From 5c66263962667dda3c6f7960c966e0e2e6760952 Mon Sep 17 00:00:00 2001 From: Jenny Empawi Date: Fri, 9 Oct 2026 11:39:58 -0400 Subject: [PATCH 1/9] Redesign the site layouts over hugo-book and add page metadata headers - site/: home page, data catalog with cohort x modality grid and filters, dataset summary card, inventory and analysis coverage pages, dark mode - Metadata headers on dataset pages; page text is unchanged. Sample size, status, release, access and method status are left blank for curators. - New pages: how to get the data, inventory, coverage - hugo_generator.py copies site/ into the build; CI installs PyYAML and pins the hugo-book theme --- .github/ISSUE_TEMPLATE/propose-dataset.yml | 53 ++ content/coverage.md | 7 + content/how_to_get_data.md | 48 ++ content/inventory.md | 7 + .../gwas/ADGC_GWAS_imputation_protocol.md | 3 + content/xqtl-data/gwas/AD_GWAS.md | 1 + content/xqtl-data/gwas/Bellenguez_AD.md | 3 + content/xqtl-data/gwas/Jansen_AD.md | 3 + content/xqtl-data/gwas/Kunkle_AD.md | 3 + content/xqtl-data/gwas/Wightman_AD.md | 3 + .../omics/covariates/ROSMAP_covariates.md | 12 + .../Knight_ADRC_brain_expression.md | 13 + .../omics/expression/MSBB_brain_expression.md | 15 + .../expression/MetaBrain_brain_expression.md | 12 + .../omics/expression/MiGA_brain_expression.md | 15 + .../omics/expression/ROSMAP_AC_expression.md | 13 + .../expression/ROSMAP_DLPFC_expression.md | 15 + .../omics/expression/ROSMAP_PCC_expression.md | 13 + .../expression/ROSMAP_microglia_expression.md | 13 + .../expression/ROSMAP_monocyte_expression.md | 13 + .../expression/ROSMAP_snRNAseq_pseudo_bulk.md | 13 + .../omics/expression/STARNET_macrophage.md | 13 + .../omics/genotype/Knight_ADRC_genotype.md | 14 + content/xqtl-data/omics/genotype/MSBB_WGS.md | 15 + .../xqtl-data/omics/genotype/MiGA_genotype.md | 12 + .../xqtl-data/omics/genotype/ROSMAP_WGS.md | 15 + .../omics/genotype/STARNET_genotype.md | 14 + .../ROSMAP_DLPFC_glycoproteomics.md | 13 + .../ROSMAP_DLPFC_ChIPSeq_H3K9ac.md | 15 + .../Knight_ADRC_brain_metabolomics.md | 13 + .../metabolomics/ROSMAP_DLPFC_metabolomics.md | 15 + .../Knight_ADRC_brain_methylation.md | 13 + .../methylation/MSBB_brain_methylation.md | 13 + .../methylation/ROSMAP_DLPFC_methylation.md | 15 + .../Knight_ADRC_brain_proteomics.md | 15 + .../omics/proteomics/MSBB_proteomics.md | 13 + .../proteomics/ROSMAP_DLPFC_proteomics.md | 15 + .../omics/snATAC/ROSMAP_snuc_caQTL.md | 14 + .../omics/snRNA_seq/ROSMAP_snuc_CUIMC1.md | 13 + .../omics/snRNA_seq/ROSMAP_snuc_MIT.md | 13 + .../omics/snRNA_seq/ROSMAP_snuc_mega.md | 15 + .../splicing/Knight_ADRC_brain_splicing.md | 13 + .../omics/splicing/MSBB_brain_splicing.md | 13 + .../omics/splicing/ROSMAP_AC_splicing.md | 13 + .../omics/splicing/ROSMAP_DLPFC_splicing.md | 13 + .../omics/splicing/ROSMAP_PCC_splicing.md | 13 + .../omics/splicing/ROSMAP_snuc_splicing.md | 13 + .../qtl/FunGen_xQTL_protocol_data.md | 11 + .../qtl/caQTL/ROSMAP_snuc_caQTL_qtl.md | 14 + .../eQTL/Knight_ADRC_brain_expression_qtl.md | 15 + .../qtl/eQTL/MSBB_brain_expression_qtl.md | 15 + .../eQTL/MetaBrain_brain_expression_qtl.md | 14 + .../qtl/eQTL/MiGA_brain_expression_qtl.md | 2 + .../qtl/eQTL/ROSMAP_AC_expression_qtl.md | 15 + .../qtl/eQTL/ROSMAP_DLPFC_expression_qtl.md | 15 + .../qtl/eQTL/ROSMAP_PCC_expression_qtl.md | 15 + .../eQTL/ROSMAP_microglia_expression_qtl.md | 15 + .../eQTL/ROSMAP_monocyte_expression_qtl.md | 15 + .../eQTL/ROSMAP_snRNAseq_pseudo_bulk_qtl.md | 15 + .../qtl/eQTL/STARNET_macrophage_qtl.md | 14 + .../gpQTL/ROSMAP_DLPFC_glycoproteomics_qtl.md | 2 + .../haQTL/ROSMAP_DLPFC_ChIPSeq_H3K9ac_qtl.md | 15 + .../mQTL/Knight_ADRC_brain_methylation_qtl.md | 15 + .../qtl/mQTL/MSBB_brain_methylation_qtl.md | 15 + .../qtl/mQTL/ROSMAP_DLPFC_methylation_qtl.md | 15 + .../Knight_ADRC_brain_metabolomics_qtl.md | 13 + .../metQTL/ROSMAP_DLPFC_metabolomics_qtl.md | 14 + .../pQTL/Knight_ADRC_brain_proteomics_qtl.md | 15 + .../xqtl-data/qtl/pQTL/MSBB_proteomics_qtl.md | 15 + .../qtl/pQTL/ROSMAP_DLPFC_proteomics_qtl.md | 15 + .../sQTL/Knight_ADRC_brain_splicing_qtl.md | 15 + .../qtl/sQTL/MSBB_brain_splicing_qtl.md | 15 + .../qtl/sQTL/ROSMAP_AC_splicing_qtl.md | 15 + .../qtl/sQTL/ROSMAP_DLPFC_splicing_qtl.md | 15 + .../qtl/sQTL/ROSMAP_PCC_splicing_qtl.md | 15 + .../qtl/sQTL/ROSMAP_snuc_splicing_qtl.md | 14 + .../xqtl-data/reference_data/ld_reference.md | 13 + content/xqtl-data/study_info/KnightADRC.md | 1 + content/xqtl-data/study_info/MSBB.md | 1 + content/xqtl-data/study_info/MiGA.md | 1 + content/xqtl-data/study_info/ROSMAP.md | 1 + content/xqtl-data/study_info/STARNET.md | 1 + hugo.toml | 17 +- scripts/audit_catalog.py | 6 +- scripts/hugo_generator.py | 133 +++- site/README.md | 20 + site/assets/xqtl/catalog.js | 147 ++++ site/assets/xqtl/site.css | 631 ++++++++++++++++++ site/assets/xqtl/site.js | 96 +++ site/data/next_phase.yaml | 31 + site/data/xqtl.yaml | 104 +++ site/layouts/_markup/render-codeblock.html | 10 + site/layouts/_partials/ds/info.html | 66 ++ site/layouts/_partials/ds/page.html | 171 +++++ site/layouts/_partials/ds/rows.html | 21 + site/layouts/_partials/site/breadcrumb.html | 17 + site/layouts/_partials/site/doc.html | 12 + site/layouts/_partials/site/facet-opt.html | 7 + site/layouts/_partials/site/head.html | 21 + site/layouts/_partials/site/header.html | 25 + site/layouts/_partials/site/nav-link.html | 9 + site/layouts/_partials/site/nav.html | 93 +++ site/layouts/_partials/site/page-foot.html | 4 + site/layouts/_partials/site/toc.html | 21 + site/layouts/_partials/ui/access.html | 4 + site/layouts/_partials/ui/logo.html | 9 + site/layouts/_partials/ui/mark.html | 6 + site/layouts/_partials/ui/status.html | 4 + site/layouts/_shortcodes/access-defs.html | 7 + site/layouts/_shortcodes/callout.html | 2 + site/layouts/_shortcodes/status-defs.html | 6 + site/layouts/_shortcodes/steps.html | 2 + site/layouts/baseof.html | 24 + site/layouts/catalog.html | 126 ++++ site/layouts/coverage.html | 65 ++ site/layouts/home.html | 107 +++ site/layouts/inventory.html | 86 +++ site/layouts/page.html | 13 + site/layouts/section.html | 42 ++ site/static/favicon.svg | 1 + template/metadata_header.md | 10 +- 121 files changed, 3210 insertions(+), 16 deletions(-) create mode 100644 .github/ISSUE_TEMPLATE/propose-dataset.yml create mode 100644 content/coverage.md create mode 100644 content/how_to_get_data.md create mode 100644 content/inventory.md create mode 100644 site/README.md create mode 100644 site/assets/xqtl/catalog.js create mode 100644 site/assets/xqtl/site.css create mode 100644 site/assets/xqtl/site.js create mode 100644 site/data/next_phase.yaml create mode 100644 site/data/xqtl.yaml create mode 100644 site/layouts/_markup/render-codeblock.html create mode 100644 site/layouts/_partials/ds/info.html create mode 100644 site/layouts/_partials/ds/page.html create mode 100644 site/layouts/_partials/ds/rows.html create mode 100644 site/layouts/_partials/site/breadcrumb.html create mode 100644 site/layouts/_partials/site/doc.html create mode 100644 site/layouts/_partials/site/facet-opt.html create mode 100644 site/layouts/_partials/site/head.html create mode 100644 site/layouts/_partials/site/header.html create mode 100644 site/layouts/_partials/site/nav-link.html create mode 100644 site/layouts/_partials/site/nav.html create mode 100644 site/layouts/_partials/site/page-foot.html create mode 100644 site/layouts/_partials/site/toc.html create mode 100644 site/layouts/_partials/ui/access.html create mode 100644 site/layouts/_partials/ui/logo.html create mode 100644 site/layouts/_partials/ui/mark.html create mode 100644 site/layouts/_partials/ui/status.html create mode 100644 site/layouts/_shortcodes/access-defs.html create mode 100644 site/layouts/_shortcodes/callout.html create mode 100644 site/layouts/_shortcodes/status-defs.html create mode 100644 site/layouts/_shortcodes/steps.html create mode 100644 site/layouts/baseof.html create mode 100644 site/layouts/catalog.html create mode 100644 site/layouts/coverage.html create mode 100644 site/layouts/home.html create mode 100644 site/layouts/inventory.html create mode 100644 site/layouts/page.html create mode 100644 site/layouts/section.html create mode 100644 site/static/favicon.svg diff --git a/.github/ISSUE_TEMPLATE/propose-dataset.yml b/.github/ISSUE_TEMPLATE/propose-dataset.yml new file mode 100644 index 0000000..10e3414 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/propose-dataset.yml @@ -0,0 +1,53 @@ +name: Propose a dataset +description: Suggest a new or expanded dataset for the FunGen-xQTL catalog. A curator turns it into a page. +title: "Dataset proposal: " +labels: [dataset-proposal] +body: + - type: markdown + attributes: + value: | + Give public identifiers only: a Synapse ID or a public URL. Do not paste cluster, HPC or FTP paths, emails, or participant-level details. + - type: input + id: name + attributes: + label: Dataset name + placeholder: e.g. MSSM PsychAD snRNA-seq + validations: + required: true + - type: input + id: cohort + attributes: + label: Cohort + placeholder: e.g. ROSMAP, MSBB, Knight-ADRC, MiGA + validations: + required: true + - type: input + id: context + attributes: + label: Context (organ, tissue or cell type) + placeholder: e.g. DLPFC, microglia, 7 cell types + - type: input + id: modality + attributes: + label: Modality + placeholder: e.g. snRNA-seq, methylation, proteomics + validations: + required: true + - type: input + id: n + attributes: + label: Sample size (aggregate) + - type: dropdown + id: access + attributes: + label: Access + options: [open, controlled, requested, not known yet] + - type: input + id: synapse + attributes: + label: Synapse ID or public URL + placeholder: syn... + - type: textarea + id: why + attributes: + label: Why it belongs in the atlas diff --git a/content/coverage.md b/content/coverage.md new file mode 100644 index 0000000..885948b --- /dev/null +++ b/content/coverage.md @@ -0,0 +1,7 @@ +--- +layout: coverage +--- + +# Analysis coverage + +Which methods from the [xQTL protocol](https://statfungen.github.io/xqtl-protocol) have been run on each dataset: cis-QTL mapping, SuSiE and fSuSiE fine-mapping, ColocBoost colocalization, TWAS, cTWAS, Mendelian randomization, LF2 and scEEMS. diff --git a/content/how_to_get_data.md b/content/how_to_get_data.md new file mode 100644 index 0000000..09a4d9a --- /dev/null +++ b/content/how_to_get_data.md @@ -0,0 +1,48 @@ +# How to get the data + +This site describes the data but does not host it. Every dataset page gives a Synapse ID or a public URL. The access label on the page tells you what you need before you can download. + +{{< access-defs >}} + +## Synapse and the AD Knowledge Portal + +Omics data, QTL results, xQTL models and reference files are on Synapse. Most cohort data are controlled. + +{{% steps %}} +1. **Create a Synapse account.** Register at [synapse.org](https://www.synapse.org/) and verify your profile. +2. **Become a certified user.** Pass the short Synapse certification quiz on data governance. +3. **Request access.** For controlled data, submit the data use certificate for the cohort through the [AD Knowledge Portal](https://adknowledgeportal.synapse.org/). Approval is per cohort, not per dataset. +4. **Download.** Use the web interface, the Synapse command-line client, or the Python or R client with the Synapse ID from the dataset page. +{{% /steps %}} + +```python +import synapseclient +syn = synapseclient.login() +entity = syn.get("syn69670632", downloadLocation=".") +``` + +The four top-level FunGen-xQTL folders on Synapse are [variant and gene summaries (syn69865684)](https://www.synapse.org/Synapse:syn69865684), [xQTL models (syn69670588)](https://www.synapse.org/Synapse:syn69670588), [raw QTL data (syn69670632)](https://www.synapse.org/Synapse:syn69670632) and [reference files (syn69670634)](https://www.synapse.org/Synapse:syn69670634). + +## NIAGADS + +AD GWAS summary statistics and ADSP genomics are distributed by NIAGADS. Summary statistics marked Open can be downloaded from the dataset's public URL. Harmonized xQTL summary statistics and fine-mapping results are open access on NIAGADS DSS as [NG00184.v1](https://dss.niagads.org/datasets/ng00184/) (GRCh38). No application is needed. Individual-level data stay controlled and are requested through DSS under their own accessions. + +{{% callout %}} +**NG00184 downloads are packaged archives, one per QTL type and result type:** `ADSP_FunGen_xQTL.v1...tar` + +| Result type | What it holds | +|---|---| +| `hmt_significant` | Best default: high-confidence associations | +| `bh_significant` | Broader, still FDR-filtered | +| `all` | Every tested association | +| `single_context_finemapping_cs95` | Variants in 95% credible sets | +| `single_context_finemapping_all` | Full fine-mapping output | + +QTL types in NG00184: eQTL, snuc-eQTL, sQTL, pQTL, mQTL, haQTL. Each archive holds `.bed.gz` files with tabix indexes, metadata and a manifest. +{{% /callout %}} + +To search significant associations without downloading, use the [xQTL Atlas](https://xqtl.niagads.org/): look up a variant, gene or region, view tracks in its genome browser, and download matching rows as TSV. + +## Release status + +{{< status-defs >}} diff --git a/content/inventory.md b/content/inventory.md new file mode 100644 index 0000000..1257661 --- /dev/null +++ b/content/inventory.md @@ -0,0 +1,7 @@ +--- +layout: inventory +--- + +# Dataset inventory + +The catalog seen through the next phase of the atlas: every omics dataset behind the current release, plus new and expanded datasets being curated. Acquisition stage comes from each page's release status; datasets without a page yet are listed in `site/data/next_phase.yaml`. diff --git a/content/xqtl-data/gwas/ADGC_GWAS_imputation_protocol.md b/content/xqtl-data/gwas/ADGC_GWAS_imputation_protocol.md index 87dc143..fbb0ce6 100644 --- a/content/xqtl-data/gwas/ADGC_GWAS_imputation_protocol.md +++ b/content/xqtl-data/gwas/ADGC_GWAS_imputation_protocol.md @@ -1,6 +1,9 @@ --- type: gwas +short_title: ADGC imputation protocol status: +access: +release: synapse_ids: [] lead_analysts: [Xuanhe Chen] last_verified: diff --git a/content/xqtl-data/gwas/AD_GWAS.md b/content/xqtl-data/gwas/AD_GWAS.md index fb3453e..9395619 100644 --- a/content/xqtl-data/gwas/AD_GWAS.md +++ b/content/xqtl-data/gwas/AD_GWAS.md @@ -1,5 +1,6 @@ --- type: gwas +short_title: AD GWAS overview status: synapse_ids: [syn69670651, syn69670652, syn69670653, syn69670656, syn69670625, syn69696846, syn69865824] lead_analysts: [] diff --git a/content/xqtl-data/gwas/Bellenguez_AD.md b/content/xqtl-data/gwas/Bellenguez_AD.md index 2d4e0d3..88b7eba 100644 --- a/content/xqtl-data/gwas/Bellenguez_AD.md +++ b/content/xqtl-data/gwas/Bellenguez_AD.md @@ -1,6 +1,9 @@ --- type: gwas +short_title: Bellenguez 2022 status: +access: +release: synapse_ids: [syn69670625, syn69670630, syn69865816, syn69865824, syn70095142, syn70095143] lead_analysts: [Oluwatosin Olayinka, Hao Sun, Rui Dong] last_verified: diff --git a/content/xqtl-data/gwas/Jansen_AD.md b/content/xqtl-data/gwas/Jansen_AD.md index 04e433b..975c1a1 100644 --- a/content/xqtl-data/gwas/Jansen_AD.md +++ b/content/xqtl-data/gwas/Jansen_AD.md @@ -1,6 +1,9 @@ --- type: gwas +short_title: Jansen 2019 status: +access: +release: synapse_ids: [syn69670625, syn69670626, syn69670630, syn69696846, syn69865816, syn69865824, syn70095142, syn70095143] lead_analysts: [Oluwatosin Olayinka] last_verified: diff --git a/content/xqtl-data/gwas/Kunkle_AD.md b/content/xqtl-data/gwas/Kunkle_AD.md index 14172bb..ac7f1d3 100644 --- a/content/xqtl-data/gwas/Kunkle_AD.md +++ b/content/xqtl-data/gwas/Kunkle_AD.md @@ -1,6 +1,9 @@ --- type: gwas +short_title: Kunkle 2019 status: +access: +release: synapse_ids: [syn69670625, syn69670626, syn69670630, syn69696846, syn69865816, syn69865824, syn70095142, syn70095143] lead_analysts: [Oluwatosin Olayinka] last_verified: diff --git a/content/xqtl-data/gwas/Wightman_AD.md b/content/xqtl-data/gwas/Wightman_AD.md index 102b041..3f4009d 100644 --- a/content/xqtl-data/gwas/Wightman_AD.md +++ b/content/xqtl-data/gwas/Wightman_AD.md @@ -1,6 +1,9 @@ --- type: gwas +short_title: Wightman 2021 status: +access: +release: synapse_ids: [syn69670625, syn69670626, syn69670630, syn69696846, syn69865816, syn69865824, syn70095142, syn70095143] lead_analysts: [Oluwatosin Olayinka] last_verified: diff --git a/content/xqtl-data/omics/covariates/ROSMAP_covariates.md b/content/xqtl-data/omics/covariates/ROSMAP_covariates.md index 6f75d57..b7f3d77 100644 --- a/content/xqtl-data/omics/covariates/ROSMAP_covariates.md +++ b/content/xqtl-data/omics/covariates/ROSMAP_covariates.md @@ -1,3 +1,15 @@ +--- +type: omics +modality: covariates +short_title: ROSMAP covariates +cohort: ROSMAP +access: controlled +status: +synapse_ids: [] +lead_analysts: [] +last_verified: +--- + # ROSMAP Covariates data Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) covariates data diff --git a/content/xqtl-data/omics/expression/Knight_ADRC_brain_expression.md b/content/xqtl-data/omics/expression/Knight_ADRC_brain_expression.md index 5f07963..b331605 100644 --- a/content/xqtl-data/omics/expression/Knight_ADRC_brain_expression.md +++ b/content/xqtl-data/omics/expression/Knight_ADRC_brain_expression.md @@ -1,3 +1,16 @@ +--- +type: omics +modality: expression +short_title: Knight ADRC brain +cohort: Knight-ADRC +context: parietal cortex +access: controlled +status: +synapse_ids: [syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] +lead_analysts: [Chunming Liu] +last_verified: +--- + # Knight ADRC brain gene expression ## Contact diff --git a/content/xqtl-data/omics/expression/MSBB_brain_expression.md b/content/xqtl-data/omics/expression/MSBB_brain_expression.md index abfa662..4a130c5 100644 --- a/content/xqtl-data/omics/expression/MSBB_brain_expression.md +++ b/content/xqtl-data/omics/expression/MSBB_brain_expression.md @@ -1,3 +1,18 @@ +--- +type: omics +modality: expression +short_title: MSBB brain +cohort: MSBB +context: 4 brain regions +sample_size: +access: controlled +status: +release: +synapse_ids: [syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] +lead_analysts: [Minghui Wang] +last_verified: +--- + # MSBB brain gene expression ## Contact diff --git a/content/xqtl-data/omics/expression/MetaBrain_brain_expression.md b/content/xqtl-data/omics/expression/MetaBrain_brain_expression.md index eff9c9f..0a69c0d 100644 --- a/content/xqtl-data/omics/expression/MetaBrain_brain_expression.md +++ b/content/xqtl-data/omics/expression/MetaBrain_brain_expression.md @@ -1,3 +1,15 @@ +--- +type: omics +modality: expression +short_title: MetaBrain +cohort: MetaBrain +context: multi-region +status: +synapse_ids: [syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] +lead_analysts: [] +last_verified: +--- + # MetaBrain Brain Expression ## Summary diff --git a/content/xqtl-data/omics/expression/MiGA_brain_expression.md b/content/xqtl-data/omics/expression/MiGA_brain_expression.md index b1421ec..93678da 100644 --- a/content/xqtl-data/omics/expression/MiGA_brain_expression.md +++ b/content/xqtl-data/omics/expression/MiGA_brain_expression.md @@ -1,3 +1,18 @@ +--- +type: omics +modality: expression +short_title: MiGA microglia +cohort: MiGA +context: "microglia, 4 regions" +sample_size: +access: controlled +status: +release: +synapse_ids: [syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] +lead_analysts: [Travyse Edwards] +last_verified: +--- + # MiGA multi-brain region gene expression A genetic and transcriptomic resource comprised of 255 primary human microglia samples isolated ex vivo from four different brain regions of 100 human subjects with neurodegenerative, neurological, or neuropsychiatric disorders, as well as unaffected controls. diff --git a/content/xqtl-data/omics/expression/ROSMAP_AC_expression.md b/content/xqtl-data/omics/expression/ROSMAP_AC_expression.md index 416bdef..6f728c1 100644 --- a/content/xqtl-data/omics/expression/ROSMAP_AC_expression.md +++ b/content/xqtl-data/omics/expression/ROSMAP_AC_expression.md @@ -1,3 +1,16 @@ +--- +type: omics +modality: expression +short_title: ROSMAP AC +cohort: ROSMAP +context: AC +access: controlled +status: +synapse_ids: [syn3388564, syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] +lead_analysts: [Frank Grenn] +last_verified: +--- + # ROSMAP AC gene expression Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) AC gene expression. diff --git a/content/xqtl-data/omics/expression/ROSMAP_DLPFC_expression.md b/content/xqtl-data/omics/expression/ROSMAP_DLPFC_expression.md index 940b0d5..117dbce 100644 --- a/content/xqtl-data/omics/expression/ROSMAP_DLPFC_expression.md +++ b/content/xqtl-data/omics/expression/ROSMAP_DLPFC_expression.md @@ -1,3 +1,18 @@ +--- +type: omics +modality: expression +short_title: ROSMAP DLPFC +cohort: ROSMAP +context: DLPFC +sample_size: +access: controlled +status: +release: +synapse_ids: [syn3388564, syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] +lead_analysts: [Xuanhe Chen] +last_verified: +--- + # ROSMAP DLPFC gene expression Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) DLPFC gene expression. diff --git a/content/xqtl-data/omics/expression/ROSMAP_PCC_expression.md b/content/xqtl-data/omics/expression/ROSMAP_PCC_expression.md index a07e5d6..acc41e2 100644 --- a/content/xqtl-data/omics/expression/ROSMAP_PCC_expression.md +++ b/content/xqtl-data/omics/expression/ROSMAP_PCC_expression.md @@ -1,3 +1,16 @@ +--- +type: omics +modality: expression +short_title: ROSMAP PCC +cohort: ROSMAP +context: PCC +access: controlled +status: +synapse_ids: [syn3157322, syn3388564, syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] +lead_analysts: [Frank Grenn] +last_verified: +--- + # ROSMAP PCC gene expression Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) PCC alternative splicing. diff --git a/content/xqtl-data/omics/expression/ROSMAP_microglia_expression.md b/content/xqtl-data/omics/expression/ROSMAP_microglia_expression.md index 4970174..2597ea6 100644 --- a/content/xqtl-data/omics/expression/ROSMAP_microglia_expression.md +++ b/content/xqtl-data/omics/expression/ROSMAP_microglia_expression.md @@ -1,3 +1,16 @@ +--- +type: omics +modality: expression +short_title: ROSMAP microglia +cohort: ROSMAP +context: microglia +access: controlled +status: +synapse_ids: [syn2580853, syn11468526, syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] +lead_analysts: [Travyse Edwards] +last_verified: +--- + # ROSMAP RNA-seq microglia gene expression Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) microglia data-set. diff --git a/content/xqtl-data/omics/expression/ROSMAP_monocyte_expression.md b/content/xqtl-data/omics/expression/ROSMAP_monocyte_expression.md index 5b9ce08..ef0183e 100644 --- a/content/xqtl-data/omics/expression/ROSMAP_monocyte_expression.md +++ b/content/xqtl-data/omics/expression/ROSMAP_monocyte_expression.md @@ -1,3 +1,16 @@ +--- +type: omics +modality: expression +short_title: ROSMAP monocyte +cohort: ROSMAP +context: monocyte +access: controlled +status: +synapse_ids: [syn22024496, syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] +lead_analysts: [Travyse Edwards] +last_verified: +--- + # ROSMAP RNA-seq monocyte gene expression Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) monocyte data-set. diff --git a/content/xqtl-data/omics/expression/ROSMAP_snRNAseq_pseudo_bulk.md b/content/xqtl-data/omics/expression/ROSMAP_snRNAseq_pseudo_bulk.md index 28b7a3a..d3cba29 100644 --- a/content/xqtl-data/omics/expression/ROSMAP_snRNAseq_pseudo_bulk.md +++ b/content/xqtl-data/omics/expression/ROSMAP_snRNAseq_pseudo_bulk.md @@ -1,3 +1,16 @@ +--- +type: omics +modality: expression +short_title: ROSMAP pseudo-bulk +cohort: ROSMAP +context: "DLPFC, cell types" +access: controlled +status: +synapse_ids: [syn31512863, syn52293417, syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] +lead_analysts: [Hao Sun, Masashi Fujita] +last_verified: +--- + # ROSMAP snRNA-seq pseudo-bulk gene expression Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) snRNA-seq from different cells in Dorsolateral Prefrontal Cortex (DLPFC). diff --git a/content/xqtl-data/omics/expression/STARNET_macrophage.md b/content/xqtl-data/omics/expression/STARNET_macrophage.md index a850367..d7f4d93 100644 --- a/content/xqtl-data/omics/expression/STARNET_macrophage.md +++ b/content/xqtl-data/omics/expression/STARNET_macrophage.md @@ -1,3 +1,16 @@ +--- +type: omics +modality: expression +short_title: STARNET macrophage +cohort: STARNET +context: macrophage +access: controlled +status: +synapse_ids: [syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] +lead_analysts: [Travyse Edwards] +last_verified: +--- + # STARNET macrophage gene expression QTL STARNET is an RNA expression study of various disease-relevant tissues obtained from living patients with cardiovascular disease (CVD). The inclusion criterion for patients was eligibility for coronary artery by-pass graft (CABG) surgery. diff --git a/content/xqtl-data/omics/genotype/Knight_ADRC_genotype.md b/content/xqtl-data/omics/genotype/Knight_ADRC_genotype.md index ccafc5b..8ffe7d5 100644 --- a/content/xqtl-data/omics/genotype/Knight_ADRC_genotype.md +++ b/content/xqtl-data/omics/genotype/Knight_ADRC_genotype.md @@ -1,3 +1,17 @@ +--- +type: omics +modality: genotype +short_title: Knight ADRC genotype +cohort: Knight-ADRC +context: blood +access: controlled +status: +release: +synapse_ids: [] +lead_analysts: [Zining Qi] +last_verified: +--- + # Knight ADRC genotype data ## Contact diff --git a/content/xqtl-data/omics/genotype/MSBB_WGS.md b/content/xqtl-data/omics/genotype/MSBB_WGS.md index 92f9753..4184119 100644 --- a/content/xqtl-data/omics/genotype/MSBB_WGS.md +++ b/content/xqtl-data/omics/genotype/MSBB_WGS.md @@ -1,3 +1,18 @@ +--- +type: omics +modality: genotype +short_title: MSBB WGS +cohort: MSBB +context: blood +sample_size: +access: controlled +status: +release: +synapse_ids: [] +lead_analysts: [Minghui Wang, Julia TCW] +last_verified: +--- + # MSBB WGS data MSBB whole-genome sequence data. diff --git a/content/xqtl-data/omics/genotype/MiGA_genotype.md b/content/xqtl-data/omics/genotype/MiGA_genotype.md index 35f4015..bb81a46 100644 --- a/content/xqtl-data/omics/genotype/MiGA_genotype.md +++ b/content/xqtl-data/omics/genotype/MiGA_genotype.md @@ -1,3 +1,15 @@ +--- +type: omics +modality: genotype +short_title: MiGA genotype +cohort: MiGA +access: controlled +status: +synapse_ids: [] +lead_analysts: [Travyse Edwards] +last_verified: +--- + # MiGA genotype data Microglia Genomic Atlas from the Netherlands Brain Bank (NBB) and the Neuropathology Brain Bank and Research CoRE at Mount Sinai Hospital. The permission to collect human brain material was obtained from the Ethical Committee of the VU University Medical Center, Amsterdam, The Netherlands, and the Mount Sinai Institutional Review Board. For the Netherlands Brain bank, informed consent for autopsy, the use of brain tissue and accompanied clinical information for research purposes was obtained per donor ante-mortem. diff --git a/content/xqtl-data/omics/genotype/ROSMAP_WGS.md b/content/xqtl-data/omics/genotype/ROSMAP_WGS.md index 6d15e0f..a9313f7 100644 --- a/content/xqtl-data/omics/genotype/ROSMAP_WGS.md +++ b/content/xqtl-data/omics/genotype/ROSMAP_WGS.md @@ -1,3 +1,18 @@ +--- +type: omics +modality: genotype +short_title: ROSMAP WGS +cohort: ROSMAP +context: "blood, brain" +sample_size: +access: controlled +status: +release: +synapse_ids: [] +lead_analysts: [Hao Sun, Xuanhe Chen] +last_verified: +--- + # ROSMAP WGS data Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) whole-genome sequence data diff --git a/content/xqtl-data/omics/genotype/STARNET_genotype.md b/content/xqtl-data/omics/genotype/STARNET_genotype.md index b0460c2..f3125ac 100644 --- a/content/xqtl-data/omics/genotype/STARNET_genotype.md +++ b/content/xqtl-data/omics/genotype/STARNET_genotype.md @@ -1,3 +1,17 @@ +--- +type: omics +modality: genotype +short_title: STARNET genotype +cohort: STARNET +context: blood +access: controlled +status: +release: +synapse_ids: [] +lead_analysts: [Travyse Edwards] +last_verified: +--- + # STARNET genotype data STARNET is an RNA expression study of various disease-relevant tissues obtained from living patients with cardiovascular disease (CVD). The inclusion criterion for patients was eligibility for coronary artery by-pass graft (CABG) surgery. diff --git a/content/xqtl-data/omics/glycoproteomics/ROSMAP_DLPFC_glycoproteomics.md b/content/xqtl-data/omics/glycoproteomics/ROSMAP_DLPFC_glycoproteomics.md index 61bd7ba..05c4173 100644 --- a/content/xqtl-data/omics/glycoproteomics/ROSMAP_DLPFC_glycoproteomics.md +++ b/content/xqtl-data/omics/glycoproteomics/ROSMAP_DLPFC_glycoproteomics.md @@ -1,3 +1,16 @@ +--- +type: omics +modality: glycoproteomics +short_title: ROSMAP DLPFC +cohort: ROSMAP +context: DLPFC +access: +status: +synapse_ids: [syn17015098, syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] +lead_analysts: [FunGen-xQTL Analysis Working Group] +last_verified: +--- + # ROSMAP DLPFC Glycoproteomics Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) DLPFC glycoproteomics (N-glycosylation proteomics). diff --git a/content/xqtl-data/omics/histone_ChIPSeq/ROSMAP_DLPFC_ChIPSeq_H3K9ac.md b/content/xqtl-data/omics/histone_ChIPSeq/ROSMAP_DLPFC_ChIPSeq_H3K9ac.md index d369578..822057b 100644 --- a/content/xqtl-data/omics/histone_ChIPSeq/ROSMAP_DLPFC_ChIPSeq_H3K9ac.md +++ b/content/xqtl-data/omics/histone_ChIPSeq/ROSMAP_DLPFC_ChIPSeq_H3K9ac.md @@ -1,3 +1,18 @@ +--- +type: omics +modality: histone_ChIPSeq +short_title: ROSMAP DLPFC H3K9ac +cohort: ROSMAP +context: DLPFC +sample_size: +access: controlled +status: +release: +synapse_ids: [syn4896408, syn17016212, syn69670592, syn69670597, syn69670630, syn69865816] +lead_analysts: [Xuanhe Chen, Hao Sun, Hans Klein] +last_verified: +--- + # ROSMAP DLPFC H3K9ac Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) h3k9ac data-set. diff --git a/content/xqtl-data/omics/metabolomics/Knight_ADRC_brain_metabolomics.md b/content/xqtl-data/omics/metabolomics/Knight_ADRC_brain_metabolomics.md index 776ba2c..fe5025d 100644 --- a/content/xqtl-data/omics/metabolomics/Knight_ADRC_brain_metabolomics.md +++ b/content/xqtl-data/omics/metabolomics/Knight_ADRC_brain_metabolomics.md @@ -1,3 +1,16 @@ +--- +type: omics +modality: metabolomics +short_title: Knight ADRC brain +cohort: Knight-ADRC +context: parietal cortex +access: controlled +status: +synapse_ids: [] +lead_analysts: [Zining Qi] +last_verified: +--- + # Knight ADRC brain metabolomics ## Contact diff --git a/content/xqtl-data/omics/metabolomics/ROSMAP_DLPFC_metabolomics.md b/content/xqtl-data/omics/metabolomics/ROSMAP_DLPFC_metabolomics.md index 8606b46..c74d081 100644 --- a/content/xqtl-data/omics/metabolomics/ROSMAP_DLPFC_metabolomics.md +++ b/content/xqtl-data/omics/metabolomics/ROSMAP_DLPFC_metabolomics.md @@ -1,3 +1,18 @@ +--- +type: omics +modality: metabolomics +short_title: ROSMAP DLPFC +cohort: ROSMAP +context: DLPFC +sample_size: +access: controlled +status: +release: +synapse_ids: [syn69670592, syn69670597, syn69670630, syn69865816] +lead_analysts: [] +last_verified: +--- + # ROSMAP DLPFC Metabolomics ## Summary diff --git a/content/xqtl-data/omics/methylation/Knight_ADRC_brain_methylation.md b/content/xqtl-data/omics/methylation/Knight_ADRC_brain_methylation.md index b72a862..a4387b0 100644 --- a/content/xqtl-data/omics/methylation/Knight_ADRC_brain_methylation.md +++ b/content/xqtl-data/omics/methylation/Knight_ADRC_brain_methylation.md @@ -1,3 +1,16 @@ +--- +type: omics +modality: methylation +short_title: Knight ADRC brain +cohort: Knight-ADRC +context: parietal cortex +access: controlled +status: +synapse_ids: [syn69670592, syn69670597, syn69670630, syn69865816] +lead_analysts: [Alexandre Pelletier] +last_verified: +--- + # Knight ADRC brain methylation ## Contact diff --git a/content/xqtl-data/omics/methylation/MSBB_brain_methylation.md b/content/xqtl-data/omics/methylation/MSBB_brain_methylation.md index 567809f..6871079 100644 --- a/content/xqtl-data/omics/methylation/MSBB_brain_methylation.md +++ b/content/xqtl-data/omics/methylation/MSBB_brain_methylation.md @@ -1,3 +1,16 @@ +--- +type: omics +modality: methylation +short_title: MSBB brain +cohort: MSBB +context: brain +access: controlled +status: +synapse_ids: [syn69670592, syn69670597, syn69670630, syn69865816] +lead_analysts: [Alexandre Pelletier] +last_verified: +--- + # MSBB brain methylation ## Contact diff --git a/content/xqtl-data/omics/methylation/ROSMAP_DLPFC_methylation.md b/content/xqtl-data/omics/methylation/ROSMAP_DLPFC_methylation.md index e9f7f9c..3ff59da 100644 --- a/content/xqtl-data/omics/methylation/ROSMAP_DLPFC_methylation.md +++ b/content/xqtl-data/omics/methylation/ROSMAP_DLPFC_methylation.md @@ -1,3 +1,18 @@ +--- +type: omics +modality: methylation +short_title: ROSMAP DLPFC +cohort: ROSMAP +context: DLPFC +sample_size: +access: controlled +status: +release: +synapse_ids: [syn3157275, syn69670592, syn69670597, syn69670630, syn69865816] +lead_analysts: [Alexandre Pelletier, Jiajun Tao] +last_verified: +--- + # ROSMAP DLPFC methylation Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) DLPFC methylation data-set. diff --git a/content/xqtl-data/omics/proteomics/Knight_ADRC_brain_proteomics.md b/content/xqtl-data/omics/proteomics/Knight_ADRC_brain_proteomics.md index 7be1afe..f6eb571 100644 --- a/content/xqtl-data/omics/proteomics/Knight_ADRC_brain_proteomics.md +++ b/content/xqtl-data/omics/proteomics/Knight_ADRC_brain_proteomics.md @@ -1,3 +1,18 @@ +--- +type: omics +modality: proteomics +short_title: Knight ADRC brain +cohort: Knight-ADRC +context: parietal cortex +sample_size: +access: controlled +status: +release: +synapse_ids: [syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] +lead_analysts: [Zining Qi] +last_verified: +--- + # Knight ADRC brain proteomics Charles F And Joanne Knight Alzheimer's Disease Research Center (Knight-ADRC) diff --git a/content/xqtl-data/omics/proteomics/MSBB_proteomics.md b/content/xqtl-data/omics/proteomics/MSBB_proteomics.md index b6a8293..8bc48e9 100644 --- a/content/xqtl-data/omics/proteomics/MSBB_proteomics.md +++ b/content/xqtl-data/omics/proteomics/MSBB_proteomics.md @@ -1,3 +1,16 @@ +--- +type: omics +modality: proteomics +short_title: MSBB brain +cohort: MSBB +context: brain +access: controlled +status: +synapse_ids: [syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] +lead_analysts: [Minghui Wang] +last_verified: +--- + # MSBB brain proteomics ## Contact diff --git a/content/xqtl-data/omics/proteomics/ROSMAP_DLPFC_proteomics.md b/content/xqtl-data/omics/proteomics/ROSMAP_DLPFC_proteomics.md index b977625..2561256 100644 --- a/content/xqtl-data/omics/proteomics/ROSMAP_DLPFC_proteomics.md +++ b/content/xqtl-data/omics/proteomics/ROSMAP_DLPFC_proteomics.md @@ -1,3 +1,18 @@ +--- +type: omics +modality: proteomics +short_title: ROSMAP DLPFC +cohort: ROSMAP +context: DLPFC +sample_size: +access: controlled +status: +release: +synapse_ids: [syn17015098, syn21449447, syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] +lead_analysts: [Zining Qi] +last_verified: +--- + # ROSMAP DLPFC protein expression Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) DLPFC protein expression. diff --git a/content/xqtl-data/omics/snATAC/ROSMAP_snuc_caQTL.md b/content/xqtl-data/omics/snATAC/ROSMAP_snuc_caQTL.md index 12cbd26..e8fd408 100644 --- a/content/xqtl-data/omics/snATAC/ROSMAP_snuc_caQTL.md +++ b/content/xqtl-data/omics/snATAC/ROSMAP_snuc_caQTL.md @@ -1,3 +1,17 @@ +--- +type: omics +modality: snATAC +short_title: ROSMAP snATAC-seq +cohort: ROSMAP +context: "DLPFC, cell types" +sample_size: +access: controlled +status: +synapse_ids: [syn69670592, syn69670597, syn69670630, syn69865816] +lead_analysts: [] +last_verified: +--- + # ROSMAP snATAC-seq Chromatin Accessibility ## Summary diff --git a/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_CUIMC1.md b/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_CUIMC1.md index 5182766..8da53cc 100644 --- a/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_CUIMC1.md +++ b/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_CUIMC1.md @@ -1,3 +1,16 @@ +--- +type: omics +modality: snRNA_seq +short_title: ROSMAP CUIMC +cohort: ROSMAP +context: DLPFC +access: controlled +status: +synapse_ids: [syn31512863, syn69670592, syn69670597, syn69670630, syn69865816] +lead_analysts: [Anjing Liu] +last_verified: +--- + # ROSMAP CUIMC snRNA-seq expression Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) single-nucleus RNA-seq expression data from Columbia University Irving Medical Center (CUIMC). diff --git a/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_MIT.md b/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_MIT.md index 992bc9a..290b799 100644 --- a/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_MIT.md +++ b/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_MIT.md @@ -1,3 +1,16 @@ +--- +type: omics +modality: snRNA_seq +short_title: ROSMAP MIT +cohort: ROSMAP +context: DLPFC +access: controlled +status: +synapse_ids: [syn52293417, syn69670592, syn69670597, syn69670630, syn69865816] +lead_analysts: [Anjing Liu] +last_verified: +--- + # ROSMAP MIT snRNA-seq expression Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) single-nucleus RNA-seq expression data from Massachusetts Institute of Technology (MIT). diff --git a/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_mega.md b/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_mega.md index 4257fd5..c3bde93 100644 --- a/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_mega.md +++ b/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_mega.md @@ -1,3 +1,18 @@ +--- +type: omics +modality: snRNA_seq +short_title: ROSMAP Mega +cohort: ROSMAP +context: DLPFC +sample_size: +access: controlled +status: +release: +synapse_ids: [syn31512863, syn52293417, syn69670592, syn69670597, syn69670630, syn69865816] +lead_analysts: [Anjing Liu] +last_verified: +--- + # ROSMAP Mega snRNA-seq expression Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) mega-analysis combining single-nucleus RNA-seq data from CUIMC and MIT. diff --git a/content/xqtl-data/omics/splicing/Knight_ADRC_brain_splicing.md b/content/xqtl-data/omics/splicing/Knight_ADRC_brain_splicing.md index 66ade1a..fd3478d 100644 --- a/content/xqtl-data/omics/splicing/Knight_ADRC_brain_splicing.md +++ b/content/xqtl-data/omics/splicing/Knight_ADRC_brain_splicing.md @@ -1,3 +1,16 @@ +--- +type: omics +modality: splicing +short_title: Knight ADRC brain +cohort: Knight-ADRC +context: parietal cortex +access: controlled +status: +synapse_ids: [syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] +lead_analysts: [Xuanhe Chen] +last_verified: +--- + # Knight ADRC brain splicing ## Contact diff --git a/content/xqtl-data/omics/splicing/MSBB_brain_splicing.md b/content/xqtl-data/omics/splicing/MSBB_brain_splicing.md index 8eeb7fb..beeac3c 100644 --- a/content/xqtl-data/omics/splicing/MSBB_brain_splicing.md +++ b/content/xqtl-data/omics/splicing/MSBB_brain_splicing.md @@ -1,3 +1,16 @@ +--- +type: omics +modality: splicing +short_title: MSBB brain +cohort: MSBB +context: 4 brain regions +access: controlled +status: +synapse_ids: [syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] +lead_analysts: [Minghui Wang] +last_verified: +--- + # MSBB brain alternative splicing ## Contact diff --git a/content/xqtl-data/omics/splicing/ROSMAP_AC_splicing.md b/content/xqtl-data/omics/splicing/ROSMAP_AC_splicing.md index 69e1d39..f52cf8f 100644 --- a/content/xqtl-data/omics/splicing/ROSMAP_AC_splicing.md +++ b/content/xqtl-data/omics/splicing/ROSMAP_AC_splicing.md @@ -1,3 +1,16 @@ +--- +type: omics +modality: splicing +short_title: ROSMAP AC +cohort: ROSMAP +context: AC +access: controlled +status: +synapse_ids: [syn3388564, syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] +lead_analysts: [Frank Grenn] +last_verified: +--- + # ROSMAP AC alternative splicing Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) AC alternative splicing. diff --git a/content/xqtl-data/omics/splicing/ROSMAP_DLPFC_splicing.md b/content/xqtl-data/omics/splicing/ROSMAP_DLPFC_splicing.md index f6b1caf..d070864 100644 --- a/content/xqtl-data/omics/splicing/ROSMAP_DLPFC_splicing.md +++ b/content/xqtl-data/omics/splicing/ROSMAP_DLPFC_splicing.md @@ -1,3 +1,16 @@ +--- +type: omics +modality: splicing +short_title: ROSMAP DLPFC +cohort: ROSMAP +context: DLPFC +access: controlled +status: +synapse_ids: [syn3388564, syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] +lead_analysts: [Xuanhe Chen, Shrishtee Kandoi] +last_verified: +--- + # ROSMAP DLPFC alternative splicing Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) DLPFC alternative splicing. diff --git a/content/xqtl-data/omics/splicing/ROSMAP_PCC_splicing.md b/content/xqtl-data/omics/splicing/ROSMAP_PCC_splicing.md index 555cbb6..ca5e14f 100644 --- a/content/xqtl-data/omics/splicing/ROSMAP_PCC_splicing.md +++ b/content/xqtl-data/omics/splicing/ROSMAP_PCC_splicing.md @@ -1,3 +1,16 @@ +--- +type: omics +modality: splicing +short_title: ROSMAP PCC +cohort: ROSMAP +context: PCC +access: controlled +status: +synapse_ids: [syn3157322, syn3388564, syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] +lead_analysts: [Frank Grenn] +last_verified: +--- + # ROSMAP PCC alternative splicing Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) PCC alternative splicing. diff --git a/content/xqtl-data/omics/splicing/ROSMAP_snuc_splicing.md b/content/xqtl-data/omics/splicing/ROSMAP_snuc_splicing.md index 7e56292..b4c790b 100644 --- a/content/xqtl-data/omics/splicing/ROSMAP_snuc_splicing.md +++ b/content/xqtl-data/omics/splicing/ROSMAP_snuc_splicing.md @@ -1,3 +1,16 @@ +--- +type: omics +modality: splicing +short_title: ROSMAP ISSAC +cohort: ROSMAP +context: "DLPFC, cell types" +access: controlled +status: +synapse_ids: [syn31512863, syn52293417, syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] +lead_analysts: [] +last_verified: +--- + # ROSMAP snRNA-seq Splicing (ISSAC) Single-nucleus RNA-seq splicing QTL analysis using the ISSAC (Integrative Single-cell Splicing Analysis with Context) method, applied to harmonized CUIMC and MIT single-nucleus data from ROSMAP DLPFC. diff --git a/content/xqtl-data/qtl/FunGen_xQTL_protocol_data.md b/content/xqtl-data/qtl/FunGen_xQTL_protocol_data.md index b7648a5..8f63020 100644 --- a/content/xqtl-data/qtl/FunGen_xQTL_protocol_data.md +++ b/content/xqtl-data/qtl/FunGen_xQTL_protocol_data.md @@ -1,3 +1,14 @@ +--- +type: qtl +short_title: Protocol toy data +cohort: ROSMAP +sample_size: +status: +synapse_ids: [syn36416601, syn4164376, syn21088596] +lead_analysts: [] +last_verified: +--- + # FunGen-xQTL protocol data A toy data-set consisting of 49 de-identified samples from ROSMAP project, used to illustrates the computational protocols we developed for the detection and analysis of molecular QTLs (xQTLs). diff --git a/content/xqtl-data/qtl/caQTL/ROSMAP_snuc_caQTL_qtl.md b/content/xqtl-data/qtl/caQTL/ROSMAP_snuc_caQTL_qtl.md index 435af72..4cb089a 100644 --- a/content/xqtl-data/qtl/caQTL/ROSMAP_snuc_caQTL_qtl.md +++ b/content/xqtl-data/qtl/caQTL/ROSMAP_snuc_caQTL_qtl.md @@ -1,3 +1,17 @@ +--- +type: qtl +modality: caQTL +short_title: ROSMAP single-nucleus +cohort: ROSMAP +context: "DLPFC, cell types" +sample_size: +access: controlled +status: +synapse_ids: [syn69670592, syn69670597, syn69865816, syn69670630] +lead_analysts: [FunGen-xQTL Analysis Team] +last_verified: +--- + # ROSMAP Single-Nucleus Chromatin Accessibility QTL (caQTL) Single-nucleus ATAC-seq chromatin accessibility QTL analysis from ROSMAP donors, covering MIT snATAC-seq and CUIMC & MIT harmonized Multiome ATAC data. diff --git a/content/xqtl-data/qtl/eQTL/Knight_ADRC_brain_expression_qtl.md b/content/xqtl-data/qtl/eQTL/Knight_ADRC_brain_expression_qtl.md index fdb9b17..feb8f95 100644 --- a/content/xqtl-data/qtl/eQTL/Knight_ADRC_brain_expression_qtl.md +++ b/content/xqtl-data/qtl/eQTL/Knight_ADRC_brain_expression_qtl.md @@ -1,3 +1,18 @@ +--- +type: qtl +modality: eQTL +short_title: Knight ADRC brain +cohort: Knight-ADRC +context: parietal cortex +sample_size: +access: controlled +status: +release: +synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] +lead_analysts: [Chunming Liu] +last_verified: +--- + # Knight ADRC brain gene expression QTL ## Contact diff --git a/content/xqtl-data/qtl/eQTL/MSBB_brain_expression_qtl.md b/content/xqtl-data/qtl/eQTL/MSBB_brain_expression_qtl.md index 8c60b20..7f80b18 100644 --- a/content/xqtl-data/qtl/eQTL/MSBB_brain_expression_qtl.md +++ b/content/xqtl-data/qtl/eQTL/MSBB_brain_expression_qtl.md @@ -1,3 +1,18 @@ +--- +type: qtl +modality: eQTL +short_title: MSBB brain +cohort: MSBB +context: 4 brain regions +sample_size: +access: controlled +status: +release: +synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] +lead_analysts: [Minghui Wang] +last_verified: +--- + # MSBB brain gene expression QTL ## Contact diff --git a/content/xqtl-data/qtl/eQTL/MetaBrain_brain_expression_qtl.md b/content/xqtl-data/qtl/eQTL/MetaBrain_brain_expression_qtl.md index f616865..97e1115 100644 --- a/content/xqtl-data/qtl/eQTL/MetaBrain_brain_expression_qtl.md +++ b/content/xqtl-data/qtl/eQTL/MetaBrain_brain_expression_qtl.md @@ -1,3 +1,17 @@ +--- +type: qtl +modality: eQTL +short_title: MetaBrain +cohort: MetaBrain +context: multi-region +access: +status: +release: +synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] +lead_analysts: [FunGen-xQTL Analysis Team] +last_verified: +--- + # MetaBrain Brain Gene Expression QTL MetaBrain multi-region bulk RNA-seq gene expression data used for validation of eQTL signals in the FunGen-xQTL flagship study. diff --git a/content/xqtl-data/qtl/eQTL/MiGA_brain_expression_qtl.md b/content/xqtl-data/qtl/eQTL/MiGA_brain_expression_qtl.md index faf11dd..07a5992 100644 --- a/content/xqtl-data/qtl/eQTL/MiGA_brain_expression_qtl.md +++ b/content/xqtl-data/qtl/eQTL/MiGA_brain_expression_qtl.md @@ -1,11 +1,13 @@ --- type: qtl modality: expression +short_title: MiGA microglia cohort: MiGA context: microglia sample_size: 255 access: controlled status: +release: synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] lead_analysts: [Travyse Edwards] last_verified: diff --git a/content/xqtl-data/qtl/eQTL/ROSMAP_AC_expression_qtl.md b/content/xqtl-data/qtl/eQTL/ROSMAP_AC_expression_qtl.md index 38799f6..34762c9 100644 --- a/content/xqtl-data/qtl/eQTL/ROSMAP_AC_expression_qtl.md +++ b/content/xqtl-data/qtl/eQTL/ROSMAP_AC_expression_qtl.md @@ -1,3 +1,18 @@ +--- +type: qtl +modality: eQTL +short_title: ROSMAP AC +cohort: ROSMAP +context: AC +sample_size: +access: controlled +status: +release: +synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] +lead_analysts: [Frank Grenn] +last_verified: +--- + # ROSMAP AC gene expression QTL Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) AC gene expression. diff --git a/content/xqtl-data/qtl/eQTL/ROSMAP_DLPFC_expression_qtl.md b/content/xqtl-data/qtl/eQTL/ROSMAP_DLPFC_expression_qtl.md index 7fe7b87..ef79d92 100644 --- a/content/xqtl-data/qtl/eQTL/ROSMAP_DLPFC_expression_qtl.md +++ b/content/xqtl-data/qtl/eQTL/ROSMAP_DLPFC_expression_qtl.md @@ -1,3 +1,18 @@ +--- +type: qtl +modality: eQTL +short_title: ROSMAP DLPFC +cohort: ROSMAP +context: DLPFC +sample_size: +access: controlled +status: +release: +synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] +lead_analysts: [Shrishtee Kandoi, Frank Grenn] +last_verified: +--- + # ROSMAP DLPFC gene expression QTL Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) DLPFC gene expression. diff --git a/content/xqtl-data/qtl/eQTL/ROSMAP_PCC_expression_qtl.md b/content/xqtl-data/qtl/eQTL/ROSMAP_PCC_expression_qtl.md index 8a31448..1868232 100644 --- a/content/xqtl-data/qtl/eQTL/ROSMAP_PCC_expression_qtl.md +++ b/content/xqtl-data/qtl/eQTL/ROSMAP_PCC_expression_qtl.md @@ -1,3 +1,18 @@ +--- +type: qtl +modality: eQTL +short_title: ROSMAP PCC +cohort: ROSMAP +context: PCC +sample_size: +access: controlled +status: +release: +synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] +lead_analysts: [Frank Grenn] +last_verified: +--- + # ROSMAP PCC Expression QTL Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) PCC alternative splicing. diff --git a/content/xqtl-data/qtl/eQTL/ROSMAP_microglia_expression_qtl.md b/content/xqtl-data/qtl/eQTL/ROSMAP_microglia_expression_qtl.md index 643032f..81bcdbd 100644 --- a/content/xqtl-data/qtl/eQTL/ROSMAP_microglia_expression_qtl.md +++ b/content/xqtl-data/qtl/eQTL/ROSMAP_microglia_expression_qtl.md @@ -1,3 +1,18 @@ +--- +type: qtl +modality: eQTL +short_title: ROSMAP microglia +cohort: ROSMAP +context: microglia +sample_size: +access: controlled +status: +release: +synapse_ids: [syn2580853, syn11468526, syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] +lead_analysts: [Travyse Edwards] +last_verified: +--- + # ROSMAP RNA-seq microglia gene expression QTL Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) microglia data-set. diff --git a/content/xqtl-data/qtl/eQTL/ROSMAP_monocyte_expression_qtl.md b/content/xqtl-data/qtl/eQTL/ROSMAP_monocyte_expression_qtl.md index 87c8e2c..62fb30c 100644 --- a/content/xqtl-data/qtl/eQTL/ROSMAP_monocyte_expression_qtl.md +++ b/content/xqtl-data/qtl/eQTL/ROSMAP_monocyte_expression_qtl.md @@ -1,3 +1,18 @@ +--- +type: qtl +modality: eQTL +short_title: ROSMAP monocyte +cohort: ROSMAP +context: monocyte +sample_size: +access: controlled +status: +release: +synapse_ids: [syn22024496, syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] +lead_analysts: [Travyse Edwards] +last_verified: +--- + # ROSMAP RNA-seq monocyte QTL Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) monocyte data-set. diff --git a/content/xqtl-data/qtl/eQTL/ROSMAP_snRNAseq_pseudo_bulk_qtl.md b/content/xqtl-data/qtl/eQTL/ROSMAP_snRNAseq_pseudo_bulk_qtl.md index 5069a46..9897967 100644 --- a/content/xqtl-data/qtl/eQTL/ROSMAP_snRNAseq_pseudo_bulk_qtl.md +++ b/content/xqtl-data/qtl/eQTL/ROSMAP_snRNAseq_pseudo_bulk_qtl.md @@ -1,3 +1,18 @@ +--- +type: qtl +modality: eQTL +short_title: ROSMAP snuc-eQTL +cohort: ROSMAP +context: "DLPFC, 7 cell types" +sample_size: +access: controlled +status: +release: +synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] +lead_analysts: [Hao Sun, Masashi Fujita] +last_verified: +--- + # ROSMAP snRNA-seq pseudo-bulk gene expression QTL Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) snRNA-seq from different cells in Dorsolateral Prefrontal Cortex (DLPFC). diff --git a/content/xqtl-data/qtl/eQTL/STARNET_macrophage_qtl.md b/content/xqtl-data/qtl/eQTL/STARNET_macrophage_qtl.md index a0b210f..5344cdc 100644 --- a/content/xqtl-data/qtl/eQTL/STARNET_macrophage_qtl.md +++ b/content/xqtl-data/qtl/eQTL/STARNET_macrophage_qtl.md @@ -1,3 +1,17 @@ +--- +type: qtl +modality: eQTL +short_title: STARNET macrophage +cohort: STARNET +context: macrophage +access: controlled +status: +release: +synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] +lead_analysts: [Travyse Edwards] +last_verified: +--- + # STARNET macrophage gene expression QTL STARNET is an RNA expression study of various disease-relevant tissues obtained from living patients with cardiovascular disease (CVD). The inclusion criterion for patients was eligibility for coronary artery by-pass graft (CABG) surgery. diff --git a/content/xqtl-data/qtl/gpQTL/ROSMAP_DLPFC_glycoproteomics_qtl.md b/content/xqtl-data/qtl/gpQTL/ROSMAP_DLPFC_glycoproteomics_qtl.md index d36f14c..a4f79cd 100644 --- a/content/xqtl-data/qtl/gpQTL/ROSMAP_DLPFC_glycoproteomics_qtl.md +++ b/content/xqtl-data/qtl/gpQTL/ROSMAP_DLPFC_glycoproteomics_qtl.md @@ -1,9 +1,11 @@ --- type: qtl modality: gpQTL +short_title: ROSMAP DLPFC cohort: ROSMAP context: DLPFC status: +access: synapse_ids: [syn69865744, syn70094703, syn76495192, syn77828034, syn76489398, syn76490205, syn75180848] lead_analysts: [] last_verified: diff --git a/content/xqtl-data/qtl/haQTL/ROSMAP_DLPFC_ChIPSeq_H3K9ac_qtl.md b/content/xqtl-data/qtl/haQTL/ROSMAP_DLPFC_ChIPSeq_H3K9ac_qtl.md index 63947e1..16ecdfb 100644 --- a/content/xqtl-data/qtl/haQTL/ROSMAP_DLPFC_ChIPSeq_H3K9ac_qtl.md +++ b/content/xqtl-data/qtl/haQTL/ROSMAP_DLPFC_ChIPSeq_H3K9ac_qtl.md @@ -1,3 +1,18 @@ +--- +type: qtl +modality: haQTL +short_title: ROSMAP DLPFC H3K9ac +cohort: ROSMAP +context: DLPFC +sample_size: +access: controlled +status: +release: +synapse_ids: [syn69670592, syn69670597, syn69865816, syn69670630] +lead_analysts: [Xuanhe Chen] +last_verified: +--- + # ROSMAP DLPFC H3K9ac QTL Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) h3k9ac QTL analysis using the FGC xQTL pipeline. diff --git a/content/xqtl-data/qtl/mQTL/Knight_ADRC_brain_methylation_qtl.md b/content/xqtl-data/qtl/mQTL/Knight_ADRC_brain_methylation_qtl.md index 9acc153..4da6ed4 100644 --- a/content/xqtl-data/qtl/mQTL/Knight_ADRC_brain_methylation_qtl.md +++ b/content/xqtl-data/qtl/mQTL/Knight_ADRC_brain_methylation_qtl.md @@ -1,3 +1,18 @@ +--- +type: qtl +modality: mQTL +short_title: Knight ADRC brain +cohort: Knight-ADRC +context: parietal cortex +sample_size: +access: controlled +status: +release: +synapse_ids: [syn69670592, syn69670597, syn69865816, syn69670630] +lead_analysts: [Alexandre Pelletier] +last_verified: +--- + # Knight ADRC brain methylation QTL ## Contact diff --git a/content/xqtl-data/qtl/mQTL/MSBB_brain_methylation_qtl.md b/content/xqtl-data/qtl/mQTL/MSBB_brain_methylation_qtl.md index 6a1f014..e153733 100644 --- a/content/xqtl-data/qtl/mQTL/MSBB_brain_methylation_qtl.md +++ b/content/xqtl-data/qtl/mQTL/MSBB_brain_methylation_qtl.md @@ -1,3 +1,18 @@ +--- +type: qtl +modality: mQTL +short_title: MSBB brain +cohort: MSBB +context: brain +sample_size: +access: controlled +status: +release: +synapse_ids: [syn69670592, syn69670597, syn69865816, syn69670630] +lead_analysts: [Alexandre Pelletier] +last_verified: +--- + # MSBB brain methylation QTL ## Contact diff --git a/content/xqtl-data/qtl/mQTL/ROSMAP_DLPFC_methylation_qtl.md b/content/xqtl-data/qtl/mQTL/ROSMAP_DLPFC_methylation_qtl.md index d935267..928b97b 100644 --- a/content/xqtl-data/qtl/mQTL/ROSMAP_DLPFC_methylation_qtl.md +++ b/content/xqtl-data/qtl/mQTL/ROSMAP_DLPFC_methylation_qtl.md @@ -1,3 +1,18 @@ +--- +type: qtl +modality: mQTL +short_title: ROSMAP DLPFC +cohort: ROSMAP +context: DLPFC +sample_size: +access: controlled +status: +release: +synapse_ids: [syn69670592, syn69670597, syn69865816, syn69670630] +lead_analysts: [Alexandre Pelletier] +last_verified: +--- + # ROSMAP DLPFC methylation QTL Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) DLPFC methylation data-set. diff --git a/content/xqtl-data/qtl/metQTL/Knight_ADRC_brain_metabolomics_qtl.md b/content/xqtl-data/qtl/metQTL/Knight_ADRC_brain_metabolomics_qtl.md index 04f9967..fccf108 100644 --- a/content/xqtl-data/qtl/metQTL/Knight_ADRC_brain_metabolomics_qtl.md +++ b/content/xqtl-data/qtl/metQTL/Knight_ADRC_brain_metabolomics_qtl.md @@ -1,3 +1,16 @@ +--- +type: qtl +modality: metQTL +short_title: Knight ADRC brain +cohort: Knight-ADRC +context: parietal cortex +access: controlled +status: +synapse_ids: [] +lead_analysts: [Zining Qi] +last_verified: +--- + # Knight ADRC brain metabolomics QTL ## Contact diff --git a/content/xqtl-data/qtl/metQTL/ROSMAP_DLPFC_metabolomics_qtl.md b/content/xqtl-data/qtl/metQTL/ROSMAP_DLPFC_metabolomics_qtl.md index 2367710..5a8a15a 100644 --- a/content/xqtl-data/qtl/metQTL/ROSMAP_DLPFC_metabolomics_qtl.md +++ b/content/xqtl-data/qtl/metQTL/ROSMAP_DLPFC_metabolomics_qtl.md @@ -1,3 +1,17 @@ +--- +type: qtl +modality: metQTL +short_title: ROSMAP DLPFC +cohort: ROSMAP +context: DLPFC +sample_size: +access: controlled +status: +synapse_ids: [syn69670592, syn69670597, syn69865816, syn69670630] +lead_analysts: [FunGen-xQTL Analysis Team] +last_verified: +--- + # ROSMAP DLPFC Brain Metabolomics QTL Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) brain tissue metabolomics QTL analysis. diff --git a/content/xqtl-data/qtl/pQTL/Knight_ADRC_brain_proteomics_qtl.md b/content/xqtl-data/qtl/pQTL/Knight_ADRC_brain_proteomics_qtl.md index d8693cb..890e4ff 100644 --- a/content/xqtl-data/qtl/pQTL/Knight_ADRC_brain_proteomics_qtl.md +++ b/content/xqtl-data/qtl/pQTL/Knight_ADRC_brain_proteomics_qtl.md @@ -1,3 +1,18 @@ +--- +type: qtl +modality: pQTL +short_title: Knight ADRC brain +cohort: Knight-ADRC +context: parietal cortex +sample_size: +access: controlled +status: +release: +synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] +lead_analysts: [Zining Qi] +last_verified: +--- + # Knight ADRC brain proteomics QTL Charles F. And Joanne Knight Alzheimer's Disease Research Center (Knight-ADRC) diff --git a/content/xqtl-data/qtl/pQTL/MSBB_proteomics_qtl.md b/content/xqtl-data/qtl/pQTL/MSBB_proteomics_qtl.md index 4879e45..b97ced9 100644 --- a/content/xqtl-data/qtl/pQTL/MSBB_proteomics_qtl.md +++ b/content/xqtl-data/qtl/pQTL/MSBB_proteomics_qtl.md @@ -1,3 +1,18 @@ +--- +type: qtl +modality: pQTL +short_title: MSBB brain +cohort: MSBB +context: brain +sample_size: +access: controlled +status: +release: +synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] +lead_analysts: [Minghui Wang] +last_verified: +--- + # MSBB brain proteomics QTL ## Contact diff --git a/content/xqtl-data/qtl/pQTL/ROSMAP_DLPFC_proteomics_qtl.md b/content/xqtl-data/qtl/pQTL/ROSMAP_DLPFC_proteomics_qtl.md index 20af49a..81d49ad 100644 --- a/content/xqtl-data/qtl/pQTL/ROSMAP_DLPFC_proteomics_qtl.md +++ b/content/xqtl-data/qtl/pQTL/ROSMAP_DLPFC_proteomics_qtl.md @@ -1,3 +1,18 @@ +--- +type: qtl +modality: pQTL +short_title: ROSMAP DLPFC +cohort: ROSMAP +context: DLPFC +sample_size: +access: controlled +status: +release: +synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] +lead_analysts: [Zining Qi] +last_verified: +--- + # ROSMAP DLPFC protein expression QTL Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) DLPFC protein expression. diff --git a/content/xqtl-data/qtl/sQTL/Knight_ADRC_brain_splicing_qtl.md b/content/xqtl-data/qtl/sQTL/Knight_ADRC_brain_splicing_qtl.md index daf3439..9074949 100644 --- a/content/xqtl-data/qtl/sQTL/Knight_ADRC_brain_splicing_qtl.md +++ b/content/xqtl-data/qtl/sQTL/Knight_ADRC_brain_splicing_qtl.md @@ -1,3 +1,18 @@ +--- +type: qtl +modality: sQTL +short_title: Knight ADRC brain +cohort: Knight-ADRC +context: parietal cortex +sample_size: +access: controlled +status: +release: +synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] +lead_analysts: [Xuanhe Chen] +last_verified: +--- + # Knight ADRC brain splicing QTL ## Contact diff --git a/content/xqtl-data/qtl/sQTL/MSBB_brain_splicing_qtl.md b/content/xqtl-data/qtl/sQTL/MSBB_brain_splicing_qtl.md index 8fafe83..bb262cf 100644 --- a/content/xqtl-data/qtl/sQTL/MSBB_brain_splicing_qtl.md +++ b/content/xqtl-data/qtl/sQTL/MSBB_brain_splicing_qtl.md @@ -1,3 +1,18 @@ +--- +type: qtl +modality: sQTL +short_title: MSBB brain +cohort: MSBB +context: 4 brain regions +sample_size: +access: controlled +status: +release: +synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] +lead_analysts: [Minghui Wang] +last_verified: +--- + # MSBB brain alternative splicing QTL ## Contact diff --git a/content/xqtl-data/qtl/sQTL/ROSMAP_AC_splicing_qtl.md b/content/xqtl-data/qtl/sQTL/ROSMAP_AC_splicing_qtl.md index 2d00f00..8406157 100644 --- a/content/xqtl-data/qtl/sQTL/ROSMAP_AC_splicing_qtl.md +++ b/content/xqtl-data/qtl/sQTL/ROSMAP_AC_splicing_qtl.md @@ -1,3 +1,18 @@ +--- +type: qtl +modality: sQTL +short_title: ROSMAP AC +cohort: ROSMAP +context: AC +sample_size: +access: controlled +status: +release: +synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] +lead_analysts: [Ru Feng] +last_verified: +--- + # ROSMAP AC alternative splicing QTL Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) AC alternative splicing. diff --git a/content/xqtl-data/qtl/sQTL/ROSMAP_DLPFC_splicing_qtl.md b/content/xqtl-data/qtl/sQTL/ROSMAP_DLPFC_splicing_qtl.md index ac4f3ff..8de8693 100644 --- a/content/xqtl-data/qtl/sQTL/ROSMAP_DLPFC_splicing_qtl.md +++ b/content/xqtl-data/qtl/sQTL/ROSMAP_DLPFC_splicing_qtl.md @@ -1,3 +1,18 @@ +--- +type: qtl +modality: sQTL +short_title: ROSMAP DLPFC +cohort: ROSMAP +context: DLPFC +sample_size: +access: controlled +status: +release: +synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] +lead_analysts: [Shrishtee Kandoi, Xuanhe Chen] +last_verified: +--- + # ROSMAP DLPFC alternative splicing QTL Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) DLPFC alternative splicing. diff --git a/content/xqtl-data/qtl/sQTL/ROSMAP_PCC_splicing_qtl.md b/content/xqtl-data/qtl/sQTL/ROSMAP_PCC_splicing_qtl.md index c19fb8c..ecc2d4f 100644 --- a/content/xqtl-data/qtl/sQTL/ROSMAP_PCC_splicing_qtl.md +++ b/content/xqtl-data/qtl/sQTL/ROSMAP_PCC_splicing_qtl.md @@ -1,3 +1,18 @@ +--- +type: qtl +modality: sQTL +short_title: ROSMAP PCC +cohort: ROSMAP +context: PCC +sample_size: +access: controlled +status: +release: +synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] +lead_analysts: [Frank Grenn] +last_verified: +--- + # ROSMAP PCC alternative splicing QTL Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) PCC alternative splicing. diff --git a/content/xqtl-data/qtl/sQTL/ROSMAP_snuc_splicing_qtl.md b/content/xqtl-data/qtl/sQTL/ROSMAP_snuc_splicing_qtl.md index 7170b4b..6c34b03 100644 --- a/content/xqtl-data/qtl/sQTL/ROSMAP_snuc_splicing_qtl.md +++ b/content/xqtl-data/qtl/sQTL/ROSMAP_snuc_splicing_qtl.md @@ -1,3 +1,17 @@ +--- +type: qtl +modality: sQTL +short_title: ROSMAP single-nucleus +cohort: ROSMAP +context: "DLPFC, 7 cell types" +sample_size: +access: controlled +status: +synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] +lead_analysts: [FunGen-xQTL Analysis Team] +last_verified: +--- + # ROSMAP Single-Nucleus Alternative Splicing QTL (snSplicing) Single-nucleus alternative splicing QTL analysis from CUIMC & MIT harmonized snRNA-seq / Multiome data across seven major cell types. diff --git a/content/xqtl-data/reference_data/ld_reference.md b/content/xqtl-data/reference_data/ld_reference.md index 33b98a2..4ac83f7 100644 --- a/content/xqtl-data/reference_data/ld_reference.md +++ b/content/xqtl-data/reference_data/ld_reference.md @@ -1,3 +1,16 @@ +--- +type: reference +short_title: LD reference panel +cohort: ADSP +sample_size: +access: controlled +status: +release: +synapse_ids: [syn53171227, syn69670651, syn69670652] +lead_analysts: [Oluwatosin Olayinka] +last_verified: +--- + # Non-Hispanic White Linkage Disequilibrium Reference Panel LD matrices calculated from whole genome sequencing data from 16571 non-Hispanic white individuals obtained from the Genome Center for Alzheimer's Disease (GCAD). Correlation matrices were calculated between SNPs within 1361 LD blocks which were obtained from [this Github page](https://github.com/jmacdon/LDblocks_GRCh38/) (generated from 1000 Genomes EUR samples). diff --git a/content/xqtl-data/study_info/KnightADRC.md b/content/xqtl-data/study_info/KnightADRC.md index 4234b6c..a8958f9 100644 --- a/content/xqtl-data/study_info/KnightADRC.md +++ b/content/xqtl-data/study_info/KnightADRC.md @@ -1,5 +1,6 @@ --- type: study +short_title: Knight-ADRC cohort: Knight-ADRC status: synapse_ids: [syn69670592, syn69670600, syn69670597, syn69865816] diff --git a/content/xqtl-data/study_info/MSBB.md b/content/xqtl-data/study_info/MSBB.md index 81c4f55..734303b 100644 --- a/content/xqtl-data/study_info/MSBB.md +++ b/content/xqtl-data/study_info/MSBB.md @@ -1,5 +1,6 @@ --- type: study +short_title: MSBB cohort: MSBB context: brain status: diff --git a/content/xqtl-data/study_info/MiGA.md b/content/xqtl-data/study_info/MiGA.md index 2da6c8b..9a7b6dd 100644 --- a/content/xqtl-data/study_info/MiGA.md +++ b/content/xqtl-data/study_info/MiGA.md @@ -1,5 +1,6 @@ --- type: study +short_title: MiGA cohort: MiGA context: microglia sample_size: 255 diff --git a/content/xqtl-data/study_info/ROSMAP.md b/content/xqtl-data/study_info/ROSMAP.md index ebf6db1..cd92b6e 100644 --- a/content/xqtl-data/study_info/ROSMAP.md +++ b/content/xqtl-data/study_info/ROSMAP.md @@ -1,5 +1,6 @@ --- type: study +short_title: ROSMAP cohort: ROSMAP context: brain status: diff --git a/content/xqtl-data/study_info/STARNET.md b/content/xqtl-data/study_info/STARNET.md index 90cf459..35dfca5 100644 --- a/content/xqtl-data/study_info/STARNET.md +++ b/content/xqtl-data/study_info/STARNET.md @@ -1,5 +1,6 @@ --- type: study +short_title: STARNET cohort: STARNET context: macrophage status: diff --git a/hugo.toml b/hugo.toml index 4de3f15..dd5238b 100644 --- a/hugo.toml +++ b/hugo.toml @@ -26,7 +26,7 @@ home = [ "HTML", "RSS"] # (Optional, default light) Sets color theme: light, dark or auto. # Theme 'auto' switches between dark and light modes based on browser/os preferences - BookTheme = 'light' + BookTheme = 'auto' # (Optional, default true) Controls table of contents visibility on right side of pages. # Start and end levels can be controlled with markup.tableOfContents setting. @@ -49,7 +49,7 @@ home = [ "HTML", "RSS"] # Set source repository location. # Used for 'Last Modified' and 'Edit this page' links. - BookRepo = 'https://github.com/cumc/xqtl-data' + BookRepo = 'https://github.com/StatFunGen/xqtl-resources' # Specifies commit portion of the link to the page's last modified commit hash for 'doc' page # type. @@ -87,7 +87,18 @@ home = [ "HTML", "RSS"] # /!\ This is an experimental feature, might be removed or changed at any time # (Optional, experimental, default false) Enables service worker that caches visited pages and resources for offline use. - BookServiceWorker = true + # Off: the site layouts in site/ do not register it, and a stale cache hides catalog updates + BookServiceWorker = false + + # Used by the site layouts in site/ (header links, home page numbers, edit links) + repoURL = 'https://github.com/StatFunGen/xqtl-resources' + repoBranch = 'main' + protocolURL = 'https://statfungen.github.io/xqtl-protocol' + atlasURL = 'https://xqtl.niagads.org/' + +[markup.tableOfContents] + startLevel = 2 + endLevel = 2 [markup.goldmark.renderer] unsafe = true diff --git a/scripts/audit_catalog.py b/scripts/audit_catalog.py index 4063b1e..c3394c7 100644 --- a/scripts/audit_catalog.py +++ b/scripts/audit_catalog.py @@ -37,7 +37,11 @@ def flag(p, check, detail=""): rows.append((rel(p), check, detail)) for p in pages: t = open(p, encoding="utf-8").read() lines = t.split("\n") - title = lines[0].lstrip("# ").strip() if lines and lines[0].startswith("#") else "" + # the title is the first heading after the optional YAML metadata header + body = lines + if t.startswith("---\n") and "\n---" in t[4:]: + body = t[t.find("\n---", 4) + 4:].lstrip("\n").split("\n") + title = body[0].lstrip("# ").strip() if body and body[0].startswith("#") else "" if not title: flag(p, "no_title") titles.setdefault(title, []).append(p) has_header = t.startswith("---\n") diff --git a/scripts/hugo_generator.py b/scripts/hugo_generator.py index ba7abbd..26a8f7e 100644 --- a/scripts/hugo_generator.py +++ b/scripts/hugo_generator.py @@ -14,8 +14,13 @@ import urllib.request import zipfile import tempfile +import json from pathlib import Path from collections import defaultdict +try: + import yaml +except ImportError: + yaml = None # Configuration defaults DEFAULT_CONTENT_DIR = 'content' @@ -23,6 +28,12 @@ DEFAULT_BASE_URL = 'https://statfungen.github.io/xqtl-resources/' DEFAULT_GITHUB_URL = 'https://github.com/StatFunGen/xqtl-resources/tree/main/' HUGO_BOOK_THEME_URL = 'https://github.com/alex-shpak/hugo-book/archive/refs/heads/master.zip' +# Site layouts, styles and data that override hugo-book (copied into the website directory) +DEFAULT_SITE_DIR = 'site' +# Header keys that are Hugo page settings rather than dataset metadata +HUGO_KEYS = {'layout', 'weight', 'description', 'linkTitle', 'bookHidden', 'bookToc'} +# Pages that use a dedicated layout, by source path relative to the content directory +PAGE_LAYOUTS = {'xqtl-data/README.md': 'catalog'} OMICS_TITLES = {'histone_ChIPSeq': 'Histone ChIP-seq', 'snATAC': 'snATAC-seq', 'snRNA_seq': 'snRNA-seq'} @@ -107,6 +118,23 @@ def download_theme(self, force=False): if os.path.exists(tmp_path): os.remove(tmp_path) + def copy_site_overlay(self, site_dir=DEFAULT_SITE_DIR): + """Copy the site layouts, styles, scripts and data that override hugo-book""" + if not os.path.isdir(site_dir): + self.log(f"No {site_dir}/ directory, using hugo-book defaults", 'warning') + return False + for name in os.listdir(site_dir): + src = os.path.join(site_dir, name) + dest = os.path.join(self.website_dir, name) + if os.path.isdir(src): + if os.path.exists(dest): + shutil.rmtree(dest) + shutil.copytree(src, dest) + else: + shutil.copy2(src, dest) + self.log(f"Copied site layouts and styles from {site_dir}/", 'success') + return True + def create_hugo_config(self): """Copy Hugo configuration file from source repository""" source_config = 'hugo.toml' @@ -140,7 +168,8 @@ def escape_braces(match, is_block=False): return f'```{code}```' if is_block else f'`{code}`' content = re.sub(r'```(.*?)```', lambda m: escape_braces(m, True), content, flags=re.DOTALL) - content = re.sub(r'`([^`]+)`', lambda m: escape_braces(m, False), content) + # Inline code never spans lines; matching across lines would pair backticks from different spans + content = re.sub(r'`([^`\n]+)`', lambda m: escape_braces(m, False), content) # Remove Pandoc-style attributes content = re.sub(r'\{\.[\w\s-]+\}', '', content) @@ -177,7 +206,63 @@ def strip_source_header(self, content): return content[end + 4:].lstrip('\n') return content - def add_frontmatter(self, content, title, filepath, depth_level=1): + def parse_source_header(self, content, filepath): + """Return the source metadata header as a dict, without the internal field""" + if not content.startswith('---\n') or content.find('\n---', 4) < 0: + return {} + if yaml is None: + self.log(f"PyYAML not installed, metadata header ignored: {filepath}", 'warning') + return {} + try: + meta = yaml.safe_load(content[4:content.find('\n---', 4)]) or {} + except yaml.YAMLError as e: + self.log(f"Invalid metadata header in {filepath}: {e}", 'warning') + return {} + if not isinstance(meta, dict): + return {} + meta.pop('internal', None) + return meta + + def split_title_and_lead(self, content): + """Remove the first-level heading (the layout prints the title) and the opening + paragraphs before the first section heading (the layout prints them as the lead). + Returns (lead, body). Nothing is dropped: the lead is shown above the body.""" + lines = content.split('\n') + i = 0 + while i < len(lines) and not lines[i].strip(): + i += 1 + if i < len(lines) and re.match(r'^#\s+', lines[i]): + lines = lines[i + 1:] + else: + return '', content + # Lead: up to two plain paragraphs. Stop at headings, lists, tables, code, HTML and rules + block_start = re.compile(r'^\s*(#|\||[-*+]\s|\d+\.\s|```|<|>|---|\*\*\*|\{\{)') + lead, para, n_para, j = [], [], 0, 0 + while j < len(lines): + line = lines[j] + if not line.strip(): + if para: + lead.append('\n'.join(para)) + para, n_para = [], n_para + 1 + if n_para == 2: + break + j += 1 + continue + if block_start.match(line): + break + para.append(line) + j += 1 + if para: + # a paragraph that runs straight into a list or heading stays in the body + j -= len(para) + return '\n\n'.join(lead), '\n'.join(lines[j:]).lstrip('\n') + + def is_generated_list(self, content): + """True for section READMEs written by toc.py --subfolder-readme (a title and links only)""" + lines = [l for l in content.split('\n') if l.strip()] + return bool(lines) and all(re.match(r'^(#\s|\*\s+\[[^\]]+\]\([^)]+\)\s*$)', l) for l in lines) + + def add_frontmatter(self, content, title, filepath, depth_level=1, meta=None, extra=None): """Add Hugo frontmatter to markdown content Hugo Book theme automatically generates navigation based on: @@ -206,10 +291,23 @@ def add_frontmatter(self, content, title, filepath, depth_level=1): title: "{safe_title}" weight: {weight} bookToc: true -{book_collapse}{book_hidden}--- - -""" - return frontmatter + content +{book_collapse}{book_hidden}""" + # Page settings from the source header, then dataset metadata under one key + # so that fields such as `type` do not collide with Hugo's own front matter + fields = {} + meta = dict(meta or {}) + for key in list(meta): + if key in HUGO_KEYS: + fields[key] = meta.pop(key) + if meta.get('short_title'): + fields.setdefault('linkTitle', meta['short_title']) + if meta: + fields['dataset'] = meta + fields.update(extra or {}) + for key, value in fields.items(): + # JSON is valid YAML, and it keeps dates and lists unambiguous + frontmatter += f"{key}: {json.dumps(value, default=str, ensure_ascii=False)}\n" + return frontmatter + "---\n\n" + content def process_markdown_file(self, source_file, dest_file, depth_level=1): """Process a single markdown file with all transformations""" @@ -218,16 +316,28 @@ def process_markdown_file(self, source_file, dest_file, depth_level=1): with open(source_file, 'r', encoding='utf-8', errors='replace') as f: content = f.read() - # Strip the optional source metadata header (--- ... ---) so that it is not - # rendered and does not collide with the Hugo front matter added below + # Read the optional source metadata header (--- ... ---), then strip it so that it + # is not rendered. Its public fields are passed to the layouts as front matter. + meta = self.parse_source_header(content, source_file) content = self.strip_source_header(content) # Extract title and sanitize content title = self.extract_title_from_content(content, source_file) content = self.sanitize_markdown_content(content) - + + rel_path = os.path.relpath(source_file, self.source_content_dir).replace(os.sep, '/') + extra = {'source_path': f"{self.source_content_dir}/{rel_path}"} + if rel_path in PAGE_LAYOUTS: + extra['layout'] = PAGE_LAYOUTS[rel_path] + if self.is_generated_list(content): + extra['generated_list'] = True + else: + lead, content = self.split_title_and_lead(content) + if lead: + extra['lead'] = lead + # Add frontmatter - content = self.add_frontmatter(content, title, source_file, depth_level) + content = self.add_frontmatter(content, title, source_file, depth_level, meta, extra) # Ensure destination directory exists os.makedirs(os.path.dirname(dest_file), exist_ok=True) @@ -622,7 +732,8 @@ def run_full_pipeline(self, download_theme=True, generate_readme=True, self.log("Theme download failed but continuing...", 'warning') else: self.log("\nStep 2: Skipping theme download", 'info') - + self.copy_site_overlay() + # Step 3: Content self.log("\nStep 3: Processing content files...", 'info') file_count = self.copy_content_files() diff --git a/site/README.md b/site/README.md new file mode 100644 index 0000000..e0ded51 --- /dev/null +++ b/site/README.md @@ -0,0 +1,20 @@ +# Site layouts + +The files here override the hugo-book theme. `scripts/hugo_generator.py` copies this folder into `website/` before Hugo runs, so authors keep editing Markdown in `content/` only. + +| Path | What it does | +|---|---| +| `layouts/baseof.html` | Page shell: header with search and theme toggle, left menu, content, "On this page" | +| `layouts/home.html` | Home page. Counts are computed from the dataset pages; the Markdown in `content/README.md` is shown under it | +| `layouts/catalog.html`, `assets/xqtl/catalog.js` | Data catalog: cohort x modality matrix, facets and table. Every row is in the HTML, so it works without JavaScript. Filters are kept in the URL, for example `?kind=qtl&cohort=ROSMAP&family=Expression` | +| `layouts/page.html`, `layouts/_partials/ds/page.html` | Dataset page: summary card and access table from the metadata header, then the page's Markdown, then Analyses and Related datasets | +| `layouts/section.html` | Folder pages (eQTL, Expression ...): a table of the datasets in the folder | +| `layouts/inventory.html`, `layouts/coverage.html` | Dataset inventory and analysis coverage grid | +| `layouts/_partials/ds/info.html` | Works out a page's kind, modality label, colour, status and access in one place | +| `data/xqtl.yaml` | Shared vocabulary: modality colours and labels, cohorts, status and access wording, Synapse folders, home page participant count | +| `data/next_phase.yaml` | Datasets being curated that do not have a page yet | +| `assets/xqtl/site.css` | All styles. Colour tokens at the top, light and dark | + +Page metadata lives in each page's header; see `template/metadata_header.md`. + +To preview locally: install Hugo extended (0.158 or newer) and PyYAML, clone hugo-book into `website/themes/hugo-book`, then run `python scripts/hugo_generator.py --no-theme-download --no-readme --serve`. diff --git a/site/assets/xqtl/catalog.js b/site/assets/xqtl/catalog.js new file mode 100644 index 0000000..95b9e7d --- /dev/null +++ b/site/assets/xqtl/catalog.js @@ -0,0 +1,147 @@ +// Data catalog filters. Rows, facets and the cohort x modality matrix are rendered by +// layouts/catalog.html; this script shows and hides rows in place. Filter state is kept +// in the URL (?q=&cohort=&family=...) so a filtered view can be linked, for example from +// the coverage matrix on the home page. +(function () { + var root = document.querySelector('[data-catalog]'); + if (!root) return; + + var KEYS = ['kind', 'cohort', 'family', 'tissue', 'status', 'access']; + var rows = Array.prototype.slice.call(root.querySelectorAll('[data-row]')); + var opts = Array.prototype.slice.call(root.querySelectorAll('[data-facet]')); + var qInput = root.querySelector('[data-q]'); + var countEl = root.querySelector('[data-count]'); + var emptyEl = root.querySelector('[data-empty]'); + var filterCountEl = root.querySelector('[data-filter-count]'); + var clearBtns = root.querySelectorAll('[data-clear]'); + var state = { q: '' }; + KEYS.forEach(function (k) { state[k] = null; }); + + // Read the initial state from the URL + var params = new URLSearchParams(location.search); + KEYS.forEach(function (k) { if (params.get(k)) state[k] = params.get(k); }); + state.q = params.get('q') || ''; + qInput.value = state.q; + + function matches(row, except) { + for (var i = 0; i < KEYS.length; i++) { + var k = KEYS[i]; + if (k !== except && state[k] && row.dataset[k] !== state[k]) return false; + } + var q = state.q.trim().toLowerCase(); + if (q) { + var words = q.split(/\s+/); + for (var j = 0; j < words.length; j++) if (row.dataset.search.indexOf(words[j]) < 0) return false; + } + return true; + } + + function writeURL() { + var p = new URLSearchParams(); + if (state.q) p.set('q', state.q); + KEYS.forEach(function (k) { if (state[k]) p.set(k, state[k]); }); + var s = p.toString(); + history.replaceState(null, '', location.pathname + (s ? '?' + s : '') + location.hash); + } + + function render() { + var shown = 0; + rows.forEach(function (r) { + var ok = matches(r); + r.hidden = !ok; + if (ok) shown++; + }); + // Facet counts: how many rows each option would give, given the other filters + opts.forEach(function (o) { + var k = o.dataset.facet, v = o.dataset.value, on = state[k] === v; + var n = 0; + rows.forEach(function (r) { if (r.dataset[k] === v && matches(r, k)) n++; }); + o.setAttribute('aria-pressed', on ? 'true' : 'false'); + var c = o.querySelector('[data-count-for]'); + if (c) c.textContent = n; + if (o.classList.contains('fopt')) o.disabled = !n && !on; + }); + // Matrix: highlight the selected cell, row or column, dim the rest + root.querySelectorAll('[data-matrix-cell]').forEach(function (b) { + var cf = b.dataset.matrixCell.split('|'); + var on = state.cohort === cf[0] && state.family === cf[1]; + var dim = (state.cohort && state.cohort !== cf[0]) || (state.family && state.family !== cf[1]); + b.setAttribute('aria-pressed', on ? 'true' : 'false'); + b.classList.toggle('is-dim', !!dim); + }); + root.querySelectorAll('[data-matrix-row]').forEach(function (tr) { + tr.classList.toggle('is-selected', state.cohort === tr.dataset.matrixRow); + }); + root.querySelectorAll('[data-matrix-col]').forEach(function (b) { + b.classList.toggle('is-selected', state.family === b.dataset.matrixCol); + }); + var nF = KEYS.filter(function (k) { return state[k]; }).length; + countEl.textContent = shown + ' of ' + rows.length + ' shown'; + emptyEl.hidden = shown > 0; + if (filterCountEl) filterCountEl.textContent = nF; + clearBtns.forEach(function (b) { if (b.closest('.catalog__mobilebar')) b.hidden = !(nF || state.q); }); + writeURL(); + } + + opts.forEach(function (o) { + o.addEventListener('click', function () { + var k = o.dataset.facet, v = o.dataset.value; + state[k] = state[k] === v ? null : v; + render(); + }); + }); + + var t; + qInput.addEventListener('input', function () { + clearTimeout(t); + t = setTimeout(function () { state.q = qInput.value; render(); }, 120); + }); + + clearBtns.forEach(function (b) { + b.addEventListener('click', function () { + KEYS.forEach(function (k) { state[k] = null; }); + state.q = ''; qInput.value = ''; + render(); + }); + }); + + root.querySelectorAll('[data-matrix-cell]').forEach(function (b) { + b.addEventListener('click', function () { + var cf = b.dataset.matrixCell.split('|'); + var on = state.cohort === cf[0] && state.family === cf[1]; + state.cohort = on ? null : cf[0]; + state.family = on ? null : cf[1]; + state.kind = on ? null : 'qtl'; + render(); + }); + }); + root.querySelectorAll('[data-matrix-row-btn]').forEach(function (b) { + b.addEventListener('click', function () { + var c = b.dataset.matrixRowBtn, on = state.cohort === c && !state.family; + state.cohort = on ? null : c; state.family = null; + render(); + }); + }); + root.querySelectorAll('[data-matrix-col]').forEach(function (b) { + b.addEventListener('click', function () { + var f = b.dataset.matrixCol, on = state.family === f && !state.cohort; + state.family = on ? null : f; state.cohort = null; + render(); + }); + }); + + // Phones: facets open as a sheet + var facets = root.querySelector('#facets'); + var openBtn = root.querySelector('[data-filters-open]'); + var closeBtn = root.querySelector('[data-filters-close]'); + function sheet(open) { + facets.classList.toggle('is-open', open); + openBtn.setAttribute('aria-expanded', open ? 'true' : 'false'); + if (open) facets.querySelector('button').focus(); else openBtn.focus(); + } + openBtn.addEventListener('click', function () { sheet(true); }); + closeBtn.addEventListener('click', function () { sheet(false); }); + facets.addEventListener('keydown', function (e) { if (e.key === 'Escape') sheet(false); }); + + render(); +})(); diff --git a/site/assets/xqtl/site.css b/site/assets/xqtl/site.css new file mode 100644 index 0000000..e3c3f13 --- /dev/null +++ b/site/assets/xqtl/site.css @@ -0,0 +1,631 @@ +/* FunGen-xQTL Resources: site styles. + Tokens follow the style guide (design 5a). Light is the default; dark applies under + prefers-color-scheme or the header toggle (data-theme on ). 4-px spacing base; + radius 6 controls, 8 chips and code, 10-12 cards; 1-px borders, no shadows. */ + +/* ---------- Tokens ---------- */ +:root { + --bg: #f8f9f9; + --sf: #ffffff; + --sk: #f1f3f4; + --ink: #15191e; + --ink2: #47505b; + --ink3: #626b77; + --ln: #e0e4e8; + --pr: #22313f; + --on-pr: #ffffff; + --ac: oklch(0.55 0.18 38); + --acs: oklch(0.96 0.02 245); + --okb: oklch(0.94 0.05 155); + --okf: oklch(0.4 0.1 155); + --stb: oklch(0.94 0.07 85); + --stf: oklch(0.43 0.09 70); + --code: #f1f3f4; + --empty: #dfe3e6; + --dim: #cfd5da; + --next: oklch(0.985 0.012 60); + --mk-ink: #22313f; + --mk-mute: #b8c0c8; + + --sans: 'IBM Plex Sans', system-ui, -apple-system, 'Segoe UI', sans-serif; + --mono: 'IBM Plex Mono', ui-monospace, Menlo, Consolas, monospace; + --serif: 'Source Serif 4', Georgia, 'Times New Roman', serif; + --topbar: 56px; + color-scheme: light; +} +@media (prefers-color-scheme: dark) { + :root:not([data-theme="light"]) { + --bg: #111417; --sf: #181c20; --sk: #20252a; --ink: #e8ebee; --ink2: #b3bac2; --ink3: #8d959f; + --ln: #2c3238; --pr: oklch(0.86 0.04 240); --on-pr: #111417; --ac: oklch(0.74 0.15 45); + --acs: oklch(0.3 0.04 245); --okb: oklch(0.33 0.05 155); --okf: oklch(0.87 0.1 155); + --stb: oklch(0.35 0.05 85); --stf: oklch(0.9 0.09 85); --code: #0d1013; + --empty: #2a3036; --dim: #3a424a; --next: oklch(0.24 0.02 60); + --mk-ink: #dfe5ea; --mk-mute: #4a545e; + color-scheme: dark; + } +} +:root[data-theme="dark"] { + --bg: #111417; --sf: #181c20; --sk: #20252a; --ink: #e8ebee; --ink2: #b3bac2; --ink3: #8d959f; + --ln: #2c3238; --pr: oklch(0.86 0.04 240); --on-pr: #111417; --ac: oklch(0.74 0.15 45); + --acs: oklch(0.3 0.04 245); --okb: oklch(0.33 0.05 155); --okf: oklch(0.87 0.1 155); + --stb: oklch(0.35 0.05 85); --stf: oklch(0.9 0.09 85); --code: #0d1013; + --empty: #2a3036; --dim: #3a424a; --next: oklch(0.24 0.02 60); + --mk-ink: #dfe5ea; --mk-mute: #4a545e; + color-scheme: dark; +} + +/* ---------- Base ---------- */ +*, *::before, *::after { box-sizing: border-box; } +html { -webkit-text-size-adjust: 100%; scroll-padding-top: calc(var(--topbar) + 16px); } +body { + margin: 0; background: var(--bg); color: var(--ink); + font: 400 15px/1.6 var(--sans); -webkit-font-smoothing: antialiased; +} +a { color: inherit; text-decoration: none; } +a:hover { text-decoration: underline; } +:focus-visible { outline: 2px solid var(--ac); outline-offset: 2px; border-radius: 3px; } +button { font: inherit; color: inherit; } +img { max-width: 100%; height: auto; } +code, kbd, pre { font-family: var(--mono); } +[hidden] { display: none !important; } +.sr-only { position: absolute; width: 1px; height: 1px; overflow: hidden; clip: rect(0 0 0 0); white-space: nowrap; } +.skip-link { position: absolute; left: 8px; top: -48px; z-index: 50; background: var(--pr); color: var(--on-pr); padding: 8px 12px; border-radius: 6px; } +.skip-link:focus { top: 8px; } + +.mono { font-family: var(--mono); } +.strong { font-weight: 600; } +.muted { color: var(--ink2); } +.subtle { color: var(--ink3); } +.accent { color: var(--ac); } +.nowrap { white-space: nowrap; } +.r { text-align: right; } +.label { font: 500 10.5px/1.2 var(--mono); letter-spacing: .08em; text-transform: uppercase; color: var(--ink3); } +.eyebrow { font: 500 11.5px/1.2 var(--mono); letter-spacing: .06em; text-transform: uppercase; color: var(--ac); } +.note { margin: 0; font-size: 12.5px; line-height: 1.5; color: var(--ink3); } +.note a { color: var(--ac); } +.link { color: var(--ac); font-weight: 500; background: none; border: 0; padding: 0; cursor: pointer; font-size: inherit; } +.link--strong { font-weight: 600; } + +/* ---------- Header ---------- */ +.topbar { + position: sticky; top: 0; z-index: 30; height: var(--topbar); + display: flex; align-items: center; gap: 20px; padding: 0 20px; + background: var(--sf); border-bottom: 1px solid var(--ln); +} +.brand { display: flex; align-items: center; gap: 10px; width: 228px; flex: none; } +.brand:hover { text-decoration: none; } +.brand__name { font: 700 17px/1 var(--serif); letter-spacing: -.005em; white-space: nowrap; } +.brand__sub { font-weight: 600; color: var(--ink2); } +.logo-mark { flex: none; display: block; } +.logo-mark .lm-line { fill: var(--ac); opacity: .5; } +.logo-mark .lm-ink { fill: var(--mk-ink); } +.logo-mark .lm-mute { fill: var(--mk-mute); } +.logo-mark .lm-lead { fill: var(--ac); } + +.search { + position: relative; flex: 1; max-width: 520px; height: 36px; + display: flex; align-items: center; gap: 10px; padding: 0 12px; + border: 1px solid var(--ln); border-radius: 8px; background: var(--bg); +} +.search:focus-within { border-color: var(--ink3); } +.search__icon { width: 11px; height: 11px; flex: none; border: 1.5px solid var(--ink3); border-radius: 50%; position: relative; } +.search__icon::after { content: ""; position: absolute; width: 5px; height: 1.5px; background: var(--ink3); right: -4px; bottom: -2px; transform: rotate(45deg); } +.search input { flex: 1; min-width: 0; border: 0; outline: 0; background: transparent; font: 400 13.5px var(--sans); color: var(--ink); } +.search input::placeholder { color: var(--ink3); } +.search input::-webkit-search-cancel-button { display: none; } +.search__key { font: 500 11px var(--mono); color: var(--ink3); border: 1px solid var(--ln); border-radius: 4px; padding: 1px 5px; } +.search__results { + position: absolute; left: -1px; right: -1px; top: calc(100% + 6px); margin: 0; padding: 0; list-style: none; + background: var(--sf); border: 1px solid var(--ln); border-radius: 10px; overflow: hidden; +} +.search__results:empty { display: none; } +.search__results li + li { border-top: 1px solid var(--ln); } +.search__results a { display: block; padding: 10px 14px 2px; font-weight: 600; font-size: 14px; } +.search__results small { display: block; padding: 0 14px 10px; color: var(--ink2); font-size: 12.5px; line-height: 1.45; } +.search__results mark { background: var(--acs); color: inherit; border-radius: 2px; } + +.topbar__links { margin-left: auto; display: flex; align-items: center; gap: 18px; font-size: 13.5px; color: var(--ink2); white-space: nowrap; } +.icon-btn { + width: 32px; height: 32px; flex: none; display: grid; place-items: center; cursor: pointer; + border: 1px solid var(--ln); border-radius: 8px; background: var(--sf); color: var(--ink2); +} +.theme-toggle__icon { width: 12px; height: 12px; border-radius: 50%; border: 1.5px solid currentColor; background: linear-gradient(90deg, currentColor 50%, transparent 50%); } +:root[data-theme-pref="light"] .theme-toggle__icon { background: transparent; } +:root[data-theme-pref="dark"] .theme-toggle__icon { background: currentColor; } +.topbar__menu { display: none; border: 0; width: 44px; height: 44px; } +.burger { display: flex; flex-direction: column; gap: 4px; } +.burger span { width: 18px; height: 2px; background: var(--ink); display: block; } + +/* ---------- Shell ---------- */ +.shell { display: grid; grid-template-columns: 248px minmax(0, 1fr) auto; align-items: start; min-height: calc(100vh - var(--topbar)); } +.nav-toggle { position: absolute; opacity: 0; pointer-events: none; } +.nav-scrim { display: none; } +.sidenav { + position: sticky; top: var(--topbar); height: calc(100vh - var(--topbar)); overflow-y: auto; + border-right: 1px solid var(--ln); padding: 22px 12px 40px; overscroll-behavior: contain; +} +.main { min-width: 0; outline: none; } + +/* ---------- Left menu ---------- */ +.nav { display: flex; flex-direction: column; gap: 20px; } +.nav ul { list-style: none; margin: 0; padding: 0; display: flex; flex-direction: column; gap: 1px; } +.nav-group__title { font: 500 10.5px/1 var(--mono); letter-spacing: .08em; text-transform: uppercase; color: var(--ink3); padding: 0 10px 8px; } +.nav-item { display: flex; align-items: center; gap: 9px; padding: 5px 10px; border-radius: 6px; font-size: 13.5px; line-height: 1.35; color: var(--ink); } +.nav-item:hover { background: var(--sk); text-decoration: none; } +.nav-item.is-active { color: var(--ac); background: var(--acs); font-weight: 600; } +.nav-item.is-open { font-weight: 600; } +.nav-item--sub { margin-left: 17px; } +.nav-item__label { flex: 1; min-width: 0; } +.nav-item__hint { font-size: 11.5px; font-weight: 400; color: var(--ink3); } + +/* ---------- Marks, badges, access ---------- */ +.sq { width: 9px; height: 9px; flex: none; display: inline-block; border-radius: 2px; vertical-align: -1px; margin-right: 7px; } +.nav .sq, .fopt .sq { width: 8px; height: 8px; margin-right: 0; } +.sq--fill { background: var(--c); } +.sq--ring { box-shadow: inset 0 0 0 1.5px var(--c); } +.sq--muted { background: var(--ink3); } +.sq--none { background: transparent; } + +.badge { + display: inline-flex; align-items: center; gap: 5px; height: 22px; padding: 0 8px; border-radius: 11px; + font: 600 11.5px var(--sans); white-space: nowrap; +} +.badge::before { content: ""; width: 6px; height: 6px; border-radius: 50%; background: currentColor; } +.badge--released { background: var(--okb); color: var(--okf); } +.badge--staged { background: var(--stb); color: var(--stf); } +.badge--planned, .badge--deprecated { background: transparent; color: var(--ink2); box-shadow: inset 0 0 0 1px var(--ln); } + +.acc { display: inline-flex; align-items: center; gap: 6px; font-size: 12.5px; color: var(--ink2); white-space: nowrap; } +.acc__mark { width: 9px; height: 9px; flex: none; box-shadow: inset 0 0 0 1.5px var(--ink2); } +.acc--controlled .acc__mark { border-radius: 2px; background: var(--ink2); } +.acc--open .acc__mark { border-radius: 50%; } +.acc--requested .acc__mark { border-radius: 50%; background: linear-gradient(90deg, var(--ink2) 50%, transparent 50%); } +.acc--pending .acc__mark { border-radius: 2px; background: transparent; } + +/* ---------- Buttons, chips, cards ---------- */ +.btn { + display: inline-flex; align-items: center; justify-content: center; gap: 6px; height: 36px; padding: 0 14px; + border: 1px solid var(--ln); border-radius: 8px; background: var(--sf); color: var(--ink); + font: 500 14px var(--sans); cursor: pointer; white-space: nowrap; +} +.btn:hover { text-decoration: none; border-color: var(--ink3); } +.btn--primary { background: var(--pr); border-color: var(--pr); color: var(--on-pr); font-weight: 600; } +.btn--primary:hover { border-color: var(--pr); filter: brightness(1.12); } +.btn--lg { height: 40px; padding: 0 18px; } +.btn--sm { height: 30px; padding: 0 10px; font-size: 12.5px; border-radius: 6px; } +.btn--outline { border-color: var(--ink); font-weight: 600; } +.btn--ghost { border-color: transparent; background: transparent; color: var(--ac); } + +.chip { + display: inline-flex; align-items: center; gap: 8px; min-height: 34px; padding: 0 12px; + border: 1px solid var(--ln); background: var(--sf); border-radius: 8px; font-size: 13.5px; +} +.chip .sq { margin-right: 0; } +.chip:hover { text-decoration: none; border-color: var(--ink3); } +.chip--mono { font: 500 12.5px var(--mono); color: var(--ac); min-height: 28px; padding: 0 8px; } + +.card { background: var(--sf); border: 1px solid var(--ln); border-radius: 10px; } + +/* ---------- Page ---------- */ +.page { padding: 32px 56px 64px; display: flex; flex-direction: column; gap: 40px; max-width: 1040px; } +.page__head { display: flex; flex-direction: column; gap: 14px; } +.crumbs { display: flex; flex-wrap: wrap; gap: 6px; font-size: 13px; color: var(--ink3); } +.page__title { margin: 0; font: 700 34px/1.15 var(--serif); letter-spacing: -.015em; text-wrap: balance; } +.page__lead { font-size: 16.5px; line-height: 1.6; color: var(--ink2); max-width: 720px; text-wrap: pretty; } +.page__lead p { margin: 0 0 10px; } +.page__lead p:last-child { margin-bottom: 0; } +.page__lead a, .prose a, .muted a { color: var(--ac); } +.page__foot { border-top: 1px solid var(--ln); padding-top: 16px; display: flex; justify-content: space-between; gap: 16px; font-size: 13px; color: var(--ink3); } +.page__foot a { color: var(--ac); } + +/* Right-hand "On this page" */ +.pagetoc { width: 200px; position: sticky; top: var(--topbar); padding: 40px 20px 24px 0; max-height: calc(100vh - var(--topbar)); overflow-y: auto; font-size: 13px; color: var(--ink2); } +.pagetoc__title { font: 500 10.5px var(--mono); letter-spacing: .08em; text-transform: uppercase; color: var(--ink3); padding-bottom: 8px; } +.pagetoc ul { list-style: none; margin: 0; padding: 0; display: flex; flex-direction: column; gap: 8px; } +.pagetoc a { display: block; padding-left: 10px; margin-left: -12px; border-left: 2px solid transparent; line-height: 1.35; } +.pagetoc a.is-current { color: var(--ink); font-weight: 600; border-left-color: var(--ac); } + +/* ---------- Summary card (dataset page) ---------- */ +.summary { border-radius: 12px; overflow: hidden; } +.summary__grid { display: grid; grid-template-columns: repeat(4, minmax(0, 1fr)); margin: 0; } +.summary__cell { padding: 16px 20px; border-right: 1px solid var(--ln); border-bottom: 1px solid var(--ln); margin-right: -1px; display: flex; flex-direction: column; gap: 6px; min-width: 0; } +.summary__cell dt { font: 500 10.5px var(--mono); letter-spacing: .08em; text-transform: uppercase; color: var(--ink3); } +.summary__cell dd { margin: 0; display: flex; align-items: center; font-size: 15px; font-weight: 600; overflow-wrap: anywhere; } +.summary__cell dd .sq { width: 10px; height: 10px; margin-right: 8px; } +.summary__cell dd.num { font-family: var(--mono); font-weight: 500; } +.summary__cell dd.summary__sub { font-size: 12.5px; font-weight: 400; color: var(--ink2); } +.summary__cell dd a:hover { color: var(--ac); } +.summary__cell .acc { font-size: 15px; font-weight: 600; color: var(--ink); gap: 8px; } +.summary__cell .acc__mark { width: 10px; height: 10px; } +.summary__bar { display: flex; align-items: center; flex-wrap: wrap; gap: 10px 12px; padding: 16px 20px; background: var(--acs); margin-top: -1px; } +.summary__bar .label { color: var(--ink2); } +.summary__id { font: 600 16px var(--mono); color: var(--ink); } +.summary__bar .spacer { flex: 1; } +.summary__bar .link { font-size: 13.5px; } + +/* ---------- Dataset sections and Markdown body ---------- */ +.ds-section { display: flex; flex-direction: column; gap: 14px; } +.ds-section h2, .prose h2 { margin: 0; font: 600 22px/1.3 var(--sans); padding-bottom: 10px; border-bottom: 1px solid var(--ln); } +.ds-section > p { margin: 0; font-size: 14.5px; line-height: 1.6; max-width: 720px; } +.ds-section .codeblock { margin: 0; } +.ids { display: flex; flex-wrap: wrap; align-items: center; gap: 6px; margin: 0; } +.ids .label { margin-right: 6px; } + +.prose { font-size: 15px; line-height: 1.65; color: var(--ink); max-width: 820px; overflow-wrap: break-word; } +.prose > :first-child { margin-top: 0; } +.prose h2 { margin: 44px 0 16px; } +.prose h3 { margin: 28px 0 10px; font: 600 17px/1.35 var(--sans); } +.prose h4, .prose h5, .prose h6 { margin: 22px 0 8px; font: 600 15px/1.4 var(--sans); } +.prose p, .prose ul, .prose ol, .prose blockquote, .prose dl { margin: 0 0 14px; } +.prose ul, .prose ol { padding-left: 22px; } +.prose li { margin: 3px 0; } +.prose li > ul, .prose li > ol { margin: 4px 0; } +.prose strong { font-weight: 600; } +.prose hr { border: 0; border-top: 1px solid var(--ln); margin: 28px 0; } +.prose blockquote { padding: 12px 14px; border-radius: 8px; background: var(--acs); color: var(--ink); } +.prose blockquote > :last-child { margin-bottom: 0; } +.prose :not(pre) > code { font: 500 .87em var(--mono); background: var(--sk); padding: 2px 5px; border-radius: 5px; overflow-wrap: anywhere; } +.prose img { border-radius: 8px; border: 1px solid var(--ln); } +.prose table, .dtable { + width: 100%; border-collapse: separate; border-spacing: 0; margin: 0 0 16px; + font-size: 13.5px; line-height: 1.45; background: var(--sf); + border: 1px solid var(--ln); border-radius: 10px; overflow: hidden; +} +.prose table { display: block; overflow-x: auto; width: max-content; max-width: 100%; } +.prose th, .dtable th { + text-align: left; padding: 10px 14px; background: var(--sk); white-space: nowrap; + font: 500 11px var(--mono); letter-spacing: .05em; text-transform: uppercase; color: var(--ink3); +} +.prose td, .dtable td { padding: 9px 14px; border-top: 1px solid var(--ln); vertical-align: baseline; } +.dtable th.r, .dtable td.r { text-align: right; } +.dtable td .mono, .dtable td.mono { font-size: 12.5px; } +.table-card { overflow-x: auto; border-radius: 10px; } +.table-card .dtable { margin: 0; } +.dtable .strong { font-weight: 600; } +.dtable a.mono { color: var(--ac); font-weight: 500; } +.dtable code { font: 500 12px var(--mono); } +.dtable--list td:first-child a:hover { color: var(--ac); } + +/* Code blocks */ +.codeblock { border: 1px solid var(--ln); border-radius: 10px; overflow: hidden; margin: 0 0 16px; background: var(--code); } +.codeblock__bar { display: flex; align-items: center; justify-content: space-between; padding: 6px 8px 6px 14px; background: var(--sk); border-bottom: 1px solid var(--ln); font: 500 12px var(--mono); color: var(--ink2); } +.codeblock__copy { border: 0; background: transparent; color: var(--ink2); font: 500 12px var(--mono); cursor: pointer; padding: 2px 6px; border-radius: 4px; } +.codeblock__copy:hover { background: var(--ln); } +.codeblock pre, .codeblock .highlight pre { margin: 0; padding: 14px 16px; overflow-x: auto; background: transparent !important; font: 400 13px/1.7 var(--mono); color: var(--ink); } +.codeblock code { font: inherit; background: none; padding: 0; } +.chroma .c, .chroma .c1, .chroma .cm, .chroma .ch, .chroma .cs { color: var(--ink3); font-style: italic; } +.chroma .k, .chroma .kn, .chroma .kd, .chroma .kc, .chroma .nb, .chroma .ow { color: var(--pr); font-weight: 500; } +.chroma .s, .chroma .s1, .chroma .s2, .chroma .sb, .chroma .sd { color: var(--okf); } +.chroma .m, .chroma .mi, .chroma .mf { color: var(--stf); } + +/* Analyses and related */ +.method-chips { list-style: none; margin: 0; padding: 0; display: flex; flex-wrap: wrap; gap: 8px; } +.method-chip { height: 32px; padding: 0 12px 0 8px; border: 1px solid var(--ln); background: var(--sf); border-radius: 8px; display: flex; align-items: center; gap: 8px; font-size: 12.5px; } +.method-chip .mono { font-weight: 500; } +.mcell { width: 16px; height: 16px; flex: none; border-radius: 4px; display: inline-grid; place-items: center; font: 600 10px/1 var(--mono); color: var(--ink3); } +.mcell--done { background: var(--pr); } +.mcell--running { background: linear-gradient(90deg, var(--pr) 50%, var(--sk) 50%); box-shadow: inset 0 0 0 1.5px var(--pr); } +.mcell--not_run { background: var(--sf); box-shadow: inset 0 0 0 2px var(--ac); } +.mcell--awaiting { background: var(--sk); box-shadow: inset 0 0 0 1px var(--ln); } +.mcell--decide { background: transparent; box-shadow: inset 0 0 0 1px var(--ln); } +.related { list-style: none; margin: 0; padding: 0; display: flex; flex-wrap: wrap; gap: 8px; } +.related .mono { font-size: 12px; } + +/* ---------- Home ---------- */ +.home { padding: 52px 64px 56px; display: flex; flex-direction: column; gap: 52px; max-width: 940px; } +.hero { display: flex; flex-direction: column; gap: 18px; } +.hero__title { margin: 0; font: 700 42px/1.12 var(--serif); letter-spacing: -.02em; max-width: 720px; text-wrap: balance; } +.hero__lead { margin: 0; font-size: 17px; line-height: 1.6; color: var(--ink2); max-width: 680px; text-wrap: pretty; } +.hero__actions { display: flex; flex-wrap: wrap; align-items: center; gap: 10px; margin-top: 6px; } +.hero__actions .link { padding: 0 6px; font-size: 14px; } +.stats { display: grid; grid-template-columns: repeat(3, minmax(0, 1fr)); border-top: 1px solid var(--ink); border-bottom: 1px solid var(--ln); } +.stat { padding: 20px 0 22px; display: flex; flex-direction: column; gap: 4px; } +.stat + .stat { padding-left: 24px; border-left: 1px solid var(--ln); } +.stat__n { font: 500 40px/1 var(--mono); letter-spacing: -.02em; } +.stat__l { font-size: 14px; color: var(--ink2); } +.stats__note { margin: -38px 0 0; font-size: 12.5px; line-height: 1.5; color: var(--ink3); max-width: 720px; } +.home__block { display: flex; flex-direction: column; gap: 18px; } +.home__block > h2, .home__blockhead h2 { margin: 0; font: 600 22px/1.3 var(--sans); } +.home__blockhead { display: flex; flex-wrap: wrap; align-items: baseline; gap: 6px 14px; } +.home__blockhead .muted { font-size: 13px; color: var(--ink3); } +.browse { display: grid; grid-template-columns: repeat(3, minmax(0, 1fr)); gap: 16px; align-items: start; } +.browse__card { padding: 18px 18px 12px; display: flex; flex-direction: column; gap: 4px; } +.browse__card > .label { padding-bottom: 8px; } +.browse__list { list-style: none; margin: 0; padding: 0; } +.browse__list a { display: flex; flex-direction: column; gap: 1px; padding: 7px 0; border-top: 1px solid var(--ln); } +.browse__list a:hover { text-decoration: none; } +.browse__list a:hover .strong { color: var(--ac); } +.browse__list .strong { font-size: 14.5px; } +.browse__list .muted { font-size: 12.5px; line-height: 1.4; } +.modgrid { list-style: none; margin: 0 0 6px; padding: 0; display: grid; grid-template-columns: 1fr 1fr; gap: 6px; } +.modgrid a { display: flex; flex-direction: column; gap: 2px; padding: 9px 10px; border: 1px solid var(--ln); border-radius: 8px; height: 100%; } +.modgrid a:hover { text-decoration: none; border-color: var(--ink3); } +.modgrid__id { display: flex; align-items: center; font-weight: 600; font-size: 14px; } +.modgrid .muted { font-size: 11.5px; line-height: 1.3; } +.repos { list-style: none; margin: 0; padding: 0; display: grid; grid-template-columns: repeat(3, minmax(0, 1fr)); gap: 10px; } +.repo { padding: 14px; display: flex; flex-direction: column; gap: 6px; height: 100%; } +.repo:hover { text-decoration: none; border-color: var(--ink3); } +.repo .strong { font-size: 14px; line-height: 1.3; } +.repo .mono { font-size: 12.5px; font-weight: 500; } +.home__about { border-top: 1px solid var(--ln); padding-top: 8px; } +.home__about .prose h2 { margin-top: 28px; } +.home__foot { border-top: 1px solid var(--ln); padding-top: 18px; font-size: 13px; color: var(--ink3); display: flex; justify-content: space-between; gap: 20px; } +.home__footlinks { display: flex; gap: 16px; white-space: nowrap; } + +/* ---------- Coverage matrix (home and catalog) ---------- */ +.matrix { padding: 4px 18px 8px; } +.matrix__head { display: flex; flex-wrap: wrap; align-items: baseline; gap: 4px 12px; padding: 14px 0 6px; } +.matrix__head h2 { margin: 0; font: 600 15px var(--sans); } +.matrix__head .muted { font-size: 13px; color: var(--ink3); } +.matrix__scroll { overflow-x: auto; } +.matrix__table { width: 100%; border-collapse: collapse; min-width: 560px; } +.matrix__table th, .matrix__table td { border-bottom: 1px solid var(--ln); text-align: center; padding: 0; } +.matrix__table tbody tr:last-child > * { border-bottom: 0; } +.matrix__table thead th { padding: 10px 0; font: 500 12px var(--mono); color: var(--ink2); } +.matrix__table tbody th { text-align: left; width: 140px; height: 42px; font-size: 13.5px; font-weight: 600; white-space: nowrap; } +.matrix__table tr.is-selected { background: var(--acs); } +.matrix__cell { + min-width: 26px; height: 26px; padding: 0 5px; display: inline-grid; place-items: center; vertical-align: middle; + border: 0; border-radius: 5px; background: var(--c); color: #fff; font: 600 11.5px/1 var(--mono); cursor: pointer; +} +a.matrix__cell:hover { text-decoration: none; filter: brightness(1.08); } +.matrix__cell.is-dim { background: var(--dim); } +.matrix__cell[aria-pressed="true"] { box-shadow: 0 0 0 2px var(--sf), 0 0 0 4px var(--ink); } +.matrix__empty { width: 6px; height: 6px; display: inline-block; border-radius: 2px; background: var(--empty); vertical-align: middle; } +.matrix__col, .matrix__row { border: 0; background: transparent; cursor: pointer; padding: 0; font: inherit; color: inherit; } +.matrix__col { display: inline-flex; flex-direction: column; align-items: center; gap: 5px; font: 600 12.5px var(--mono); color: var(--ink2); } +.matrix__col.is-selected { color: var(--ink); } +.matrix__bar { width: 44px; max-width: 100%; height: 3px; border-radius: 2px; background: var(--c); } +.matrix__row { font: 600 13.5px var(--sans); } + +/* ---------- Catalog ---------- */ +.catalog { display: flex; flex-direction: column; } +.catalog__head { padding: 28px 32px 18px; border-bottom: 1px solid var(--ln); background: var(--sf); display: flex; flex-direction: column; gap: 14px; } +.catalog__titlebar { display: flex; align-items: flex-end; gap: 24px; } +.catalog__titlebar .page__title { flex: 1; font-size: 30px; letter-spacing: -.01em; } +.catalog__titlebar .muted { font-size: 13px; } +.field { display: flex; align-items: center; gap: 10px; padding: 0 14px; height: 42px; max-width: 640px; border: 1px solid var(--ln); border-radius: 8px; background: var(--bg); } +.field:focus-within { border-color: var(--ink3); } +.field input { flex: 1; min-width: 0; border: 0; outline: 0; background: transparent; font: 400 14.5px var(--sans); color: var(--ink); } +.field input::placeholder { color: var(--ink3); } +.catalog__mobilebar, .chips--scroll { display: none; } +.catalog > .matrix { margin: 20px 32px 0; } +.catalog__body { display: grid; grid-template-columns: 240px minmax(0, 1fr); margin-top: 20px; border-top: 1px solid var(--ln); } +.facets { padding: 20px 20px 32px; border-right: 1px solid var(--ln); display: flex; flex-direction: column; gap: 22px; } +.facets__mobilehead { display: none; } +.facet { display: flex; flex-direction: column; gap: 2px; } +.facet__title { font: 500 10.5px var(--mono); letter-spacing: .08em; text-transform: uppercase; color: var(--ink3); padding-bottom: 6px; } +.fopt { display: flex; align-items: center; gap: 9px; width: 100%; padding: 5px 8px; border: 0; border-radius: 6px; background: transparent; cursor: pointer; text-align: left; font: 400 13.5px var(--sans); color: var(--ink); } +.fopt:hover { background: var(--sk); } +.fopt:disabled { color: var(--ink3); cursor: default; background: transparent; } +.fopt__box { width: 14px; height: 14px; flex: none; border-radius: 3px; border: 1.5px solid var(--ln); background: var(--sf); } +.fopt__label { flex: 1; } +.fopt__count { font: 400 12px var(--mono); color: var(--ink3); } +.fopt .acc { gap: 0; } +.fopt[aria-pressed="true"] { background: var(--acs); } +.fopt[aria-pressed="true"] .fopt__box { border-color: var(--pr); background: var(--pr); box-shadow: inset 0 0 0 2px var(--sf); } +.fopt[aria-pressed="true"] .fopt__label { font-weight: 600; } +.catalog__results { min-width: 0; padding: 0 0 24px; overflow-x: auto; } +.dtable--catalog { border: 0; border-radius: 0; background: transparent; margin: 0; } +.dtable--catalog th { padding: 12px 10px; background: var(--sf); border-bottom: 1px solid var(--ln); } +.dtable--catalog th:first-child, .dtable--catalog td:first-child { padding-left: 24px; } +.dtable--catalog td { padding: 9px 10px; border-top: 0; border-bottom: 1px solid var(--ln); vertical-align: middle; } +.dtable--catalog tbody tr:nth-child(even) { background: var(--bg); } +.dtable--catalog tbody tr:nth-child(odd) { background: var(--sf); } +.dtable--catalog .c-name { min-width: 220px; } +.dtable--catalog .c-name a { font-weight: 500; } +.dtable--catalog .c-name a:hover { color: var(--ac); } +.dtable--catalog .c-cohort, .dtable--catalog .c-tissue { color: var(--ink2); } +.dtable--catalog .c-type { white-space: nowrap; font-weight: 500; } +.dtable--catalog .c-n { color: var(--ink2); } +.dtable--catalog .c-loc span { display: block; white-space: nowrap; } +.dtable--catalog .c-loc .subtle { font-size: 11px; } +.empty { padding: 48px 24px; text-align: center; color: var(--ink2); } +.catalog__results > .note { padding: 14px 24px 0; } +.az { margin: 8px 32px 40px; border: 1px solid var(--ln); border-radius: 10px; background: var(--sf); } +.az summary { cursor: pointer; padding: 14px 18px; font-weight: 600; } +.az .prose { padding: 0 18px 18px; max-width: none; } + +/* ---------- Inventory and coverage ---------- */ +.wide { padding: 0 0 40px; display: flex; flex-direction: column; } +.wide__head { padding: 28px 32px 20px; background: var(--sf); border-bottom: 1px solid var(--ln); display: flex; flex-direction: column; gap: 16px; } +.wide__titlebar { display: flex; flex-wrap: wrap; align-items: flex-end; gap: 16px 20px; } +.wide__titlebar > div:first-child { flex: 1; display: flex; flex-direction: column; gap: 6px; min-width: 240px; } +.wide__titlebar .page__title { font-size: 30px; } +.wide__intro { max-width: 820px; font-size: 14.5px; color: var(--ink2); } +.wide__intro p { margin: 0 0 8px; } +.wide__intro a { color: var(--ac); } +.wide__body { padding: 0 32px; overflow-x: auto; } +.wide__foot { padding: 14px 32px 0; } +.tabs { display: inline-flex; border: 1px solid var(--ln); border-radius: 8px; overflow: hidden; } +.tabs button { height: 34px; padding: 0 14px; border: 0; border-right: 1px solid var(--ln); background: var(--sf); color: var(--ink); font: 500 13px var(--sans); cursor: pointer; } +.tabs button:last-child { border-right: 0; } +.tabs button[aria-pressed="true"] { background: var(--pr); color: var(--on-pr); } +.stages { display: grid; grid-template-columns: repeat(4, minmax(0, 1fr)); gap: 10px; } +.stage { border: 1px solid var(--ln); border-radius: 8px; padding: 10px 14px; display: flex; align-items: center; gap: 12px; } +.stage__n { font: 500 24px/1 var(--mono); } +.stage__t { display: flex; flex-direction: column; gap: 1px; font-size: 12px; color: var(--ink2); } +.aq { display: inline-flex; align-items: center; gap: 6px; font-size: 12.5px; font-weight: 600; white-space: nowrap; } +.aq::before { content: ""; width: 9px; height: 9px; border-radius: 50%; flex: none; } +.aq--in_hand { color: var(--okf); } .aq--in_hand::before { background: var(--okf); } +.aq--reviewing { color: var(--stf); } .aq--reviewing::before { background: var(--stf); } +.aq--requested { color: var(--ac); } .aq--requested::before { box-shadow: inset 0 0 0 2px var(--ac); } +.aq--to_identify { color: var(--ink3); } .aq--to_identify::before { box-shadow: inset 0 0 0 1.5px var(--ink3); } +.stage .aq { font-size: 13.5px; color: var(--ink); } +.dtable--wide { border: 0; border-radius: 0; background: transparent; margin: 0; } +.dtable--wide th { background: var(--sf); border-bottom: 1px solid var(--ln); padding: 12px 10px; } +.dtable--wide td { border-top: 0; border-bottom: 1px solid var(--ln); padding: 10px; vertical-align: middle; background: var(--sf); } +.dtable--wide tr.is-next td { background: var(--next); } +.dtable--wide .phase { font: 500 11.5px var(--mono); color: var(--ink3); white-space: nowrap; } +.dtable--wide tr.is-next .phase { color: var(--ac); } +.dtable--wide .sub { display: block; font-size: 12px; color: var(--ink3); } +.dtable--wide td:first-child a:hover { color: var(--ac); } +.propose { display: inline-flex; align-items: center; height: 32px; padding: 0 12px; border: 1px dashed var(--ink3); border-radius: 8px; font-weight: 600; white-space: nowrap; color: var(--ink); } +.propose:hover { text-decoration: none; border-color: var(--ink); } +.wide__foot.flex { display: flex; flex-wrap: wrap; align-items: center; gap: 10px 14px; font-size: 13px; color: var(--ink2); } +.legend { display: flex; flex-wrap: wrap; gap: 8px 14px; align-items: center; font-size: 12.5px; color: var(--ink2); } +.legend span { display: inline-flex; align-items: center; gap: 6px; } +.legend .mcell { width: 14px; height: 14px; font-size: 9px; } +.cov { border-collapse: collapse; width: 100%; min-width: 900px; } +.cov th, .cov td { border-bottom: 1px solid var(--ln); padding: 0; height: 42px; } +.cov thead th { padding: 14px 0 10px; height: auto; font: 600 12px var(--mono); color: var(--ink2); text-align: center; width: 72px; } +.cov thead th.r { text-align: right; font: 500 11px var(--mono); color: var(--ink3); width: 64px; } +.cov thead th:first-child { width: auto; } +.cov tbody th { text-align: left; font-weight: 500; font-size: 13.5px; white-space: nowrap; } +.cov tbody th a { display: inline-flex; align-items: center; } +.cov tbody th .tag { font: 500 11px var(--mono); color: var(--ink3); margin-left: 9px; } +.cov td { text-align: center; } +.cov td.r { text-align: right; font: 500 12px var(--mono); color: var(--ink2); } +.cov .mcell { width: 22px; height: 22px; border-radius: 5px; font-size: 11px; } +.cov tr.is-next { background: var(--next); } +.cov.ready-only .mcell:not(.mcell--not_run) { opacity: .18; } +.btn--toggle { color: var(--ac); border-color: var(--ac); font-weight: 600; } +.btn--toggle[aria-pressed="true"] { background: var(--ac); color: #fff; } + +/* ---------- How to get the data (shortcodes) ---------- */ +.defs { display: grid; grid-template-columns: repeat(3, minmax(0, 1fr)); gap: 12px; margin: 0 0 18px; } +.def { padding: 16px; display: flex; flex-direction: column; gap: 8px; } +.def .acc { font-size: 15px; font-weight: 600; color: var(--ink); gap: 8px; } +.def .acc__mark { width: 11px; height: 11px; } +.def p { margin: 0; font-size: 13.5px; line-height: 1.5; color: var(--ink2); } +.statusdefs { display: flex; flex-direction: column; gap: 10px; margin: 0 0 16px; } +.statusdefs > div { display: grid; grid-template-columns: 110px minmax(0, 1fr); gap: 16px; align-items: center; font-size: 14px; color: var(--ink2); } +.prose ol.steps { list-style: none; padding: 0; counter-reset: step; } +.prose ol.steps > li { counter-increment: step; position: relative; padding: 14px 0 12px 50px; margin: 0; border-bottom: 1px solid var(--ln); } +.prose ol.steps > li::before { content: counter(step); position: absolute; left: 0; top: 12px; width: 28px; height: 28px; border-radius: 50%; border: 1.5px solid var(--ink); display: grid; place-items: center; font: 600 13px var(--mono); } +.callout { background: var(--sf); border: 1px solid var(--ln); border-radius: 10px; padding: 14px 16px; margin: 0 0 16px; } +.callout > :last-child { margin-bottom: 0; } + +/* Wide pages (catalog, inventory, coverage) use the full width; the menu opens as a drawer */ +.is-wide .topbar__menu { display: grid; margin-left: -12px; } +.is-wide .brand { width: auto; } +.is-wide .shell { grid-template-columns: minmax(0, 1fr); } +.is-wide .sidenav { + position: fixed; z-index: 40; top: 0; left: 0; bottom: 0; height: auto; width: min(300px, 86vw); + background: var(--sf); transform: translateX(-100%); transition: transform .2s ease; visibility: hidden; padding-top: 18px; +} +.is-wide .nav-toggle:checked ~ .sidenav { transform: none; visibility: visible; } +.is-wide .nav-toggle:checked ~ .nav-scrim { display: block; position: fixed; inset: 0; z-index: 35; background: rgb(0 0 0 / .35); } + +/* ---------- Responsive ---------- */ +@media (max-width: 1180px) { + .pagetoc { display: none; } + .page { padding: 32px 40px 56px; } +} +@media (max-width: 1100px) { + .browse, .repos { grid-template-columns: repeat(2, minmax(0, 1fr)); } + .summary__grid { grid-template-columns: repeat(2, minmax(0, 1fr)); } +} +@media (max-width: 900px) { + .topbar { gap: 4px; padding: 0 4px; } + .topbar__menu { display: grid; } + .brand { width: auto; flex: 1; min-width: 0; } + .brand__name { font-size: 15px; } + .topbar__links { display: none; } + .theme-toggle { margin-right: 4px; } + /* Search collapses to an icon; tapping it shows the field under the header */ + .search { position: static; flex: none; width: 44px; height: 44px; padding: 0; border: 0; background: transparent; justify-content: center; } + .search__icon { width: 14px; height: 14px; border-width: 2px; border-color: var(--ink); pointer-events: none; } + .search__icon::after { background: var(--ink); width: 6px; height: 2px; } + .search input { position: absolute; inset: 0; opacity: 0; cursor: pointer; } + .search:focus-within input, .search input:not(:placeholder-shown) { + position: fixed; inset: auto 8px auto 8px; top: calc(var(--topbar) + 8px); height: 44px; padding: 0 12px; opacity: 1; cursor: text; + border: 1px solid var(--ink3); border-radius: 8px; background: var(--sf); font-size: 15px; z-index: 31; + } + .search__key { display: none; } + .search__results { position: fixed; left: 8px; right: 8px; top: calc(var(--topbar) + 58px); z-index: 31; } + .shell { grid-template-columns: minmax(0, 1fr); } + .sidenav { + position: fixed; z-index: 40; top: 0; left: 0; bottom: 0; height: auto; width: min(300px, 86vw); + background: var(--sf); transform: translateX(-100%); transition: transform .2s ease; visibility: hidden; padding-top: 18px; + } + .nav-toggle:checked ~ .sidenav { transform: none; visibility: visible; } + .nav-toggle:checked ~ .nav-scrim { display: block; position: fixed; inset: 0; z-index: 35; background: rgb(0 0 0 / .35); } + .nav-item { min-height: 40px; } + .page { padding: 22px 16px 32px; gap: 28px; } + .page__title { font-size: 26px; line-height: 1.2; } + .page__lead { font-size: 15px; line-height: 1.55; } + .home { padding: 28px 20px 32px; gap: 28px; } + .hero { gap: 12px; } + .hero__title { font-size: 30px; line-height: 1.15; } + .hero__lead { font-size: 15px; line-height: 1.55; } + .hero__actions .btn--primary { width: 100%; height: 48px; font-size: 15px; } + .stat { padding: 12px 0; } + .stat + .stat { padding-left: 12px; } + .stat__n { font-size: 26px; } + .stat__l { font-size: 12px; } + .stats__note { margin-top: -18px; } + .browse, .repos { grid-template-columns: minmax(0, 1fr); } + .home__foot { flex-direction: column; } + .catalog__head { padding: 12px 16px; position: sticky; top: var(--topbar); z-index: 10; gap: 10px; } + .catalog__head .crumbs, .catalog__titlebar { display: none; } + .catalog > .matrix { display: none; } + .field { height: 44px; max-width: none; } + .catalog__mobilebar { display: flex; gap: 8px; } + .catalog__mobilebar .btn { height: 44px; } + .chips--scroll { display: flex; gap: 6px; overflow-x: auto; margin: 0 -16px; padding: 0 16px 2px; scrollbar-width: none; } + .fchip { flex: none; height: 36px; padding: 0 12px; border-radius: 18px; border: 1px solid var(--ln); background: var(--sf); color: var(--ink); font: 500 13.5px var(--sans); display: flex; align-items: center; gap: 6px; cursor: pointer; } + .fchip .sq { margin: 0; width: 8px; height: 8px; } + .fchip[aria-pressed="true"] { background: var(--pr); border-color: var(--pr); color: var(--on-pr); } + .catalog__body { grid-template-columns: minmax(0, 1fr); margin-top: 0; border-top: 0; } + .facets { position: fixed; z-index: 45; inset: auto 0 0 0; max-height: 82vh; overflow-y: auto; background: var(--sf); border: 0; border-top: 1px solid var(--ln); border-radius: 14px 14px 0 0; transform: translateY(105%); visibility: hidden; transition: transform .2s ease; padding: 0 16px 24px; } + .facets.is-open { transform: none; visibility: visible; box-shadow: 0 -8px 40px rgb(0 0 0 / .25); } + .facets__mobilehead { display: flex; justify-content: space-between; align-items: center; position: sticky; top: 0; z-index: 1; background: var(--sf); padding: 14px 0 10px; } + .fopt { min-height: 40px; } + /* Rows become cards (design 2d) */ + .catalog__results { overflow: visible; } + .dtable--catalog, .dtable--catalog tbody { display: block; } + .dtable--catalog thead { display: none; } + .dtable--catalog tbody tr { display: flex; flex-wrap: wrap; align-items: center; gap: 6px 10px; padding: 14px 16px; border-bottom: 1px solid var(--ln); background: var(--bg) !important; } + .dtable--catalog td { display: block; padding: 0 !important; border: 0; } + .dtable--catalog .c-type { order: 1; font-size: 11.5px; color: var(--ink2); } + .dtable--catalog .c-cohort { order: 2; font: 500 11.5px var(--mono); } + .dtable--catalog .c-name { order: 3; flex: 1 0 100%; min-width: 0; } + .dtable--catalog .c-name a { font: 600 15.5px/1.3 var(--sans); } + .dtable--catalog .c-status { order: 4; } + .dtable--catalog .c-access { order: 5; } + .dtable--catalog .c-tissue, .dtable--catalog .c-n, .dtable--catalog .c-loc { display: none; } + .catalog__results > .note { padding: 14px 16px 0; } + .az { margin: 16px; } + .summary__grid { grid-template-columns: repeat(2, minmax(0, 1fr)); } + .summary__bar { flex-direction: column; align-items: stretch; gap: 10px; padding: 14px; } + .summary__bar .spacer, .summary__bar .label { display: none; } + .summary__bar .btn { height: 48px; font-size: 15px; } + .summary__bar .btn--sm { height: 32px; font-size: 12.5px; align-self: flex-start; } + .summary__bar .btn--primary { order: 3; } + .summary__bar .btn:not(.btn--primary):not(.btn--sm) { order: 4; } + .summary__bar .link { order: 5; } + .summary__cell { padding: 12px 14px; } + .summary__cell dd { font-size: 14px; } + .summary__cell dd.summary__sub { display: none; } + .wide__head { padding: 22px 16px 16px; } + .wide__body { padding: 0; } + .wide__foot { padding: 14px 16px 0; } + .stages { grid-template-columns: repeat(2, minmax(0, 1fr)); } + .defs { grid-template-columns: minmax(0, 1fr); } + .prose table { font-size: 13px; } + /* Folded Markdown sections on phones (design 3b) */ + .fold { border-bottom: 1px solid var(--ln); } + .fold:first-of-type { border-top: 1px solid var(--ln); } + .fold > summary { min-height: 52px; display: flex; align-items: center; justify-content: space-between; gap: 12px; font: 600 15.5px var(--sans); cursor: pointer; list-style: none; } + .fold > summary::-webkit-details-marker { display: none; } + .fold > summary::after { content: "+"; font-size: 20px; font-weight: 400; color: var(--ink3); } + .fold[open] > summary::after { content: "−"; } + .fold[open] { padding-bottom: 12px; } +} + +/* ---------- Print ---------- */ +@media print { + :root { --bg: #fff; --sf: #fff; --sk: #f3f4f5; --acs: #f1f4f8; --ink: #111; --ink2: #333; --ink3: #555; --ln: #ccc; color-scheme: light; } + body { font-size: 11pt; background: #fff; } + .topbar, .sidenav, .pagetoc, .nav-scrim, .skip-link, .btn, .codeblock__copy, .catalog__mobilebar, .chips--scroll, + .facets, .catalog > .matrix, .home__foot, .page__foot a, [data-empty], .az { display: none !important; } + .shell, .catalog__body { display: block; } + .page, .home { padding: 0; max-width: none; gap: 20px; } + .summary, table, pre, .codeblock { break-inside: avoid; } + .prose a[href^="http"]::after, .ds-section a.mono[href^="http"]::after { content: " (" attr(href) ")"; font-size: 9pt; color: #555; overflow-wrap: anywhere; } + .prose h2, .ds-section h2 { break-after: avoid; } +} +@media (prefers-reduced-motion: reduce) { + * { transition: none !important; scroll-behavior: auto !important; } +} diff --git a/site/assets/xqtl/site.js b/site/assets/xqtl/site.js new file mode 100644 index 0000000..c9a3eab --- /dev/null +++ b/site/assets/xqtl/site.js @@ -0,0 +1,96 @@ +// Site behaviour shared by every page: theme toggle, copy buttons, "On this page" +// highlighting and collapsible sections on phones. Everything degrades to plain links. +(function () { + var doc = document.documentElement; + + // Theme: automatic (follows the system), light or dark. The choice is kept per browser. + var btn = document.getElementById('theme-toggle'); + var order = ['auto', 'light', 'dark']; + function current() { + try { return localStorage.getItem('xqtl-theme') || 'auto'; } catch (e) { return 'auto'; } + } + function apply(mode) { + if (mode === 'auto') doc.removeAttribute('data-theme'); else doc.setAttribute('data-theme', mode); + doc.setAttribute('data-theme-pref', mode); + if (btn) btn.setAttribute('aria-label', 'Colour theme: ' + (mode === 'auto' ? 'automatic' : mode)); + } + apply(current()); + if (btn) btn.addEventListener('click', function () { + var next = order[(order.indexOf(current()) + 1) % order.length]; + try { localStorage.setItem('xqtl-theme', next); } catch (e) {} + apply(next); + }); + + // Copy buttons: [data-copy] copies its value, code blocks copy their text + function copy(text, el) { + var done = function () { + var old = el.textContent; + el.textContent = 'Copied'; + setTimeout(function () { el.textContent = old; }, 1400); + }; + if (navigator.clipboard) navigator.clipboard.writeText(text).then(done, function () {}); + } + document.addEventListener('click', function (e) { + var b = e.target.closest('[data-copy]'); + if (b) { copy(b.getAttribute('data-copy'), b); return; } + var c = e.target.closest('[data-copy-code]'); + if (c) { + var code = c.closest('.codeblock').querySelector('pre code, pre'); + copy(code.innerText.replace(/\n$/, ''), c); + } + }); + + // Close the phone menu with Escape + var navToggle = document.getElementById('nav-toggle'); + document.addEventListener('keydown', function (e) { + if (e.key === 'Escape' && navToggle && navToggle.checked) navToggle.checked = false; + }); + document.querySelectorAll('.topbar__menu').forEach(function (l) { + l.addEventListener('keydown', function (e) { + if (e.key === 'Enter' || e.key === ' ') { e.preventDefault(); navToggle.checked = !navToggle.checked; } + }); + }); + + // "On this page": mark the section in view + var toc = document.querySelector('.pagetoc'); + if (toc && 'IntersectionObserver' in window) { + var links = Array.prototype.slice.call(toc.querySelectorAll('a[href^="#"]')); + var targets = links.map(function (a) { return document.getElementById(decodeURIComponent(a.hash.slice(1))); }); + var io = new IntersectionObserver(function (entries) { + entries.forEach(function (en) { + if (!en.isIntersecting) return; + var i = targets.indexOf(en.target); + if (i < 0) return; + links.forEach(function (a) { a.classList.remove('is-current'); }); + links[i].classList.add('is-current'); + }); + }, { rootMargin: '0px 0px -70% 0px' }); + targets.forEach(function (t) { if (t) io.observe(t); }); + } + + // Phones: the Markdown sections of a dataset page fold under their headings (design 3b) + var prose = document.querySelector('.page--dataset .prose'); + if (prose && window.matchMedia('(max-width: 720px)').matches) { + var hs = Array.prototype.slice.call(prose.children).filter(function (n) { return n.tagName === 'H2'; }); + hs.forEach(function (h) { + var det = document.createElement('details'); + det.className = 'fold'; + var sum = document.createElement('summary'); + sum.innerHTML = h.innerHTML; + sum.id = h.id; + det.appendChild(sum); + var n = h.nextSibling; + while (n && n.tagName !== 'H2') { var nx = n.nextSibling; det.appendChild(n); n = nx; } + h.replaceWith(det); + }); + if (location.hash) { + var t = document.getElementById(decodeURIComponent(location.hash.slice(1))); + var d = t && t.closest('details'); if (d) d.open = true; + } + } + + // The previous theme registered a service worker; remove it so pages are never stale + if ('serviceWorker' in navigator) { + navigator.serviceWorker.getRegistrations().then(function (rs) { rs.forEach(function (r) { r.unregister(); }); }).catch(function () {}); + } +})(); diff --git a/site/data/next_phase.yaml b/site/data/next_phase.yaml new file mode 100644 index 0000000..1ac53a0 --- /dev/null +++ b/site/data/next_phase.yaml @@ -0,0 +1,31 @@ +# Datasets being curated for the next phase of the atlas that do not have a page yet. +# They appear in the inventory and the analysis coverage grid. When a dataset gets its +# own page under content/xqtl-data, remove it here. +# acquisition: in_hand | reviewing | requested | to_identify +# methods: same statuses as a page header (done, running, not_run, awaiting, decide) + +- name: ROSMAP snRNA-seq gene expression (expanded) + cohort: ROSMAP + context: Brain, cell types + omics: snRNA_seq + modality: snuc-eQTL + access: controlled + acquisition: reviewing + synapse: syn57373409 + note: Review and add to the atlas + methods: {cis-QTL: awaiting, SuSiE: awaiting, ColocBoost: awaiting, TWAS: awaiting, cTWAS: awaiting, MR: awaiting, LF2: decide, scEEMS: awaiting} + +- name: MSSM PsychAD snRNA-seq (Towfique lab) + cohort: MSSM PsychAD + context: Prefrontal cortex, cell types + omics: snRNA_seq + modality: snuc-eQTL + access: controlled + acquisition: requested + synapse: syn52160016 + note: Access being arranged + methods: {cis-QTL: awaiting, SuSiE: awaiting, ColocBoost: awaiting, TWAS: awaiting, cTWAS: awaiting, MR: awaiting, LF2: decide, scEEMS: awaiting} + +- name: Other new or expanded datasets + acquisition: to_identify + note: Add candidates with + Propose a dataset diff --git a/site/data/xqtl.yaml b/site/data/xqtl.yaml new file mode 100644 index 0000000..4582b91 --- /dev/null +++ b/site/data/xqtl.yaml @@ -0,0 +1,104 @@ +# Shared vocabulary for the site layouts in site/layouts. +# Labels, colours and descriptions live here so that menus, the catalog, the dataset +# summary card and the home page always agree. Page-level facts live in each page's +# metadata header (see template/metadata_header.md). + +# Headline numbers on the home page. Dataset and modality counts are computed from the +# pages at build time; participants cannot be, so it is set here. +home: + participants: "2,328" + participants_note: >- + Counts are participants. One participant can contribute several tissues, + cell types and assays. + updated: "October 2026" + +# QTL modalities, in menu order. `folder` is the folder under content/xqtl-data/qtl and +# `omics` the matching folders under content/xqtl-data/omics. Colour: oklch(0.6 0.13 hue). +modalities: + - {id: eQTL, family: Expression, what: Gene expression, hue: 250, omics: [expression, snRNA_seq]} + - {id: sQTL, family: Splicing, what: Alternative splicing, hue: 300, omics: [splicing]} + - {id: mQTL, family: Methylation, what: DNA methylation, hue: 350, omics: [methylation]} + - {id: caQTL, family: Chromatin, what: Chromatin accessibility, hue: 30, omics: [snATAC]} + - {id: haQTL, family: Histone, what: Histone acetylation, hue: 70, omics: [histone_ChIPSeq]} + - {id: metQTL, family: Metabolomics, what: Metabolites, hue: 110, omics: [metabolomics]} + - {id: pQTL, family: Proteomics, what: Protein abundance, hue: 155, omics: [proteomics]} + - {id: gpQTL, family: Glycoproteomics, what: Glycopeptides, hue: 200, omics: [glycoproteomics]} + +# Omics folders, in menu order, with the label shown on the site +omics: + - {folder: expression, label: Expression, family: Expression} + - {folder: splicing, label: Splicing, family: Splicing} + - {folder: methylation, label: Methylation, family: Methylation} + - {folder: proteomics, label: Proteomics, family: Proteomics} + - {folder: glycoproteomics, label: Glycoproteomics, family: Glycoproteomics} + - {folder: metabolomics, label: Metabolomics, family: Metabolomics} + - {folder: histone_ChIPSeq, label: Histone ChIP-seq, family: Histone} + - {folder: snRNA_seq, label: snRNA-seq, family: Expression} + - {folder: snATAC, label: snATAC-seq, family: Chromatin} + - {folder: genotype, label: Genotype / WGS, family: Genotype} + - {folder: covariates, label: Covariates, family: ""} + +# Study cohorts, in menu order. `page` is the study page under content/xqtl-data/study_info +cohorts: + - {name: ROSMAP, desc: Religious Orders Study and Rush Memory and Aging Project, page: ROSMAP} + - {name: MSBB, desc: Mount Sinai Brain Bank, page: MSBB} + - {name: Knight-ADRC, desc: Knight Alzheimer Disease Research Center, page: KnightADRC} + - {name: MiGA, desc: Microglia Genomic Atlas, page: MiGA} + - {name: STARNET, desc: "Cardiovascular tissues, macrophages", page: STARNET} + - {name: MetaBrain, desc: External replication resource, url: "https://www.metabrain.nl/"} + +# AD GWAS entries on the home page, by page file name under content/xqtl-data/gwas +gwas: + - {page: Bellenguez_AD, name: Bellenguez et al. 2022, desc: "Main, no-biobank and no-proxy analyses"} + - {page: Wightman_AD, name: Wightman et al. 2021, desc: Summary statistics} + - {page: Kunkle_AD, name: Kunkle et al. 2019, desc: Summary statistics} + - {page: Jansen_AD, name: Jansen et al. 2019, desc: Summary statistics} + - {page: ADGC_GWAS_imputation_protocol, name: ADGC imputation protocol, desc: Adapted from the ADGC GWAS QC protocol} + +# Release status badges +status: + released: {label: Released, desc: "Files are on Synapse or a public URL and can be requested or downloaded now."} + staged: {label: Staged, desc: "Files are uploaded but not yet shared. The page documents what will be released."} + planned: {label: Planned, desc: "Analysis in progress. No files yet."} + deprecated: {label: Deprecated, desc: "Replaced by a newer page, which this page links to."} + +# Access labels +access: + open: {label: Open, desc: "Download without an application: a public URL, an open Synapse folder or the NIAGADS open-access portal."} + controlled: {label: Controlled, desc: "Needs a Synapse account and an approved data use certificate for the cohort."} + requested: {label: Requested, desc: "Shared on request from the data owner before general release."} + pending: {label: Pending, desc: "Access terms are still being set."} + +# NIAGADS DSS NG00184 holds open xQTL summary statistics and fine-mapping for these +# modalities and cohorts. Released pages that match get an "+ NG00184 open" note. +ng00184: + id: NG00184.v1 + url: "https://dss.niagads.org/datasets/ng00184/" + modalities: [eQTL, snuc-eQTL, sQTL, pQTL, mQTL, haQTL] + cohorts: [ROSMAP, MSBB, Knight-ADRC, MiGA] + +# Home page: where the data are hosted +repos: + - {host: Synapse, name: Variant and gene summaries, id: syn69865684, url: "https://www.synapse.org/Synapse:syn69865684"} + - {host: Synapse, name: xQTL models, id: syn69670588, url: "https://www.synapse.org/Synapse:syn69670588"} + - {host: Synapse, name: Raw QTL data, id: syn69670632, url: "https://www.synapse.org/Synapse:syn69670632"} + - {host: Synapse, name: Reference files, id: syn69670634, url: "https://www.synapse.org/Synapse:syn69670634"} + - {host: NIAGADS DSS · open, name: xQTL summary statistics and fine-mapping, id: NG00184.v1, url: "https://dss.niagads.org/datasets/ng00184/"} + - {host: NIAGADS, name: xQTL Atlas · query and genome browser, id: xqtl.niagads.org, url: "https://xqtl.niagads.org/"} + +# xQTL protocol methods for the analysis coverage grid, in column order. A page lists the +# methods that apply to it in a `methods:` map in its metadata header. +methods: [cis-QTL, SuSiE, fSuSiE, ColocBoost, TWAS, cTWAS, MR, LF2, scEEMS] +method_status: + done: {label: Done, glyph: ""} + running: {label: Running, glyph: ""} + not_run: {label: Not yet run, glyph: ""} + awaiting: {label: Awaiting data, glyph: "·"} + decide: {label: Scope to decide, glyph: "?"} + +# Inventory acquisition stages +acquisition: + in_hand: {label: In hand, desc: "On Synapse or DSS, usable now"} + reviewing: {label: Reviewing, desc: "Located; checking fit and QC"} + requested: {label: Requested, desc: "Outreach under way"} + to_identify: {label: To identify, desc: "Candidates not yet found"} diff --git a/site/layouts/_markup/render-codeblock.html b/site/layouts/_markup/render-codeblock.html new file mode 100644 index 0000000..490c16f --- /dev/null +++ b/site/layouts/_markup/render-codeblock.html @@ -0,0 +1,10 @@ +{{- /* Code block with a language label and a Copy button (design 3a). */ -}} +{{- $lang := .Type | default "text" -}} +
+
{{ $lang }}
+ {{- if transform.CanHighlight $lang }} + {{ transform.Highlight .Inner $lang (dict "noClasses" false) }} + {{- else }} + 
{{ .Inner }}
+ {{- end }} +
diff --git a/site/layouts/_partials/ds/info.html b/site/layouts/_partials/ds/info.html new file mode 100644 index 0000000..ec1f1e2 --- /dev/null +++ b/site/layouts/_partials/ds/info.html @@ -0,0 +1,66 @@ +{{- /* + Everything the layouts need to know about one page, computed in one place. + Input: a page. Returns a dict: + kind qtl | omics | gwas | reference | study | other + kindLabel "QTL results", "Omics data", ... + folder modality or omics folder name, when there is one + label eQTL, snuc-eQTL, Expression, snRNA-seq, GWAS, ... + family Expression, Splicing, ... (colour family) + color CSS colour of the modality square, or "" + mark fill (QTL results) | ring (omics data) | muted (other) + cohort, context, n, status, access, analysts, synapse (first ID), synapseIDs + ng00184 true when the open NIAGADS DSS archive covers this page + short short label for menus +*/ -}} +{{- $p := . -}} +{{- $d := $p.Params.dataset | default dict -}} +{{- $x := hugo.Data.xqtl -}} +{{- $parts := slice -}} +{{- with $p.File }}{{ $parts = split (strings.TrimSuffix "/" .Dir) "/" }}{{ end -}} +{{- /* Section pages: the folder of the _index.md is the section itself */ -}} +{{- $kind := "other" -}} +{{- $folder := "" -}} +{{- if and (ge (len $parts) 2) (eq (index $parts 0) "xqtl-data") -}} + {{- $top := index $parts 1 -}} + {{- $kind = index (dict "qtl" "qtl" "omics" "omics" "gwas" "gwas" "reference_data" "reference" "study_info" "study") $top | default "other" -}} + {{- if ge (len $parts) 3 }}{{ $folder = index $parts 2 }}{{ end -}} +{{- end -}} +{{- with $d.type }}{{ $kind = . }}{{ end -}} +{{- $kindLabel := index (dict "qtl" "QTL results" "omics" "Omics data" "gwas" "GWAS" "reference" "Reference" "study" "Study cohort" "other" "Page") $kind -}} + +{{- $label := "" -}}{{- $family := "" -}}{{- $color := "" -}}{{- $mark := "muted" -}} +{{- if eq $kind "qtl" -}} + {{- range $x.modalities }}{{ if eq .id $folder }}{{ $label = .id }}{{ $family = .family }}{{ $color = printf "oklch(0.6 0.13 %v)" .hue }}{{ end }}{{ end -}} + {{- if and (eq $label "eQTL") (findRE `(?i)snRNA-seq|single-nucleus` $p.Title) }}{{ $label = "snuc-eQTL" }}{{ end -}} + {{- if $label }}{{ $mark = "fill" }}{{ else }}{{ $label = "Protocol" }}{{ end -}} +{{- else if eq $kind "omics" -}} + {{- range $x.omics }}{{ if eq .folder $folder }}{{ $label = .label }}{{ $family = .family }}{{ end }}{{ end -}} + {{- range $x.modalities }}{{ if eq .family $family }}{{ $color = printf "oklch(0.6 0.13 %v)" .hue }}{{ end }}{{ end -}} + {{- if eq $family "Genotype" }}{{ $color = "#8d959f" }}{{ end -}} + {{- if $color }}{{ $mark = "ring" }}{{ end -}} +{{- else if eq $kind "gwas" -}} + {{- $label = cond (findRE `(?i)protocol` $p.Title) "Protocol" "GWAS" -}} +{{- else if eq $kind "reference" -}} + {{- $label = "LD panel" -}} +{{- else if eq $kind "study" -}} + {{- $label = "Study" -}} +{{- end -}} + +{{- $ids := $d.synapse_ids | default slice -}} +{{- $syn := "" }}{{ with $ids }}{{ $syn = index . 0 }}{{ end -}} +{{- $cohort := $d.cohort | default "" -}} +{{- if and (not $cohort) (in (slice "gwas") $kind) }}{{ $cohort = "AD GWAS" }}{{ end -}} +{{- $analysts := $d.lead_analysts | default slice -}} +{{- $ng := false -}} +{{- if and (eq $kind "qtl") (eq $d.status "released") (in $x.ng00184.modalities $label) (in $x.ng00184.cohorts $cohort) }}{{ $ng = true }}{{ end -}} + +{{- return dict + "kind" $kind "kindLabel" $kindLabel "folder" $folder + "label" $label "family" $family "color" $color "mark" $mark + "cohort" $cohort "context" ($d.context | default "") "n" ($d.sample_size | default "") + "status" ($d.status | default "") "access" ($d.access | default "") + "analysts" $analysts "synapse" $syn "synapseIDs" $ids "ng00184" $ng + "release" ($d.release | default "") "verified" ($d.last_verified | default "") + "methods" ($d.methods | default dict) + "short" ($p.LinkTitle | default $p.Title) +-}} diff --git a/site/layouts/_partials/ds/page.html b/site/layouts/_partials/ds/page.html new file mode 100644 index 0000000..8300ecf --- /dev/null +++ b/site/layouts/_partials/ds/page.html @@ -0,0 +1,171 @@ +{{- /* Dataset page template (design 3a): summary card from the metadata header, then the + page's own Markdown unchanged, then generated Analyses and Related datasets. */ -}} +{{- $p := .page -}} +{{- $i := .info -}} +{{- $x := hugo.Data.xqtl -}} +{{- $howto := site.GetPage "/how_to_get_data" -}} + +{{- /* Source data / results counterpart: same cohort and context, matching modality family */ -}} +{{- $counter := slice -}} +{{- if in (slice "qtl" "omics") $i.kind -}} + {{- range where site.RegularPages "Params.dataset.cohort" $i.cohort -}} + {{- $o := partial "ds/info.html" . -}} + {{- /* single-nucleus data pair only with single-nucleus results, bulk with bulk */ -}} + {{- $snI := or (in (slice "snuc-eQTL" "snRNA-seq") $i.label) (findRE `(?i)snRNA|single-nucleus|snuc` $p.Title) -}} + {{- $snO := or (in (slice "snuc-eQTL" "snRNA-seq") $o.label) (findRE `(?i)snRNA|single-nucleus|snuc` .Title) -}} + {{- if and (ne . $p) (ne $o.kind $i.kind) (in (slice "qtl" "omics") $o.kind) (eq $o.family $i.family) (eq $o.context $i.context) (eq (not $snI) (not $snO)) -}} + {{- $counter = $counter | append (dict "page" . "info" $o) -}} + {{- end -}} + {{- end -}} +{{- end -}} +{{- $study := "" -}} +{{- range $x.cohorts }}{{ if and .page (eq .name $i.cohort) }}{{ $study = site.GetPage (printf "/xqtl-data/study_info/%s" .page) }}{{ end }}{{ end -}} +{{- $cohortDesc := "" -}} +{{- range $x.cohorts }}{{ if eq .name $i.cohort }}{{ $cohortDesc = .desc }}{{ end }}{{ end -}} + +
+
+ {{ partial "site/breadcrumb.html" $p }} +

