CTCF tunes gene expression in a loop-dependent and -independent manner
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 172 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
- 172 samples: 64 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 GSE275003_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 PRJNA1148927 and SRA study SRP526227. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 149 samples.
How we read this: 64 replicated groups read from 172 sample titles; they account for 149 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.
- GSM8457622 CTCF_AID_0h_rep1 CTCF_AID_0h
- GSM8457623 CTCF_AID_0h_rep2 CTCF_AID_0h
- GSM8457624 CTCF_AID_12h_rep1 CTCF_AID_12h
- GSM8457625 CTCF_AID_12h_rep2 CTCF_AID_12h
- GSM8457626 CTCF_AID_24h_rep1 CTCF_AID_24h
- GSM8457627 CTCF_AID_24h_rep2 CTCF_AID_24h
- GSM8457628 RAD21_AID_0h_rep1 RAD21_AID_0h
- GSM8457629 RAD21_AID_0h_rep2 RAD21_AID_0h
- GSM8457630 RAD21_AID_12h_rep1 RAD21_AID_12h
- GSM8457631 RAD21_AID_12h_rep2 RAD21_AID_12h
- GSM8457632 RAD21_AID_24h_rep1 RAD21_AID_24h
- GSM8457633 RAD21_AID_24h_rep2 RAD21_AID_24h
- GSM8457634 oectrl_rep1 oectrl
- GSM8457635 oectrl_rep2 oectrl
- GSM8457636 oectrl_IAA_rep1 oectrl_IAA
- GSM8457637 oectrl_IAA_rep2 oectrl_IAA
- GSM8457638 oeCTCFwt_rep1 oeCTCFwt
- GSM8457639 oeCTCFwt_rep2 oeCTCFwt
- GSM8457640 oeCTCFmut_rep1 oeCTCFmut
- GSM8457641 oeCTCFmut_rep2 oeCTCFmut
- GSM8457642 oeCTCFwt_IAA_rep1 oeCTCFwt_IAA
- GSM8457643 oeCTCFwt_IAA_rep2 oeCTCFwt_IAA
- GSM8457644 oeCTCFmut_IAA_rep1 oeCTCFmut_IAA
- GSM8457645 oeCTCFmut_IAA_rep2 oeCTCFmut_IAA
- 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
+ 132 more — browse all 172 samples with per-sample file links →
- GSE274792 CTCF tunes gene expression in a loop-dependent and -independent manner [ChIP-Seq] 30 samples shares ctcf, loop-dependent, independent, manner, tunes
- GSE274789 CTCF tunes gene expression in a loop-dependent and -independent manner [ATAC-Seq] 24 samples shares ctcf, loop-dependent, independent, manner, tunes
- GSE269216 Hoxblinc lncRNA reprograms CTCF-independent TADs to drive leukemic transcription and HSC dysregulation in NUP98 fusion transformed leukemia [ATAC-Seq] 10 samples shares ctcf, independent
- GSE300925 Lyn expression in macrophages promotes TLR activation and restricts proliferation in an isoform-independent manner 48 samples shares independent, manner
- GSE269171 Gingival spatial analysis reveals geographic immunological variation in a microbiota-dependent and -independent manner 10 samples shares independent, manner
- GSE244681 CTCF-mediated 3D chromatin predetermines the gene expression program in the male germline 26 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
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.