Binding domain mutations provide insight into CTCF's relationship with chromatin and its contribution to gene regulation (Omni-ATAC)
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 20 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
- 20 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
- Binding domain mutations provide insight into CTCF's relationship with chromatin and its contribution to gene regulationCell genomics · 2025
Read the full summary ↓
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 GSE270626_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 PRJNA1127588. 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 20 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.
- GSM8348503 OmniATAC_H455R_ID_rep1 OmniATAC_H455R_ID
- GSM8348504 OmniATAC_H455R_ID_rep2 OmniATAC_H455R_ID
- GSM8348505 OmniATAC_K365T_ID_rep1 OmniATAC_K365T_ID
- GSM8348506 OmniATAC_K365T_ID_rep2 OmniATAC_K365T_ID
- GSM8348507 OmniATAC_Q418R_ID_rep1 OmniATAC_Q418R_ID
- GSM8348508 OmniATAC_Q418R_ID_rep2 OmniATAC_Q418R_ID
- GSM8348509 OmniATAC_R339Q_ID_rep1 OmniATAC_R339Q_ID
- GSM8348510 OmniATAC_R339Q_ID_rep2 OmniATAC_R339Q_ID
- GSM8348511 OmniATAC_R342C_ID_rep1 OmniATAC_R342C_ID
- GSM8348512 OmniATAC_R342C_ID_rep2 OmniATAC_R342C_ID
- GSM8348513 OmniATAC_R377C_ID_rep1 OmniATAC_R377C_ID
- GSM8348514 OmniATAC_R377C_ID_rep2 OmniATAC_R377C_ID
- GSM8348515 OmniATAC_R377H_ID_rep1 OmniATAC_R377H_ID
- GSM8348516 OmniATAC_R377H_ID_rep2 OmniATAC_R377H_ID
- GSM8348517 OmniATAC_R448Q_ID_rep1 OmniATAC_R448Q_ID
- GSM8348518 OmniATAC_R448Q_ID_rep2 OmniATAC_R448Q_ID
- GSM8348519 OmniATAC_S354F_ID_rep1 OmniATAC_S354F_ID
- GSM8348520 OmniATAC_S354F_ID_rep2 OmniATAC_S354F_ID
- GSM8348521 OmniATAC_WT_ID_rep1 OmniATAC_WT_ID
- GSM8348522 OmniATAC_WT_ID_rep2 OmniATAC_WT_ID
- GSE270669 Binding domain mutations provide insight into CTCF's relationship with chromatin and its contribution to gene regulation 130 samples shares ctcf, relationship, contribution, mutations, chromatin, binding, provide
- 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
- GSE288516 A proteomics screen uncovers CTCF as a key G-quadruplex binding protein [CUT&Tag] 28 samples shares ctcf, binding
- GSE280719 Interplay between CTCF-binding and CTCF-lacking regulatory elements in generating an architectural stripe at the Igh locus 16 samples shares ctcf, binding
- 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
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.