{{ $p.Title }}

+ {{ with $p.Params.lead }}
{{ $p.RenderString . }}
{{ end }} +
+ +
+
+ {{- if $i.cohort }} +
Cohort
{{ with $study }}{{ $i.cohort }}{{ else }}{{ $i.cohort }}{{ end }}
{{ with $cohortDesc }}
{{ . }}
{{ end }}
+ {{- end }} + {{- if and $i.label (ne $i.kind "study") }} +
{{ cond (eq $i.kind "omics") "Data type" "Modality" }}
{{ partial "ui/mark.html" $i }}{{ $i.label }}
{{ $i.kindLabel }}
+ {{- end }} + {{- with $i.context }} +
Tissue or cell type
{{ . }}
+ {{- end }} + {{- if or $i.n (in (slice "qtl" "omics") $i.kind) }} +
Sample size
{{ with $i.n }}{{ lang.FormatNumberCustom 0 . }}{{ else }}—{{ end }}
samples
+ {{- end }} + {{- if ne $i.kind "study" }} +
Status
{{ with $i.status }}{{ partial "ui/status.html" . }}{{ else }}—{{ end }}
+
{{ with $i.release }}{{ . }}{{ end }}{{ if and $i.status (not $i.verified) }}{{ if $i.release }} · {{ end }}not yet verified{{ end }}{{ with $i.verified }}{{ if $i.release }} · {{ end }}verified {{ . }}{{ end }}
+ {{- end }} + {{- with $i.access }} +
Access
{{ partial "ui/access.html" . }}
{{ index (dict "open" "No application" "controlled" "Data use certificate" "requested" "Ask the data owner" "pending" "Terms being set") . }}
+ {{- end }} + {{- with $i.analysts }} +
Lead analysts
{{ delimit . ", " }}
Contact by name
+ {{- end }} + {{- with $counter }} +
{{ cond (eq $i.kind "qtl") "Source data" "QTL results" }}
+ {{- range . }}
{{ partial "ui/mark.html" .info }}{{ .page.LinkTitle }} {{ .info.label }}
{{ end -}} +
+ {{- end }} +
+ {{- if or $i.synapse (eq $i.kind "qtl") }} +
+ {{- with $i.synapse }} + Synapse + {{ . }} + + {{- end }} + + {{ with $howto }}How to request access{{ end }} + {{- if eq $i.kind "qtl" }} + Query in xQTL Atlas ↗ + {{- end }} + {{- with $i.synapse }} + Open in Synapse ↗ + {{- end }} +
+ {{- end }} +
+ +
+

Access

+

+ {{- if eq $i.access "open" }}Open access. Download from the links below without an application. + {{- else if eq $i.access "requested" }}Shared on request from the data owner before general release. + {{- else if eq $i.access "controlled" }}Controlled access through the AD Knowledge Portal on Synapse. You need a Synapse account and an approved data use certificate{{ with $i.cohort }} for {{ . }}{{ end }}. + {{- else }}Access terms for this page are not set yet.{{ end }} + {{ with $howto }}See How to get the data.{{ end }} +

+ {{- if or $i.synapseIDs $i.ng00184 }} +
+ + + + {{- with $i.synapse }} + + + {{- end }} + {{- if $i.ng00184 }} + + + {{- end }} + +
WhereIDAccessWhat you get
Synapse{{ . }}{{ partial "ui/access.html" ($i.access | default "controlled") }}{{ if eq $i.kind "qtl" }}{{ if eq . "syn69670632" }}Raw QTL data folder, with the per-dataset results described below{{ else }}Results described below{{ end }}{{ else }}Files described below{{ end }}
NIAGADS DSS{{ $x.ng00184.id }}{{ partial "ui/access.html" "open" }}Harmonized summary statistics and SuSiE fine-mapping in ADSP_FunGen_xQTL.v1.{{ $i.label }}.*.tar
+
+ {{- end }} + {{- if gt (len $i.synapseIDs) 1 }} +

Other Synapse IDs on this page + {{- range after 1 $i.synapseIDs }} {{ . }}{{ end }}

+ {{- end }} + {{- with $i.synapse }} + {{ $code := printf "pip install synapseclient\nsynapse login\nsynapse get -r %s" . }} + {{ $p.RenderString (printf "```shell\n%s\n```" $code) }} + {{- end }} +
+ +
+ {{ $p.Content }} +
+ + {{- with $i.methods }} +
+

Analyses

+
    + {{- range $m := $x.methods }} + {{- with index $i.methods $m }} + {{- $st := index $x.method_status . }} +
  • {{ $m }}{{ with $st }}{{ .label }}{{ end }}
    • + {{- end }} + {{- end }} +
+

Read from the methods: map in this page's metadata header{{ with site.GetPage "/coverage" }}, the same data as the analysis coverage grid{{ end }}.

+
+ {{- end }} + + {{- /* Related: counterpart, same cohort and context in other modalities, same modality in other contexts, cohort study page */ -}} + {{- $rel := slice -}} + {{- range $counter }}{{ $rel = $rel | append (dict "rel" (cond (eq $i.kind "qtl") "source" "results") "page" .page "info" .info) }}{{ end -}} + {{- if in (slice "qtl" "omics") $i.kind -}} + {{- range where site.RegularPages "Params.dataset.cohort" $i.cohort -}} + {{- $o := partial "ds/info.html" . -}} + {{- if and (ne . $p) (eq $o.kind $i.kind) -}} + {{- if and $i.context (eq $o.context $i.context) (ne $o.label $i.label) }}{{ $rel = $rel | append (dict "rel" "same tissue" "page" . "info" $o) }} + {{- else if and (eq $o.label $i.label) (ne $o.context $i.context) }}{{ $rel = $rel | append (dict "rel" "other context" "page" . "info" $o) }}{{ end -}} + {{- end -}} + {{- end -}} + {{- if eq $i.label "eQTL" -}} + {{- with site.GetPage "/xqtl-data/qtl/eQTL/MetaBrain_brain_expression_qtl" }}{{ if ne . $p }}{{ $rel = $rel | append (dict "rel" "replication" "page" . "info" (partial "ds/info.html" .)) }}{{ end }}{{ end -}} + {{- end -}} + {{- end -}} + {{- if eq $i.kind "study" -}} + {{- range (where site.RegularPages "Params.dataset.cohort" $i.cohort).ByTitle -}} + {{- $o := partial "ds/info.html" . -}} + {{- if in (slice "qtl" "omics") $o.kind }}{{ $rel = $rel | append (dict "rel" (cond (eq $o.kind "qtl") "QTL" "omics") "page" . "info" $o) }}{{ end -}} + {{- end -}} + {{- end -}} + {{- with $study }}{{ if ne . $p }}{{ $rel = $rel | append (dict "rel" "cohort" "page" . "info" (dict "mark" "none")) }}{{ end }}{{ end -}} + {{- if $rel }} + + {{- end }} + + {{ partial "site/page-foot.html" $p }} +
diff --git a/site/layouts/_partials/ds/rows.html b/site/layouts/_partials/ds/rows.html new file mode 100644 index 0000000..1936c15 --- /dev/null +++ b/site/layouts/_partials/ds/rows.html @@ -0,0 +1,21 @@ +{{- /* All catalog rows (QTL results, omics data, GWAS, reference), as dicts ready for JSON. Cached per build. */ -}} +{{- $rows := slice -}} +{{- $root := site.GetPage "/xqtl-data" -}} +{{- with $root -}} +{{- range .RegularPagesRecursive -}} + {{- $i := partial "ds/info.html" . -}} + {{- if in (slice "qtl" "omics" "gwas" "reference") $i.kind -}} + {{- $loc := $i.synapse -}} + {{- if and (not $loc) (eq $i.kind "gwas") }}{{ $loc = "Public URL" }}{{ end -}} + {{- $rows = $rows | append (dict + "title" .Title "href" .RelPermalink "short" $i.short + "kind" $i.kind "kindLabel" $i.kindLabel "label" $i.label "family" ($i.family | default (cond (eq $i.kind "gwas") "GWAS" (cond (eq $i.kind "reference") "Reference" ""))) "color" $i.color "mark" $i.mark + "cohort" $i.cohort "context" $i.context "n" $i.n + "status" $i.status "access" $i.access "analysts" $i.analysts + "loc" $loc "ng" $i.ng00184 "lead" (.Params.lead | default "" | plainify | htmlUnescape | truncate 220) + "methods" $i.methods + ) -}} + {{- end -}} +{{- end -}} +{{- end -}} +{{- return sort $rows "title" -}} diff --git a/site/layouts/_partials/site/breadcrumb.html b/site/layouts/_partials/site/breadcrumb.html new file mode 100644 index 0000000..fff95a3 --- /dev/null +++ b/site/layouts/_partials/site/breadcrumb.html @@ -0,0 +1,17 @@ +{{- /* Breadcrumb from the section tree, skipping the home page. Uses short labels. */ -}} +{{- $crumbs := slice -}} +{{- range .Ancestors.Reverse -}} + {{- if not .IsHome -}} + {{- $label := .LinkTitle -}} + {{- if eq .Path "/xqtl-data" }}{{ $label = "Data catalog" }}{{ end -}} + {{- $i := partial "ds/info.html" . -}} + {{- if and .IsSection $i.label }}{{ $label = $i.label }}{{ end -}} + {{- if and .IsSection (eq $i.folder "") }}{{ $label = index (dict "qtl" "QTL results" "omics" "Omics data" "gwas" "AD GWAS" "reference" "Reference data" "study" "Study cohorts") $i.kind | default $label }}{{ end -}} + {{- $crumbs = $crumbs | append (dict "href" .RelPermalink "label" $label) -}} + {{- end -}} +{{- end -}} +{{- with $crumbs -}} + +{{- end -}} diff --git a/site/layouts/_partials/site/doc.html b/site/layouts/_partials/site/doc.html new file mode 100644 index 0000000..40f837c --- /dev/null +++ b/site/layouts/_partials/site/doc.html @@ -0,0 +1,12 @@ +{{- /* A plain content page: breadcrumb, serif title, lead, then the Markdown body unchanged. */ -}} +
+
+ {{ partial "site/breadcrumb.html" . }} +

{{ .Title }}

+ {{ with .Params.lead }}
{{ $.RenderString . }}
{{ end }} +
+
+ {{ .Content }} +
+ {{ partial "site/page-foot.html" . }} +
diff --git a/site/layouts/_partials/site/facet-opt.html b/site/layouts/_partials/site/facet-opt.html new file mode 100644 index 0000000..9367698 --- /dev/null +++ b/site/layouts/_partials/site/facet-opt.html @@ -0,0 +1,7 @@ + diff --git a/site/layouts/_partials/site/head.html b/site/layouts/_partials/site/head.html new file mode 100644 index 0000000..26eb2d3 --- /dev/null +++ b/site/layouts/_partials/site/head.html @@ -0,0 +1,21 @@ + + + + + + +{{ if .IsHome }}{{ site.Title }}{{ else }}{{ .Title }} · FunGen-xQTL Resources{{ end }} + + +{{- /* Apply the stored theme before first paint so the page does not flash */}} + + + + +{{ $css := resources.Get "xqtl/site.css" | resources.Minify | resources.Fingerprint -}} + +{{- /* Full-text search from hugo-book (MiniSearch). The header holds its input and results list. */}} +{{- if default true site.Params.BookSearch -}} + {{- $searchJS := resources.Get "search.js" | resources.ExecuteAsTemplate (printf "%s.search.js" site.Language.Lang) . | resources.Minify | resources.Fingerprint -}} + +{{- end }} diff --git a/site/layouts/_partials/site/header.html b/site/layouts/_partials/site/header.html new file mode 100644 index 0000000..7e1e9d3 --- /dev/null +++ b/site/layouts/_partials/site/header.html @@ -0,0 +1,25 @@ +{{- $howto := site.GetPage "/how_to_get_data" -}} +
+ + + {{ partial "ui/logo.html" . }} + FunGen-xQTL Resources + + + + +
diff --git a/site/layouts/_partials/site/nav-link.html b/site/layouts/_partials/site/nav-link.html new file mode 100644 index 0000000..058c2c9 --- /dev/null +++ b/site/layouts/_partials/site/nav-link.html @@ -0,0 +1,9 @@ +{{- /* (dict "cur" page "page" page "label" .. "hint" .. "mark" dict "sub" bool "href" ..) */ -}} + {{- $href := .href -}} + {{- with .page }}{{ $href = .RelPermalink }}{{ end -}} + {{- $on := and .page (eq .page.RelPermalink .cur.RelPermalink) -}} +
  • + {{- if .mark }}{{ partial "ui/mark.html" .mark }}{{ else if not .sub }}{{ end -}} + {{ .label }} + {{- with .hint }}{{ . }}{{ end -}} +
    • diff --git a/site/layouts/_partials/site/nav.html b/site/layouts/_partials/site/nav.html new file mode 100644 index 0000000..a9e8256 --- /dev/null +++ b/site/layouts/_partials/site/nav.html @@ -0,0 +1,93 @@ +{{- /* Left menu: fixed groups with consistent labels (eQTL, sQTL, caQTL ...). The current + modality or omics type expands to list its datasets. */ -}} +{{- $cur := . -}} +{{- $x := hugo.Data.xqtl -}} + + diff --git a/site/layouts/_partials/site/page-foot.html b/site/layouts/_partials/site/page-foot.html new file mode 100644 index 0000000..54de69e --- /dev/null +++ b/site/layouts/_partials/site/page-foot.html @@ -0,0 +1,4 @@ +
    + {{ with .GitInfo }}Last updated {{ .AuthorDate.Format "January 2006" }}{{ else }}{{ with .Lastmod }}{{ if gt .Year 1 }}Last updated {{ .Format "January 2006" }}{{ end }}{{ end }}{{ end }} + {{ with .Params.source_path }}Edit this page on GitHub{{ end }} +
    diff --git a/site/layouts/_partials/site/toc.html b/site/layouts/_partials/site/toc.html new file mode 100644 index 0000000..5c570fe --- /dev/null +++ b/site/layouts/_partials/site/toc.html @@ -0,0 +1,21 @@ +{{- /* Right-hand "On this page". Dataset pages add the generated sections around the Markdown headings. */ -}} +{{- $p := .page -}} +{{- $items := slice -}} +{{- if .dataset }}{{ $items = $items | append (dict "href" "#summary" "label" "Summary") (dict "href" "#access" "label" "Access") }}{{ end -}} +{{- range findRESubmatch `(.*?)` $p.TableOfContents -}} + {{- $items = $items | append (dict "href" (index . 1) "label" (index . 2 | plainify | htmlUnescape)) -}} +{{- end -}} +{{- if .dataset -}} + {{- with .info.methods }}{{ $items = $items | append (dict "href" "#analyses" "label" "Analyses") }}{{ end -}} + {{- $items = $items | append (dict "href" "#related" "label" "Related datasets") -}} +{{- end -}} +{{- if gt (len $items) 1 -}} + +{{- end -}} diff --git a/site/layouts/_partials/ui/access.html b/site/layouts/_partials/ui/access.html new file mode 100644 index 0000000..827e727 --- /dev/null +++ b/site/layouts/_partials/ui/access.html @@ -0,0 +1,4 @@ +{{- /* Access label: a shape plus text (filled square controlled, circle open, half circle requested). Input: access key. */ -}} +{{- with index hugo.Data.xqtl.access . -}} +{{ .label }} +{{- end -}} diff --git a/site/layouts/_partials/ui/logo.html b/site/layouts/_partials/ui/logo.html new file mode 100644 index 0000000..01f8236 --- /dev/null +++ b/site/layouts/_partials/ui/logo.html @@ -0,0 +1,9 @@ +{{- /* Logo 8a: a Manhattan plot with one lead variant above the significance line. viewBox matches the 60 x 44 design grid. */ -}} + diff --git a/site/layouts/_partials/ui/mark.html b/site/layouts/_partials/ui/mark.html new file mode 100644 index 0000000..7dac4c2 --- /dev/null +++ b/site/layouts/_partials/ui/mark.html @@ -0,0 +1,6 @@ +{{- /* Modality square. Input: the dict from ds/info, or (dict "color" .. "mark" ..). Filled for QTL results, outlined for omics data. */ -}} +{{- if .color -}} + +{{- else -}} + +{{- end -}} diff --git a/site/layouts/_partials/ui/status.html b/site/layouts/_partials/ui/status.html new file mode 100644 index 0000000..c6cec15 --- /dev/null +++ b/site/layouts/_partials/ui/status.html @@ -0,0 +1,4 @@ +{{- /* Release status badge. Input: status key. Always shows a text label. */ -}} +{{- with index hugo.Data.xqtl.status . -}} +{{ .label }} +{{- end -}} diff --git a/site/layouts/_shortcodes/access-defs.html b/site/layouts/_shortcodes/access-defs.html new file mode 100644 index 0000000..243543b --- /dev/null +++ b/site/layouts/_shortcodes/access-defs.html @@ -0,0 +1,7 @@ +{{- /* Cards explaining each access label, from data/xqtl.yaml */ -}} +
    + {{- range slice "open" "controlled" "requested" }} + {{- $a := index hugo.Data.xqtl.access . }} +
    {{ partial "ui/access.html" . }}

    {{ $a.desc }}

    + {{- end }} +
    diff --git a/site/layouts/_shortcodes/callout.html b/site/layouts/_shortcodes/callout.html new file mode 100644 index 0000000..ac3ac62 --- /dev/null +++ b/site/layouts/_shortcodes/callout.html @@ -0,0 +1,2 @@ +{{- /* A bordered note box for Markdown content */ -}} +
    {{ .Page.RenderString .Inner }}
    diff --git a/site/layouts/_shortcodes/status-defs.html b/site/layouts/_shortcodes/status-defs.html new file mode 100644 index 0000000..9b35672 --- /dev/null +++ b/site/layouts/_shortcodes/status-defs.html @@ -0,0 +1,6 @@ +{{- /* Release status badges with their meaning, from data/xqtl.yaml */ -}} +
    + {{- range slice "released" "staged" "planned" }} +
    {{ partial "ui/status.html" . }}{{ (index hugo.Data.xqtl.status .).desc }}
    + {{- end }} +
    diff --git a/site/layouts/_shortcodes/steps.html b/site/layouts/_shortcodes/steps.html new file mode 100644 index 0000000..ff81691 --- /dev/null +++ b/site/layouts/_shortcodes/steps.html @@ -0,0 +1,2 @@ +{{- /* Numbered steps: wrap a Markdown ordered list. Overrides hugo-book's steps shortcode. */ -}} +{{ replace (.Page.RenderString .Inner) "
      " `
        ` | safeHTML }} diff --git a/site/layouts/baseof.html b/site/layouts/baseof.html new file mode 100644 index 0000000..fc587ea --- /dev/null +++ b/site/layouts/baseof.html @@ -0,0 +1,24 @@ + + + + {{ partial "site/head.html" . }} + + + + {{ partial "site/header.html" . }} +
        + + + +
        + {{ block "main" . }}{{ end }} +
        + {{ block "toc" . }}{{ end }} +
        + {{ $js := resources.Get "xqtl/site.js" | resources.Minify | resources.Fingerprint }} + + {{ block "scripts" . }}{{ end }} + + diff --git a/site/layouts/catalog.html b/site/layouts/catalog.html new file mode 100644 index 0000000..9a831a6 --- /dev/null +++ b/site/layouts/catalog.html @@ -0,0 +1,126 @@ +{{ define "main" }} +{{- /* Data catalog (designs 2a + 2c, 2d on phones). Every row is rendered here so the page + works without JavaScript; assets/xqtl/catalog.js filters the rows in place. */ -}} +{{- $x := hugo.Data.xqtl -}} +{{- $rows := partialCached "ds/rows.html" . "rows" -}} +{{- $qtl := where $rows "kind" "qtl" -}} +
        +
        + {{ partial "site/breadcrumb.html" . }} +
        +

        Data catalog

        + {{ len $rows }} datasets +
        + +
        + + +
        +
        + {{- range $x.modalities }} + + {{- end }} +
        +
        + +
        +
        +

        QTL results by cohort and modality

        + Each cell counts QTL datasets. Select a cell, a row or a column to filter. +
        +
        + + + {{- range $x.modalities }} + + {{- end }} + + + {{- range $c := $x.cohorts }} + {{- $cr := where $qtl "cohort" $c.name -}} + + + {{- range $m := $x.modalities }} + {{- $n := len (where $cr "family" $m.family) }} + + {{- end }} + + {{- end }} + +
        {{ if $n }}{{ else }}{{ end }}
        +
        +
        + +
        + + +
        + + + + + {{- range $rows }} + {{- $tissue := "" }}{{ with .context }}{{ $tissue = index (split . ",") 0 | strings.TrimSpace }}{{ end }} + + + + + + + + + + + {{- end }} + +
        Datasets in the FunGen-xQTL catalog
        Dataset ↑CohortTypeTissue / cellNStatusAccessLocation
        {{ .title }}{{ .cohort }}{{ partial "ui/mark.html" . }}{{ .label }}{{ .context }}{{ with .n }}{{ lang.FormatNumberCustom 0 . }}{{ else }}—{{ end }}{{ with .status }}{{ partial "ui/status.html" . }}{{ end }}{{ with .access }}{{ partial "ui/access.html" . }}{{ end }}{{ .loc | default "—" }}{{ if .ng }}+ NG00184 open{{ end }}
        + +

        Study cohorts are described on their own pages. The access label describes the Synapse copy; "+ NG00184 open" marks results that are also open on NIAGADS DSS.

        +
        +
        + + {{- with .Content }} +
        + A–Z list with descriptions and lead analysts +
        {{ . }}
        +
        + {{- end }} +
        +{{ end }} + +{{ define "scripts" }} +{{ $js := resources.Get "xqtl/catalog.js" | resources.Minify | resources.Fingerprint }} + +{{ end }} diff --git a/site/layouts/coverage.html b/site/layouts/coverage.html new file mode 100644 index 0000000..d2f7c58 --- /dev/null +++ b/site/layouts/coverage.html @@ -0,0 +1,65 @@ +{{ define "main" }} +{{- /* Analysis coverage (design 9b): dataset x xQTL protocol method, from the `methods:` map + in each page header plus data/next_phase.yaml. */ -}} +{{- $x := hugo.Data.xqtl -}} +{{- $grid := slice -}} +{{- range where (partialCached "ds/rows.html" . "rows") "kind" "qtl" -}} + {{- if .methods }}{{ $grid = $grid | append (dict "name" .short "href" .href "tag" .label "color" .color "methods" .methods "next" false) }}{{ end -}} +{{- end -}} +{{- range hugo.Data.next_phase -}} + {{- if .methods -}} + {{- $grid = $grid | append (dict "name" .name "href" "" "tag" (printf "%s · next phase" .modality) "color" "oklch(0.6 0.13 250)" "methods" .methods "next" true) -}} + {{- end -}} +{{- end -}} +{{- $ready := 0 -}} +{{- range $grid }}{{ range $m, $s := .methods }}{{ if eq $s "not_run" }}{{ $ready = add $ready 1 }}{{ end }}{{ end }}{{ end -}} +
        +
        + {{ partial "site/breadcrumb.html" . }} +
        +
        xQTL protocol

        {{ .Title }}

        +
        + {{- range $k := slice "done" "running" "not_run" "awaiting" "decide" }}{{ $s := index $x.method_status $k }}{{ $s.label }}{{ end }} +
        + +
        + {{ with .Params.lead }}
        {{ $.RenderString . }}
        {{ end }} +
        +
        + + {{ range $x.methods }}{{ end }} + + {{- range $grid }} + {{- $r := . -}} + {{- $done := 0 }}{{ $app := 0 -}} + {{- range $m, $s := .methods }}{{ $app = add $app 1 }}{{ if eq $s "done" }}{{ $done = add $done 1 }}{{ end }}{{ end }} + + + {{- range $m := $x.methods }} + {{- $s := index $r.methods $m }} + + {{- end }} + + + {{- end }} + +
        Dataset{{ . }}DONE
        {{ if .href }}{{ partial "ui/mark.html" (dict "color" .color "mark" "fill") }}{{ .name }}{{ else }}{{ partial "ui/mark.html" (dict "color" .color "mark" "ring") }}{{ .name }}{{ end }}{{ .tag }}{{ with $s }}{{ $d := index $x.method_status . }}{{ with $d }}{{ .glyph }}{{ end }}{{ with $d }}{{ .label }}{{ end }}{{ else }}–{{ end }}{{ $done }}/{{ $app }}
        +
        +

        Statuses come from a methods: map in each page's metadata header; datasets without a page yet are listed in site/data/next_phase.yaml. "Not yet run" marks a method that applies to data already in hand, a quick way to see what can be run next.

