CTCF binding landscape is established by the epigenetic status of the nucleosome, well-positioned relative to CTCF motif orientation
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 30 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
- 30 samples: 30 samples, each with a distinct title — no replicated groupsGroups 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 binding landscape is shaped by the epigenetic state of the N-terminal nucleosome in relation to CTCF motif orientationNucleic acids research · 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 GSE277826_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 PRJNA1164285 and SRA study SRP534256. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 9 samples read as cases, 6 as controls.
How we read this: Read from 30 sample titles: 30 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.
- GSM8532260 MNase-Seq Assisted H3 ChIP-seq in wtCH12 cells
- GSM8532261 MNase-Seq Assisted H3 ChIP-seq in mutCH12 cells
- GSM8532262 MNase-Seq Assisted H3 ChIP-seq in mutCH12+FL-CTCF cells
- GSM8532263 MNase-Seq Assisted H3 ChIP-seq in mutCH12+deltaN-CTCF cells
- GSM8532264 MNase-Seq Assisted H3 ChIP-seq in mutCH12+deltaC-CTCF cells
- GSM8532265 MNase-Seq Assisted H3 ChIP-seq in mutCH12+BORIS cells
- GSM8532266 ATAC-seq on wtCH12 cells
- GSM8532267 ATAC-seq on mutant CH12 cells (mutCH12)
- GSM8532268 ATAC-seq on mutant CH12 cells, ectopically expressing Full-Length (FL)-CTCF (mutCH12_FLCTCF)
- GSM8532269 ATAC-seq on mutant CH12 cells, ectopically expressing deltaN-CTCF (mutCH12_deltaN)
- GSM8532270 ATAC-seq on mutant CH12 cells, ectopically expressing deltaC-CTCF (mutCH12_deltaC)
- GSM8532271 ATAC-seq on mutant CH12 cells, ectopically expressing human BORIS (mutCH12_BORIS)
- GSM8532272 meDIP-seq with 5mC Abs on wtCH12 cells
- GSM8532273 meDIP-seq with 5mC Abs on mutCH12 cells
- GSM8532274 Input for meDIP-seq with 5mC Abs on wtCH12 cells
- GSM8532275 Input for meDIP-seq with 5mC Abs on mutCH12 cells
- GSM8532276 ChIP-seq on wtCH12 cells with H3K9me3 antibodies
- GSM8532277 ChIP-seq on mutCH12 cells with H3K9me3 antibodies
- GSM8532278 ChIP-seq on wtCH12 cells with Snf2h antibodies
- GSM8532279 ChIP-seq on mutCH12 cells with Snf2h antibodies
- GSM8532280 ChIP-seq on mutant CH12 cells, ectopically expressing Full-Length (FL)-CTCF (mutCH12_FLCTCF) with Snf2h Antibodies
- GSM8532281 ChIP-seq on mutant CH12 cells, ectopically expressing deltaN-CTCF (mutCH12_deltaN) with Snf2h Antibodies
- GSM8532282 ChIP-seq on mutant CH12 cells, ectopically expressing deltaC-CTCF (mutCH12_deltaC) with Snf2h Antibodies
- GSM8532283 ChIP-seq on mutant CH12 cells, ectopically expressing human BORIS (mutCH12_BORIS) with Snf2h Antibodies
- GSM8532284 ChIP-seq on NIH3T3+EV cells with SMC1 Antibodies
- GSM8532285 ChIP-seq on NIH3T3+EV cells with RAD21 Antibodies
- GSM8532286 ChIP-seq on NIH3T3+EV cells with SMC3 Antibodies
- GSM8532287 ChIP-seq on NIH3T3+BORIS (cl.2) cells with SMC1 Antibodies
- GSM8532288 ChIP-seq on NIH3T3+BORIS (cl.2) cells with RAD21 Antibodies
- GSM8532289 ChIP-seq on NIH3T3+BORIS (cl.2) cells with SMC3 Antibodies
- GSE72720 CTCF binding polarity determines chromatin looping 506 samples shares ctcf, binding
- GSE72539 CTCF binding polarity determines chromatin looping [4C] 504 samples shares ctcf, binding
- GSE270669 Binding domain mutations provide insight into CTCF's relationship with chromatin and its contribution to gene regulation 130 samples shares ctcf, binding
- 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
- GSE270620 Binding domain mutations provide insight into CTCF's relationship with chromatin and its contribution to gene regulation (chip-seq) 48 samples shares ctcf, binding
- GSE330560 A proteomics screen uncovers CTCF as a key G-quadruplex binding protein 43 samples shares ctcf, binding
- GSE293581 H3K27 and H3K9 Methylation Mask Potential CTCF Binding Sites to Maintain 3D Genome Integrity 40 samples shares ctcf, binding
- GSE288516 A proteomics screen uncovers CTCF as a key G-quadruplex binding protein [CUT&Tag] 28 samples shares ctcf, binding
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.