GEO series
Disentangling the architectural and non-architectural functions of CTCF and cohesin in global gene regulation
GSE262521
Mus musculus (mouse)
ChIP-seq / ATAC-seq (genome binding and open chromatin)
68 samples
Submitted 2025/08/27
Platform GPL30172
At a glance
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 68 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Mus musculus (mouse)
- Samples
- 68 samples: 60 distinct titles, 8 of them repeatedGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- Disentangling the architectural and non-architectural functions of CTCF and cohesin in gene regulationNature genetics · 2025
Summary (written by the submitters)
Cohesin- and CTCF-mediated chromatin loops shape enhancer-promoter interactions, but their global impact on gene regulation remains unclear. We show that cohesin and CTCF regulate hundreds of genes in mouse cells, though the magnitude of expression changes is modest. Acute loss of cohesin loops mainly downregulates CBP/p300-dependent enhancer targets, while CTCF depletion can both up- and downregulate putative enhancer targets.
Read the full summary ↓
Interestingly, beyond regulating enhancer-dependent transcription via loop anchoring, CTCF acts as a transcriptional activator or repressor of sense and antisense transcripts, depending on its binding position and orientation in promoters. Mechanistically, promoter-bound CTCF enhances DNA accessibility and RNA polymerase II recruitment, thereby activating housekeeping genes essential for mammalian cell proliferation. CTCF’s transcriptional activation function—but not its loop-anchoring role—is shared with its vertebrate-specific paralog, CTCFL. These findings resolve cohesin and CTCF’s roles in global gene regulation, offering a unified model that integrates their enhancer-dependent and -independent functions in transcription control.
Published in
Narita T, Kilic S, Higashijima Y et al.
· Nature genetics 2025
· PMID 41254162
· doi:10.1038/s41588-025-02404-x
This dataset
Download · which file do I need?
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
1 · Just have a look
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
2 · Re-analyse it
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE262521_RAW.tar (it can run to tens of gigabytes).
3 · Start from the raw reads
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1092101 and SRA study SRP497965. Searching any of these in the dataset finder brings you back here.
Study design
60 distinct titles, 8 of them repeated
ATAC-seq on GFP-dTAG-Ctcf ESC, control, ×2
ATAC-seq on GFP-dTAG-Ctcf ESC, dTAG13 100nM … ×2
Pol II ChIP-seq on GFP-dTAG-Ctcf ESC, control, ×2
Pol II ChIP-seq on GFP-dTAG-Ctcf ESC, dTAG13… ×2
Stranded EU-seq of bTAG-ΔN-CTCF/dTAG-CTCF-ΔC … ×2
Stranded EU-seq of bTAG-ΔN-CTCF/dTAG-CTCF-ΔC … ×2
Stranded EU-seq of bTAG-ΔN-CTCF/dTAG-CTCF-ΔC … ×2
Stranded EU-seq of bTAG-ΔN-CTCF/dTAG-CTCF-ΔC … ×2
Supports a case/control comparison: 30 samples read as cases, 26 as controls.
How we read this: Read from 68 sample titles: 60 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
Samples in this study
- GSM8170804 ATAC-seq on GFP-dTAG-Ctcf ESC, control, replicate1
- GSM8170805 ATAC-seq on GFP-dTAG-Ctcf ESC, control, replicate2
- GSM8170806 ATAC-seq on GFP-dTAG-Ctcf ESC, dTAG13 100nM treatment for 3hrs, replicate1
- GSM8170807 ATAC-seq on GFP-dTAG-Ctcf ESC, dTAG13 100nM treatment for 3hrs, replicate2
- GSM8170895 Pol II ChIP-seq on GFP-dTAG-Ctcf ESC, control, replicate1
- GSM8170896 Pol II ChIP-seq on GFP-dTAG-Ctcf ESC, control, replicate2
- GSM8170897 Pol II ChIP-seq on GFP-dTAG-Ctcf ESC, dTAG13 100nM treatment for 4hrs, replicate1
- GSM8170898 Pol II ChIP-seq on GFP-dTAG-Ctcf ESC, dTAG13 100nM treatment for 4hrs, replicate2
- GSM8170899 EU-seq of GFP-AID-Ctcf mouse ESC control, replicate1.
- GSM8170900 EU-seq of GFP-AID-Ctcf mouse ESC control, replicate2.
- GSM8170901 Stranded EU-seq of GFP-AID-Ctcf mouse ESC control, replicate1.
- GSM8170902 Stranded EU-seq of GFP-AID-Ctcf mouse ESC control, replicate2.
- GSM8170903 EU-seq of GFP-AID-Ctcf mouse ESC treated with IAA for 6hr, replicate1.