        + {{ with .Content }}
        {{ . }}
        {{ end }} +
        +{{ end }} + +{{ define "scripts" }} + +{{ end }} diff --git a/site/layouts/home.html b/site/layouts/home.html new file mode 100644 index 0000000..727e435 --- /dev/null +++ b/site/layouts/home.html @@ -0,0 +1,107 @@ +{{ define "main" }} +{{- /* Home page (designs 1a and 1b). Counts are computed from the pages at build time. + The Markdown in content/README.md is shown in full under "About FunGen-AD". */ -}} +{{- $x := hugo.Data.xqtl -}} +{{- $rows := partialCached "ds/rows.html" . "rows" -}} +{{- $qtl := where $rows "kind" "qtl" -}} +{{- $catalog := site.GetPage "/xqtl-data" -}} +{{- $howto := site.GetPage "/how_to_get_data" -}} +
        +
        +
        ADSP Functional Genomics Consortium · FunGen-AD
        +

        Find and access the FunGen-xQTL datasets

        +

        FunGen-xQTL maps genetic effects on gene expression, splicing, DNA methylation, proteins, chromatin and metabolites in brain and immune cells, and integrates them with AD GWAS. This catalog describes each dataset and where to get it. To look up associations by variant, gene or region, use the xQTL Atlas on NIAGADS.

        +
        + {{ with $catalog }}Browse the catalog{{ end }} + {{ with $howto }}How to get the data{{ end }} + Query the xQTL Atlas ↗ +
        +
        + +
        +
        {{ len $rows }}datasets documented
        +
        {{ len $x.modalities }}QTL modalities
        +
        {{ $x.home.participants }}participants
        +
        +

        {{ $x.home.participants_note }}

        + +
        +

        Browse by

        +
        +
        +
        Study cohort
        +
          + {{- range $x.cohorts }} + {{- $href := .url -}} + {{- with .page }}{{ with site.GetPage (printf "/xqtl-data/study_info/%s" .) }}{{ $href = .RelPermalink }}{{ end }}{{ end }} +
        • {{ .name }}{{ .desc }}
          • + {{- end }} +
        +
        +
        +
        QTL modality
        + +
        +
        +
        AD GWAS summary statistics
        +
          + {{- range $x.gwas }} + {{- $g := . -}} + {{- with site.GetPage (printf "/xqtl-data/gwas/%s" .page) }} +
        • {{ $g.name }}{{ $g.desc }}
          • + {{- end }} + {{- end }} +
        +
        +
        +
        + +
        +

        Coverage by cohort and modality

        Number of QTL datasets. Select a cell to open the filtered catalog.
        +
        +
        + + {{ range $x.modalities }}{{ end }} + + {{- range $c := $x.cohorts }} + {{- $cr := where $qtl "cohort" $c.name }} + + {{- range $m := $x.modalities }} + {{- $n := len (where $cr "family" $m.family) }} + + {{- end }} + + {{- end }} + +
        {{ .id }}
        {{ $c.name }}{{ if $n }}{{ $n }}{{ else }}{{ end }}
        +
        +
        +
        + +
        +

        Where the data are hosted

        + +
        + + {{- with .Content }} +
        +
        {{ . }}
        +
        + {{- end }} + + +
        +{{ end }} diff --git a/site/layouts/inventory.html b/site/layouts/inventory.html new file mode 100644 index 0000000..a06ee70 --- /dev/null +++ b/site/layouts/inventory.html @@ -0,0 +1,86 @@ +{{ define "main" }} +{{- /* Dataset inventory (design 9a): the omics data behind the atlas plus datasets being + curated for the next phase (data/next_phase.yaml). */ -}} +{{- $x := hugo.Data.xqtl -}} +{{- $rows := slice -}} +{{- range where (partialCached "ds/rows.html" . "rows") "kind" "omics" -}} + {{- if ne .family "" -}} + {{- $rows = $rows | append (dict "name" .title "href" .href "cohort" .cohort "context" .context "label" .label "color" .color "mark" "ring" "n" .n "access" .access + "acq" (cond (eq .status "released") "in_hand" (cond (eq .status "") "" "reviewing")) "phase" "v1" "src" .loc "note" "") -}} + {{- end -}} +{{- end -}} +{{- range hugo.Data.next_phase -}} + {{- $label := "" }}{{ $color := "" -}} + {{- $o := .omics -}} + {{- range $x.omics }}{{ if eq .folder $o }}{{ $label = .label }}{{ $fam := .family }}{{ range $x.modalities }}{{ if eq .family $fam }}{{ $color = printf "oklch(0.6 0.13 %v)" .hue }}{{ end }}{{ end }}{{ end }}{{ end -}} + {{- $rows = $rows | append (dict "name" .name "href" "" "cohort" (.cohort | default "—") "context" (.context | default "—") "label" ($label | default "—") "color" $color "mark" "ring" "n" "" "access" (.access | default "") + "acq" .acquisition "phase" "next" "src" (.synapse | default "—") "note" (.note | default "")) -}} +{{- end -}} +
        +
        + {{ partial "site/breadcrumb.html" . }} +
        +

        {{ .Title }}

        +
        + + + +
        +
        + {{ with .Params.lead }}
        {{ $.RenderString . }}
        {{ end }} +
        + {{- range $k := slice "in_hand" "reviewing" "requested" "to_identify" }} + {{- $s := index $x.acquisition $k }} +
        {{ len (where $rows "acq" $k) }} + {{ $s.label }}{{ $s.desc }}
        + {{- end }} +
        +
        +
        + + + + {{- range $rows }} + + + + + + + + + + + + {{- end }} + +
        DatasetCohortContextModalityNAccessAcquisitionPhaseSource
        {{ if .href }}{{ .name }}{{ else }}{{ .name }}{{ end }}{{ with .note }}{{ . }}{{ end }}{{ .cohort }}{{ .context }}{{ partial "ui/mark.html" . }}{{ .label }}{{ with .n }}{{ lang.FormatNumberCustom 0 . }}{{ else }}—{{ end }}{{ with .access }}{{ partial "ui/access.html" . }}{{ else }}—{{ end }}{{ with .acq }}{{ (index $x.acquisition .).label }}{{ else }}Not set{{ end }}{{ if eq .phase "v1" }}Atlas v1{{ else }}Next phase{{ end }}{{ if hasPrefix .src "syn" }}{{ .src }}{{ else }}{{ .src }}{{ end }}
        +
        +
        + + Propose a dataset + Opens a GitHub issue that asks for cohort, context, modality, N, access and Synapse ID. A curator turns it into a page. +
        + {{ with .Content }}
        {{ . }}
        {{ end }} +
        +{{ end }} + +{{ define "scripts" }} + +{{ end }} diff --git a/site/layouts/page.html b/site/layouts/page.html new file mode 100644 index 0000000..0ebe8a0 --- /dev/null +++ b/site/layouts/page.html @@ -0,0 +1,13 @@ +{{ define "main" }} +{{- $i := partial "ds/info.html" . -}} +{{- if in (slice "qtl" "omics" "gwas" "reference" "study") $i.kind -}} + {{ partial "ds/page.html" (dict "page" . "info" $i) }} +{{- else -}} + {{ partial "site/doc.html" . }} +{{- end -}} +{{ end }} + +{{ define "toc" }} +{{- $i := partial "ds/info.html" . -}} +{{ partial "site/toc.html" (dict "page" . "dataset" (in (slice "qtl" "omics" "gwas" "reference" "study") $i.kind) "info" $i) }} +{{ end }} diff --git a/site/layouts/section.html b/site/layouts/section.html new file mode 100644 index 0000000..68c2a50 --- /dev/null +++ b/site/layouts/section.html @@ -0,0 +1,42 @@ +{{ define "main" }} +{{- $i := partial "ds/info.html" . -}} +
        +
        + {{ partial "site/breadcrumb.html" . }} +

        {{ if and $i.label (in (slice "qtl" "omics") $i.kind) }}{{ $i.label }}{{ if eq $i.kind "omics" }} data{{ end }}{{ else }}{{ .Title }}{{ end }}

