CTCF tunes gene expression in a loop-dependent and -independent manner [ATAC-Seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 24 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
- 24 samples: 10 conditions, mostly in duplicateGroups 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
- CTCF's loop-independent functions prevail over chromatin looping in the acute degradation systemProtein & cell · 2026
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE274789_RAW.tar (it can run to tens of gigabytes).
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 PRJNA1148056 and SRA study SRP526319. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 20 samples.
How we read this: 10 replicated groups read from 24 sample titles; they account for 20 of them. 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.
- GSM8457932 [ATAC-Seq] oectrl_rep1 [ATAC-Seq] oectrl
- GSM8457933 [ATAC-Seq] oectrl_rep2 [ATAC-Seq] oectrl
- GSM8457934 [ATAC-Seq] oectrl_IAA_rep1 [ATAC-Seq] oectrl_IAA
- GSM8457935 [ATAC-Seq] oectrl_IAA_rep2 [ATAC-Seq] oectrl_IAA
- GSM8457936 [ATAC-Seq] oeCTCFwt_IAA_rep1 [ATAC-Seq] oeCTCFwt_IAA
- GSM8457937 [ATAC-Seq] oeCTCFwt_IAA_rep2 [ATAC-Seq] oeCTCFwt_IAA
- GSM8457938 [ATAC-Seq] oeCTCFmut_IAA_rep1 [ATAC-Seq] oeCTCFmut_IAA
- GSM8457939 [ATAC-Seq] oeCTCFmut_IAA_rep2 [ATAC-Seq] oeCTCFmut_IAA
- GSM8457940 [ATAC-Seq] chd4_shluci_rep1 [ATAC-Seq] chd4_shluci
- GSM8457941 [ATAC-Seq] chd4_shluci_rep2 [ATAC-Seq] chd4_shluci
- GSM8457942 [ATAC-Seq] chd4_shRNA1_rep1 [ATAC-Seq] chd4_shRNA1
- GSM8457943 [ATAC-Seq] chd4_shRNA1_rep2 [ATAC-Seq] chd4_shRNA1
- GSM8457944 [ATAC-Seq] chd4_shRNA2_rep1 [ATAC-Seq] chd4_shRNA2
- GSM8457945 [ATAC-Seq] chd4_shRNA2_rep2 [ATAC-Seq] chd4_shRNA2
- GSM8457946 [ATAC-Seq] chd8_shluci_rep1 [ATAC-Seq] chd8_shluci
- GSM8457947 [ATAC-Seq] chd8_shluci_rep2 [ATAC-Seq] chd8_shluci
- GSM8457948 [ATAC-Seq] chd8_shRNA1_rep1 [ATAC-Seq] chd8_shRNA1
- GSM8457949 [ATAC-Seq] chd8_shRNA1_rep2 [ATAC-Seq] chd8_shRNA1
- GSM8457950 [ATAC-Seq] chd8_shRNA2_rep1 [ATAC-Seq] chd8_shRNA2
- GSM8457951 [ATAC-Seq] chd8_shRNA2_rep2 [ATAC-Seq] chd8_shRNA2
- GSM9161150 CTCF_0h_ATAC_rep1_serum
- GSM9161151 CTCF_0h_ATAC_rep2_serum
- GSM9161152 CTCF_12h_ATAC_rep1_serum
- GSM9161153 CTCF_12h_ATAC_rep2_serum
- GSE300925 Lyn expression in macrophages promotes TLR activation and restricts proliferation in an isoform-independent manner 48 samples shares independent, manner
- GSE234251 Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF [Mnase-seq] 21 samples shares ctcf
- GSE234288 Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF [Cut&Run] 12 samples shares ctcf
- GSE262521 Disentangling the architectural and non-architectural functions of CTCF and cohesin in global gene regulation 68 samples shares ctcf
- GSE72539 CTCF binding polarity determines chromatin looping [4C] 504 samples shares ctcf
- GSE267881 Foxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for effector Treg cell differentiation [ATAC-Seq] 30 samples shares atac-seq
- GSE234248 Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF [RNA-seq] 24 samples shares ctcf
- GSE328495 Gene expression + ATAC profiling of trisomic hippocampal neurons upon SAHA treatment [ATAC-seq] 16 samples shares atac-seq
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.