- GSM8170904 EU-seq of GFP-AID-Ctcf mouse ESC treated with IAA for 6hr, replicate2.
- GSM8170905 Stranded EU-seq of GFP-AID-Ctcf mouse ESC treated with IAA for 6hr, replicate1.
- GSM8170906 Stranded EU-seq of GFP-AID-Ctcf mouse ESC treated with IAA for 6hr, replicate2.
- GSM8170907 EU-seq of GFP-FKBP12F36V-Ctcf (Y226A/F228A) ESC mutant control, replicate1.
- GSM8170908 EU-seq of GFP-FKBP12F36V-Ctcf (Y226A/F228A) ESC mutant control, replicate2.
- GSM8170909 EU-seq of GFP-FKBP12F36V-Ctcf (Y226A/F228A) ESC mutant treated with dTAG13 for 2hr, replicate1.
- GSM8170910 EU-seq of GFP-FKBP12F36V-Ctcf (Y226A/F228A) ESC mutant treated with dTAG13 for 2hr, replicate2.
- GSM8170911 EU-seq of GFP-FKBP12F36V-Ctcf (Y226A/F228A) ESC mutant treated with dTAG13 for 4hr, replicate1.
- GSM8170912 EU-seq of GFP-FKBP12F36V-Ctcf (Y226A/F228A) ESC mutant treated with dTAG13 for 4hr, replicate2.
- GSM8170917 EU-seq of GFP-AID-Rad21 mouse ESC control, replicate1.
- GSM8170918 EU-seq of GFP-AID-Rad21 mouse ESC control, replicate2.
- GSM8170919 EU-seq of GFP-AID-Rad21 mouse ESC treated with IAA for 4hr, replicate1.
- GSM8170920 EU-seq of GFP-AID-Rad21 mouse ESC treated with IAA for 4hr, replicate2.
- GSM8664049 EU-seq of GFP-AID-Rad21 NPC, control, replicate1.
- GSM8664050 EU-seq of GFP-AID-Rad21 NPC, control, replicate2.
- GSM8664051 EU-seq of GFP-AID-Rad21 NPC, treated with 500uM IAA for 1hr, replicate1.
- GSM8664052 EU-seq of GFP-AID-Rad21 NPC, treated with 500uM IAA for 1hr, replicate2.
- GSM8664053 EU-seq of GFP-AID-Rad21 NPC, treated with 500uM IAA for 2hr, replicate1.
- GSM8664054 EU-seq of GFP-AID-Rad21 NPC, treated with 500uM IAA for 2hr, replicate2.
- GSM8664055 EU-seq of GFP-AID-Rad21 NPC, treated with 500uM IAA for 4hr, replicate1.
- GSM8664056 EU-seq of GFP-AID-Rad21 NPC, treated with 500uM IAA for 4hr, replicate2.
- GSM8664057 EU-seq of GFP-AID-Rad21 NPC, treated with 10uM A-485 for 1hr, replicate1.
- GSM8664058 EU-seq of GFP-AID-Rad21 NPC, treated with 10uM A-485 for 1hr, replicate2.
- GSM8664059 EU-seq of GFP-AID-Rad21 ESC, control, replicate1.
- GSM8664060 EU-seq of GFP-AID-Rad21 ESC, control, replicate2.
- GSM8664061 EU-seq of GFP-AID-Rad21 ESC, control, replicate3.
- GSM8664062 EU-seq of GFP-AID-Rad21 ESC, control, replicate4.
+ 28 more — browse all 68 samples with per-sample file links →
Datasets on a similar topic
- GSE269683 CTCF regulates global chromatin accessibility and transcription during rod photoreceptor development 26 samples shares ctcf, global
- GSE285578 CTCF N-terminal Domain Regulates Clustered Protocadherin Gene Expression by Enhancing Cohesin Processivity [ChIP-seq] 20 samples shares ctcf, cohesin
- GSE280719 Interplay between CTCF-binding and CTCF-lacking regulatory elements in generating an architectural stripe at the Igh locus 16 samples shares ctcf, architectural
- GSE277289 Cohesin-mediated chromatin remodeling controls the differentiation and function of conventional dendritic cells (RAD21 and CTCF ChIP-seq of Hoxb8-FL differentiation) 9 samples shares ctcf, cohesin
- GSE90994 CTCF and cohesin regulate chromatin loop stability with distinct dynamics 8 samples shares ctcf, cohesin
- GSE72720 CTCF binding polarity determines chromatin looping 506 samples shares ctcf
- GSE246984 The impact of the embryonic DNA methylation program on CTCF-mediated genome regulation 28 samples shares ctcf
- GSE244681 CTCF-mediated 3D chromatin predetermines the gene expression program in the male germline 26 samples shares ctcf
Share this dataset
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.