        + {{ with .Params.lead }}
        {{ $.RenderString . }}
        {{ end }} +
        + + {{- /* Datasets in this section and below, in the catalog row style */ -}} + {{- $pages := slice -}} + {{- range .RegularPagesRecursive.ByTitle }}{{ $o := partial "ds/info.html" . }}{{ if ne $o.kind "other" }}{{ $pages = $pages | append (dict "page" . "info" $o) }}{{ end }}{{ end -}} + {{- with $pages }} +
        + + + + {{- range . }} + + + + + + + + + + {{- end }} + +
        DatasetCohortTypeTissue / cellNStatusAccess
        {{ .page.Title }}{{ .info.cohort }}{{ partial "ui/mark.html" .info }}{{ .info.label }}{{ .info.context }}{{ with .info.n }}{{ lang.FormatNumberCustom 0 . }}{{ else }}—{{ end }}{{ with .info.status }}{{ partial "ui/status.html" . }}{{ end }}{{ with .info.access }}{{ partial "ui/access.html" . }}{{ end }}
        +
        + {{- end }} + + {{- /* A hand-written section page keeps its Markdown. Generated link lists are replaced by the table above. */ -}} + {{- if and .Content (not .Params.generated_list) }} +
        {{ .Content }}
        + {{- end }} + {{ partial "site/page-foot.html" . }} +
        +{{ end }} + +{{ define "toc" }}{{ partial "site/toc.html" (dict "page" . "dataset" false) }}{{ end }} diff --git a/site/static/favicon.svg b/site/static/favicon.svg new file mode 100644 index 0000000..6db67be --- /dev/null +++ b/site/static/favicon.svg @@ -0,0 +1 @@ + diff --git a/template/metadata_header.md b/template/metadata_header.md index 4975dea..80c0d01 100644 --- a/template/metadata_header.md +++ b/template/metadata_header.md @@ -1,6 +1,6 @@ # Dataset page metadata header -Every dataset page under `content/xqtl-data/{gwas,omics,qtl,study_info,reference_data}` can start with a YAML header between two `---` lines. The catalog generator (`scripts/toc.py`) and the checker (`scripts/audit_catalog.py`) read it. `scripts/hugo_generator.py` removes it before the page is built, so it is never shown on the site. Pages without a header keep working and the catalog falls back to the first sentence of the page. +Every dataset page under `content/xqtl-data/{gwas,omics,qtl,study_info,reference_data}` can start with a YAML header between two `---` lines. The catalog generator (`scripts/toc.py`) and the checker (`scripts/audit_catalog.py`) read it. `scripts/hugo_generator.py` removes it from the page text and passes its public fields to the site layouts in `site/`, which use them for the summary card, the catalog, the menu and the analysis coverage grid. The `internal` field is dropped and never reaches the site. Pages without a header keep working and the catalog falls back to the first sentence of the page. The header sits next to the NIAGADS fields described in the other templates in this folder. It does not replace them. @@ -8,6 +8,7 @@ The header sits next to the NIAGADS fields described in the other templates in t --- type: omics # study | gwas | omics | qtl | reference modality: expression # omics and qtl pages. Use the modality folder name, for example expression, splicing, eQTL, sQTL +short_title: MiGA microglia # optional, label in the menu and in "Related datasets" cohort: MiGA # study, omics and qtl pages context: microglia # optional, tissue or cell type sample_size: 255 # optional, number of samples @@ -18,6 +19,9 @@ synapse_ids: [syn69670592] # public Synapse IDs only. May be empty for staged or lead_analysts: [Travyse Edwards] last_verified: 2026-10-07 # required for released pages. May be blank during the migration replaced_by: # required for deprecated pages. Path of the replacing page +methods: # optional, qtl pages. Analyses run on this dataset, shown on the page and in the coverage grid + cis-QTL: done # done | running | not_run | awaiting | decide. Leave out methods that do not apply + SuSiE: done internal: # optional. Not shown on the site. Staging IDs go here. Never file-system paths: the field is still visible in the repository staging_ids: [] --- @@ -37,4 +41,8 @@ internal: # optional. Not shown on the site. Staging IDs go her | `lead_analysts` | always | list of names | | `last_verified` | released | date of the last Synapse check, may be blank during the migration | | `replaced_by` | deprecated | path of the replacing page | +| `short_title` | optional | short label for menus, for example `ROSMAP DLPFC` | +| `methods` | optional | map of method to `done`, `running`, `not_run`, `awaiting` or `decide`. Methods: cis-QTL, SuSiE, fSuSiE, ColocBoost, TWAS, cTWAS, MR, LF2, scEEMS | | `internal` | optional | excluded from the build | + +Values marked `# TODO: verify (design placeholder)` came from the site redesign mockup, not from the analysts. Replace them with checked values and remove the comment; `scripts/audit_catalog.py` lists them as placeholders until then. From fe2ee1005672e7bccb637bdb08b173cf610c37ce Mon Sep 17 00:00:00 2001 From: Jenny Empawi Date: Fri, 9 Oct 2026 11:54:20 -0400 Subject: [PATCH 2/9] Rename gpQTL to glycoQTL in page text, links and the side menu Synapse file names and analysis repository paths that contain gpQTL are unchanged. --- README.md | 2 +- content/README.md | 2 +- .../xqtl-data/omics/glycoproteomics/README.md | 2 +- .../ROSMAP_DLPFC_glycoproteomics.md | 2 +- content/xqtl-data/qtl/README.md | 4 +- content/xqtl-data/qtl/glycoQTL/README.md | 54 +++++++++++++++++++ .../ROSMAP_DLPFC_glycoproteomics_qtl.md | 6 +-- content/xqtl-data/qtl/gpQTL/README.md | 54 ------------------- content/xqtl-data/study_info/ROSMAP.md | 2 +- content/xqtl_resource_description.md | 10 ++-- content/xqtl_resource_format.md | 8 +-- scripts/hugo_generator.py | 2 +- site/data/xqtl.yaml | 2 +- 13 files changed, 75 insertions(+), 75 deletions(-) create mode 100644 content/xqtl-data/qtl/glycoQTL/README.md rename content/xqtl-data/qtl/{gpQTL => glycoQTL}/ROSMAP_DLPFC_glycoproteomics_qtl.md (82%) delete mode 100644 content/xqtl-data/qtl/gpQTL/README.md diff --git a/README.md b/README.md index 6592278..992de9b 100644 --- a/README.md +++ b/README.md @@ -23,7 +23,7 @@ FunGen-xQTL maps molecular quantitative trait loci (QTL) across multiple molecul - Metabolomics of brain. - Single-nucleus RNA-seq (ROSMAP DLPFC, in the CUIMC, MIT and mega cohorts). - Whole-genome sequencing genotypes and covariates. -* **[xQTL data](xqtl-data/qtl/)** are molecular QTL associations organized by modality, namely [eQTL](xqtl-data/qtl/eQTL), [sQTL](xqtl-data/qtl/sQTL), [pQTL](xqtl-data/qtl/pQTL), [gpQTL](xqtl-data/qtl/gpQTL), [mQTL](xqtl-data/qtl/mQTL), [haQTL](xqtl-data/qtl/haQTL), [caQTL](xqtl-data/qtl/caQTL) and [metQTL](xqtl-data/qtl/metQTL). They also include ROSMAP transcriptomic pattern QTL (tpQTL) and trans-xQTL. +* **[xQTL data](xqtl-data/qtl/)** are molecular QTL associations organized by modality, namely [eQTL](xqtl-data/qtl/eQTL), [sQTL](xqtl-data/qtl/sQTL), [pQTL](xqtl-data/qtl/pQTL), [glycoQTL](xqtl-data/qtl/glycoQTL), [mQTL](xqtl-data/qtl/mQTL), [haQTL](xqtl-data/qtl/haQTL), [caQTL](xqtl-data/qtl/caQTL) and [metQTL](xqtl-data/qtl/metQTL). They also include ROSMAP transcriptomic pattern QTL (tpQTL) and trans-xQTL. * **[FGMB Atlas](fgmb_weights_database)** provides multi-context regulome-wide association study (RWAS) prediction models, with Synapse accessions for the models, gene-level association results and causal fine-mapping outputs. * **AD loci integration summary** gives the 195-locus AD GWAS and xQTL summary from the October 2026 release on Synapse ([syn69865823](https://www.synapse.org/Synapse:syn69865823)). The same data can be browsed in the interactive [xQTL-AD-loci-explorer](https://wanggroup.org/xQTL-AD-loci-explorer/). * **[Reference data](xqtl-data/reference_data/)** include ADSP-based LD reference panels (16,905 European ancestry samples), an LD sketch panel, and other analytical resources. diff --git a/content/README.md b/content/README.md index f080749..4f668cf 100644 --- a/content/README.md +++ b/content/README.md @@ -21,7 +21,7 @@ The FunGen-xQTL project provides comprehensive molecular quantitative trait loci - Metabolomics (brain) - Single-nucleus RNA-seq (ROSMAP DLPFC: CUIMC, MIT, and mega cohorts) - Genotype (WGS) and covariates -* **[xQTL Data](xqtl-data/qtl/)** - Molecular QTL associations organized by modality: [eQTL](xqtl-data/qtl/eQTL), [sQTL](xqtl-data/qtl/sQTL), [pQTL](xqtl-data/qtl/pQTL), [gpQTL](xqtl-data/qtl/gpQTL), [mQTL](xqtl-data/qtl/mQTL), [haQTL](xqtl-data/qtl/haQTL), [caQTL](xqtl-data/qtl/caQTL), [metQTL](xqtl-data/qtl/metQTL), plus ROSMAP transcriptomic pattern QTLs (tpQTL) and trans-xQTLs +* **[xQTL Data](xqtl-data/qtl/)** - Molecular QTL associations organized by modality: [eQTL](xqtl-data/qtl/eQTL), [sQTL](xqtl-data/qtl/sQTL), [pQTL](xqtl-data/qtl/pQTL), [glycoQTL](xqtl-data/qtl/glycoQTL), [mQTL](xqtl-data/qtl/mQTL), [haQTL](xqtl-data/qtl/haQTL), [caQTL](xqtl-data/qtl/caQTL), [metQTL](xqtl-data/qtl/metQTL), plus ROSMAP transcriptomic pattern QTLs (tpQTL) and trans-xQTLs * **[FGMB Atlas](fgmb_weights_database)** - Multi-context regulome-wide association study (RWAS) prediction model resources, including Synapse accessions for models, gene-level association results, causal fine-mapping outputs. * **AD Loci Integration Summary** - The 195-locus AD GWAS × xQTL summary (October 2026 release) on Synapse ([syn69865823](https://www.synapse.org/Synapse:syn69865823)), also browsable in the interactive [xQTL-AD-loci-explorer](https://wanggroup.org/xQTL-AD-loci-explorer/) * **[Reference Data](xqtl-data/reference_data/)** - ADSP-based LD reference panels (16,905 European ancestry samples), including an LD sketch panel, and other analytical resources diff --git a/content/xqtl-data/omics/glycoproteomics/README.md b/content/xqtl-data/omics/glycoproteomics/README.md index 9beaae1..94456e7 100644 --- a/content/xqtl-data/omics/glycoproteomics/README.md +++ b/content/xqtl-data/omics/glycoproteomics/README.md @@ -1,6 +1,6 @@ # Glycoproteomics Data -Glycopeptide-level mass spectrometry measurements of protein glycosylation from brain tissue, used for gpQTL mapping. → See [gpQTL results](../../qtl/gpQTL) +Glycopeptide-level mass spectrometry measurements of protein glycosylation from brain tissue, used for glycoQTL mapping. → See [glycoQTL results](../../qtl/glycoQTL) ## Brain Tissue diff --git a/content/xqtl-data/omics/glycoproteomics/ROSMAP_DLPFC_glycoproteomics.md b/content/xqtl-data/omics/glycoproteomics/ROSMAP_DLPFC_glycoproteomics.md index 05c4173..fc64284 100644 --- a/content/xqtl-data/omics/glycoproteomics/ROSMAP_DLPFC_glycoproteomics.md +++ b/content/xqtl-data/omics/glycoproteomics/ROSMAP_DLPFC_glycoproteomics.md @@ -48,7 +48,7 @@ Glycopeptide abundance matrices normalized from TMT-based mass spectrometry data ## QTL Analysis -QTL analysis for this dataset is documented in [../../qtl/gpQTL/ROSMAP_DLPFC_glycoproteomics_qtl.md](../../qtl/gpQTL/ROSMAP_DLPFC_glycoproteomics_qtl.md). +QTL analysis for this dataset is documented in [../../qtl/glycoQTL/ROSMAP_DLPFC_glycoproteomics_qtl.md](../../qtl/glycoQTL/ROSMAP_DLPFC_glycoproteomics_qtl.md). Flagship paper analyses: - Fine-mapping (SuSiE-RSS): [syn69670592](https://www.synapse.org/Synapse:syn69670592) diff --git a/content/xqtl-data/qtl/README.md b/content/xqtl-data/qtl/README.md index 2e580a3..d54171a 100644 --- a/content/xqtl-data/qtl/README.md +++ b/content/xqtl-data/qtl/README.md @@ -6,7 +6,7 @@ All QTL datasets are hosted on Synapse under [xQTL_data](https://www.synapse.org * [Expression QTLs (eQTL)](eQTL) — ROSMAP (DLPFC/PCC/AC/microglia/monocyte/snRNA-seq), MSBB, MiGA, MetaBrain, Knight ADRC, STARNET * [Splicing QTLs (sQTL)](sQTL) — ROSMAP (DLPFC/PCC/AC/snuc), MSBB, Knight ADRC -* [Glycosylation QTLs (gpQTL)](gpQTL) — ROSMAP DLPFC +* [Glycosylation QTLs (glycoQTL)](glycoQTL) — ROSMAP DLPFC * [Methylation QTLs (mQTL)](mQTL) — ROSMAP DLPFC, MSBB, Knight ADRC * [Histone acetylation QTLs (haQTL)](haQTL) — ROSMAP DLPFC * [Chromatin accessibility QTLs (caQTL)](caQTL) — ROSMAP snuc @@ -29,7 +29,7 @@ All QTL datasets are hosted on Synapse under [xQTL_data](https://www.synapse.org * [ROSMAP AC gene expression QTL](eQTL/ROSMAP_AC_expression_qtl) * [ROSMAP DLPFC alternative splicing QTL](sQTL/ROSMAP_DLPFC_splicing_qtl) * [ROSMAP DLPFC gene expression QTL](eQTL/ROSMAP_DLPFC_expression_qtl) -* [ROSMAP DLPFC glycoproteomics QTL](gpQTL/ROSMAP_DLPFC_glycoproteomics_qtl) +* [ROSMAP DLPFC glycoproteomics QTL](glycoQTL/ROSMAP_DLPFC_glycoproteomics_qtl) * [ROSMAP DLPFC H3K9ac QTL](haQTL/ROSMAP_DLPFC_ChIPSeq_H3K9ac_qtl) * [ROSMAP DLPFC metabolomics QTL](metQTL/ROSMAP_DLPFC_metabolomics_qtl) * [ROSMAP DLPFC methylation QTL](mQTL/ROSMAP_DLPFC_methylation_qtl) diff --git a/content/xqtl-data/qtl/glycoQTL/README.md b/content/xqtl-data/qtl/glycoQTL/README.md new file mode 100644 index 0000000..0d5c523 --- /dev/null +++ b/content/xqtl-data/qtl/glycoQTL/README.md @@ -0,0 +1,54 @@ +# Glycoproteomics QTL (glycoQTL) Resources + +Glycoproteomics quantitative trait loci (glycoQTL) identify genetic variants that influence protein glycosylation levels. Glycosylation is a key post-translational modification affecting protein folding, stability, and function, and is particularly relevant to neurodegeneration and amyloid processing in Alzheimer's disease. This resource provides glycoQTL summary statistics, fine-mapping results, TWAS/qTWAS pre-trained models, and trans-glycoQTL analyses. + +## Overview + +glycoQTL mapping was performed on glycopeptide-level mass spectrometry data from brain tissue, using the [FunGen-xQTL pipeline](https://statfungen.github.io/xqtl-protocol/README.html). Glycopeptide abundances were normalized and regressed on covariates before tensorQTL-based association testing. Fine-mapping was performed using SuSiE-RSS. This represents one of the first large-scale brain glycoQTL resources integrated with AD genetics. + +## Available Datasets + +### Brain Tissue + +| Dataset | Cohort / Brain Region | Synapse | +|---------|-----------------------|---------| +| [ROSMAP DLPFC](ROSMAP_DLPFC_glycoproteomics_qtl) | ROSMAP dorsolateral prefrontal cortex | [syn69670592](https://www.synapse.org/Synapse:syn69670592) | + +## Analyses Performed + +### Single-Context Fine-Mapping + +Fine-mapping using **SuSiE-RSS** per glycopeptide, yielding: +- Posterior inclusion probabilities (PIPs) +- 95% credible sets +- Effect sizes on glycosylation levels + +### Multi-Gene Fine-Mapping + +Multi-gene fine-mapping for glycoQTLs jointly models co-regulated glycoproteins to resolve shared signals. Results available at [syn69670592](https://www.synapse.org/Synapse:syn69670592). + +### Trans-glycoQTL Fine-Mapping + +Genome-wide trans-glycoQTL analyses identify distant genetic influences on glycosylation patterns. Trans-glycoQTL fine-mapping results for ROSMAP DLPFC are provided at [ROSMAP DLPFC](ROSMAP_DLPFC_glycoproteomics_qtl). + +### TWAS / qTWAS Models + +Pre-trained glycoQTL-based TWAS models: +- **TWAS weight models** ([syn69670600](https://www.synapse.org/Synapse:syn69670600)): ROSMAP DLPFC +- **qTWAS models** ([syn69670611](https://www.synapse.org/Synapse:syn69670611)): quantile regression glycoQTL models +- **cTWAS inputs** ([syn70095142](https://www.synapse.org/Synapse:syn70095142)): causal TWAS formatted inputs + +### Colocalization + +AD GWAS–glycoQTL colocalization analyses identify glycosylation-level mechanisms of AD risk variants. Results at [syn69865816](https://www.synapse.org/Synapse:syn69865816) and [syn69670630](https://www.synapse.org/Synapse:syn69670630). + +## Data Access + +| Resource | Synapse ID | +|----------|------------| +| Fine-mapping models (glycoQTL) | [syn69670592](https://www.synapse.org/Synapse:syn69670592) | +| TWAS weight models (glycoQTL) | [syn69670600](https://www.synapse.org/Synapse:syn69670600) | +| qTWAS models (glycoQTL) | [syn69670611](https://www.synapse.org/Synapse:syn69670611) | +| cTWAS input files | [syn70095142](https://www.synapse.org/Synapse:syn70095142) | +| AD–glycoQTL colocalization results | [syn69865816](https://www.synapse.org/Synapse:syn69865816) | +| AD–glycoQTL colocalization models | [syn69670630](https://www.synapse.org/Synapse:syn69670630) | diff --git a/content/xqtl-data/qtl/gpQTL/ROSMAP_DLPFC_glycoproteomics_qtl.md b/content/xqtl-data/qtl/glycoQTL/ROSMAP_DLPFC_glycoproteomics_qtl.md similarity index 82% rename from content/xqtl-data/qtl/gpQTL/ROSMAP_DLPFC_glycoproteomics_qtl.md rename to content/xqtl-data/qtl/glycoQTL/ROSMAP_DLPFC_glycoproteomics_qtl.md index a4f79cd..c5c3f91 100644 --- a/content/xqtl-data/qtl/gpQTL/ROSMAP_DLPFC_glycoproteomics_qtl.md +++ b/content/xqtl-data/qtl/glycoQTL/ROSMAP_DLPFC_glycoproteomics_qtl.md @@ -1,6 +1,6 @@ --- type: qtl -modality: gpQTL +modality: glycoQTL short_title: ROSMAP DLPFC cohort: ROSMAP context: DLPFC @@ -13,7 +13,7 @@ last_verified: # ROSMAP DLPFC glycoproteomics QTL -This page documents the glycoproteomics QTL (gpQTL) analysis of dorsolateral prefrontal cortex (DLPFC) tissue from the Religious Orders Study (ROS) and the Rush Memory and Aging Project (MAP). The [ROSMAP study page](../../study_info/ROSMAP.md) gives an overview of the cohort. +This page documents the glycoproteomics QTL (glycoQTL) analysis of dorsolateral prefrontal cortex (DLPFC) tissue from the Religious Orders Study (ROS) and the Rush Memory and Aging Project (MAP). The [ROSMAP study page](../../study_info/ROSMAP.md) gives an overview of the cohort. ## Study overview @@ -36,4 +36,4 @@ This page documents the glycoproteomics QTL (gpQTL) analysis of dorsolateral pre - **TWAS weight models.** [ROSMAP_glycoQTL, syn77828034](https://www.synapse.org/Synapse:syn77828034) - **Multi-context colocalization models (ColocBoost).** [ROSMAP_glycoQTL, syn76489398](https://www.synapse.org/Synapse:syn76489398) - **AD GWAS and xQTL colocalization models.** [ROSMAP_glycoQTL, syn76490205](https://www.synapse.org/Synapse:syn76490205) -- **sLDSC LD scores.** [gpQTL, syn75180848](https://www.synapse.org/Synapse:syn75180848) +- **sLDSC LD scores.** [glycoQTL, syn75180848](https://www.synapse.org/Synapse:syn75180848) diff --git a/content/xqtl-data/qtl/gpQTL/README.md b/content/xqtl-data/qtl/gpQTL/README.md deleted file mode 100644 index a6c47f8..0000000 --- a/content/xqtl-data/qtl/gpQTL/README.md +++ /dev/null @@ -1,54 +0,0 @@ -# Glycoproteomics QTL (gpQTL) Resources - -Glycoproteomics quantitative trait loci (gpQTL) identify genetic variants that influence protein glycosylation levels. Glycosylation is a key post-translational modification affecting protein folding, stability, and function, and is particularly relevant to neurodegeneration and amyloid processing in Alzheimer's disease. This resource provides gpQTL summary statistics, fine-mapping results, TWAS/qTWAS pre-trained models, and trans-gpQTL analyses. - -## Overview - -gpQTL mapping was performed on glycopeptide-level mass spectrometry data from brain tissue, using the [FunGen-xQTL pipeline](https://statfungen.github.io/xqtl-protocol/README.html). Glycopeptide abundances were normalized and regressed on covariates before tensorQTL-based association testing. Fine-mapping was performed using SuSiE-RSS. This represents one of the first large-scale brain gpQTL resources integrated with AD genetics. - -## Available Datasets - -### Brain Tissue - -| Dataset | Cohort / Brain Region | Synapse | -|---------|-----------------------|---------| -| [ROSMAP DLPFC](ROSMAP_DLPFC_glycoproteomics_qtl) | ROSMAP dorsolateral prefrontal cortex | [syn69670592](https://www.synapse.org/Synapse:syn69670592) | - -## Analyses Performed - -### Single-Context Fine-Mapping - -Fine-mapping using **SuSiE-RSS** per glycopeptide, yielding: -- Posterior inclusion probabilities (PIPs) -- 95% credible sets -- Effect sizes on glycosylation levels - -### Multi-Gene Fine-Mapping - -Multi-gene fine-mapping for gpQTLs jointly models co-regulated glycoproteins to resolve shared signals. Results available at [syn69670592](https://www.synapse.org/Synapse:syn69670592). - -### Trans-gpQTL Fine-Mapping - -Genome-wide trans-gpQTL analyses identify distant genetic influences on glycosylation patterns. Trans-gpQTL fine-mapping results for ROSMAP DLPFC are provided at [ROSMAP DLPFC](ROSMAP_DLPFC_glycoproteomics_qtl). - -### TWAS / qTWAS Models - -Pre-trained gpQTL-based TWAS models: -- **TWAS weight models** ([syn69670600](https://www.synapse.org/Synapse:syn69670600)): ROSMAP DLPFC -- **qTWAS models** ([syn69670611](https://www.synapse.org/Synapse:syn69670611)): quantile regression gpQTL models -- **cTWAS inputs** ([syn70095142](https://www.synapse.org/Synapse:syn70095142)): causal TWAS formatted inputs - -### Colocalization - -AD GWAS–gpQTL colocalization analyses identify glycosylation-level mechanisms of AD risk variants. Results at [syn69865816](https://www.synapse.org/Synapse:syn69865816) and [syn69670630](https://www.synapse.org/Synapse:syn69670630). - -## Data Access - -| Resource | Synapse ID | -|----------|------------| -| Fine-mapping models (gpQTL) | [syn69670592](https://www.synapse.org/Synapse:syn69670592) | -| TWAS weight models (gpQTL) | [syn69670600](https://www.synapse.org/Synapse:syn69670600) | -| qTWAS models (gpQTL) | [syn69670611](https://www.synapse.org/Synapse:syn69670611) | -| cTWAS input files | [syn70095142](https://www.synapse.org/Synapse:syn70095142) | -| AD–gpQTL colocalization results | [syn69865816](https://www.synapse.org/Synapse:syn69865816) | -| AD–gpQTL colocalization models | [syn69670630](https://www.synapse.org/Synapse:syn69670630) | diff --git a/content/xqtl-data/study_info/ROSMAP.md b/content/xqtl-data/study_info/ROSMAP.md index cd92b6e..3005d4a 100644 --- a/content/xqtl-data/study_info/ROSMAP.md +++ b/content/xqtl-data/study_info/ROSMAP.md @@ -59,7 +59,7 @@ The FunGen-xQTL flagship paper used ROSMAP datasets in these xQTL analyses. | DLPFC H3K9ac ChIP-seq | haQTL | [ROSMAP_DLPFC_ChIPSeq_H3K9ac_qtl](../qtl/haQTL/ROSMAP_DLPFC_ChIPSeq_H3K9ac_qtl.md) | | snATAC-seq (CUIMC + MIT) | caQTL | [ROSMAP_snuc_caQTL_qtl](../qtl/caQTL/ROSMAP_snuc_caQTL_qtl.md) | | DLPFC proteomics | pQTL | [ROSMAP_DLPFC_proteomics_qtl](../qtl/pQTL/ROSMAP_DLPFC_proteomics_qtl.md) | -| DLPFC glycoproteomics | gpQTL | [ROSMAP_DLPFC_glycoproteomics_qtl](../qtl/gpQTL/ROSMAP_DLPFC_glycoproteomics_qtl.md) | +| DLPFC glycoproteomics | glycoQTL | [ROSMAP_DLPFC_glycoproteomics_qtl](../qtl/glycoQTL/ROSMAP_DLPFC_glycoproteomics_qtl.md) | | Brain metabolomics | metQTL | [ROSMAP_DLPFC_metabolomics_qtl](../qtl/metQTL/ROSMAP_DLPFC_metabolomics_qtl.md) | The flagship paper also used these datasets for fine-mapping ([syn69670592](https://www.synapse.org/Synapse:syn69670592)), TWAS models ([syn69670600](https://www.synapse.org/Synapse:syn69670600)) and colocalization ([syn69670597](https://www.synapse.org/Synapse:syn69670597), [syn69865816](https://www.synapse.org/Synapse:syn69865816)). diff --git a/content/xqtl_resource_description.md b/content/xqtl_resource_description.md index 6ca15d2..12deab4 100644 --- a/content/xqtl_resource_description.md +++ b/content/xqtl_resource_description.md @@ -22,7 +22,7 @@ Our xQTL analyses span diverse brain regions and cell types across multiple coho - **[Protein QTLs (pQTL)](xqtl-data/qtl/pQTL):** [ROSMAP DLPFC](xqtl-data/qtl/pQTL/ROSMAP_DLPFC_proteomics_qtl), [MSBB](xqtl-data/qtl/pQTL/MSBB_proteomics_qtl), [Knight ADRC brain](xqtl-data/qtl/pQTL/Knight_ADRC_brain_proteomics_qtl) -- **[Glycosylation QTLs (gpQTL)](xqtl-data/qtl/gpQTL):** [ROSMAP DLPFC](xqtl-data/qtl/gpQTL/ROSMAP_DLPFC_glycoproteomics_qtl) +- **[Glycosylation QTLs (glycoQTL)](xqtl-data/qtl/glycoQTL):** [ROSMAP DLPFC](xqtl-data/qtl/glycoQTL/ROSMAP_DLPFC_glycoproteomics_qtl) - **[Methylation QTLs (mQTL)](xqtl-data/qtl/mQTL):** [ROSMAP DLPFC](xqtl-data/qtl/mQTL/ROSMAP_DLPFC_methylation_qtl), [MSBB](xqtl-data/qtl/mQTL/MSBB_brain_methylation_qtl), [Knight ADRC](xqtl-data/qtl/mQTL/Knight_ADRC_brain_methylation_qtl) @@ -32,7 +32,7 @@ Our xQTL analyses span diverse brain regions and cell types across multiple coho - **[Metabolome QTLs (metQTL)](xqtl-data/qtl/metQTL):** [ROSMAP DLPFC](xqtl-data/qtl/metQTL/ROSMAP_DLPFC_metabolomics_qtl), [Knight ADRC brain](xqtl-data/qtl/metQTL/Knight_ADRC_brain_metabolomics_qtl) -We provide [multi-context fine-mapping](https://www.synapse.org/Synapse:syn69865754) that integrates signals across brain regions for ROSMAP and MSBB cohorts, and [multi-gene fine-mapping](https://www.synapse.org/Synapse:syn69865757) with separate analyses for eQTLs and pQTLs that jointly model multiple genes. Additionally, [trans-QTL fine-mapping](https://www.synapse.org/Synapse:syn69865773) identifies distant regulatory relationships for trans-eQTLs ([ROSMAP DLPFC](xqtl-data/qtl/eQTL/ROSMAP_DLPFC_expression_qtl)), trans-pQTLs ([ROSMAP DLPFC](xqtl-data/qtl/pQTL/ROSMAP_DLPFC_proteomics_qtl)), trans-gpQTLs ([ROSMAP DLPFC](xqtl-data/qtl/gpQTL/ROSMAP_DLPFC_glycoproteomics_qtl)), and metabolome QTLs ([ROSMAP DLPFC](xqtl-data/qtl/metQTL/ROSMAP_DLPFC_metabolomics_qtl)). Transcriptomic pattern QTLs (tpQTL), derived from ROSMAP splicing factor analyses, are included in the fine-mapping, colocalization and TWAS resources. +We provide [multi-context fine-mapping](https://www.synapse.org/Synapse:syn69865754) that integrates signals across brain regions for ROSMAP and MSBB cohorts, and [multi-gene fine-mapping](https://www.synapse.org/Synapse:syn69865757) with separate analyses for eQTLs and pQTLs that jointly model multiple genes. Additionally, [trans-QTL fine-mapping](https://www.synapse.org/Synapse:syn69865773) identifies distant regulatory relationships for trans-eQTLs ([ROSMAP DLPFC](xqtl-data/qtl/eQTL/ROSMAP_DLPFC_expression_qtl)), trans-pQTLs ([ROSMAP DLPFC](xqtl-data/qtl/pQTL/ROSMAP_DLPFC_proteomics_qtl)), trans-glycoQTLs ([ROSMAP DLPFC](xqtl-data/qtl/glycoQTL/ROSMAP_DLPFC_glycoproteomics_qtl)), and metabolome QTLs ([ROSMAP DLPFC](xqtl-data/qtl/metQTL/ROSMAP_DLPFC_metabolomics_qtl)). Transcriptomic pattern QTLs (tpQTL), derived from ROSMAP splicing factor analyses, are included in the fine-mapping, colocalization and TWAS resources. To understand relationships between molecular traits, we conducted colocalization analyses including [multi-context colocalization](https://www.synapse.org/Synapse:syn69865796) using [ColocBoost](https://www.medrxiv.org/content/10.1101/2025.04.17.25326042v1) across cohorts ([syn69865796](https://www.synapse.org/Synapse:syn69865796); models: [syn69670597](https://www.synapse.org/Synapse:syn69670597)) and [pairwise colocalization](https://www.synapse.org/Synapse:syn69865800) using SuSiE-COLOC to specifically examine [caQTL-eQTL](https://www.synapse.org/Synapse:syn69865800) relationships. ColocBoost colocalization among ROSMAP trans-xQTL (transmap) signals is provided separately as [trans colocalization](https://www.synapse.org/Synapse:syn77579916) ([syn77579916](https://www.synapse.org/Synapse:syn77579916)). @@ -76,12 +76,12 @@ We provide complete statistical models as RDS files for researchers to conduct c - **eQTL:** [ROSMAP DLPFC](xqtl-data/qtl/eQTL/ROSMAP_DLPFC_expression_qtl), [ROSMAP PCC](xqtl-data/qtl/eQTL/ROSMAP_PCC_expression_qtl), [ROSMAP AC](xqtl-data/qtl/eQTL/ROSMAP_AC_expression_qtl), [ROSMAP microglia](xqtl-data/qtl/eQTL/ROSMAP_microglia_expression_qtl), [ROSMAP monocyte](xqtl-data/qtl/eQTL/ROSMAP_monocyte_expression_qtl), [MSBB](xqtl-data/qtl/eQTL/MSBB_brain_expression_qtl), [Knight ADRC](xqtl-data/qtl/eQTL/Knight_ADRC_brain_expression_qtl), [MiGA](xqtl-data/qtl/eQTL/MiGA_brain_expression_qtl), [MetaBrain](xqtl-data/qtl/eQTL/MetaBrain_brain_expression_qtl) - **sQTL:** [ROSMAP DLPFC](xqtl-data/qtl/sQTL/ROSMAP_DLPFC_splicing_qtl), [ROSMAP PCC](xqtl-data/qtl/sQTL/ROSMAP_PCC_splicing_qtl), [ROSMAP AC](xqtl-data/qtl/sQTL/ROSMAP_AC_splicing_qtl), [ROSMAP snuc](xqtl-data/qtl/sQTL/ROSMAP_snuc_splicing_qtl), [MSBB](xqtl-data/qtl/sQTL/MSBB_brain_splicing_qtl), [Knight ADRC](xqtl-data/qtl/sQTL/Knight_ADRC_brain_splicing_qtl) - **pQTL:** [ROSMAP DLPFC](xqtl-data/qtl/pQTL/ROSMAP_DLPFC_proteomics_qtl), [MSBB](xqtl-data/qtl/pQTL/MSBB_proteomics_qtl), [Knight ADRC brain](xqtl-data/qtl/pQTL/Knight_ADRC_brain_proteomics_qtl) -- **gpQTL:** [ROSMAP DLPFC](xqtl-data/qtl/gpQTL/ROSMAP_DLPFC_glycoproteomics_qtl) +- **glycoQTL:** [ROSMAP DLPFC](xqtl-data/qtl/glycoQTL/ROSMAP_DLPFC_glycoproteomics_qtl) - **mQTL:** [ROSMAP DLPFC](xqtl-data/qtl/mQTL/ROSMAP_DLPFC_methylation_qtl), [MSBB](xqtl-data/qtl/mQTL/MSBB_brain_methylation_qtl), [Knight ADRC](xqtl-data/qtl/mQTL/Knight_ADRC_brain_methylation_qtl) - **haQTL:** [ROSMAP DLPFC](xqtl-data/qtl/haQTL/ROSMAP_DLPFC_ChIPSeq_H3K9ac_qtl) - **caQTL:** [ROSMAP snuc](xqtl-data/qtl/caQTL/ROSMAP_snuc_caQTL_qtl) -[Colocalization models](https://www.synapse.org/Synapse:syn69670597) preserve the probabilistic framework for identifying shared genetic signals, allowing exploration of alternative colocalization thresholds and model assessment ([syn69670597](https://www.synapse.org/Synapse:syn69670597)). TWAS weight models ([syn69670600](https://www.synapse.org/Synapse:syn69670600)) and qTWAS models ([syn69670611](https://www.synapse.org/Synapse:syn69670611)) are provided for eQTL ([ROSMAP DLPFC](xqtl-data/qtl/eQTL/ROSMAP_DLPFC_expression_qtl), [ROSMAP PCC](xqtl-data/qtl/eQTL/ROSMAP_PCC_expression_qtl), [ROSMAP AC](xqtl-data/qtl/eQTL/ROSMAP_AC_expression_qtl), [MSBB](xqtl-data/qtl/eQTL/MSBB_brain_expression_qtl), [Knight ADRC](xqtl-data/qtl/eQTL/Knight_ADRC_brain_expression_qtl)), pQTL ([ROSMAP DLPFC](xqtl-data/qtl/pQTL/ROSMAP_DLPFC_proteomics_qtl), [MSBB](xqtl-data/qtl/pQTL/MSBB_proteomics_qtl), [Knight ADRC](xqtl-data/qtl/pQTL/Knight_ADRC_brain_proteomics_qtl)), gpQTL ([ROSMAP DLPFC](xqtl-data/qtl/gpQTL/ROSMAP_DLPFC_glycoproteomics_qtl)), and sQTL ([ROSMAP DLPFC](xqtl-data/qtl/sQTL/ROSMAP_DLPFC_splicing_qtl), [ROSMAP PCC](xqtl-data/qtl/sQTL/ROSMAP_PCC_splicing_qtl), [ROSMAP AC](xqtl-data/qtl/sQTL/ROSMAP_AC_splicing_qtl), [MSBB](xqtl-data/qtl/sQTL/MSBB_brain_splicing_qtl), [Knight ADRC](xqtl-data/qtl/sQTL/Knight_ADRC_brain_splicing_qtl)), incorporating non-linear QTL effects. +[Colocalization models](https://www.synapse.org/Synapse:syn69670597) preserve the probabilistic framework for identifying shared genetic signals, allowing exploration of alternative colocalization thresholds and model assessment ([syn69670597](https://www.synapse.org/Synapse:syn69670597)). TWAS weight models ([syn69670600](https://www.synapse.org/Synapse:syn69670600)) and qTWAS models ([syn69670611](https://www.synapse.org/Synapse:syn69670611)) are provided for eQTL ([ROSMAP DLPFC](xqtl-data/qtl/eQTL/ROSMAP_DLPFC_expression_qtl), [ROSMAP PCC](xqtl-data/qtl/eQTL/ROSMAP_PCC_expression_qtl), [ROSMAP AC](xqtl-data/qtl/eQTL/ROSMAP_AC_expression_qtl), [MSBB](xqtl-data/qtl/eQTL/MSBB_brain_expression_qtl), [Knight ADRC](xqtl-data/qtl/eQTL/Knight_ADRC_brain_expression_qtl)), pQTL ([ROSMAP DLPFC](xqtl-data/qtl/pQTL/ROSMAP_DLPFC_proteomics_qtl), [MSBB](xqtl-data/qtl/pQTL/MSBB_proteomics_qtl), [Knight ADRC](xqtl-data/qtl/pQTL/Knight_ADRC_brain_proteomics_qtl)), glycoQTL ([ROSMAP DLPFC](xqtl-data/qtl/glycoQTL/ROSMAP_DLPFC_glycoproteomics_qtl)), and sQTL ([ROSMAP DLPFC](xqtl-data/qtl/sQTL/ROSMAP_DLPFC_splicing_qtl), [ROSMAP PCC](xqtl-data/qtl/sQTL/ROSMAP_PCC_splicing_qtl), [ROSMAP AC](xqtl-data/qtl/sQTL/ROSMAP_AC_splicing_qtl), [MSBB](xqtl-data/qtl/sQTL/MSBB_brain_splicing_qtl), [Knight ADRC](xqtl-data/qtl/sQTL/Knight_ADRC_brain_splicing_qtl)), incorporating non-linear QTL effects. ### Alzheimer's Disease Analysis Models @@ -134,7 +134,7 @@ All FunGen-xQTL flagship paper datasets are hosted on [Synapse](https://www.syna | scEEMS scores | Single-cell eQTL effect models and predictions | [syn69670587](https://www.synapse.org/Synapse:syn69670587) | | Single-nucleus sQTL (ISSAC GLMM) | Cell-type and subtype sQTL summary statistics | [syn69670647](https://www.synapse.org/Synapse:syn69670647) | | Colocalization models | ColocBoost multi-context + SuSiE-coloc pairwise models | [syn69670597](https://www.synapse.org/Synapse:syn69670597) | -| TWAS weight models | Pre-trained TWAS weight models (eQTL, sQTL, pQTL, gpQTL) | [syn69670600](https://www.synapse.org/Synapse:syn69670600) | +| TWAS weight models | Pre-trained TWAS weight models (eQTL, sQTL, pQTL, glycoQTL) | [syn69670600](https://www.synapse.org/Synapse:syn69670600) | | qTWAS models | Quantile TWAS weight models | [syn69670611](https://www.synapse.org/Synapse:syn69670611) | | AD GWAS fine-mapping | SuSiE-RSS fine-mapping results for AD GWAS | [syn69670625](https://www.synapse.org/Synapse:syn69670625) | | AD GWAS colocalization results | Cross-GWAS ColocBoost colocalization summary | [syn69865814](https://www.synapse.org/Synapse:syn69865814) | diff --git a/content/xqtl_resource_format.md b/content/xqtl_resource_format.md index 7d60c4e..9e2caf9 100644 --- a/content/xqtl_resource_format.md +++ b/content/xqtl_resource_format.md @@ -54,8 +54,8 @@ The following table catalogs all fine-mapped QTL and AD GWAS integration results | eQTL | ROSMAP | Oli_mega | single_context_finemapping | analysis_result/single_context/ROSMAP_eQTL/export/summary/context_specific/Oli_mega_eQTL.exported.toploci.bed.gz | | eQTL | ROSMAP | PCC | single_context_finemapping | analysis_result/single_context/ROSMAP_eQTL/export/summary/context_specific/PCC_DeJager_eQTL.exported.toploci.bed.gz | | pQTL | ROSMAP | DLPFC_Bennett | single_context_finemapping | analysis_result/single_context/ROSMAP_pQTL/export/summary/context_specific/DLPFC_Bennett_pQTL.exported.toploci.bed.gz | -| gpQTL | ROSMAP | DLPFC_Klein_adjusted | single_context_finemapping | analysis_result/single_context/ROSMAP_pQTL/export/summary/context_specific/DLPFC_Klein_gpQTL_adjusted.exported.toploci.bed.gz | -| gpQTL | ROSMAP | DLPFC_Klein_unadjusted | single_context_finemapping | analysis_result/single_context/ROSMAP_pQTL/export/summary/context_specific/DLPFC_Klein_gpQTL_unadjusted.exported.toploci.bed.gz | +| glycoQTL | ROSMAP | DLPFC_Klein_adjusted | single_context_finemapping | analysis_result/single_context/ROSMAP_pQTL/export/summary/context_specific/DLPFC_Klein_gpQTL_adjusted.exported.toploci.bed.gz | +| glycoQTL | ROSMAP | DLPFC_Klein_unadjusted | single_context_finemapping | analysis_result/single_context/ROSMAP_pQTL/export/summary/context_specific/DLPFC_Klein_gpQTL_unadjusted.exported.toploci.bed.gz | | eQTL | ROSMAP | monocyte | single_context_finemapping | analysis_result/single_context/ROSMAP_pQTL/export/summary/context_specific/monocyte_ROSMAP_eQTL.exported.toploci.bed.gz | | sQTL | ROSMAP | AC | single_context_finemapping | analysis_result/single_context/ROSMAP_sQTL/LeafCutter2/export/summary/context_specific/ROSMAP_AC_sQTL.exported.toploci.bed.gz | | sQTL | ROSMAP | DLPFC | single_context_finemapping | analysis_result/single_context/ROSMAP_sQTL/LeafCutter2/export/summary/context_specific/ROSMAP_DLPFC_sQTL.exported.toploci.bed.gz | @@ -116,8 +116,8 @@ The following table catalogs all fine-mapped QTL and AD GWAS integration results | eQTL | ROSMAP | mega_Oli | trans_finemapping | analysis_result/trans/export/summary/context_specific/ROSMAP_mega_eQTL_Oli.exported.toploci.bed.gz | | metabolome | ROSMAP | - | trans_finemapping | analysis_result/trans/export/summary/context_specific/ROSMAP_metabolome.exported.toploci.bed.gz | | eQTL | STARNET | Mac | trans_finemapping | analysis_result/trans/export/summary/context_specific/STARNET_eQTL.exported.toploci.bed.gz | -| gpQTL | ROSMAP | DLPFC_Klein_adjusted | trans_finemapping | analysis_result/trans/export/summary/context_specific/ROSMAP_adjusted_gpQTL.exported.toploci.bed.gz | -| gpQTL | ROSMAP | DLPFC_Klein_unadjusted | trans_finemapping | analysis_result/trans/export/summary/context_specific/ROSMAP_gpQTL.exported.toploci.bed.gz | +| glycoQTL | ROSMAP | DLPFC_Klein_adjusted | trans_finemapping | analysis_result/trans/export/summary/context_specific/ROSMAP_adjusted_gpQTL.exported.toploci.bed.gz | +| glycoQTL | ROSMAP | DLPFC_Klein_unadjusted | trans_finemapping | analysis_result/trans/export/summary/context_specific/ROSMAP_gpQTL.exported.toploci.bed.gz | | GWAS | AD_Bellenguez_2022 | - | AD_GWAS_finemapping | analysis_result/AD_GWAS_finemapping/export/context_specific/AD_Bellenguez_2022.exported.toploci.bed.gz | | GWAS | AD_Jansen_2021 | - | AD_GWAS_finemapping | analysis_result/AD_GWAS_finemapping/export/context_specific/AD_Jansen_2021.exported.toploci.bed.gz | | GWAS | AD_Wightman_Full_2021 | - | AD_GWAS_finemapping | analysis_result/AD_GWAS_finemapping/export/context_specific/AD_Wightman_Full_2021.exported.toploci.bed.gz | diff --git a/scripts/hugo_generator.py b/scripts/hugo_generator.py index 26a8f7e..8b5e77a 100644 --- a/scripts/hugo_generator.py +++ b/scripts/hugo_generator.py @@ -698,7 +698,7 @@ def fix_qtl_section_titles(self): for d in Path(self.website_content_dir).rglob('*'): if not d.is_dir(): continue - if re.fullmatch(r'(?i)(ca|gp|ha|met|e|m|p|s)qtl', d.name): + if re.fullmatch(r'(?i)(ca|glyco|gp|ha|met|e|m|p|s)qtl', d.name): title = d.name[:-3].lower() + 'QTL' elif d.name in OMICS_TITLES: title = OMICS_TITLES[d.name] diff --git a/site/data/xqtl.yaml b/site/data/xqtl.yaml index 4582b91..871a724 100644 --- a/site/data/xqtl.yaml +++ b/site/data/xqtl.yaml @@ -22,7 +22,7 @@ modalities: - {id: haQTL, family: Histone, what: Histone acetylation, hue: 70, omics: [histone_ChIPSeq]} - {id: metQTL, family: Metabolomics, what: Metabolites, hue: 110, omics: [metabolomics]} - {id: pQTL, family: Proteomics, what: Protein abundance, hue: 155, omics: [proteomics]} - - {id: gpQTL, family: Glycoproteomics, what: Glycopeptides, hue: 200, omics: [glycoproteomics]} + - {id: glycoQTL, family: Glycoproteomics, what: Glycopeptides, hue: 200, omics: [glycoproteomics]} # Omics folders, in menu order, with the label shown on the site omics: From b8c860db640c250601827975a92c521c76737c8c Mon Sep 17 00:00:00 2001 From: Jenny Empawi Date: Fri, 9 Oct 2026 12:02:12 -0400 Subject: [PATCH 3/9] Name snRNA-seq datasets CUIMC1 and MIT instead of by lab PI names, Synapse file names and analysis repository links are unchanged. --- content/README.md | 2 +- .../expression/ROSMAP_snRNAseq_pseudo_bulk.md | 8 ++++---- content/xqtl-data/omics/snRNA_seq/README.md | 4 ++-- .../omics/snRNA_seq/ROSMAP_snuc_CUIMC1.md | 6 +++--- .../xqtl-data/omics/snRNA_seq/ROSMAP_snuc_MIT.md | 2 +- .../omics/snRNA_seq/ROSMAP_snuc_mega.md | 10 +++++----- .../omics/splicing/ROSMAP_snuc_splicing.md | 16 ++++++++-------- content/xqtl-data/qtl/eQTL/README.md | 2 +- .../qtl/eQTL/ROSMAP_snRNAseq_pseudo_bulk_qtl.md | 8 ++++---- content/xqtl-data/qtl/sQTL/README.md | 2 +- .../qtl/sQTL/ROSMAP_snuc_splicing_qtl.md | 6 +++--- 11 files changed, 33 insertions(+), 33 deletions(-) diff --git a/content/README.md b/content/README.md index 4f668cf..5ab3e3c 100644 --- a/content/README.md +++ b/content/README.md @@ -19,7 +19,7 @@ The FunGen-xQTL project provides comprehensive molecular quantitative trait loci - Histone modification (H3K9ac ChIP-seq) - Chromatin accessibility (snATAC-seq) - Metabolomics (brain) - - Single-nucleus RNA-seq (ROSMAP DLPFC: CUIMC, MIT, and mega cohorts) + - Single-nucleus RNA-seq (ROSMAP DLPFC: CUIMC1, MIT, and mega cohorts) - Genotype (WGS) and covariates * **[xQTL Data](xqtl-data/qtl/)** - Molecular QTL associations organized by modality: [eQTL](xqtl-data/qtl/eQTL), [sQTL](xqtl-data/qtl/sQTL), [pQTL](xqtl-data/qtl/pQTL), [glycoQTL](xqtl-data/qtl/glycoQTL), [mQTL](xqtl-data/qtl/mQTL), [haQTL](xqtl-data/qtl/haQTL), [caQTL](xqtl-data/qtl/caQTL), [metQTL](xqtl-data/qtl/metQTL), plus ROSMAP transcriptomic pattern QTLs (tpQTL) and trans-xQTLs * **[FGMB Atlas](fgmb_weights_database)** - Multi-context regulome-wide association study (RWAS) prediction model resources, including Synapse accessions for models, gene-level association results, causal fine-mapping outputs. diff --git a/content/xqtl-data/omics/expression/ROSMAP_snRNAseq_pseudo_bulk.md b/content/xqtl-data/omics/expression/ROSMAP_snRNAseq_pseudo_bulk.md index d3cba29..ba0d779 100644 --- a/content/xqtl-data/omics/expression/ROSMAP_snRNAseq_pseudo_bulk.md +++ b/content/xqtl-data/omics/expression/ROSMAP_snRNAseq_pseudo_bulk.md @@ -31,7 +31,7 @@ Hao Sun and Masashi Fujita - Study name : ROSMAP snRNA-seq pseudo-bulk gene expression - Study Description : - Disease : Alzheimer’s Disease -- Data Citation : Omics data: [syn31512863](https://www.synapse.org/Synapse:syn31512863) (CUIMC), [syn52293417](https://www.synapse.org/Synapse:syn52293417) (MIT); Genetics data: [ng00067](https://dss.niagads.org/datasets/ng00067/) +- Data Citation : Omics data: [syn31512863](https://www.synapse.org/Synapse:syn31512863) (CUIMC1), [syn52293417](https://www.synapse.org/Synapse:syn52293417) (MIT); Genetics data: [ng00067](https://dss.niagads.org/datasets/ng00067/) - Additional study information : ## Dataset Description @@ -84,10 +84,10 @@ Here, I use astrocytes as an example. But all other cell types have the same fol ### Other key data files -Annotations used by De Jager Lab analysis +Annotations used by the CUIMC1 analysis -- Transcription start sites (TSS) of genes in GRCh38, De Jager Lab -- GTF file used to generate the TSS file, De Jager Lab +- Transcription start sites (TSS) of genes in GRCh38, CUIMC1 analysis +- GTF file used to generate the TSS file, CUIMC1 analysis ## QTL Analysis QTL analysis for this dataset is documented in [../../qtl/eQTL/ROSMAP_snRNAseq_pseudo_bulk_qtl.md](../../qtl/eQTL/ROSMAP_snRNAseq_pseudo_bulk_qtl.md). diff --git a/content/xqtl-data/omics/snRNA_seq/README.md b/content/xqtl-data/omics/snRNA_seq/README.md index 41e1efb..7d022b7 100644 --- a/content/xqtl-data/omics/snRNA_seq/README.md +++ b/content/xqtl-data/omics/snRNA_seq/README.md @@ -1,6 +1,6 @@ # Single-Nucleus RNA-seq Data -Raw single-nucleus RNA-seq (snRNA-seq) datasets from ROSMAP brain tissue, processed separately by site (CUIMC and MIT) before integration. These datasets underlie the pseudo-bulk eQTL and ISSAC sQTL analyses. → See [expression data](../expression) and [splicing data](../splicing) +Raw single-nucleus RNA-seq (snRNA-seq) datasets from ROSMAP brain tissue, processed separately by site (CUIMC1 and MIT) before integration. These datasets underlie the pseudo-bulk eQTL and ISSAC sQTL analyses. → See [expression data](../expression) and [splicing data](../splicing) ## ROSMAP Datasets @@ -8,4 +8,4 @@ Raw single-nucleus RNA-seq (snRNA-seq) datasets from ROSMAP brain tissue, proces |---------|------|--------|--------| | [ROSMAP snuc CUIMC1](ROSMAP_snuc_CUIMC1) | Columbia University (CUIMC) | 424 | — | | [ROSMAP snuc MIT](ROSMAP_snuc_MIT) | MIT | 298 | — | -| [ROSMAP snuc Mega](ROSMAP_snuc_mega) | Combined CUIMC + MIT | 530 (192 shared) | 3,177,748 | +| [ROSMAP snuc Mega](ROSMAP_snuc_mega) | Combined CUIMC1 + MIT | 530 (192 shared) | 3,177,748 | diff --git a/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_CUIMC1.md b/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_CUIMC1.md index 8da53cc..625984d 100644 --- a/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_CUIMC1.md +++ b/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_CUIMC1.md @@ -1,7 +1,7 @@ --- type: omics modality: snRNA_seq -short_title: ROSMAP CUIMC +short_title: ROSMAP CUIMC1 cohort: ROSMAP context: DLPFC access: controlled @@ -11,7 +11,7 @@ lead_analysts: [Anjing Liu] last_verified: --- -# ROSMAP CUIMC snRNA-seq expression +# ROSMAP CUIMC1 snRNA-seq expression Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) single-nucleus RNA-seq expression data from Columbia University Irving Medical Center (CUIMC). Please refer to [this document](../../study_info/ROSMAP) for an overview of the ROSMAP project. @@ -32,7 +32,7 @@ Acknowledgement : Study data were generated from postmortem brain tissue provide Study name : ROSMAP CUIMC snRNA-seq expression -Study Description : Single-nucleus RNA-seq expression data from 424 ROSMAP donors generated at Columbia University Irving Medical Center (CUIMC) by the De Jager lab. Nuclei were isolated from dorsolateral prefrontal cortex (DLPFC) postmortem brain tissue and profiled using droplet-based 10x Genomics snRNA-seq. Cell types covered: Astrocytes (Ast), Excitatory neurons (Exc), Inhibitory neurons (Inh), Microglia (Mic), Oligodendrocytes (Oli), and Oligodendrocyte progenitor cells (OPC). Pseudo-bulk expression matrices were generated per cell type for use in cis-eQTL analysis. +Study Description : Single-nucleus RNA-seq expression data from 424 ROSMAP donors generated at Columbia University Irving Medical Center (CUIMC1 dataset). Nuclei were isolated from dorsolateral prefrontal cortex (DLPFC) postmortem brain tissue and profiled using droplet-based 10x Genomics snRNA-seq. Cell types covered: Astrocytes (Ast), Excitatory neurons (Exc), Inhibitory neurons (Inh), Microglia (Mic), Oligodendrocytes (Oli), and Oligodendrocyte progenitor cells (OPC). Pseudo-bulk expression matrices were generated per cell type for use in cis-eQTL analysis. Disease : Alzheimer's Disease diff --git a/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_MIT.md b/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_MIT.md index 290b799..b38cdef 100644 --- a/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_MIT.md +++ b/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_MIT.md @@ -32,7 +32,7 @@ Acknowledgement : The results published here are in whole or in part based on da Study name : ROSMAP MIT snRNA-seq expression -Study Description : Single-nucleus RNA-seq expression data from 427 ROSMAP donors generated at Massachusetts Institute of Technology (MIT) by the Kellis lab. Nuclei were isolated from prefrontal cortex (PFC) postmortem brain tissue and profiled using 10x Genomics snRNA-seq to generate a comprehensive single-cell atlas of the aged human prefrontal cortex spanning more than 2.3 million nuclei. Cell types covered: Astrocytes (Ast), Excitatory neurons (Exc), Inhibitory neurons (Inh), Microglia (Mic), Oligodendrocytes (Oli), and Oligodendrocyte progenitor cells (OPC). Pseudo-bulk expression matrices were generated per cell type for use in cis-eQTL analysis. +Study Description : Single-nucleus RNA-seq expression data from 427 ROSMAP donors generated at Massachusetts Institute of Technology (MIT dataset). Nuclei were isolated from prefrontal cortex (PFC) postmortem brain tissue and profiled using 10x Genomics snRNA-seq to generate a comprehensive single-cell atlas of the aged human prefrontal cortex spanning more than 2.3 million nuclei. Cell types covered: Astrocytes (Ast), Excitatory neurons (Exc), Inhibitory neurons (Inh), Microglia (Mic), Oligodendrocytes (Oli), and Oligodendrocyte progenitor cells (OPC). Pseudo-bulk expression matrices were generated per cell type for use in cis-eQTL analysis. Disease : Alzheimer's Disease diff --git a/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_mega.md b/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_mega.md index c3bde93..4f0e6e8 100644 --- a/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_mega.md +++ b/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_mega.md @@ -14,7 +14,7 @@ last_verified: --- # ROSMAP Mega snRNA-seq expression -Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) mega-analysis combining single-nucleus RNA-seq data from CUIMC and MIT. +Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) mega-analysis combining single-nucleus RNA-seq data from CUIMC1 and MIT. Please refer to [this document](../../study_info/ROSMAP) for an overview of the ROSMAP project. @@ -34,11 +34,11 @@ Acknowledgement : Study data were generated from postmortem brain tissue provide Study name : ROSMAP Mega snRNA-seq expression -Study Description : Mega-analysis combining single-nucleus RNA-seq data from the CUIMC (De Jager lab) and MIT (Kellis lab) ROSMAP datasets. The merged dataset integrates nuclei from DLPFC/PFC postmortem brain tissue across a total of approximately 848 ROSMAP donors (with overlapping donors harmonized). This larger combined resource increases statistical power for cell-type-specific cis-eQTL discovery. Cell types covered: Astrocytes (Ast), Excitatory neurons (Exc), Inhibitory neurons (Inh), Microglia (Mic), Oligodendrocytes (Oli), and Oligodendrocyte progenitor cells (OPC). Pseudo-bulk expression matrices were generated per cell type for use in cis-eQTL analysis. +Study Description : Mega-analysis combining single-nucleus RNA-seq data from the CUIMC1 and MIT ROSMAP datasets. The merged dataset integrates nuclei from DLPFC/PFC postmortem brain tissue across a total of approximately 848 ROSMAP donors (with overlapping donors harmonized). This larger combined resource increases statistical power for cell-type-specific cis-eQTL discovery. Cell types covered: Astrocytes (Ast), Excitatory neurons (Exc), Inhibitory neurons (Inh), Microglia (Mic), Oligodendrocytes (Oli), and Oligodendrocyte progenitor cells (OPC). Pseudo-bulk expression matrices were generated per cell type for use in cis-eQTL analysis. Disease : Alzheimer's Disease -Data Citation : Omics data: https://www.synapse.org/Synapse:syn31512863 (CUIMC), https://www.synapse.org/Synapse:syn52293417 (MIT) +Data Citation : Omics data: https://www.synapse.org/Synapse:syn31512863 (CUIMC1), https://www.synapse.org/Synapse:syn52293417 (MIT) Genetics data: https://dss.niagads.org/datasets/ng00067/ @@ -50,7 +50,7 @@ PIs : Phil De Jager (Columbia University) and Manolis Kellis (Massachusetts Inst ### Raw data -Nuclei were isolated from DLPFC/PFC postmortem brain tissue of ROSMAP participants from two complementary datasets: the CUIMC dataset (424 donors, De Jager lab; Synapse [syn31512863](https://www.synapse.org/Synapse:syn31512863)) and the MIT dataset (427 donors, Kellis lab; Synapse [syn52293417](https://www.synapse.org/Synapse:syn52293417)). Overlapping donors between the two datasets were identified and handled appropriately during harmonization. Single-nucleus RNA-seq was performed using the 10x Genomics Chromium platform in both studies. Raw reads were aligned to the GRCh38 reference genome following the respective lab preprocessing workflows. +Nuclei were isolated from DLPFC/PFC postmortem brain tissue of ROSMAP participants from two complementary datasets: the CUIMC1 dataset (424 donors; Synapse [syn31512863](https://www.synapse.org/Synapse:syn31512863)) and the MIT dataset (427 donors; Synapse [syn52293417](https://www.synapse.org/Synapse:syn52293417)). Overlapping donors between the two datasets were identified and handled appropriately during harmonization. Single-nucleus RNA-seq was performed using the 10x Genomics Chromium platform in both studies. Raw reads were aligned to the GRCh38 reference genome following the respective lab preprocessing workflows. ### Molecular phenotype matrices @@ -58,7 +58,7 @@ Pseudo-bulk count matrices were independently generated for each dataset by aggr ### Phenotype preprocessing -Pseudo-bulk expression matrices from both datasets were normalized and filtered following standard pipelines prior to merging. Batch effects between the CUIMC and MIT datasets were accounted for during covariate modeling. Covariates for eQTL analysis include sex, age at death, postmortem interval (PMI), study (ROS or MAP), dataset (CUIMC or MIT), total genes detected, top genotype principal components, and expression principal components. +Pseudo-bulk expression matrices from both datasets were normalized and filtered following standard pipelines prior to merging. Batch effects between the CUIMC1 and MIT datasets were accounted for during covariate modeling. Covariates for eQTL analysis include sex, age at death, postmortem interval (PMI), study (ROS or MAP), dataset (CUIMC1 or MIT), total genes detected, top genotype principal components, and expression principal components. ## Analysis Status diff --git a/content/xqtl-data/omics/splicing/ROSMAP_snuc_splicing.md b/content/xqtl-data/omics/splicing/ROSMAP_snuc_splicing.md index b4c790b..dc9dca9 100644 --- a/content/xqtl-data/omics/splicing/ROSMAP_snuc_splicing.md +++ b/content/xqtl-data/omics/splicing/ROSMAP_snuc_splicing.md @@ -13,7 +13,7 @@ last_verified: # ROSMAP snRNA-seq Splicing (ISSAC) -Single-nucleus RNA-seq splicing QTL analysis using the ISSAC (Integrative Single-cell Splicing Analysis with Context) method, applied to harmonized CUIMC and MIT single-nucleus data from ROSMAP DLPFC. +Single-nucleus RNA-seq splicing QTL analysis using the ISSAC (Integrative Single-cell Splicing Analysis with Context) method, applied to harmonized CUIMC1 and MIT single-nucleus data from ROSMAP DLPFC. Please refer to [this document](../../study_info/ROSMAP.md) for an overview of the ROSMAP project. @@ -28,7 +28,7 @@ FunGen-xQTL Analysis Working Group - **Publication**: PMID: 38514782, PMID: 39048816, PMID: 37774677, PMID: 40060644 - **Genetics publication**: PMID: 40407102 - **Acknowledgement**: Study data were generated from postmortem brain tissue provided by the Religious Orders Study and Rush Memory and Aging Project (ROSMAP) cohort at Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago. This work was funded by NIH grants U01AG061356 (De Jager/Bennett), RF1AG057473 (De Jager/Bennett), and U01AG046152 (De Jager/Bennett) as part of the AMP-AD consortium, as well as NIH grants R01AG066831 (Menon) and U01AG072572 (De Jager/St George-Hyslop). This work was also supported in part by the Cure Alzheimer's Fund, NIH grants AG058002, AG062377, NS110453, NS115064, AG062335, AG074003, NS127187, MH119509, HG008155 (M.K.), RF1AG062377, RF1AG054321, RO1AG054012 (L.-H.T.) and the NIH training grant GM087237 (to C.A.B.). ROSMAP is supported by P30AG10161, P30AG72975, R01AG15819, R01AG17917, U01AG46152, U01AG61356. -- **Omics data**: [syn31512863](https://www.synapse.org/Synapse:syn31512863) (CUIMC), [syn52293417](https://www.synapse.org/Synapse:syn52293417) (MIT) +- **Omics data**: [syn31512863](https://www.synapse.org/Synapse:syn31512863) (CUIMC1), [syn52293417](https://www.synapse.org/Synapse:syn52293417) (MIT) - **Genetics data**: [ng00067](https://dss.niagads.org/datasets/ng00067/) - **Disease**: Alzheimer's Disease @@ -38,7 +38,7 @@ FunGen-xQTL Analysis Working Group This study utilized single-nucleus RNA sequencing data from the dorsolateral prefrontal cortex (DLPFC, Brodmann Area 9) of post-mortem human brain tissue from two cohorts as part of the FunGen-xQTL harmonized aging brain resource project: -- **CUIMC cohort** (Columbia University Irving Medical Center, also known as CUIMC1 or CUMC): 424 donors +- **CUIMC1 cohort** (Columbia University Irving Medical Center, also known as CUIMC1 or CUMC): 424 donors - **MIT cohort**: 298 donors - **Shared donors**: 192 donors shared between cohorts - **Total**: 530 unique donors across 722 specimens @@ -46,19 +46,19 @@ This study utilized single-nucleus RNA sequencing data from the dorsolateral pre ### Sample Processing -**CUIMC cohort:** Dorsolateral prefrontal cortex tissue specimens were received frozen and processed on ice. Gray matter was carefully dissected to remove white matter and meninges when present. Approximately 50–100 mg of gray matter tissue was transferred into a dounce homogenizer with 2 mL of NP40 Lysis Buffer (0.1% NP40, 10 mM Tris, 146 mM NaCl, 1 mM CaCl2, 21 mM MgCl2, 40 U/mL of RNase inhibitor). Tissue was gently dounced on ice 25 times with Pestle A followed by 25 times with Pestle B, then transferred to a 15 mL conical tube. 3 mL of PBS + 0.01% BSA and 40 U/mL of RNase inhibitor were added for a final volume of 5 mL and immediately centrifuged at 500g for 5 min at 4°C. Nuclei pellets were resuspended in 500 µL of PBS + 0.01% BSA and 40 U/mL of RNase inhibitor and filtered through 20 µm pre-separation filters. +**CUIMC1 cohort:** Dorsolateral prefrontal cortex tissue specimens were received frozen and processed on ice. Gray matter was carefully dissected to remove white matter and meninges when present. Approximately 50–100 mg of gray matter tissue was transferred into a dounce homogenizer with 2 mL of NP40 Lysis Buffer (0.1% NP40, 10 mM Tris, 146 mM NaCl, 1 mM CaCl2, 21 mM MgCl2, 40 U/mL of RNase inhibitor). Tissue was gently dounced on ice 25 times with Pestle A followed by 25 times with Pestle B, then transferred to a 15 mL conical tube. 3 mL of PBS + 0.01% BSA and 40 U/mL of RNase inhibitor were added for a final volume of 5 mL and immediately centrifuged at 500g for 5 min at 4°C. Nuclei pellets were resuspended in 500 µL of PBS + 0.01% BSA and 40 U/mL of RNase inhibitor and filtered through 20 µm pre-separation filters. **MIT cohort:** Single nuclei were isolated from frozen tissue following the DroNc-seq protocol (Habib et al. 2017) modified to work on the 10x Genomics Chromium platform. ### Library Batching and Preparation -**CUIMC cohort:** Approximately 5,000 nuclei from each of 8 participants were pooled into one sample (40,000 nuclei total). Libraries were generated from pooled samples: 222 libraries contained samples from 8 donors each; 4 libraries from 7 donors each; and 8 libraries from a single donor each. Libraries were created as two replicates (e.g., B10-A and B10-B), each sequenced twice at different sequencing centers (Broad Institute and NYGC). The pooled nuclei were run on the 10x Genomics Single Cell RNA-Seq Platform using Chromium Single Cell 3' Reagent Kits version 3. +**CUIMC1 cohort:** Approximately 5,000 nuclei from each of 8 participants were pooled into one sample (40,000 nuclei total). Libraries were generated from pooled samples: 222 libraries contained samples from 8 donors each; 4 libraries from 7 donors each; and 8 libraries from a single donor each. Libraries were created as two replicates (e.g., B10-A and B10-B), each sequenced twice at different sequencing centers (Broad Institute and NYGC). The pooled nuclei were run on the 10x Genomics Single Cell RNA-Seq Platform using Chromium Single Cell 3' Reagent Kits version 3. **MIT cohort:** Nuclei from individual samples were loaded on a single channel on the 10x Genomics Chromium chip. Library construction was performed per the Chromium Single Cell 3' Reagent Kit v2 protocol (CG00052). ### Sequencing -**CUIMC:** Libraries from 4 channels were pooled and sequenced on 1 lane of Illumina HiSeqX at the Broad Institute's Genomics Platform or NYGC, targeting approximately 1 million reads per channel. +**CUIMC1:** Libraries from 4 channels were pooled and sequenced on 1 lane of Illumina HiSeqX at the Broad Institute's Genomics Platform or NYGC, targeting approximately 1 million reads per channel. **MIT:** Sequenced on Illumina HiSeq4000 using paired-end sequencing: Read 1 (UMI + 10x barcode) – 26 cycles; i7 sample index – 8 cycles; Read 2 (transcript) – 98 cycles. @@ -66,9 +66,9 @@ This study utilized single-nucleus RNA sequencing data from the dorsolateral pre Raw sequencing reads were processed using CellRanger (v3.0 or later) and aligned to GRCh38 (hg38). Nuclei with fewer than 400 detected genes were excluded. Doublets were identified and removed. The two cohorts were integrated using Harmony batch correction. The final dataset comprised 3,177,748 high-quality nuclei. -### Demultiplexing (CUIMC Pooled Libraries) +### Demultiplexing (CUIMC1 Pooled Libraries) -Because CUIMC libraries consisted of pooled nuclei from eight individuals, original individuals were inferred from SNPs in snRNA-seq reads. When all eight individuals were genotyped, **demuxlet** was used. When fewer were genotyped, **freemuxlet** was used to cluster droplets into 8 groups, with snRNA-seq-based genotypes compared to WGS using `bcftools gtcheck`. +Because CUIMC1 libraries consisted of pooled nuclei from eight individuals, original individuals were inferred from SNPs in snRNA-seq reads. When all eight individuals were genotyped, **demuxlet** was used. When fewer were genotyped, **freemuxlet** was used to cluster droplets into 8 groups, with snRNA-seq-based genotypes compared to WGS using `bcftools gtcheck`. ### Cell Type Annotation diff --git a/content/xqtl-data/qtl/eQTL/README.md b/content/xqtl-data/qtl/eQTL/README.md index 360f213..9dac494 100644 --- a/content/xqtl-data/qtl/eQTL/README.md +++ b/content/xqtl-data/qtl/eQTL/README.md @@ -17,7 +17,7 @@ eQTL mapping was performed using the [FunGen-xQTL pipeline](https://statfungen.g | [ROSMAP AC](ROSMAP_AC_expression_qtl) | Anterior cingulate cortex (bulk RNA-seq) | — | | [ROSMAP microglia](ROSMAP_microglia_expression_qtl) | Microglia (bulk RNA-seq) | — | | [ROSMAP monocyte](ROSMAP_monocyte_expression_qtl) | Peripheral blood monocytes | — | -| [ROSMAP snRNA-seq pseudo-bulk](ROSMAP_snRNAseq_pseudo_bulk_qtl) | Single-nucleus RNA-seq, 7 major cell types (CUIMC + MIT) | — | +| [ROSMAP snRNA-seq pseudo-bulk](ROSMAP_snRNAseq_pseudo_bulk_qtl) | Single-nucleus RNA-seq, 7 major cell types (CUIMC1 + MIT) | — | ### Brain Tissue — Other Cohorts diff --git a/content/xqtl-data/qtl/eQTL/ROSMAP_snRNAseq_pseudo_bulk_qtl.md b/content/xqtl-data/qtl/eQTL/ROSMAP_snRNAseq_pseudo_bulk_qtl.md index 9897967..fa7deb6 100644 --- a/content/xqtl-data/qtl/eQTL/ROSMAP_snRNAseq_pseudo_bulk_qtl.md +++ b/content/xqtl-data/qtl/eQTL/ROSMAP_snRNAseq_pseudo_bulk_qtl.md @@ -94,8 +94,8 @@ df <- readRDS("matrix-eqtl.rds")$cis$eqtl ### Association scan using TensorQTL and summary statistics standardization - [TensorQTL.ipynb](https://github.com/cumc/xqtl-protocol/blob/main/code/association_scan/TensorQTL/TensorQTL.ipynb) provides the pipeline to generate TensorQTL cis association results for all QTLs. -- [ROSMAP_DeJager_snuc_eQTL](https://github.com/cumc/xqtl-analysis/blob/main/analysis/Wang_Columbia/cis_association/ROSMAP_DeJager_snuc_eQTL/command_generator.ipynb) provides information about the input files for TensorQTL cis association in the base_params variable in [generate_command_1]. -- [ROSMAP_Kellis_eQTL](https://github.com/cumc/xqtl-analysis/blob/main/analysis/Wang_Columbia/cis_association/ROSMAP_Kellis_eQTL/command_generator.ipynb) provides information about the input files for TensorQTL cis association in the base_params variable in [generate_command_1]. +- [ROSMAP CUIMC1 snuc eQTL](https://github.com/cumc/xqtl-analysis/blob/main/analysis/Wang_Columbia/cis_association/ROSMAP_DeJager_snuc_eQTL/command_generator.ipynb) provides information about the input files for TensorQTL cis association in the base_params variable in [generate_command_1]. +- [ROSMAP MIT snuc eQTL](https://github.com/cumc/xqtl-analysis/blob/main/analysis/Wang_Columbia/cis_association/ROSMAP_Kellis_eQTL/command_generator.ipynb) provides information about the input files for TensorQTL cis association in the base_params variable in [generate_command_1]. - [ROSMAP_mega_eQTL](https://github.com/cumc/xqtl-analysis/blob/main/analysis/Wang_Columbia/cis_association/ROSMAP_mega_eQTL/command_generator.ipynb) provides information about the input files for TensorQTL cis association in the base_params variable in [generate_command_1]. @@ -123,12 +123,12 @@ AD GWAS–xQTL colocalization results: [syn69865816](https://www.synapse.org/Syn AD GWAS–xQTL colocalization models: [syn69670630](https://www.synapse.org/Synapse:syn69670630) ## Links to QTL analysis notebooks -pseudo_bulk_eQTL_DeJager: +CUIMC1: [Preprocess_bundle](https://github.com/cumc/xqtl-analysis/blob/main/analysis/Wang_Columbia/ROSMAP/pseudo_bulk_eQTL_DeJager/Preprocess_bundle.ipynb) provides commands to preprocess genotype, phenotype and covariate data all at once. [Phenotype_preprocessing](https://github.com/cumc/xqtl-analysis/blob/main/analysis/Wang_Columbia/ROSMAP/pseudo_bulk_eQTL_DeJager/ALL/phenotype_preprocessing.ipynb) shows the commands used for the phenotype data processing and preparation steps for all cell types. Cell-specific phenotype preprocessing are listed [here in different folders](https://github.com/cumc/xqtl-analysis/tree/main/analysis/Wang_Columbia/ROSMAP/pseudo_bulk_eQTL_DeJager). -pseudo_bulk_eQTL_Kellis: +MIT: [Preprocess_bundle](https://github.com/cumc/xqtl-analysis/blob/main/analysis/Wang_Columbia/ROSMAP/pseudo_bulk_eQTL_Kellis/Preprocess_bundle.ipynb) provides commands to preprocess genotype, phenotype and covariate data all at once. [Genotype_pca](https://github.com/cumc/xqtl-analysis/blob/main/analysis/Wang_Columbia/ROSMAP/pseudo_bulk_eQTL_Kellis/genotype_pca.ipynb) provides steps for PCA analysis for genotype data. [Phenotype_preprocessing](https://github.com/cumc/xqtl-analysis/blob/main/analysis/Wang_Columbia/ROSMAP/pseudo_bulk_eQTL_Kellis/phenotype_preprocessing.ipynb) shows the commands used for the phenotype data processing and preparation steps. diff --git a/content/xqtl-data/qtl/sQTL/README.md b/content/xqtl-data/qtl/sQTL/README.md index 916d989..32d1dc2 100644 --- a/content/xqtl-data/qtl/sQTL/README.md +++ b/content/xqtl-data/qtl/sQTL/README.md @@ -41,7 +41,7 @@ Fine-mapping using **SuSiE-RSS** is applied per splicing phenotype (intron clust ### ISSAC — Single-Nucleus sQTL Method For ROSMAP snuc data, **ISSAC** implements: -- **Metacell aggregation**: 23,143 metacells for 7 major cell types and 87,936 metacells for 67 retained subcell types, from 3,177,748 nuclei (530 unique donors from 722 specimens: CUIMC N=424, MIT N=298, 192 shared donors) +- **Metacell aggregation**: 23,143 metacells for 7 major cell types and 87,936 metacells for 67 retained subcell types, from 3,177,748 nuclei (530 unique donors from 722 specimens: CUIMC1 N=424, MIT N=298, 192 shared donors) - **Splice site usage quantification** with junctools (UMI-level collapsed) - **Binomial GLMM** sQTL mapping with PCG/REML for random effects - **Context-dependent sQTL** analyses: AD-biased (FDR < 0.01), sex-biased (FDR < 0.05), and cell-state-dependent diff --git a/content/xqtl-data/qtl/sQTL/ROSMAP_snuc_splicing_qtl.md b/content/xqtl-data/qtl/sQTL/ROSMAP_snuc_splicing_qtl.md index 6c34b03..bc1b2de 100644 --- a/content/xqtl-data/qtl/sQTL/ROSMAP_snuc_splicing_qtl.md +++ b/content/xqtl-data/qtl/sQTL/ROSMAP_snuc_splicing_qtl.md @@ -14,7 +14,7 @@ last_verified: # ROSMAP Single-Nucleus Alternative Splicing QTL (snSplicing) -Single-nucleus alternative splicing QTL analysis from CUIMC & MIT harmonized snRNA-seq / Multiome data across seven major cell types. +Single-nucleus alternative splicing QTL analysis from CUIMC1 & MIT harmonized snRNA-seq / Multiome data across seven major cell types. Please refer to [this document](../../study_info/ROSMAP.md) for an overview of the ROSMAP project. @@ -25,8 +25,8 @@ FunGen-xQTL Analysis Team ## Study Overview - Study name: ROSMAP snRNA-seq alternative splicing QTL -- Study Description: Splicing quantitative trait loci (sQTL) derived from single-nucleus RNA-seq data using the CUIMC & MIT harmonized mega dataset (530 unique donors: CUIMC N=424, MIT N=298). Splice-site usage was quantified using the ISSAC pipeline, producing per-cell-type pseudo-bulk splicing phenotypes across 7 major cell types and up to 95 subcell types (67 retained with >3,000 cells). -- Dataset: CUIMC & MIT harmonized (mega) +- Study Description: Splicing quantitative trait loci (sQTL) derived from single-nucleus RNA-seq data using the CUIMC1 & MIT harmonized mega dataset (530 unique donors: CUIMC1 N=424, MIT N=298). Splice-site usage was quantified using the ISSAC pipeline, producing per-cell-type pseudo-bulk splicing phenotypes across 7 major cell types and up to 95 subcell types (67 retained with >3,000 cells). +- Dataset: CUIMC1 & MIT harmonized (mega) - Cell types: Excitatory neurons (Exc), Inhibitory neurons (Inh), Astrocytes (Ast), Oligodendrocytes (Oli), OPCs (OPC), Microglia (Mic), Endothelial cells (End) ## Analysis Details From d4674a514bb739d4cefe397d8a4cf825ff1af5d7 Mon Sep 17 00:00:00 2001 From: Jenny Empawi Date: Fri, 9 Oct 2026 12:05:34 -0400 Subject: [PATCH 4/9] Name the snATAC multiome data CUIMC2, as in the flagship paper --- content/xqtl-data/omics/snATAC/ROSMAP_snuc_caQTL.md | 4 ++-- content/xqtl-data/qtl/caQTL/ROSMAP_snuc_caQTL_qtl.md | 4 ++-- content/xqtl-data/study_info/ROSMAP.md | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/content/xqtl-data/omics/snATAC/ROSMAP_snuc_caQTL.md b/content/xqtl-data/omics/snATAC/ROSMAP_snuc_caQTL.md index e8fd408..348c166 100644 --- a/content/xqtl-data/omics/snATAC/ROSMAP_snuc_caQTL.md +++ b/content/xqtl-data/omics/snATAC/ROSMAP_snuc_caQTL.md @@ -16,11 +16,11 @@ last_verified: ## Summary -Single-nucleus ATAC-seq (snATAC-seq) data from ROSMAP, profiling chromatin accessibility in individual nuclei from DLPFC brain tissue. Includes data from MIT cohort (single-site) and harmonized CUIMC + MIT Multiome ATAC data. +Single-nucleus ATAC-seq (snATAC-seq) data from ROSMAP, profiling chromatin accessibility in individual nuclei from DLPFC brain tissue. Includes data from MIT cohort (single-site) and CUIMC2 Multiome ATAC data. ## Dataset Information -- **Cohort**: ROSMAP (MIT single-site; CUIMC + MIT harmonized Multiome) +- **Cohort**: ROSMAP (MIT single-site; CUIMC2 multiome) - **Brain region**: Dorsolateral prefrontal cortex (DLPFC) - **Data type**: Single-nucleus ATAC-seq (snATAC-seq) - **Cell types**: Multiple brain cell types (neurons, oligodendrocytes, astrocytes, microglia, etc.) diff --git a/content/xqtl-data/qtl/caQTL/ROSMAP_snuc_caQTL_qtl.md b/content/xqtl-data/qtl/caQTL/ROSMAP_snuc_caQTL_qtl.md index 4cb089a..db1be26 100644 --- a/content/xqtl-data/qtl/caQTL/ROSMAP_snuc_caQTL_qtl.md +++ b/content/xqtl-data/qtl/caQTL/ROSMAP_snuc_caQTL_qtl.md @@ -14,7 +14,7 @@ last_verified: # ROSMAP Single-Nucleus Chromatin Accessibility QTL (caQTL) -Single-nucleus ATAC-seq chromatin accessibility QTL analysis from ROSMAP donors, covering MIT snATAC-seq and CUIMC & MIT harmonized Multiome ATAC data. +Single-nucleus ATAC-seq chromatin accessibility QTL analysis from ROSMAP donors, covering MIT snATAC-seq and CUIMC2 multiome ATAC data. Please refer to [this document](../../study_info/ROSMAP.md) for an overview of the ROSMAP project. @@ -25,7 +25,7 @@ FunGen-xQTL Analysis Team ## Study Overview - Study name: ROSMAP snATAC-seq caQTL -- Study Description: Chromatin accessibility quantitative trait loci (caQTL) using pseudo-bulk ATAC-seq profiles per cell type. Two datasets are included: (1) MIT snATAC-seq (Mic, Ast, Oli, OPC, Exc, Inh) and (2) CUIMC & MIT harmonized Multiome ATAC (Mic, Ast, Oli, OPC, Exc, Inh). A response caQTL (r-caQTL) analysis was also performed to identify variants affecting chromatin remodeling in context of co-measured gene expression. +- Study Description: Chromatin accessibility quantitative trait loci (caQTL) using pseudo-bulk ATAC-seq profiles per cell type. Two datasets are included: (1) MIT snATAC-seq (Mic, Ast, Oli, OPC, Exc, Inh) and (2) CUIMC2 multiome ATAC (Mic, Ast, Oli, OPC, Exc, Inh). A response caQTL (r-caQTL) analysis was also performed to identify variants affecting chromatin remodeling in context of co-measured gene expression. - Cell types: Microglia (Mic), Astrocytes (Ast), Oligodendrocytes (Oli), OPCs (OPC), Excitatory neurons (Exc), Inhibitory neurons (Inh) - Assay: 10x Genomics snATAC-seq and Multiome ATAC diff --git a/content/xqtl-data/study_info/ROSMAP.md b/content/xqtl-data/study_info/ROSMAP.md index 3005d4a..0aeabfd 100644 --- a/content/xqtl-data/study_info/ROSMAP.md +++ b/content/xqtl-data/study_info/ROSMAP.md @@ -57,7 +57,7 @@ The FunGen-xQTL flagship paper used ROSMAP datasets in these xQTL analyses. | snRNA-seq splicing (ISSAC-seq) | sQTL | [ROSMAP_snuc_splicing_qtl](../qtl/sQTL/ROSMAP_snuc_splicing_qtl.md) | | DLPFC methylation | mQTL | [ROSMAP_DLPFC_methylation_qtl](../qtl/mQTL/ROSMAP_DLPFC_methylation_qtl.md) | | DLPFC H3K9ac ChIP-seq | haQTL | [ROSMAP_DLPFC_ChIPSeq_H3K9ac_qtl](../qtl/haQTL/ROSMAP_DLPFC_ChIPSeq_H3K9ac_qtl.md) | -| snATAC-seq (CUIMC + MIT) | caQTL | [ROSMAP_snuc_caQTL_qtl](../qtl/caQTL/ROSMAP_snuc_caQTL_qtl.md) | +| snATAC-seq (MIT; CUIMC2 multiome) | caQTL | [ROSMAP_snuc_caQTL_qtl](../qtl/caQTL/ROSMAP_snuc_caQTL_qtl.md) | | DLPFC proteomics | pQTL | [ROSMAP_DLPFC_proteomics_qtl](../qtl/pQTL/ROSMAP_DLPFC_proteomics_qtl.md) | | DLPFC glycoproteomics | glycoQTL | [ROSMAP_DLPFC_glycoproteomics_qtl](../qtl/glycoQTL/ROSMAP_DLPFC_glycoproteomics_qtl.md) | | Brain metabolomics | metQTL | [ROSMAP_DLPFC_metabolomics_qtl](../qtl/metQTL/ROSMAP_DLPFC_metabolomics_qtl.md) | From fa036d26df1030ac1b411675262b7e62c59ecd74 Mon Sep 17 00:00:00 2001 From: Jenny Empawi <80464805+jaempawi@users.noreply.github.com> Date: Fri, 9 Oct 2026 12:20:52 -0400 Subject: [PATCH 5/9] Install PyYAML in Hugo workflow Added step to install PyYAML in the workflow. --- .github/workflows/hugo.yml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/.github/workflows/hugo.yml b/.github/workflows/hugo.yml index b79b098..966569b 100644 --- a/.github/workflows/hugo.yml +++ b/.github/workflows/hugo.yml @@ -29,12 +29,15 @@ jobs: hugo-version: 'latest' extended: true + - name: Install PyYAML + run: pip install pyyaml + - name: Download Hugo Book theme + # Pinned: the layouts in site/ override hugo-book and were built against this commit run: | mkdir -p website/themes - cd website/themes - git clone https://github.com/alex-shpak/hugo-book.git - cd ../.. + git clone https://github.com/alex-shpak/hugo-book.git website/themes/hugo-book + git -C website/themes/hugo-book checkout 4074906 - name: Generate xQTL Data Catalog run: | From 1af736f25c1a8c442e57c3d5c5b39026b7cf59cf Mon Sep 17 00:00:00 2001 From: Jenny Empawi Date: Fri, 9 Oct 2026 12:26:09 -0400 Subject: [PATCH 6/9] Revise site text: plainer wording, paper modality names, no internal paths on public pages --- content/coverage.md | 2 +- content/how_to_get_data.md | 14 +++++++------- content/inventory.md | 2 +- site/README.md | 2 ++ site/data/xqtl.yaml | 16 ++++++++-------- site/layouts/coverage.html | 2 +- site/layouts/home.html | 2 +- site/layouts/inventory.html | 2 +- 8 files changed, 22 insertions(+), 20 deletions(-) diff --git a/content/coverage.md b/content/coverage.md index 885948b..aa61ec9 100644 --- a/content/coverage.md +++ b/content/coverage.md @@ -4,4 +4,4 @@ layout: coverage # Analysis coverage -Which methods from the [xQTL protocol](https://statfungen.github.io/xqtl-protocol) have been run on each dataset: cis-QTL mapping, SuSiE and fSuSiE fine-mapping, ColocBoost colocalization, TWAS, cTWAS, Mendelian randomization, LF2 and scEEMS. +This grid shows which [xQTL protocol](https://statfungen.github.io/xqtl-protocol) methods have been run on each dataset, including cis-QTL mapping, SuSiE and fSuSiE fine-mapping, ColocBoost colocalization, TWAS, cTWAS, Mendelian randomization (MR), LF2 and scEEMS. diff --git a/content/how_to_get_data.md b/content/how_to_get_data.md index 09a4d9a..7b361e4 100644 --- a/content/how_to_get_data.md +++ b/content/how_to_get_data.md @@ -1,6 +1,6 @@ # How to get the data -This site describes the data but does not host it. Every dataset page gives a Synapse ID or a public URL. The access label on the page tells you what you need before you can download. +The data are hosted on Synapse and NIAGADS. Each dataset page gives a Synapse ID or public URL, and its access label states what is needed before download. {{< access-defs >}} @@ -11,7 +11,7 @@ Omics data, QTL results, xQTL models and reference files are on Synapse. Most co {{% steps %}} 1. **Create a Synapse account.** Register at [synapse.org](https://www.synapse.org/) and verify your profile. 2. **Become a certified user.** Pass the short Synapse certification quiz on data governance. -3. **Request access.** For controlled data, submit the data use certificate for the cohort through the [AD Knowledge Portal](https://adknowledgeportal.synapse.org/). Approval is per cohort, not per dataset. +3. **Request access.** For controlled data, submit the data use certificate for the cohort through the [AD Knowledge Portal](https://adknowledgeportal.synapse.org/). 4. **Download.** Use the web interface, the Synapse command-line client, or the Python or R client with the Synapse ID from the dataset page. {{% /steps %}} @@ -28,20 +28,20 @@ The four top-level FunGen-xQTL folders on Synapse are [variant and gene summarie AD GWAS summary statistics and ADSP genomics are distributed by NIAGADS. Summary statistics marked Open can be downloaded from the dataset's public URL. Harmonized xQTL summary statistics and fine-mapping results are open access on NIAGADS DSS as [NG00184.v1](https://dss.niagads.org/datasets/ng00184/) (GRCh38). No application is needed. Individual-level data stay controlled and are requested through DSS under their own accessions. {{% callout %}} -**NG00184 downloads are packaged archives, one per QTL type and result type:** `ADSP_FunGen_xQTL.v1...tar` +**NG00184 downloads are packaged archives, one per QTL type and result type, named** `ADSP_FunGen_xQTL.v1...tar` | Result type | What it holds | |---|---| -| `hmt_significant` | Best default: high-confidence associations | -| `bh_significant` | Broader, still FDR-filtered | +| `hmt_significant` | High-confidence associations (recommended starting point) | +| `bh_significant` | Associations passing the FDR threshold | | `all` | Every tested association | | `single_context_finemapping_cs95` | Variants in 95% credible sets | | `single_context_finemapping_all` | Full fine-mapping output | -QTL types in NG00184: eQTL, snuc-eQTL, sQTL, pQTL, mQTL, haQTL. Each archive holds `.bed.gz` files with tabix indexes, metadata and a manifest. +NG00184 includes eQTL, snuc-eQTL, sQTL, pQTL, mQTL and haQTL. Each archive holds `.bed.gz` files with tabix indexes, metadata and a manifest. {{% /callout %}} -To search significant associations without downloading, use the [xQTL Atlas](https://xqtl.niagads.org/): look up a variant, gene or region, view tracks in its genome browser, and download matching rows as TSV. +The [xQTL Atlas](https://xqtl.niagads.org/) lets you search significant associations by variant, gene or region, view them in a genome browser and download matching rows as TSV. ## Release status diff --git a/content/inventory.md b/content/inventory.md index 1257661..6d7d59d 100644 --- a/content/inventory.md +++ b/content/inventory.md @@ -4,4 +4,4 @@ layout: inventory # Dataset inventory -The catalog seen through the next phase of the atlas: every omics dataset behind the current release, plus new and expanded datasets being curated. Acquisition stage comes from each page's release status; datasets without a page yet are listed in `site/data/next_phase.yaml`. +This inventory lists the omics datasets in the current release and the new or expanded datasets being curated for the next phase of the atlas. diff --git a/site/README.md b/site/README.md index e0ded51..e66b361 100644 --- a/site/README.md +++ b/site/README.md @@ -17,4 +17,6 @@ The files here override the hugo-book theme. `scripts/hugo_generator.py` copies Page metadata lives in each page's header; see `template/metadata_header.md`. +The analysis coverage grid reads a `methods:` map in each page's metadata header. The inventory reads each page's release status; datasets that do not have a page yet are listed in `data/next_phase.yaml`. + To preview locally: install Hugo extended (0.158 or newer) and PyYAML, clone hugo-book into `website/themes/hugo-book`, then run `python scripts/hugo_generator.py --no-theme-download --no-readme --serve`. diff --git a/site/data/xqtl.yaml b/site/data/xqtl.yaml index 871a724..a4d2c03 100644 --- a/site/data/xqtl.yaml +++ b/site/data/xqtl.yaml @@ -9,7 +9,7 @@ home: participants: "2,328" participants_note: >- Counts are participants. One participant can contribute several tissues, - cell types and assays. + cell types and assays. The flagship paper analyzes 77 molecular datasets. updated: "October 2026" # QTL modalities, in menu order. `folder` is the folder under content/xqtl-data/qtl and @@ -19,10 +19,10 @@ modalities: - {id: sQTL, family: Splicing, what: Alternative splicing, hue: 300, omics: [splicing]} - {id: mQTL, family: Methylation, what: DNA methylation, hue: 350, omics: [methylation]} - {id: caQTL, family: Chromatin, what: Chromatin accessibility, hue: 30, omics: [snATAC]} - - {id: haQTL, family: Histone, what: Histone acetylation, hue: 70, omics: [histone_ChIPSeq]} - - {id: metQTL, family: Metabolomics, what: Metabolites, hue: 110, omics: [metabolomics]} + - {id: haQTL, family: Histone acetylation, what: Histone acetylation, hue: 70, omics: [histone_ChIPSeq]} + - {id: metQTL, family: Metabolomics, what: Metabolite abundance, hue: 110, omics: [metabolomics]} - {id: pQTL, family: Proteomics, what: Protein abundance, hue: 155, omics: [proteomics]} - - {id: glycoQTL, family: Glycoproteomics, what: Glycopeptides, hue: 200, omics: [glycoproteomics]} + - {id: glycoQTL, family: Glycoproteomics, what: Glycoprotein abundance, hue: 200, omics: [glycoproteomics]} # Omics folders, in menu order, with the label shown on the site omics: @@ -32,7 +32,7 @@ omics: - {folder: proteomics, label: Proteomics, family: Proteomics} - {folder: glycoproteomics, label: Glycoproteomics, family: Glycoproteomics} - {folder: metabolomics, label: Metabolomics, family: Metabolomics} - - {folder: histone_ChIPSeq, label: Histone ChIP-seq, family: Histone} + - {folder: histone_ChIPSeq, label: Histone ChIP-seq, family: Histone acetylation} - {folder: snRNA_seq, label: snRNA-seq, family: Expression} - {folder: snATAC, label: snATAC-seq, family: Chromatin} - {folder: genotype, label: Genotype / WGS, family: Genotype} @@ -45,11 +45,11 @@ cohorts: - {name: Knight-ADRC, desc: Knight Alzheimer Disease Research Center, page: KnightADRC} - {name: MiGA, desc: Microglia Genomic Atlas, page: MiGA} - {name: STARNET, desc: "Cardiovascular tissues, macrophages", page: STARNET} - - {name: MetaBrain, desc: External replication resource, url: "https://www.metabrain.nl/"} + - {name: MetaBrain, desc: External bulk brain eQTL replication resource, url: "https://www.metabrain.nl/"} # AD GWAS entries on the home page, by page file name under content/xqtl-data/gwas gwas: - - {page: Bellenguez_AD, name: Bellenguez et al. 2022, desc: "Main, no-biobank and no-proxy analyses"} + - {page: Bellenguez_AD, name: Bellenguez et al. 2022, desc: "2022 summary statistics and 2026 main, no-biobank and no-proxy analyses"} - {page: Wightman_AD, name: Wightman et al. 2021, desc: Summary statistics} - {page: Kunkle_AD, name: Kunkle et al. 2019, desc: Summary statistics} - {page: Jansen_AD, name: Jansen et al. 2019, desc: Summary statistics} @@ -64,7 +64,7 @@ status: # Access labels access: - open: {label: Open, desc: "Download without an application: a public URL, an open Synapse folder or the NIAGADS open-access portal."} + open: {label: Open, desc: "Download without an application from a public URL, an open Synapse folder or NIAGADS DSS."} controlled: {label: Controlled, desc: "Needs a Synapse account and an approved data use certificate for the cohort."} requested: {label: Requested, desc: "Shared on request from the data owner before general release."} pending: {label: Pending, desc: "Access terms are still being set."} diff --git a/site/layouts/coverage.html b/site/layouts/coverage.html index d2f7c58..3a92050 100644 --- a/site/layouts/coverage.html +++ b/site/layouts/coverage.html @@ -45,7 +45,7 @@ -

