Binding domain mutations provide insight into CTCF's relationship with chromatin and its contribution to gene regulation
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 130 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
- 130 samples: 65 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
- Binding domain mutations provide insight into CTCF's relationship with chromatin and its contribution to gene regulationCell genomics · 2025
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 GSE270669_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 PRJNA1127653 and SRA study SRP534291. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 130 samples.
How we read this: 65 replicated groups read from 130 sample titles; they account for 130 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.
- GSM8348376 totalRNASeq_H455R_ID_rep1 totalRNASeq_H455R_ID
- GSM8348377 totalRNASeq_H455R_ID_rep2 totalRNASeq_H455R_ID
- GSM8348378 totalRNASeq_K365T_ID_rep1 totalRNASeq_K365T_ID
- GSM8348379 totalRNASeq_K365T_ID_rep2 totalRNASeq_K365T_ID
- GSM8348380 totalRNASeq_Q418R_ID_rep1 totalRNASeq_Q418R_ID
- GSM8348381 totalRNASeq_Q418R_ID_rep2 totalRNASeq_Q418R_ID
- GSM8348382 totalRNASeq_R339Q_ID_rep1 totalRNASeq_R339Q_ID
- GSM8348383 totalRNASeq_R339Q_ID_rep2 totalRNASeq_R339Q_ID
- GSM8348384 totalRNASeq_R342C_ID_rep1 totalRNASeq_R342C_ID
- GSM8348385 totalRNASeq_R342C_ID_rep2 totalRNASeq_R342C_ID
- GSM8348386 totalRNASeq_R377C_ID_rep1 totalRNASeq_R377C_ID
- GSM8348387 totalRNASeq_R377C_ID_rep2 totalRNASeq_R377C_ID
- GSM8348388 totalRNASeq_R377H_ID_rep1 totalRNASeq_R377H_ID
- GSM8348389 totalRNASeq_R377H_ID_rep2 totalRNASeq_R377H_ID
- GSM8348390 totalRNASeq_R448Q_ID_rep1 totalRNASeq_R448Q_ID
- GSM8348391 totalRNASeq_R448Q_ID_rep2 totalRNASeq_R448Q_ID
- GSM8348392 totalRNASeq_S354F_ID_rep1 totalRNASeq_S354F_ID
- GSM8348393 totalRNASeq_S354F_ID_rep2 totalRNASeq_S354F_ID
- GSM8348394 totalRNASeq_WT_IAA_rep1 totalRNASeq_WT_IAA
- GSM8348395 totalRNASeq_WT_IAA_rep2 totalRNASeq_WT_IAA
- GSM8348396 totalRNASeq_WT_ID_rep1 totalRNASeq_WT_ID
- GSM8348397 totalRNASeq_WT_ID_rep2 totalRNASeq_WT_ID
- GSM8348398 FLAG_CTCF_H455R_ID_rep1 FLAG_CTCF_H455R_ID
- GSM8348399 FLAG_CTCF_H455R_ID_rep2 FLAG_CTCF_H455R_ID
- GSM8348400 FLAG_CTCF_K365T_ID_rep1 FLAG_CTCF_K365T_ID
- GSM8348401 FLAG_CTCF_K365T_ID_rep2 FLAG_CTCF_K365T_ID
- GSM8348402 FLAG_CTCF_Q418R_ID_rep1 FLAG_CTCF_Q418R_ID
- GSM8348403 FLAG_CTCF_Q418R_ID_rep2 FLAG_CTCF_Q418R_ID
- GSM8348404 FLAG_CTCF_R339Q_ID_rep1 FLAG_CTCF_R339Q_ID
- GSM8348405 FLAG_CTCF_R339Q_ID_rep2 FLAG_CTCF_R339Q_ID
- GSM8348406 FLAG_CTCF_R342C_ID_rep1 FLAG_CTCF_R342C_ID
- GSM8348407 FLAG_CTCF_R342C_ID_rep2 FLAG_CTCF_R342C_ID
- GSM8348410 FLAG_CTCF_R377H_ID_rep1 FLAG_CTCF_R377H_ID
- GSM8348411 FLAG_CTCF_R377H_ID_rep2 FLAG_CTCF_R377H_ID
- GSM8348412 FLAG_CTCF_R448Q_ID_rep1 FLAG_CTCF_R448Q_ID
- GSM8348413 FLAG_CTCF_R448Q_ID_rep2 FLAG_CTCF_R448Q_ID
- GSM8348414 FLAG_CTCF_S354F_ID_rep1 FLAG_CTCF_S354F_ID
- GSM8348415 FLAG_CTCF_S354F_ID_rep2 FLAG_CTCF_S354F_ID
- GSM8348416 FLAG_CTCF_WT_ID_rep1 FLAG_CTCF_WT_ID
- GSM8348417 FLAG_CTCF_WT_ID_rep2 FLAG_CTCF_WT_ID
+ 90 more — browse all 130 samples with per-sample file links →
- GSE72539 CTCF binding polarity determines chromatin looping [4C] 504 samples shares ctcf, chromatin, binding
- GSE287375 CTCF-RNA interactions orchestrate cell-specific chromatin loop organization [ChIP-seq] 54 samples shares ctcf, chromatin
- GSE278338 ChIP-seq to measure binding of NIPBL/MAU2, RAD21, and CTCF in mouse embryonic stem cells and neural progenitor cells 50 samples shares ctcf, binding
- GSE253692 Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [mESC_d0246_CTCF_MBD3_ChIP_Seq] 36 samples shares ctcf, chromatin
- GSE253693 Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [mESC_d0246_DMSO_BPK25_IAA_RNA_Seq] 36 samples shares ctcf, chromatin
- GSE277826 CTCF binding landscape is established by the epigenetic status of the nucleosome, well-positioned relative to CTCF motif orientation 30 samples shares ctcf, binding
- GSE288516 A proteomics screen uncovers CTCF as a key G-quadruplex binding protein [CUT&Tag] 28 samples shares ctcf, binding
- GSE244681 CTCF-mediated 3D chromatin predetermines the gene expression program in the male germline 26 samples shares ctcf, chromatin
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.