Code for Carter, Almassalha, et al. — "Gene transcription and chromatin packing domains form a self-organizing system." bioRxiv (2026). doi: 10.64898/2026.03.15.711889 · PMID: 41889979
Backman Lab, Northwestern University.
This repository contains the processing pipelines and downstream analysis scripts for a study of RNA Polymerase II's role in chromatin packing domain formation and maintenance, using an auxin-inducible POLR2A degron system in HCT116 cells paired with Hi-C, RNA-seq/EU-seq/RIP-seq, ChIA-PET, ATAC-seq, CUT&Tag, and multimodal imaging (ChromSTEM, STORM, PWS).
| Folder | Contents |
|---|---|
HiC_analysis/ |
Hi-C processing (Juicer), loop calling, compartments, TAD/insulation, contact scaling |
chia_loop_analysis/ |
ChIA-PET locus plotting and loop anchor analysis |
RIPseq_analysis/ |
RIP-seq (POLR2A, EZH2) processing and feature-level quantification |
EU_seq_analysis/ |
Nascent transcription (EU-seq) processing and analysis |
total_RNA_seq/ |
Total RNA-seq differential expression |
atac_analysis/ |
ATAC-seq downstream analysis (public ENCODE data) |
Chip_analysis/ |
ChIP-seq / CUT&Tag coverage analysis |
CutTag/ |
CUT&Tag processing pipeline |
long_read_COP/ |
Long-read nascent RNA-seq (RREA) splicing analysis |
imaging_analysis_scripts/ |
PWS, EU-STORM, EdU/K9-STORM, ChromSTEM analysis |
chrom_STEM/ |
ChromSTEM analysis code |
imaging_data/ |
Raw imaging data (CSVs) underlying the imaging analyses above — not code |
Each folder has its own README.md with a script-by-script breakdown and,
where confirmed, the specific figure/panel each script produces. See
FIGURES.md for the full figure-to-script index across the whole paper.
See ENVIRONMENT.md for the full list of software versions and R/Python
packages used across this repository. Most processing pipelines were run on
Northwestern's Quest HPC cluster (SLURM); paths in submission scripts will
need to be updated for other environments.
All publicly available datasets used in this study (ENCODE ChIA-PET/ATAC-seq/ ChIP-seq, GEO nanopore direct RNA-seq) are listed with accessions in Table 5 of the manuscript.
HiC_analysis/HiC_HPC_processing/juicer_src/ is excluded from this
repository — it is a modified copy of the
Juicer 2.0 toolkit (Aiden Lab, MIT
License). Install Juicer separately. The Quest-specific adaptation of the
Juicer pipeline for this study is documented in HiC_analysis/README.md.
See LICENSE.
See CITATION.cff, or cite:
Carter LM, Almassalha LM, et al. Gene transcription and chromatin packing domains form a self-organizing system. bioRxiv. 2026. doi:10.64898/2026.03.15.711889