        Statuses come from a methods: map in each page's metadata header; datasets without a page yet are listed in site/data/next_phase.yaml. "Not yet run" marks a method that applies to data already in hand, a quick way to see what can be run next.

        +

        "Not yet run" marks a method that applies to data already in hand.

        {{ with .Content }}
        {{ . }}
        {{ end }} {{ end }} diff --git a/site/layouts/home.html b/site/layouts/home.html index 727e435..0ad6da1 100644 --- a/site/layouts/home.html +++ b/site/layouts/home.html @@ -10,7 +10,7 @@
        ADSP Functional Genomics Consortium · FunGen-AD

        Find and access the FunGen-xQTL datasets

        -

        FunGen-xQTL maps genetic effects on gene expression, splicing, DNA methylation, proteins, chromatin and metabolites in brain and immune cells, and integrates them with AD GWAS. This catalog describes each dataset and where to get it. To look up associations by variant, gene or region, use the xQTL Atlas on NIAGADS.

        +

        FunGen-xQTL fine-maps molecular QTL across eight molecular modalities, from chromatin and RNA to protein and metabolites, in brain and immune cells, and reuses the resulting credible sets and posterior effect estimates to interpret AD GWAS loci. This catalog describes each dataset and where to get it. To look up associations by variant, gene or region, use the xQTL Atlas on NIAGADS.

        {{ with $catalog }}Browse the catalog{{ end }} {{ with $howto }}How to get the data{{ end }} diff --git a/site/layouts/inventory.html b/site/layouts/inventory.html index a06ee70..4b95390 100644 --- a/site/layouts/inventory.html +++ b/site/layouts/inventory.html @@ -58,7 +58,7 @@
        + Propose a dataset - Opens a GitHub issue that asks for cohort, context, modality, N, access and Synapse ID. A curator turns it into a page. + Opens a GitHub issue that asks for cohort, tissue or cell type, modality, sample size, access and Synapse ID. A curator turns it into a page.
        {{ with .Content }}
        {{ . }}
        {{ end }} From 098b74c4a95a89cbff2d71859f0226b51145016f Mon Sep 17 00:00:00 2001 From: Jenny Empawi Date: Fri, 9 Oct 2026 12:27:52 -0400 Subject: [PATCH 7/9] Show the flagship paper's dataset count; request controlled data on the AD Knowledge Portal --- content/how_to_get_data.md | 2 +- site/data/xqtl.yaml | 9 +++++---- site/layouts/_partials/ds/page.html | 2 +- site/layouts/home.html | 2 +- 4 files changed, 8 insertions(+), 7 deletions(-) diff --git a/content/how_to_get_data.md b/content/how_to_get_data.md index 7b361e4..f4579cc 100644 --- a/content/how_to_get_data.md +++ b/content/how_to_get_data.md @@ -11,7 +11,7 @@ Omics data, QTL results, xQTL models and reference files are on Synapse. Most co {{% steps %}} 1. **Create a Synapse account.** Register at [synapse.org](https://www.synapse.org/) and verify your profile. 2. **Become a certified user.** Pass the short Synapse certification quiz on data governance. -3. **Request access.** For controlled data, submit the data use certificate for the cohort through the [AD Knowledge Portal](https://adknowledgeportal.synapse.org/). +3. **Request access.** For controlled data, request data access on the [AD Knowledge Portal](https://adknowledgeportal.synapse.org/). 4. **Download.** Use the web interface, the Synapse command-line client, or the Python or R client with the Synapse ID from the dataset page. {{% /steps %}} diff --git a/site/data/xqtl.yaml b/site/data/xqtl.yaml index a4d2c03..6f8e0fd 100644 --- a/site/data/xqtl.yaml +++ b/site/data/xqtl.yaml @@ -3,13 +3,14 @@ # summary card and the home page always agree. Page-level facts live in each page's # metadata header (see template/metadata_header.md). -# Headline numbers on the home page. Dataset and modality counts are computed from the -# pages at build time; participants cannot be, so it is set here. +# Headline numbers on the home page, as reported in the flagship paper. The modality +# count is computed from the modalities list below. home: + datasets: "77" participants: "2,328" participants_note: >- Counts are participants. One participant can contribute several tissues, - cell types and assays. The flagship paper analyzes 77 molecular datasets. + cell types and assays. updated: "October 2026" # QTL modalities, in menu order. `folder` is the folder under content/xqtl-data/qtl and @@ -65,7 +66,7 @@ status: # Access labels access: open: {label: Open, desc: "Download without an application from a public URL, an open Synapse folder or NIAGADS DSS."} - controlled: {label: Controlled, desc: "Needs a Synapse account and an approved data use certificate for the cohort."} + controlled: {label: Controlled, desc: "Needs a Synapse account and data access requested on the AD Knowledge Portal."} requested: {label: Requested, desc: "Shared on request from the data owner before general release."} pending: {label: Pending, desc: "Access terms are still being set."} diff --git a/site/layouts/_partials/ds/page.html b/site/layouts/_partials/ds/page.html index 8300ecf..8376f70 100644 --- a/site/layouts/_partials/ds/page.html +++ b/site/layouts/_partials/ds/page.html @@ -84,7 +84,7 @@

        Access

        {{- if eq $i.access "open" }}Open access. Download from the links below without an application. {{- else if eq $i.access "requested" }}Shared on request from the data owner before general release. - {{- else if eq $i.access "controlled" }}Controlled access through the AD Knowledge Portal on Synapse. You need a Synapse account and an approved data use certificate{{ with $i.cohort }} for {{ . }}{{ end }}. + {{- else if eq $i.access "controlled" }}Controlled access. Request data access{{ with $i.cohort }} for {{ . }}{{ end }} on the AD Knowledge Portal; you need a Synapse account. {{- else }}Access terms for this page are not set yet.{{ end }} {{ with $howto }}See How to get the data.{{ end }}

        diff --git a/site/layouts/home.html b/site/layouts/home.html index 0ad6da1..f8796f2 100644 --- a/site/layouts/home.html +++ b/site/layouts/home.html @@ -19,7 +19,7 @@

