gaow · Oct 9, 2026 · Oct 9, 2026 · Oct 9, 2026 · Oct 9, 2026 · Oct 9, 2026
diff --git a/.github/ISSUE_TEMPLATE/propose-dataset.yml 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/.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: |

diff --git 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
@@ -19,9 +19,9 @@ 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), [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/coverage.md b/content/coverage.md
@@ -0,0 +1,7 @@
+---
+layout: coverage
+---
+
+# Analysis coverage
+
+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
@@ -0,0 +1,50 @@
+# How to get the data
+
+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 >}}
+
+## 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, 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 %}}
+
+```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
+
+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.<QTL type>.<result type>.tar`
+
+| Result type | What it holds |
+|---|---|
+| `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 |
+
+NG00184 includes eQTL, snuc-eQTL, sQTL, pQTL, mQTL and haQTL. Each archive holds `.bed.gz` files with tabix indexes, metadata and a manifest.
+{{% /callout %}}
+
+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
+
+{{< status-defs >}}
diff --git a/content/inventory.md b/content/inventory.md
@@ -0,0 +1,7 @@
+---
+layout: inventory
+---
+
+# Dataset inventory
+
+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/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
-status:
+short_title: ADGC imputation protocol
+status: staged
+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
@@ -1,6 +1,7 @@
 ---
 type: gwas
-status:
+short_title: AD GWAS overview
+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
@@ -1,6 +1,9 @@
 ---
 type: gwas
-status:
+short_title: Bellenguez 2022
+status: staged
+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
@@ -1,6 +1,9 @@
 ---
 type: gwas
-status:
+short_title: Jansen 2019
+status: staged
+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
@@ -1,6 +1,9 @@
 ---
 type: gwas
-status:
+short_title: Kunkle 2019
+status: staged
+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
@@ -1,6 +1,9 @@
 ---
 type: gwas
-status:
+short_title: Wightman 2021
+status: staged
+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
@@ -1,3 +1,15 @@
+---
+type: omics
+modality: covariates
+short_title: ROSMAP covariates
+cohort: ROSMAP
+access: controlled
+status: staged
+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
@@ -1,3 +1,16 @@
+---
+type: omics
+modality: expression
+short_title: Knight ADRC brain
+cohort: Knight-ADRC
+context: parietal cortex
+access: controlled
+status: staged
+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
@@ -1,3 +1,18 @@
+---
+type: omics
+modality: expression
+short_title: MSBB brain
+cohort: MSBB
+context: 4 brain regions
+sample_size:
+access: controlled
+status: staged
+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
@@ -1,3 +1,15 @@
+---
+type: omics
+modality: expression
+short_title: MetaBrain
+cohort: MetaBrain
+context: multi-region
+status: staged
+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
@@ -1,3 +1,18 @@
+---
+type: omics
+modality: expression
+short_title: MiGA microglia
+cohort: MiGA
+context: "microglia, 4 regions"
+sample_size:
+access: controlled
+status: staged
+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.
@@ -26,26 +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
@@ -1,3 +1,16 @@
+---
+type: omics
+modality: expression
+short_title: ROSMAP AC
+cohort: ROSMAP
+context: AC
+access: controlled
+status: staged
+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
@@ -1,3 +1,18 @@
+---
+type: omics
+modality: expression
+short_title: ROSMAP DLPFC
+cohort: ROSMAP
+context: DLPFC
+sample_size:
+access: controlled
+status: staged
+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
@@ -1,3 +1,16 @@
+---
+type: omics
+modality: expression
+short_title: ROSMAP PCC
+cohort: ROSMAP
+context: PCC
+access: controlled
+status: staged
+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.