        Find and access the FunGen-xQTL datasets

        -
        {{ len $rows }}datasets documented
        +
        {{ $x.home.datasets | default (len $rows) }}molecular datasets
        {{ len $x.modalities }}QTL modalities
        {{ $x.home.participants }}participants
        From 9f712a34338131928dfcc7640fed53a0a5d5f977 Mon Sep 17 00:00:00 2001 From: Jenny Empawi Date: Fri, 9 Oct 2026 12:37:34 -0400 Subject: [PATCH 8/9] Describe how to request NIAGADS controlled-access data --- content/how_to_get_data.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/content/how_to_get_data.md b/content/how_to_get_data.md index f4579cc..4f1c559 100644 --- a/content/how_to_get_data.md +++ b/content/how_to_get_data.md @@ -25,7 +25,9 @@ The four top-level FunGen-xQTL folders on Synapse are [variant and gene summarie ## NIAGADS -AD GWAS summary statistics and ADSP genomics are distributed by NIAGADS. Summary statistics marked Open can be downloaded from the dataset's public URL. Harmonized xQTL summary statistics and fine-mapping results are open access on NIAGADS DSS as [NG00184.v1](https://dss.niagads.org/datasets/ng00184/) (GRCh38). No application is needed. Individual-level data stay controlled and are requested through DSS under their own accessions. +NIAGADS distributes ADSP genomic data and some AD GWAS summary statistics through its Data Sharing Service (DSS). Summary statistics marked Open can be downloaded from the dataset's public URL. Harmonized xQTL summary statistics and fine-mapping results are open access on NIAGADS DSS as [NG00184.v1](https://dss.niagads.org/datasets/ng00184/) (GRCh38) and need no application. + +Individual-level data, such as ADSP genotypes, are controlled access and are requested through DSS under their own accessions. The request is submitted by a principal investigator at the level of assistant professor or above, together with the institution's Signing Official, and both need an eRA Commons ID. Since June 2026, every DSS user verifies their identity through Login.gov or ID.me before signing in. The NIAGADS ADRD Data Access Committee reviews each request. The [NIAGADS application instructions](https://niagads.scrollhelp.site/support/application-instructions) list the required documents. {{% callout %}} **NG00184 downloads are packaged archives, one per QTL type and result type, named** `ADSP_FunGen_xQTL.v1...tar` From 5fd6c44c923f9f9a7fb327e3eb25c43e3af3be7e Mon Sep 17 00:00:00 2001 From: Jenny Empawi Date: Fri, 9 Oct 2026 12:50:35 -0400 Subject: [PATCH 9/9] Fill sample sizes, staged status and analysis coverage from page text and Synapse staging; remove Minerva cluster paths --- .../gwas/ADGC_GWAS_imputation_protocol.md | 2 +- content/xqtl-data/gwas/AD_GWAS.md | 2 +- content/xqtl-data/gwas/Bellenguez_AD.md | 2 +- content/xqtl-data/gwas/Jansen_AD.md | 2 +- content/xqtl-data/gwas/Kunkle_AD.md | 2 +- content/xqtl-data/gwas/Wightman_AD.md | 2 +- .../omics/covariates/ROSMAP_covariates.md | 2 +- .../Knight_ADRC_brain_expression.md | 2 +- .../omics/expression/MSBB_brain_expression.md | 2 +- .../expression/MetaBrain_brain_expression.md | 2 +- .../omics/expression/MiGA_brain_expression.md | 17 +- .../omics/expression/ROSMAP_AC_expression.md | 2 +- .../expression/ROSMAP_DLPFC_expression.md | 2 +- .../omics/expression/ROSMAP_PCC_expression.md | 2 +- .../expression/ROSMAP_microglia_expression.md | 2 +- .../expression/ROSMAP_monocyte_expression.md | 3 +- .../expression/ROSMAP_snRNAseq_pseudo_bulk.md | 2 +- .../omics/expression/STARNET_macrophage.md | 11 +- .../omics/genotype/Knight_ADRC_genotype.md | 2 +- content/xqtl-data/omics/genotype/MSBB_WGS.md | 2 +- .../xqtl-data/omics/genotype/MiGA_genotype.md | 10 +- .../xqtl-data/omics/genotype/ROSMAP_WGS.md | 2 +- .../omics/genotype/STARNET_genotype.md | 15 +- .../ROSMAP_DLPFC_glycoproteomics.md | 4 +- .../ROSMAP_DLPFC_ChIPSeq_H3K9ac.md | 4 +- .../Knight_ADRC_brain_metabolomics.md | 2 +- .../metabolomics/ROSMAP_DLPFC_metabolomics.md | 2 +- .../Knight_ADRC_brain_methylation.md | 2 +- .../methylation/MSBB_brain_methylation.md | 2 +- .../methylation/ROSMAP_DLPFC_methylation.md | 2 +- .../Knight_ADRC_brain_proteomics.md | 4 +- .../omics/proteomics/MSBB_proteomics.md | 2 +- .../proteomics/ROSMAP_DLPFC_proteomics.md | 4 +- .../omics/snATAC/ROSMAP_snuc_caQTL.md | 2 +- .../omics/snRNA_seq/ROSMAP_snuc_CUIMC1.md | 3 +- .../omics/snRNA_seq/ROSMAP_snuc_MIT.md | 3 +- .../omics/snRNA_seq/ROSMAP_snuc_mega.md | 2 +- .../splicing/Knight_ADRC_brain_splicing.md | 2 +- .../omics/splicing/MSBB_brain_splicing.md | 2 +- .../omics/splicing/ROSMAP_AC_splicing.md | 2 +- .../omics/splicing/ROSMAP_DLPFC_splicing.md | 3 +- .../omics/splicing/ROSMAP_PCC_splicing.md | 2 +- .../omics/splicing/ROSMAP_snuc_splicing.md | 3 +- .../qtl/FunGen_xQTL_protocol_data.md | 2 +- .../qtl/caQTL/ROSMAP_snuc_caQTL_qtl.md | 2 +- .../eQTL/Knight_ADRC_brain_expression_qtl.md | 5 +- .../qtl/eQTL/MSBB_brain_expression_qtl.md | 5 +- .../eQTL/MetaBrain_brain_expression_qtl.md | 4 +- .../qtl/eQTL/MiGA_brain_expression_qtl.md | 17 +- .../qtl/eQTL/ROSMAP_AC_expression_qtl.md | 2 +- .../qtl/eQTL/ROSMAP_DLPFC_expression_qtl.md | 4 +- .../qtl/eQTL/ROSMAP_PCC_expression_qtl.md | 2 +- .../eQTL/ROSMAP_microglia_expression_qtl.md | 2 +- .../eQTL/ROSMAP_monocyte_expression_qtl.md | 3 +- .../eQTL/ROSMAP_snRNAseq_pseudo_bulk_qtl.md | 7 +- .../qtl/eQTL/STARNET_macrophage_qtl.md | 149 +----------------- .../ROSMAP_DLPFC_glycoproteomics_qtl.md | 8 +- .../haQTL/ROSMAP_DLPFC_ChIPSeq_H3K9ac_qtl.md | 4 +- .../mQTL/Knight_ADRC_brain_methylation_qtl.md | 2 +- .../qtl/mQTL/MSBB_brain_methylation_qtl.md | 2 +- .../qtl/mQTL/ROSMAP_DLPFC_methylation_qtl.md | 2 +- .../Knight_ADRC_brain_metabolomics_qtl.md | 2 +- .../metQTL/ROSMAP_DLPFC_metabolomics_qtl.md | 2 +- .../pQTL/Knight_ADRC_brain_proteomics_qtl.md | 7 +- .../xqtl-data/qtl/pQTL/MSBB_proteomics_qtl.md | 5 +- .../qtl/pQTL/ROSMAP_DLPFC_proteomics_qtl.md | 7 +- .../sQTL/Knight_ADRC_brain_splicing_qtl.md | 2 +- .../qtl/sQTL/MSBB_brain_splicing_qtl.md | 5 +- .../qtl/sQTL/ROSMAP_AC_splicing_qtl.md | 2 +- .../qtl/sQTL/ROSMAP_DLPFC_splicing_qtl.md | 4 +- .../qtl/sQTL/ROSMAP_PCC_splicing_qtl.md | 2 +- .../qtl/sQTL/ROSMAP_snuc_splicing_qtl.md | 4 +- .../xqtl-data/reference_data/ld_reference.md | 4 +- 73 files changed, 141 insertions(+), 271 deletions(-) diff --git a/content/xqtl-data/gwas/ADGC_GWAS_imputation_protocol.md b/content/xqtl-data/gwas/ADGC_GWAS_imputation_protocol.md index fbb0ce6..4b2583a 100644 --- a/content/xqtl-data/gwas/ADGC_GWAS_imputation_protocol.md +++ b/content/xqtl-data/gwas/ADGC_GWAS_imputation_protocol.md @@ -1,7 +1,7 @@ --- type: gwas short_title: ADGC imputation protocol -status: +status: staged access: release: synapse_ids: [] diff --git a/content/xqtl-data/gwas/AD_GWAS.md b/content/xqtl-data/gwas/AD_GWAS.md index 9395619..a9d94a5 100644 --- a/content/xqtl-data/gwas/AD_GWAS.md +++ b/content/xqtl-data/gwas/AD_GWAS.md @@ -1,7 +1,7 @@ --- type: gwas short_title: AD GWAS overview -status: +status: staged synapse_ids: [syn69670651, syn69670652, syn69670653, syn69670656, syn69670625, syn69696846, syn69865824] lead_analysts: [] last_verified: diff --git a/content/xqtl-data/gwas/Bellenguez_AD.md b/content/xqtl-data/gwas/Bellenguez_AD.md index 88b7eba..742c3e8 100644 --- a/content/xqtl-data/gwas/Bellenguez_AD.md +++ b/content/xqtl-data/gwas/Bellenguez_AD.md @@ -1,7 +1,7 @@ --- type: gwas short_title: Bellenguez 2022 -status: +status: staged access: release: synapse_ids: [syn69670625, syn69670630, syn69865816, syn69865824, syn70095142, syn70095143] diff --git a/content/xqtl-data/gwas/Jansen_AD.md b/content/xqtl-data/gwas/Jansen_AD.md index 975c1a1..925adb9 100644 --- a/content/xqtl-data/gwas/Jansen_AD.md +++ b/content/xqtl-data/gwas/Jansen_AD.md @@ -1,7 +1,7 @@ --- type: gwas short_title: Jansen 2019 -status: +status: staged access: release: synapse_ids: [syn69670625, syn69670626, syn69670630, syn69696846, syn69865816, syn69865824, syn70095142, syn70095143] diff --git a/content/xqtl-data/gwas/Kunkle_AD.md b/content/xqtl-data/gwas/Kunkle_AD.md index ac7f1d3..92fcf11 100644 --- a/content/xqtl-data/gwas/Kunkle_AD.md +++ b/content/xqtl-data/gwas/Kunkle_AD.md @@ -1,7 +1,7 @@ --- type: gwas short_title: Kunkle 2019 -status: +status: staged access: release: synapse_ids: [syn69670625, syn69670626, syn69670630, syn69696846, syn69865816, syn69865824, syn70095142, syn70095143] diff --git a/content/xqtl-data/gwas/Wightman_AD.md b/content/xqtl-data/gwas/Wightman_AD.md index 3f4009d..4e6809b 100644 --- a/content/xqtl-data/gwas/Wightman_AD.md +++ b/content/xqtl-data/gwas/Wightman_AD.md @@ -1,7 +1,7 @@ --- type: gwas short_title: Wightman 2021 -status: +status: staged access: release: synapse_ids: [syn69670625, syn69670626, syn69670630, syn69696846, syn69865816, syn69865824, syn70095142, syn70095143] diff --git a/content/xqtl-data/omics/covariates/ROSMAP_covariates.md b/content/xqtl-data/omics/covariates/ROSMAP_covariates.md index b7f3d77..0fda798 100644 --- a/content/xqtl-data/omics/covariates/ROSMAP_covariates.md +++ b/content/xqtl-data/omics/covariates/ROSMAP_covariates.md @@ -4,7 +4,7 @@ modality: covariates short_title: ROSMAP covariates cohort: ROSMAP access: controlled -status: +status: staged synapse_ids: [] lead_analysts: [] last_verified: diff --git a/content/xqtl-data/omics/expression/Knight_ADRC_brain_expression.md b/content/xqtl-data/omics/expression/Knight_ADRC_brain_expression.md index b331605..fd2d9f6 100644 --- a/content/xqtl-data/omics/expression/Knight_ADRC_brain_expression.md +++ b/content/xqtl-data/omics/expression/Knight_ADRC_brain_expression.md @@ -5,7 +5,7 @@ short_title: Knight ADRC brain cohort: Knight-ADRC context: parietal cortex access: controlled -status: +status: staged synapse_ids: [syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] lead_analysts: [Chunming Liu] last_verified: diff --git a/content/xqtl-data/omics/expression/MSBB_brain_expression.md b/content/xqtl-data/omics/expression/MSBB_brain_expression.md index 4a130c5..3cb174f 100644 --- a/content/xqtl-data/omics/expression/MSBB_brain_expression.md +++ b/content/xqtl-data/omics/expression/MSBB_brain_expression.md @@ -6,7 +6,7 @@ cohort: MSBB context: 4 brain regions sample_size: access: controlled -status: +status: staged release: synapse_ids: [syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] lead_analysts: [Minghui Wang] diff --git a/content/xqtl-data/omics/expression/MetaBrain_brain_expression.md b/content/xqtl-data/omics/expression/MetaBrain_brain_expression.md index 0a69c0d..f7276f4 100644 --- a/content/xqtl-data/omics/expression/MetaBrain_brain_expression.md +++ b/content/xqtl-data/omics/expression/MetaBrain_brain_expression.md @@ -4,7 +4,7 @@ modality: expression short_title: MetaBrain cohort: MetaBrain context: multi-region -status: +status: staged synapse_ids: [syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] lead_analysts: [] last_verified: diff --git a/content/xqtl-data/omics/expression/MiGA_brain_expression.md b/content/xqtl-data/omics/expression/MiGA_brain_expression.md index 93678da..55f699a 100644 --- a/content/xqtl-data/omics/expression/MiGA_brain_expression.md +++ b/content/xqtl-data/omics/expression/MiGA_brain_expression.md @@ -6,7 +6,7 @@ cohort: MiGA context: "microglia, 4 regions" sample_size: access: controlled -status: +status: staged release: synapse_ids: [syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] lead_analysts: [Travyse Edwards] @@ -41,26 +41,19 @@ Travyse Edwards We have gene expression data for four brain regions: medial frontal gyrus (GFM), superior temporal gyrus (GTS), thalamus (THA), and subventricular zone (SVZ). I have included information about the TPM matrices below for each brain region. The columns are sample names and the rows are gene ids. - GFM - - Path: `/sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/rnaseq/GFM/sample-gfm.trimmed.clean.rnaseqc.low_expression_filtered.outlier_removed.tpm.gct.gz` + - File: `sample-gfm.trimmed.clean.rnaseqc.low_expression_filtered.outlier_removed.tpm.gct.gz` - Columns: 75, Rows: 45814 - GTS - - Path: `/sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/rnaseq/GTS/sample-gts.trimmed.clean.rnaseqc.low_expression_filtered.outlier_removed.tpm.gct.gz` + - File: `sample-gts.trimmed.clean.rnaseqc.low_expression_filtered.outlier_removed.tpm.gct.gz` - Columns: 63, Rows: 45472 - THA - - Path: `/sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/rnaseq/THA/sample-tha.trimmed.clean.rnaseqc.low_expression_filtered.outlier_removed.tpm.gct.gz` + - File: `sample-tha.trimmed.clean.rnaseqc.low_expression_filtered.outlier_removed.tpm.gct.gz` - Columns: 61, Rows: 45461 - SVZ - - Path: `/sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/rnaseq/SVZ/sample-svz.trimmed.clean.rnaseqc.low_expression_filtered.outlier_removed.tpm.gct.gz` + - File: `sample-svz.trimmed.clean.rnaseqc.low_expression_filtered.outlier_removed.tpm.gct.gz` - Columns: 53, Rows: 42086 File Sizes: -``` -$ ls -lh --rw-r--r-- 1 edwart10 LOAD 11M Sep 28 12:16 sample-gfm.trimmed.clean.rnaseqc.low_expression_filtered.outlier_removed.tpm.gct.gz --rw-r--r-- 1 edwart10 LOAD 8.8M Sep 28 13:17 sample-gts.trimmed.clean.rnaseqc.low_expression_filtered.outlier_removed.tpm.gct.gz --rw-r--r-- 1 edwart10 LOAD 8.6M Sep 28 13:17 sample-tha.trimmed.clean.rnaseqc.low_expression_filtered.outlier_removed.tpm.gct.gz --rw-r--r-- 1 edwart10 LOAD 6.8M Sep 28 13:18 sample-svz.trimmed.clean.rnaseqc.low_expression_filtered.outlier_removed.tpm.gct.gz -``` ### Other Key Files diff --git a/content/xqtl-data/omics/expression/ROSMAP_AC_expression.md b/content/xqtl-data/omics/expression/ROSMAP_AC_expression.md index 6f728c1..703573b 100644 --- a/content/xqtl-data/omics/expression/ROSMAP_AC_expression.md +++ b/content/xqtl-data/omics/expression/ROSMAP_AC_expression.md @@ -5,7 +5,7 @@ short_title: ROSMAP AC cohort: ROSMAP context: AC access: controlled -status: +status: staged synapse_ids: [syn3388564, syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] lead_analysts: [Frank Grenn] last_verified: diff --git a/content/xqtl-data/omics/expression/ROSMAP_DLPFC_expression.md b/content/xqtl-data/omics/expression/ROSMAP_DLPFC_expression.md index 117dbce..a166f4c 100644 --- a/content/xqtl-data/omics/expression/ROSMAP_DLPFC_expression.md +++ b/content/xqtl-data/omics/expression/ROSMAP_DLPFC_expression.md @@ -6,7 +6,7 @@ cohort: ROSMAP context: DLPFC sample_size: access: controlled -status: +status: staged release: synapse_ids: [syn3388564, syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] lead_analysts: [Xuanhe Chen] diff --git a/content/xqtl-data/omics/expression/ROSMAP_PCC_expression.md b/content/xqtl-data/omics/expression/ROSMAP_PCC_expression.md index acc41e2..a8bb8ef 100644 --- a/content/xqtl-data/omics/expression/ROSMAP_PCC_expression.md +++ b/content/xqtl-data/omics/expression/ROSMAP_PCC_expression.md @@ -5,7 +5,7 @@ short_title: ROSMAP PCC cohort: ROSMAP context: PCC access: controlled -status: +status: staged synapse_ids: [syn3157322, syn3388564, syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] lead_analysts: [Frank Grenn] last_verified: diff --git a/content/xqtl-data/omics/expression/ROSMAP_microglia_expression.md b/content/xqtl-data/omics/expression/ROSMAP_microglia_expression.md index 2597ea6..1551fed 100644 --- a/content/xqtl-data/omics/expression/ROSMAP_microglia_expression.md +++ b/content/xqtl-data/omics/expression/ROSMAP_microglia_expression.md @@ -5,7 +5,7 @@ short_title: ROSMAP microglia cohort: ROSMAP context: microglia access: controlled -status: +status: staged synapse_ids: [syn2580853, syn11468526, syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] lead_analysts: [Travyse Edwards] last_verified: diff --git a/content/xqtl-data/omics/expression/ROSMAP_monocyte_expression.md b/content/xqtl-data/omics/expression/ROSMAP_monocyte_expression.md index ef0183e..5d7d27e 100644 --- a/content/xqtl-data/omics/expression/ROSMAP_monocyte_expression.md +++ b/content/xqtl-data/omics/expression/ROSMAP_monocyte_expression.md @@ -5,7 +5,7 @@ short_title: ROSMAP monocyte cohort: ROSMAP context: monocyte access: controlled -status: +status: staged synapse_ids: [syn22024496, syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] lead_analysts: [Travyse Edwards] last_verified: @@ -25,7 +25,6 @@ Travyse Edwards The ROSMAP monocyte data on MSSM were downloaded from [syn22024496](https://www.synapse.org/#!Synapse:syn22024496) on July 11th, 2022. (path on MSSM to be added) -- Path on MSSM cluster `/sc/arion/projects/load/data-ext/ROSMAP/raw/rnaseq_monocytes_syn23650893/Gene_Expression-RNA-seq-monocyte` ### Preview Monocyte Gene Expression Data diff --git a/content/xqtl-data/omics/expression/ROSMAP_snRNAseq_pseudo_bulk.md b/content/xqtl-data/omics/expression/ROSMAP_snRNAseq_pseudo_bulk.md index ba0d779..33405c7 100644 --- a/content/xqtl-data/omics/expression/ROSMAP_snRNAseq_pseudo_bulk.md +++ b/content/xqtl-data/omics/expression/ROSMAP_snRNAseq_pseudo_bulk.md @@ -5,7 +5,7 @@ short_title: ROSMAP pseudo-bulk cohort: ROSMAP context: "DLPFC, cell types" access: controlled -status: +status: staged synapse_ids: [syn31512863, syn52293417, syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] lead_analysts: [Hao Sun, Masashi Fujita] last_verified: diff --git a/content/xqtl-data/omics/expression/STARNET_macrophage.md b/content/xqtl-data/omics/expression/STARNET_macrophage.md index d7f4d93..d6573fc 100644 --- a/content/xqtl-data/omics/expression/STARNET_macrophage.md +++ b/content/xqtl-data/omics/expression/STARNET_macrophage.md @@ -5,10 +5,11 @@ short_title: STARNET macrophage cohort: STARNET context: macrophage access: controlled -status: +status: staged synapse_ids: [syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] lead_analysts: [Travyse Edwards] last_verified: +sample_size: 479 --- # STARNET macrophage gene expression QTL @@ -34,7 +35,6 @@ Travyse Edwards - Study Description: TBD - Disease: Alzheimer's Disease - Data Citation: - - Local Path: `/sc/arion/projects/load/data-int/STARNET/raw` - Additional Study Information: This data is not okay to use outside of the xQTL group. Information to fix: @@ -54,7 +54,6 @@ Macrophage RNA-Seq: RNA was purified from whole blood with the RNeasy Mini kit (Qiagen, Hilden, Germany). For tissue biopsies, RNA was isolated as described (36, 37). DNA was isolated from whole blood with the QIAmp DNA Blood Midi kit (Qiagen). DNA and RNA qualities were assessed with the Agilent 2100 Bioanalyzer system (Agilent Technologies, Palo Alto, CA). Samples RIN scores of >7 were accepted for RNA-seq.Sequencing libraries were prepared with the Illumina TruSeq stranded mRNA kit, the Ribo-Zero method, and Illumina TruSeq nonstranded mRNA kit with poly(A)+ selection. Samples were sequenced using the Human OmniExpressExome-8v1 bead chip via the Illumina Infinium Assay. -- STARNET macrophage dataset on MSSM cluster: `/sc/arion/projects/load/data-int/STARNET/raw` ### Molecular Phenotype Matrices @@ -66,14 +65,14 @@ The STARNET FASTQ files (paired-end, 50 - 100 bp) were processed using the ADGC Sample level RNA-seq quality control -- `/sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Molecular_Phenotypes/Sample-Level-RNA-Seq-QC/output/STARNET_ribo0_fastq.rnaseqc.low_expression_filtered.outlier_removed.geneCount.gct.gz` +- `STARNET_ribo0_fastq.rnaseqc.low_expression_filtered.outlier_removed.geneCount.gct.gz` - Contains 24669 genes (rows) from 479 samples (columns). The column names are the STARNET sample ids, the row names are the ensemble ids, and the values are the TPM counts. -- `/sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Molecular_Phenotypes/Sample-Level-RNA-Seq-QC/output/STARNET_ribo0_fastq.rnaseqc.low_expression_filtered.outlier_removed.tpm.gct.gz` +- `STARNET_ribo0_fastq.rnaseqc.low_expression_filtered.outlier_removed.tpm.gct.gz` - Contains 24669 genes (rows) from 479 samples (columns). The column names are the STARNET sample ids and the row names are the ensemble ids, and the values are the TPM counts. Bulk RNA-seq Counts Normalization -- `/sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Molecular_Phenotypes/Bulk-RNA-Seq-Counts-Normalization/output/STARNET_ribo0_fastq.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.gz` +- `STARNET_ribo0_fastq.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.bed.gz` - Contains 20751 genes (rows) from 479 samples (columns). The column names are the STARNET sample ids. The rows are organized by increasing chromosome number, start position, end position, and ensemble id. diff --git a/content/xqtl-data/omics/genotype/Knight_ADRC_genotype.md b/content/xqtl-data/omics/genotype/Knight_ADRC_genotype.md index 8ffe7d5..1bbb21d 100644 --- a/content/xqtl-data/omics/genotype/Knight_ADRC_genotype.md +++ b/content/xqtl-data/omics/genotype/Knight_ADRC_genotype.md @@ -5,7 +5,7 @@ short_title: Knight ADRC genotype cohort: Knight-ADRC context: blood access: controlled -status: +status: staged release: synapse_ids: [] lead_analysts: [Zining Qi] diff --git a/content/xqtl-data/omics/genotype/MSBB_WGS.md b/content/xqtl-data/omics/genotype/MSBB_WGS.md index 4184119..a370b82 100644 --- a/content/xqtl-data/omics/genotype/MSBB_WGS.md +++ b/content/xqtl-data/omics/genotype/MSBB_WGS.md @@ -6,7 +6,7 @@ cohort: MSBB context: blood sample_size: access: controlled -status: +status: staged release: synapse_ids: [] lead_analysts: [Minghui Wang, Julia TCW] diff --git a/content/xqtl-data/omics/genotype/MiGA_genotype.md b/content/xqtl-data/omics/genotype/MiGA_genotype.md index bb81a46..0e82390 100644 --- a/content/xqtl-data/omics/genotype/MiGA_genotype.md +++ b/content/xqtl-data/omics/genotype/MiGA_genotype.md @@ -4,7 +4,7 @@ modality: genotype short_title: MiGA genotype cohort: MiGA access: controlled -status: +status: staged synapse_ids: [] lead_analysts: [Travyse Edwards] last_verified: @@ -28,14 +28,8 @@ Further method information can be found: - [MiGA NIAGADS entry](https://dss.niagads.org/datasets/ng00105/) - [Biorxiv Paper](https://www.biorxiv.org/content/10.1101/2020.10.27.356113v1.full) -I began analysis on the post-imputation/QC VCF file provided by the Towfique lab. The path to this file on the Minerva cluster at ISMMS is below: -`/sc/arion/projects/load/data-int/MiGA/raw/raj_microglia_anno.MAF.vcf.gz` +I began analysis on the post-imputation/QC VCF file provided by the Towfique lab. -File size: -``` -$ ls -lh --rw-r----- 1 edwart10 LOAD 322M Jul 29 2022 /sc/arion/projects/load/data-int/MiGA/raw/raj_microglia_anno.MAF.vcf.gz -``` ### Other Key Files diff --git a/content/xqtl-data/omics/genotype/ROSMAP_WGS.md b/content/xqtl-data/omics/genotype/ROSMAP_WGS.md index a9313f7..007c83e 100644 --- a/content/xqtl-data/omics/genotype/ROSMAP_WGS.md +++ b/content/xqtl-data/omics/genotype/ROSMAP_WGS.md @@ -6,7 +6,7 @@ cohort: ROSMAP context: "blood, brain" sample_size: access: controlled -status: +status: staged release: synapse_ids: [] lead_analysts: [Hao Sun, Xuanhe Chen] diff --git a/content/xqtl-data/omics/genotype/STARNET_genotype.md b/content/xqtl-data/omics/genotype/STARNET_genotype.md index f3125ac..028cdbe 100644 --- a/content/xqtl-data/omics/genotype/STARNET_genotype.md +++ b/content/xqtl-data/omics/genotype/STARNET_genotype.md @@ -5,7 +5,7 @@ short_title: STARNET genotype cohort: STARNET context: blood access: controlled -status: +status: staged release: synapse_ids: [] lead_analysts: [Travyse Edwards] @@ -35,17 +35,8 @@ Post-Imputation Quality Control - MAF cutoff between common and rare of 0.005 - Rsquared for use with common variants of 0.3 -I began analysis on the post-imputation genotype data. The path to this file on the Minerva cluster at ISMMS is below: -`/sc/arion/projects/load/data-int/STARNET/raw` - -File size: -``` -$ ls -lh -total 450M --rwxr-x---+ 1 edwart10 LOAD 40M May 24 2022 plink.bim --rwxr-x---+ 1 edwart10 LOAD 25K May 24 2022 plink.fam --rwxr-x---+ 1 edwart10 LOAD 410M May 24 2022 plink.bed -``` +I began analysis on the post-imputation genotype data. + ### Other Key Files diff --git a/content/xqtl-data/omics/glycoproteomics/ROSMAP_DLPFC_glycoproteomics.md b/content/xqtl-data/omics/glycoproteomics/ROSMAP_DLPFC_glycoproteomics.md index fc64284..d5c5897 100644 --- a/content/xqtl-data/omics/glycoproteomics/ROSMAP_DLPFC_glycoproteomics.md +++ b/content/xqtl-data/omics/glycoproteomics/ROSMAP_DLPFC_glycoproteomics.md @@ -4,8 +4,8 @@ modality: glycoproteomics short_title: ROSMAP DLPFC cohort: ROSMAP context: DLPFC -access: -status: +access: controlled +status: staged synapse_ids: [syn17015098, syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] lead_analysts: [FunGen-xQTL Analysis Working Group] last_verified: diff --git a/content/xqtl-data/omics/histone_ChIPSeq/ROSMAP_DLPFC_ChIPSeq_H3K9ac.md b/content/xqtl-data/omics/histone_ChIPSeq/ROSMAP_DLPFC_ChIPSeq_H3K9ac.md index 822057b..b61b3c6 100644 --- a/content/xqtl-data/omics/histone_ChIPSeq/ROSMAP_DLPFC_ChIPSeq_H3K9ac.md +++ b/content/xqtl-data/omics/histone_ChIPSeq/ROSMAP_DLPFC_ChIPSeq_H3K9ac.md @@ -4,9 +4,9 @@ modality: histone_ChIPSeq short_title: ROSMAP DLPFC H3K9ac cohort: ROSMAP context: DLPFC -sample_size: +sample_size: 669 access: controlled -status: +status: staged release: synapse_ids: [syn4896408, syn17016212, syn69670592, syn69670597, syn69670630, syn69865816] lead_analysts: [Xuanhe Chen, Hao Sun, Hans Klein] diff --git a/content/xqtl-data/omics/metabolomics/Knight_ADRC_brain_metabolomics.md b/content/xqtl-data/omics/metabolomics/Knight_ADRC_brain_metabolomics.md index fe5025d..7db90e0 100644 --- a/content/xqtl-data/omics/metabolomics/Knight_ADRC_brain_metabolomics.md +++ b/content/xqtl-data/omics/metabolomics/Knight_ADRC_brain_metabolomics.md @@ -5,7 +5,7 @@ short_title: Knight ADRC brain cohort: Knight-ADRC context: parietal cortex access: controlled -status: +status: staged synapse_ids: [] lead_analysts: [Zining Qi] last_verified: diff --git a/content/xqtl-data/omics/metabolomics/ROSMAP_DLPFC_metabolomics.md b/content/xqtl-data/omics/metabolomics/ROSMAP_DLPFC_metabolomics.md index c74d081..63b7b1c 100644 --- a/content/xqtl-data/omics/metabolomics/ROSMAP_DLPFC_metabolomics.md +++ b/content/xqtl-data/omics/metabolomics/ROSMAP_DLPFC_metabolomics.md @@ -6,7 +6,7 @@ cohort: ROSMAP context: DLPFC sample_size: access: controlled -status: +status: staged release: synapse_ids: [syn69670592, syn69670597, syn69670630, syn69865816] lead_analysts: [] diff --git a/content/xqtl-data/omics/methylation/Knight_ADRC_brain_methylation.md b/content/xqtl-data/omics/methylation/Knight_ADRC_brain_methylation.md index a4387b0..82b75d0 100644 --- a/content/xqtl-data/omics/methylation/Knight_ADRC_brain_methylation.md +++ b/content/xqtl-data/omics/methylation/Knight_ADRC_brain_methylation.md @@ -5,7 +5,7 @@ short_title: Knight ADRC brain cohort: Knight-ADRC context: parietal cortex access: controlled -status: +status: staged synapse_ids: [syn69670592, syn69670597, syn69670630, syn69865816] lead_analysts: [Alexandre Pelletier] last_verified: diff --git a/content/xqtl-data/omics/methylation/MSBB_brain_methylation.md b/content/xqtl-data/omics/methylation/MSBB_brain_methylation.md index 6871079..8e8f832 100644 --- a/content/xqtl-data/omics/methylation/MSBB_brain_methylation.md +++ b/content/xqtl-data/omics/methylation/MSBB_brain_methylation.md @@ -5,7 +5,7 @@ short_title: MSBB brain cohort: MSBB context: brain access: controlled -status: +status: staged synapse_ids: [syn69670592, syn69670597, syn69670630, syn69865816] lead_analysts: [Alexandre Pelletier] last_verified: diff --git a/content/xqtl-data/omics/methylation/ROSMAP_DLPFC_methylation.md b/content/xqtl-data/omics/methylation/ROSMAP_DLPFC_methylation.md index 3ff59da..36e07dd 100644 --- a/content/xqtl-data/omics/methylation/ROSMAP_DLPFC_methylation.md +++ b/content/xqtl-data/omics/methylation/ROSMAP_DLPFC_methylation.md @@ -6,7 +6,7 @@ cohort: ROSMAP context: DLPFC sample_size: access: controlled -status: +status: staged release: synapse_ids: [syn3157275, syn69670592, syn69670597, syn69670630, syn69865816] lead_analysts: [Alexandre Pelletier, Jiajun Tao] diff --git a/content/xqtl-data/omics/proteomics/Knight_ADRC_brain_proteomics.md b/content/xqtl-data/omics/proteomics/Knight_ADRC_brain_proteomics.md index f6eb571..fc6c297 100644 --- a/content/xqtl-data/omics/proteomics/Knight_ADRC_brain_proteomics.md +++ b/content/xqtl-data/omics/proteomics/Knight_ADRC_brain_proteomics.md @@ -4,9 +4,9 @@ modality: proteomics short_title: Knight ADRC brain cohort: Knight-ADRC context: parietal cortex -sample_size: +sample_size: 442 access: controlled -status: +status: staged release: synapse_ids: [syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] lead_analysts: [Zining Qi] diff --git a/content/xqtl-data/omics/proteomics/MSBB_proteomics.md b/content/xqtl-data/omics/proteomics/MSBB_proteomics.md index 8bc48e9..e8c8ebf 100644 --- a/content/xqtl-data/omics/proteomics/MSBB_proteomics.md +++ b/content/xqtl-data/omics/proteomics/MSBB_proteomics.md @@ -5,7 +5,7 @@ short_title: MSBB brain cohort: MSBB context: brain access: controlled -status: +status: staged synapse_ids: [syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] lead_analysts: [Minghui Wang] last_verified: diff --git a/content/xqtl-data/omics/proteomics/ROSMAP_DLPFC_proteomics.md b/content/xqtl-data/omics/proteomics/ROSMAP_DLPFC_proteomics.md index 2561256..160653b 100644 --- a/content/xqtl-data/omics/proteomics/ROSMAP_DLPFC_proteomics.md +++ b/content/xqtl-data/omics/proteomics/ROSMAP_DLPFC_proteomics.md @@ -4,9 +4,9 @@ modality: proteomics short_title: ROSMAP DLPFC cohort: ROSMAP context: DLPFC -sample_size: +sample_size: 596 access: controlled -status: +status: staged release: synapse_ids: [syn17015098, syn21449447, syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] lead_analysts: [Zining Qi] diff --git a/content/xqtl-data/omics/snATAC/ROSMAP_snuc_caQTL.md b/content/xqtl-data/omics/snATAC/ROSMAP_snuc_caQTL.md index 348c166..449018f 100644 --- a/content/xqtl-data/omics/snATAC/ROSMAP_snuc_caQTL.md +++ b/content/xqtl-data/omics/snATAC/ROSMAP_snuc_caQTL.md @@ -6,7 +6,7 @@ cohort: ROSMAP context: "DLPFC, cell types" sample_size: access: controlled -status: +status: staged synapse_ids: [syn69670592, syn69670597, syn69670630, syn69865816] lead_analysts: [] last_verified: diff --git a/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_CUIMC1.md b/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_CUIMC1.md index 625984d..c6f6f4a 100644 --- a/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_CUIMC1.md +++ b/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_CUIMC1.md @@ -5,10 +5,11 @@ short_title: ROSMAP CUIMC1 cohort: ROSMAP context: DLPFC access: controlled -status: +status: staged synapse_ids: [syn31512863, syn69670592, syn69670597, syn69670630, syn69865816] lead_analysts: [Anjing Liu] last_verified: +sample_size: 424 --- # ROSMAP CUIMC1 snRNA-seq expression diff --git a/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_MIT.md b/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_MIT.md index b38cdef..b24d99d 100644 --- a/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_MIT.md +++ b/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_MIT.md @@ -5,10 +5,11 @@ short_title: ROSMAP MIT cohort: ROSMAP context: DLPFC access: controlled -status: +status: staged synapse_ids: [syn52293417, syn69670592, syn69670597, syn69670630, syn69865816] lead_analysts: [Anjing Liu] last_verified: +sample_size: 427 --- # ROSMAP MIT snRNA-seq expression diff --git a/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_mega.md b/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_mega.md index 4f0e6e8..9904552 100644 --- a/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_mega.md +++ b/content/xqtl-data/omics/snRNA_seq/ROSMAP_snuc_mega.md @@ -6,7 +6,7 @@ cohort: ROSMAP context: DLPFC sample_size: access: controlled -status: +status: staged release: synapse_ids: [syn31512863, syn52293417, syn69670592, syn69670597, syn69670630, syn69865816] lead_analysts: [Anjing Liu] diff --git a/content/xqtl-data/omics/splicing/Knight_ADRC_brain_splicing.md b/content/xqtl-data/omics/splicing/Knight_ADRC_brain_splicing.md index fd3478d..d25ff25 100644 --- a/content/xqtl-data/omics/splicing/Knight_ADRC_brain_splicing.md +++ b/content/xqtl-data/omics/splicing/Knight_ADRC_brain_splicing.md @@ -5,7 +5,7 @@ short_title: Knight ADRC brain cohort: Knight-ADRC context: parietal cortex access: controlled -status: +status: staged synapse_ids: [syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] lead_analysts: [Xuanhe Chen] last_verified: diff --git a/content/xqtl-data/omics/splicing/MSBB_brain_splicing.md b/content/xqtl-data/omics/splicing/MSBB_brain_splicing.md index beeac3c..77ba4e9 100644 --- a/content/xqtl-data/omics/splicing/MSBB_brain_splicing.md +++ b/content/xqtl-data/omics/splicing/MSBB_brain_splicing.md @@ -5,7 +5,7 @@ short_title: MSBB brain cohort: MSBB context: 4 brain regions access: controlled -status: +status: staged synapse_ids: [syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] lead_analysts: [Minghui Wang] last_verified: diff --git a/content/xqtl-data/omics/splicing/ROSMAP_AC_splicing.md b/content/xqtl-data/omics/splicing/ROSMAP_AC_splicing.md index f52cf8f..5af0359 100644 --- a/content/xqtl-data/omics/splicing/ROSMAP_AC_splicing.md +++ b/content/xqtl-data/omics/splicing/ROSMAP_AC_splicing.md @@ -5,7 +5,7 @@ short_title: ROSMAP AC cohort: ROSMAP context: AC access: controlled -status: +status: staged synapse_ids: [syn3388564, syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] lead_analysts: [Frank Grenn] last_verified: diff --git a/content/xqtl-data/omics/splicing/ROSMAP_DLPFC_splicing.md b/content/xqtl-data/omics/splicing/ROSMAP_DLPFC_splicing.md index d070864..7cf3124 100644 --- a/content/xqtl-data/omics/splicing/ROSMAP_DLPFC_splicing.md +++ b/content/xqtl-data/omics/splicing/ROSMAP_DLPFC_splicing.md @@ -5,10 +5,11 @@ short_title: ROSMAP DLPFC cohort: ROSMAP context: DLPFC access: controlled -status: +status: staged synapse_ids: [syn3388564, syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] lead_analysts: [Xuanhe Chen, Shrishtee Kandoi] last_verified: +sample_size: 1141 --- # ROSMAP DLPFC alternative splicing diff --git a/content/xqtl-data/omics/splicing/ROSMAP_PCC_splicing.md b/content/xqtl-data/omics/splicing/ROSMAP_PCC_splicing.md index ca5e14f..6ac9c57 100644 --- a/content/xqtl-data/omics/splicing/ROSMAP_PCC_splicing.md +++ b/content/xqtl-data/omics/splicing/ROSMAP_PCC_splicing.md @@ -5,7 +5,7 @@ short_title: ROSMAP PCC cohort: ROSMAP context: PCC access: controlled -status: +status: staged synapse_ids: [syn3157322, syn3388564, syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] lead_analysts: [Frank Grenn] last_verified: diff --git a/content/xqtl-data/omics/splicing/ROSMAP_snuc_splicing.md b/content/xqtl-data/omics/splicing/ROSMAP_snuc_splicing.md index dc9dca9..cb67c4b 100644 --- a/content/xqtl-data/omics/splicing/ROSMAP_snuc_splicing.md +++ b/content/xqtl-data/omics/splicing/ROSMAP_snuc_splicing.md @@ -5,10 +5,11 @@ short_title: ROSMAP ISSAC cohort: ROSMAP context: "DLPFC, cell types" access: controlled -status: +status: staged synapse_ids: [syn31512863, syn52293417, syn69670592, syn69670597, syn69670600, syn69670611, syn69670630, syn69865816] lead_analysts: [] last_verified: +sample_size: 530 --- # ROSMAP snRNA-seq Splicing (ISSAC) diff --git a/content/xqtl-data/qtl/FunGen_xQTL_protocol_data.md b/content/xqtl-data/qtl/FunGen_xQTL_protocol_data.md index 8f63020..1fe087f 100644 --- a/content/xqtl-data/qtl/FunGen_xQTL_protocol_data.md +++ b/content/xqtl-data/qtl/FunGen_xQTL_protocol_data.md @@ -3,7 +3,7 @@ type: qtl short_title: Protocol toy data cohort: ROSMAP sample_size: -status: +status: staged synapse_ids: [syn36416601, syn4164376, syn21088596] lead_analysts: [] last_verified: diff --git a/content/xqtl-data/qtl/caQTL/ROSMAP_snuc_caQTL_qtl.md b/content/xqtl-data/qtl/caQTL/ROSMAP_snuc_caQTL_qtl.md index db1be26..863be37 100644 --- a/content/xqtl-data/qtl/caQTL/ROSMAP_snuc_caQTL_qtl.md +++ b/content/xqtl-data/qtl/caQTL/ROSMAP_snuc_caQTL_qtl.md @@ -6,7 +6,7 @@ cohort: ROSMAP context: "DLPFC, cell types" sample_size: access: controlled -status: +status: staged synapse_ids: [syn69670592, syn69670597, syn69865816, syn69670630] lead_analysts: [FunGen-xQTL Analysis Team] last_verified: diff --git a/content/xqtl-data/qtl/eQTL/Knight_ADRC_brain_expression_qtl.md b/content/xqtl-data/qtl/eQTL/Knight_ADRC_brain_expression_qtl.md index feb8f95..c2d03e6 100644 --- a/content/xqtl-data/qtl/eQTL/Knight_ADRC_brain_expression_qtl.md +++ b/content/xqtl-data/qtl/eQTL/Knight_ADRC_brain_expression_qtl.md @@ -6,11 +6,14 @@ cohort: Knight-ADRC context: parietal cortex sample_size: access: controlled -status: +status: staged release: synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] lead_analysts: [Chunming Liu] last_verified: +methods: + SuSiE: done + TWAS: done --- # Knight ADRC brain gene expression QTL diff --git a/content/xqtl-data/qtl/eQTL/MSBB_brain_expression_qtl.md b/content/xqtl-data/qtl/eQTL/MSBB_brain_expression_qtl.md index 7f80b18..7adc831 100644 --- a/content/xqtl-data/qtl/eQTL/MSBB_brain_expression_qtl.md +++ b/content/xqtl-data/qtl/eQTL/MSBB_brain_expression_qtl.md @@ -6,11 +6,14 @@ cohort: MSBB context: 4 brain regions sample_size: access: controlled -status: +status: staged release: synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] lead_analysts: [Minghui Wang] last_verified: +methods: + SuSiE: done + TWAS: done --- # MSBB brain gene expression QTL diff --git a/content/xqtl-data/qtl/eQTL/MetaBrain_brain_expression_qtl.md b/content/xqtl-data/qtl/eQTL/MetaBrain_brain_expression_qtl.md index 97e1115..495ebae 100644 --- a/content/xqtl-data/qtl/eQTL/MetaBrain_brain_expression_qtl.md +++ b/content/xqtl-data/qtl/eQTL/MetaBrain_brain_expression_qtl.md @@ -5,11 +5,13 @@ short_title: MetaBrain cohort: MetaBrain context: multi-region access: -status: +status: staged release: synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] lead_analysts: [FunGen-xQTL Analysis Team] last_verified: +methods: + SuSiE: done --- # MetaBrain Brain Gene Expression QTL diff --git a/content/xqtl-data/qtl/eQTL/MiGA_brain_expression_qtl.md b/content/xqtl-data/qtl/eQTL/MiGA_brain_expression_qtl.md index 07a5992..a2acd8c 100644 --- a/content/xqtl-data/qtl/eQTL/MiGA_brain_expression_qtl.md +++ b/content/xqtl-data/qtl/eQTL/MiGA_brain_expression_qtl.md @@ -6,11 +6,14 @@ cohort: MiGA context: microglia sample_size: 255 access: controlled -status: +status: staged release: synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] lead_analysts: [Travyse Edwards] last_verified: +methods: + SuSiE: done + TWAS: done --- # MiGA multi-brain region gene expression @@ -39,12 +42,12 @@ Travyse Edwards Gene expression is available for four brain regions: medial frontal gyrus (GFM), superior temporal gyrus (GTS), thalamus (THA), and subventricular zone (SVZ). Each region has a TPM matrix with gene IDs in rows and sample names in columns. Low-expression genes and outlier samples were removed. -| Region | Samples (columns) | Genes (rows) | File size | Path | -|---|---|---|---|---| -| GFM | 75 | 45,814 | 11 MB | `/sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/rnaseq/GFM/sample-gfm.trimmed.clean.rnaseqc.low_expression_filtered.outlier_removed.tpm.gct.gz` | -| GTS | 63 | 45,472 | 8.8 MB | `/sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/rnaseq/GTS/sample-gts.trimmed.clean.rnaseqc.low_expression_filtered.outlier_removed.tpm.gct.gz` | -| THA | 61 | 45,461 | 8.6 MB | `/sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/rnaseq/THA/sample-tha.trimmed.clean.rnaseqc.low_expression_filtered.outlier_removed.tpm.gct.gz` | -| SVZ | 53 | 42,086 | 6.8 MB | `/sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/rnaseq/SVZ/sample-svz.trimmed.clean.rnaseqc.low_expression_filtered.outlier_removed.tpm.gct.gz` | +| Region | Samples (columns) | Genes (rows) | File size | +|---|---|---|---| +| GFM | 75 | 45,814 | 11 MB | +| GTS | 63 | 45,472 | 8.8 MB | +| THA | 61 | 45,461 | 8.6 MB | +| SVZ | 53 | 42,086 | 6.8 MB | ### Other key files diff --git a/content/xqtl-data/qtl/eQTL/ROSMAP_AC_expression_qtl.md b/content/xqtl-data/qtl/eQTL/ROSMAP_AC_expression_qtl.md index 34762c9..fe784dc 100644 --- a/content/xqtl-data/qtl/eQTL/ROSMAP_AC_expression_qtl.md +++ b/content/xqtl-data/qtl/eQTL/ROSMAP_AC_expression_qtl.md @@ -6,7 +6,7 @@ cohort: ROSMAP context: AC sample_size: access: controlled -status: +status: staged release: synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] lead_analysts: [Frank Grenn] diff --git a/content/xqtl-data/qtl/eQTL/ROSMAP_DLPFC_expression_qtl.md b/content/xqtl-data/qtl/eQTL/ROSMAP_DLPFC_expression_qtl.md index ef79d92..b0ccae0 100644 --- a/content/xqtl-data/qtl/eQTL/ROSMAP_DLPFC_expression_qtl.md +++ b/content/xqtl-data/qtl/eQTL/ROSMAP_DLPFC_expression_qtl.md @@ -4,9 +4,9 @@ modality: eQTL short_title: ROSMAP DLPFC cohort: ROSMAP context: DLPFC -sample_size: +sample_size: 839 access: controlled -status: +status: staged release: synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] lead_analysts: [Shrishtee Kandoi, Frank Grenn] diff --git a/content/xqtl-data/qtl/eQTL/ROSMAP_PCC_expression_qtl.md b/content/xqtl-data/qtl/eQTL/ROSMAP_PCC_expression_qtl.md index 1868232..baaa4d4 100644 --- a/content/xqtl-data/qtl/eQTL/ROSMAP_PCC_expression_qtl.md +++ b/content/xqtl-data/qtl/eQTL/ROSMAP_PCC_expression_qtl.md @@ -6,7 +6,7 @@ cohort: ROSMAP context: PCC sample_size: access: controlled -status: +status: staged release: synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] lead_analysts: [Frank Grenn] diff --git a/content/xqtl-data/qtl/eQTL/ROSMAP_microglia_expression_qtl.md b/content/xqtl-data/qtl/eQTL/ROSMAP_microglia_expression_qtl.md index 81bcdbd..c34de65 100644 --- a/content/xqtl-data/qtl/eQTL/ROSMAP_microglia_expression_qtl.md +++ b/content/xqtl-data/qtl/eQTL/ROSMAP_microglia_expression_qtl.md @@ -6,7 +6,7 @@ cohort: ROSMAP context: microglia sample_size: access: controlled -status: +status: staged release: synapse_ids: [syn2580853, syn11468526, syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] lead_analysts: [Travyse Edwards] diff --git a/content/xqtl-data/qtl/eQTL/ROSMAP_monocyte_expression_qtl.md b/content/xqtl-data/qtl/eQTL/ROSMAP_monocyte_expression_qtl.md index 62fb30c..9e45461 100644 --- a/content/xqtl-data/qtl/eQTL/ROSMAP_monocyte_expression_qtl.md +++ b/content/xqtl-data/qtl/eQTL/ROSMAP_monocyte_expression_qtl.md @@ -6,7 +6,7 @@ cohort: ROSMAP context: monocyte sample_size: access: controlled -status: +status: staged release: synapse_ids: [syn22024496, syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] lead_analysts: [Travyse Edwards] @@ -27,7 +27,6 @@ Travyse Edwards The ROSMAP monocyte data on MSSM were downloaded from [syn22024496](https://www.synapse.org/#!Synapse:syn22024496) on July 11th, 2022. (path on MSSM to be added) -- Path on MSSM cluster `/sc/arion/projects/load/data-ext/ROSMAP/raw/rnaseq_monocytes_syn23650893/Gene_Expression-RNA-seq-monocyte` ### Preview Monocyte Gene Expression Data diff --git a/content/xqtl-data/qtl/eQTL/ROSMAP_snRNAseq_pseudo_bulk_qtl.md b/content/xqtl-data/qtl/eQTL/ROSMAP_snRNAseq_pseudo_bulk_qtl.md index fa7deb6..e98d658 100644 --- a/content/xqtl-data/qtl/eQTL/ROSMAP_snRNAseq_pseudo_bulk_qtl.md +++ b/content/xqtl-data/qtl/eQTL/ROSMAP_snRNAseq_pseudo_bulk_qtl.md @@ -4,13 +4,16 @@ modality: eQTL short_title: ROSMAP snuc-eQTL cohort: ROSMAP context: "DLPFC, 7 cell types" -sample_size: +sample_size: 424 access: controlled -status: +status: staged release: synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] lead_analysts: [Hao Sun, Masashi Fujita] last_verified: +methods: + SuSiE: done + TWAS: done --- # ROSMAP snRNA-seq pseudo-bulk gene expression QTL diff --git a/content/xqtl-data/qtl/eQTL/STARNET_macrophage_qtl.md b/content/xqtl-data/qtl/eQTL/STARNET_macrophage_qtl.md index 5344cdc..277972c 100644 --- a/content/xqtl-data/qtl/eQTL/STARNET_macrophage_qtl.md +++ b/content/xqtl-data/qtl/eQTL/STARNET_macrophage_qtl.md @@ -5,11 +5,15 @@ short_title: STARNET macrophage cohort: STARNET context: macrophage access: controlled -status: +status: staged release: synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] lead_analysts: [Travyse Edwards] last_verified: +sample_size: 471 +methods: + SuSiE: done + TWAS: done --- # STARNET macrophage gene expression QTL @@ -125,149 +129,6 @@ Wang lab: - Genotype level imputation : - Imputation Panel : -### Path(s) to Genotype Matrix - -- Goate Lab (Minerva), `/sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/` -``` -$ ls -lh 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/sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.7.fam --rw-r-xr--+ 1 edwart10 LOAD 63M May 28 2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.8.bed --rw-r-xr--+ 1 edwart10 LOAD 19M May 28 2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.8.bim --rw-r-xr--+ 1 edwart10 LOAD 14K May 28 2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.8.fam --rw-r-xr--+ 1 edwart10 LOAD 50M May 28 2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.9.bed --rw-r-xr--+ 1 edwart10 LOAD 15M May 28 2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.9.bim --rw-r-xr--+ 1 edwart10 LOAD 14K May 28 2022 /sc/arion/projects/load/users/edwart10/projects/xQTL-STARNET-Analysis-05-24-2022/Data-Pre-Processing/Genotype-Data-Pre-Processing/output/genotype_by_chrom/STARNET_qced.9.fam -``` -### Path(s) to Phenotype Matrix - -- Goate lab, `/sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/` -``` -$ ls -lh /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/*.bed.gz --rw-r-xr--+ 1 edwart10 LOAD 1.8M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr10.bed.gz --rw-r-xr--+ 1 edwart10 LOAD 2.5M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr11.bed.gz --rw-r-xr--+ 1 edwart10 LOAD 2.5M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr12.bed.gz --rw-r-xr--+ 1 edwart10 LOAD 842K Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr13.bed.gz --rw-r-xr--+ 1 edwart10 LOAD 1.6M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr14.bed.gz --rw-r-xr--+ 1 edwart10 LOAD 1.6M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr15.bed.gz --rw-r-xr--+ 1 edwart10 LOAD 2.3M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr16.bed.gz --rw-r-xr--+ 1 edwart10 LOAD 2.8M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr17.bed.gz --rw-r-xr--+ 1 edwart10 LOAD 723K Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr18.bed.gz --rw-r-xr--+ 1 edwart10 LOAD 3.0M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr19.bed.gz --rw-r-xr--+ 1 edwart10 LOAD 4.6M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr1.bed.gz --rw-r-xr--+ 1 edwart10 LOAD 1.2M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr20.bed.gz --rw-r-xr--+ 1 edwart10 LOAD 489K Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr21.bed.gz --rw-r-xr--+ 1 edwart10 LOAD 1.2M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr22.bed.gz --rw-r-xr--+ 1 edwart10 LOAD 3.0M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr2.bed.gz --rw-r-xr--+ 1 edwart10 LOAD 2.5M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr3.bed.gz --rw-r-xr--+ 1 edwart10 LOAD 1.6M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr4.bed.gz --rw-r-xr--+ 1 edwart10 LOAD 2.0M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr5.bed.gz --rw-r-xr--+ 1 edwart10 LOAD 2.4M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr6.bed.gz --rw-r-xr--+ 1 edwart10 LOAD 2.2M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr7.bed.gz --rw-r-xr--+ 1 edwart10 LOAD 1.6M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr8.bed.gz --rw-r-xr--+ 1 edwart10 LOAD 1.8M Apr 20 12:00 /sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/data-preprocessing/phenotype/per_chrom/STARNET.tpm.gct.bed.chr9.bed.gz -``` - -### Path(s) to Covariate Matrix - -- Goate lab, `/sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/no-status/data-preprocessing/covariates/STARNET.MP.cov.merged.gz` - -``` --rw-r-x---+ 1 edwart10 LOAD 204K May 4 09:57 STARNET.MP.cov.merged.gz -``` - -### Path(s) to cis-eQTL Results - -- Goate lab, `/sc/arion/projects/load/users/edwart10/projects/04-19-2023-STARNET-PCA-Replication/output/no-status/association_scan/TensorQTL/Marchenko-Pastur-Method` - -``` -$ ls -lh *.cis_long_table.txt --rw-r-xr--+ 1 edwart10 LOAD 995M May 6 11:46 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.10.norminal.cis_long_table.txt --rw-r-xr--+ 1 edwart10 LOAD 1.3G May 6 11:49 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.11.norminal.cis_long_table.txt --rw-r-xr--+ 1 edwart10 LOAD 1.4G May 6 11:48 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.12.norminal.cis_long_table.txt --rw-r-xr--+ 1 edwart10 LOAD 516M May 6 11:45 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.13.norminal.cis_long_table.txt --rw-r-xr--+ 1 edwart10 LOAD 908M May 6 11:46 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.14.norminal.cis_long_table.txt --rw-r-xr--+ 1 edwart10 LOAD 820M May 6 11:46 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.15.norminal.cis_long_table.txt --rw-r-xr--+ 1 edwart10 LOAD 1.3G May 6 11:46 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.16.norminal.cis_long_table.txt --rw-r-xr--+ 1 edwart10 LOAD 1.5G May 6 11:46 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.17.norminal.cis_long_table.txt --rw-r-xr--+ 1 edwart10 LOAD 452M May 6 11:45 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.18.norminal.cis_long_table.txt --rw-r-xr--+ 1 edwart10 LOAD 1.8G May 6 11:47 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.19.norminal.cis_long_table.txt --rw-r-xr--+ 1 edwart10 LOAD 2.3G May 6 11:47 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.1.norminal.cis_long_table.txt --rw-r-xr--+ 1 edwart10 LOAD 638M May 6 11:45 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.20.norminal.cis_long_table.txt --rw-r-xr--+ 1 edwart10 LOAD 282M May 6 11:45 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.21.norminal.cis_long_table.txt --rw-r-xr--+ 1 edwart10 LOAD 636M May 6 11:45 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.22.norminal.cis_long_table.txt --rw-r-xr--+ 1 edwart10 LOAD 1.6G May 6 11:47 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.2.norminal.cis_long_table.txt --rw-r-xr--+ 1 edwart10 LOAD 1.4G May 6 11:46 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.3.norminal.cis_long_table.txt --rw-r-xr--+ 1 edwart10 LOAD 935M May 6 11:46 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.4.norminal.cis_long_table.txt --rw-r-xr--+ 1 edwart10 LOAD 1.1G May 6 11:46 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.5.norminal.cis_long_table.txt --rw-r-xr--+ 1 edwart10 LOAD 1.7G May 6 11:47 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.6.norminal.cis_long_table.txt --rw-r-xr--+ 1 edwart10 LOAD 1.2G May 6 11:46 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.7.norminal.cis_long_table.txt --rw-r-xr--+ 1 edwart10 LOAD 915M May 6 11:46 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.8.norminal.cis_long_table.txt --rw-r-xr--+ 1 edwart10 LOAD 922M May 6 11:46 STARNET.tpm.gct.bed.per_chrom_STARNET.MP.cov.merged.9.norminal.cis_long_table.txt -``` -### Path(s) to cis-QTL association testing - -**output of TensorQTL.ipynb** - -- ### Path(s) to fine-mapping with SuSiE RSS model Fine-mapping model objects (SuSiE-RSS, `.rds`) are available in the [finemapping models folder (syn69670592)](https://www.synapse.org/Synapse:syn69670592). diff --git a/content/xqtl-data/qtl/glycoQTL/ROSMAP_DLPFC_glycoproteomics_qtl.md b/content/xqtl-data/qtl/glycoQTL/ROSMAP_DLPFC_glycoproteomics_qtl.md index c5c3f91..e489237 100644 --- a/content/xqtl-data/qtl/glycoQTL/ROSMAP_DLPFC_glycoproteomics_qtl.md +++ b/content/xqtl-data/qtl/glycoQTL/ROSMAP_DLPFC_glycoproteomics_qtl.md @@ -4,11 +4,15 @@ modality: glycoQTL short_title: ROSMAP DLPFC cohort: ROSMAP context: DLPFC -status: -access: +status: staged +access: controlled synapse_ids: [syn69865744, syn70094703, syn76495192, syn77828034, syn76489398, syn76490205, syn75180848] lead_analysts: [] last_verified: +methods: + SuSiE: done + ColocBoost: done + TWAS: done --- # ROSMAP DLPFC glycoproteomics QTL diff --git a/content/xqtl-data/qtl/haQTL/ROSMAP_DLPFC_ChIPSeq_H3K9ac_qtl.md b/content/xqtl-data/qtl/haQTL/ROSMAP_DLPFC_ChIPSeq_H3K9ac_qtl.md index 16ecdfb..34b2f7c 100644 --- a/content/xqtl-data/qtl/haQTL/ROSMAP_DLPFC_ChIPSeq_H3K9ac_qtl.md +++ b/content/xqtl-data/qtl/haQTL/ROSMAP_DLPFC_ChIPSeq_H3K9ac_qtl.md @@ -4,9 +4,9 @@ modality: haQTL short_title: ROSMAP DLPFC H3K9ac cohort: ROSMAP context: DLPFC -sample_size: +sample_size: 596 access: controlled -status: +status: staged release: synapse_ids: [syn69670592, syn69670597, syn69865816, syn69670630] lead_analysts: [Xuanhe Chen] diff --git a/content/xqtl-data/qtl/mQTL/Knight_ADRC_brain_methylation_qtl.md b/content/xqtl-data/qtl/mQTL/Knight_ADRC_brain_methylation_qtl.md index 4da6ed4..bd2847b 100644 --- a/content/xqtl-data/qtl/mQTL/Knight_ADRC_brain_methylation_qtl.md +++ b/content/xqtl-data/qtl/mQTL/Knight_ADRC_brain_methylation_qtl.md @@ -6,7 +6,7 @@ cohort: Knight-ADRC context: parietal cortex sample_size: access: controlled -status: +status: staged release: synapse_ids: [syn69670592, syn69670597, syn69865816, syn69670630] lead_analysts: [Alexandre Pelletier] diff --git a/content/xqtl-data/qtl/mQTL/MSBB_brain_methylation_qtl.md b/content/xqtl-data/qtl/mQTL/MSBB_brain_methylation_qtl.md index e153733..23cc2ce 100644 --- a/content/xqtl-data/qtl/mQTL/MSBB_brain_methylation_qtl.md +++ b/content/xqtl-data/qtl/mQTL/MSBB_brain_methylation_qtl.md @@ -6,7 +6,7 @@ cohort: MSBB context: brain sample_size: access: controlled -status: +status: staged release: synapse_ids: [syn69670592, syn69670597, syn69865816, syn69670630] lead_analysts: [Alexandre Pelletier] diff --git a/content/xqtl-data/qtl/mQTL/ROSMAP_DLPFC_methylation_qtl.md b/content/xqtl-data/qtl/mQTL/ROSMAP_DLPFC_methylation_qtl.md index 928b97b..6f51f2b 100644 --- a/content/xqtl-data/qtl/mQTL/ROSMAP_DLPFC_methylation_qtl.md +++ b/content/xqtl-data/qtl/mQTL/ROSMAP_DLPFC_methylation_qtl.md @@ -6,7 +6,7 @@ cohort: ROSMAP context: DLPFC sample_size: access: controlled -status: +status: staged release: synapse_ids: [syn69670592, syn69670597, syn69865816, syn69670630] lead_analysts: [Alexandre Pelletier] diff --git a/content/xqtl-data/qtl/metQTL/Knight_ADRC_brain_metabolomics_qtl.md b/content/xqtl-data/qtl/metQTL/Knight_ADRC_brain_metabolomics_qtl.md index fccf108..5f9ac4b 100644 --- a/content/xqtl-data/qtl/metQTL/Knight_ADRC_brain_metabolomics_qtl.md +++ b/content/xqtl-data/qtl/metQTL/Knight_ADRC_brain_metabolomics_qtl.md @@ -5,7 +5,7 @@ short_title: Knight ADRC brain cohort: Knight-ADRC context: parietal cortex access: controlled -status: +status: staged synapse_ids: [] lead_analysts: [Zining Qi] last_verified: diff --git a/content/xqtl-data/qtl/metQTL/ROSMAP_DLPFC_metabolomics_qtl.md b/content/xqtl-data/qtl/metQTL/ROSMAP_DLPFC_metabolomics_qtl.md index 5a8a15a..5806d42 100644 --- a/content/xqtl-data/qtl/metQTL/ROSMAP_DLPFC_metabolomics_qtl.md +++ b/content/xqtl-data/qtl/metQTL/ROSMAP_DLPFC_metabolomics_qtl.md @@ -6,7 +6,7 @@ cohort: ROSMAP context: DLPFC sample_size: access: controlled -status: +status: staged synapse_ids: [syn69670592, syn69670597, syn69865816, syn69670630] lead_analysts: [FunGen-xQTL Analysis Team] last_verified: diff --git a/content/xqtl-data/qtl/pQTL/Knight_ADRC_brain_proteomics_qtl.md b/content/xqtl-data/qtl/pQTL/Knight_ADRC_brain_proteomics_qtl.md index 890e4ff..cd0a922 100644 --- a/content/xqtl-data/qtl/pQTL/Knight_ADRC_brain_proteomics_qtl.md +++ b/content/xqtl-data/qtl/pQTL/Knight_ADRC_brain_proteomics_qtl.md @@ -4,13 +4,16 @@ modality: pQTL short_title: Knight ADRC brain cohort: Knight-ADRC context: parietal cortex -sample_size: +sample_size: 412 access: controlled -status: +status: staged release: synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] lead_analysts: [Zining Qi] last_verified: +methods: + SuSiE: done + TWAS: done --- # Knight ADRC brain proteomics QTL diff --git a/content/xqtl-data/qtl/pQTL/MSBB_proteomics_qtl.md b/content/xqtl-data/qtl/pQTL/MSBB_proteomics_qtl.md index b97ced9..17a1084 100644 --- a/content/xqtl-data/qtl/pQTL/MSBB_proteomics_qtl.md +++ b/content/xqtl-data/qtl/pQTL/MSBB_proteomics_qtl.md @@ -6,11 +6,14 @@ cohort: MSBB context: brain sample_size: access: controlled -status: +status: staged release: synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] lead_analysts: [Minghui Wang] last_verified: +methods: + SuSiE: done + TWAS: done --- # MSBB brain proteomics QTL diff --git a/content/xqtl-data/qtl/pQTL/ROSMAP_DLPFC_proteomics_qtl.md b/content/xqtl-data/qtl/pQTL/ROSMAP_DLPFC_proteomics_qtl.md index 81d49ad..058a20c 100644 --- a/content/xqtl-data/qtl/pQTL/ROSMAP_DLPFC_proteomics_qtl.md +++ b/content/xqtl-data/qtl/pQTL/ROSMAP_DLPFC_proteomics_qtl.md @@ -4,13 +4,16 @@ modality: pQTL short_title: ROSMAP DLPFC cohort: ROSMAP context: DLPFC -sample_size: +sample_size: 416 access: controlled -status: +status: staged release: synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] lead_analysts: [Zining Qi] last_verified: +methods: + SuSiE: done + TWAS: done --- # ROSMAP DLPFC protein expression QTL diff --git a/content/xqtl-data/qtl/sQTL/Knight_ADRC_brain_splicing_qtl.md b/content/xqtl-data/qtl/sQTL/Knight_ADRC_brain_splicing_qtl.md index 9074949..7773785 100644 --- a/content/xqtl-data/qtl/sQTL/Knight_ADRC_brain_splicing_qtl.md +++ b/content/xqtl-data/qtl/sQTL/Knight_ADRC_brain_splicing_qtl.md @@ -6,7 +6,7 @@ cohort: Knight-ADRC context: parietal cortex sample_size: access: controlled -status: +status: staged release: synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] lead_analysts: [Xuanhe Chen] diff --git a/content/xqtl-data/qtl/sQTL/MSBB_brain_splicing_qtl.md b/content/xqtl-data/qtl/sQTL/MSBB_brain_splicing_qtl.md index bb262cf..9902140 100644 --- a/content/xqtl-data/qtl/sQTL/MSBB_brain_splicing_qtl.md +++ b/content/xqtl-data/qtl/sQTL/MSBB_brain_splicing_qtl.md @@ -6,11 +6,14 @@ cohort: MSBB context: 4 brain regions sample_size: access: controlled -status: +status: staged release: synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] lead_analysts: [Minghui Wang] last_verified: +methods: + SuSiE: done + TWAS: done --- # MSBB brain alternative splicing QTL diff --git a/content/xqtl-data/qtl/sQTL/ROSMAP_AC_splicing_qtl.md b/content/xqtl-data/qtl/sQTL/ROSMAP_AC_splicing_qtl.md index 8406157..4e0ecb1 100644 --- a/content/xqtl-data/qtl/sQTL/ROSMAP_AC_splicing_qtl.md +++ b/content/xqtl-data/qtl/sQTL/ROSMAP_AC_splicing_qtl.md @@ -6,7 +6,7 @@ cohort: ROSMAP context: AC sample_size: access: controlled -status: +status: staged release: synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] lead_analysts: [Ru Feng] diff --git a/content/xqtl-data/qtl/sQTL/ROSMAP_DLPFC_splicing_qtl.md b/content/xqtl-data/qtl/sQTL/ROSMAP_DLPFC_splicing_qtl.md index 8de8693..db79cbd 100644 --- a/content/xqtl-data/qtl/sQTL/ROSMAP_DLPFC_splicing_qtl.md +++ b/content/xqtl-data/qtl/sQTL/ROSMAP_DLPFC_splicing_qtl.md @@ -4,9 +4,9 @@ modality: sQTL short_title: ROSMAP DLPFC cohort: ROSMAP context: DLPFC -sample_size: +sample_size: 839 access: controlled -status: +status: staged release: synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] lead_analysts: [Shrishtee Kandoi, Xuanhe Chen] diff --git a/content/xqtl-data/qtl/sQTL/ROSMAP_PCC_splicing_qtl.md b/content/xqtl-data/qtl/sQTL/ROSMAP_PCC_splicing_qtl.md index ecc2d4f..5b047fc 100644 --- a/content/xqtl-data/qtl/sQTL/ROSMAP_PCC_splicing_qtl.md +++ b/content/xqtl-data/qtl/sQTL/ROSMAP_PCC_splicing_qtl.md @@ -6,7 +6,7 @@ cohort: ROSMAP context: PCC sample_size: access: controlled -status: +status: staged release: synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] lead_analysts: [Frank Grenn] diff --git a/content/xqtl-data/qtl/sQTL/ROSMAP_snuc_splicing_qtl.md b/content/xqtl-data/qtl/sQTL/ROSMAP_snuc_splicing_qtl.md index bc1b2de..6a02cc9 100644 --- a/content/xqtl-data/qtl/sQTL/ROSMAP_snuc_splicing_qtl.md +++ b/content/xqtl-data/qtl/sQTL/ROSMAP_snuc_splicing_qtl.md @@ -4,9 +4,9 @@ modality: sQTL short_title: ROSMAP single-nucleus cohort: ROSMAP context: "DLPFC, 7 cell types" -sample_size: +sample_size: 530 access: controlled -status: +status: staged synapse_ids: [syn69670592, syn69670600, syn69670611, syn69670597, syn69865816, syn69670630] lead_analysts: [FunGen-xQTL Analysis Team] last_verified: diff --git a/content/xqtl-data/reference_data/ld_reference.md b/content/xqtl-data/reference_data/ld_reference.md index 4ac83f7..16b4d6a 100644 --- a/content/xqtl-data/reference_data/ld_reference.md +++ b/content/xqtl-data/reference_data/ld_reference.md @@ -2,9 +2,9 @@ type: reference short_title: LD reference panel cohort: ADSP -sample_size: +sample_size: 16905 access: controlled -status: +status: staged release: synapse_ids: [syn53171227, syn69670651, syn69670652] lead_analysts: [Oluwatosin Olayinka]