CTCF N-terminal Domain Regulates Clustered Protocadherin Gene Expression by Enhancing Cohesin Processivity [ChIP-seq]
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: 20 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
- CCCTC-binding factor N-terminal domain regulates clustered protocadherin gene expression by enhancing cohesin processivityThe Journal of biological chemistry · 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 GSE285578_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 PRJNA1204916 and SRA study SRP554649. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 20 sample titles: 20 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.
- GSM8705132 Adult_cortex, WT, CTCF, rep1, ChIP-seq
- GSM8705133 Adult_cortex, WT, CTCF, rep2, ChIP-seq
- GSM8705134 Adult_cortex, HET, CTCF, rep1, ChIP-seq
- GSM8705135 Adult_cortex, HET, CTCF, rep2, ChIP-seq
- GSM8705136 Adult_cortex, WT, RAD21, rep1, ChIP-seq
- GSM8705137 Adult_cortex, WT, RAD21, rep2, ChIP-seq
- GSM8705138 Adult_cortex, HET, RAD21, rep1, ChIP-seq
- GSM8705139 Adult_cortex, HET, RAD21, rep2, ChIP-seq
- GSM8705140 N2A, WT, CTCF, rep1, ChIP-seq
- GSM8705141 N2A, WT, CTCF, rep2, ChIP-seq
- GSM8705142 N2A, ADA-Clone1, CTCF, rep1, ChIP-seq
- GSM8705143 N2A, ADA-Clone1, CTCF, rep2, ChIP-seq
- GSM8705144 N2A, ADA-Clone2, CTCF, rep1, ChIP-seq
- GSM8705145 N2A, ADA-Clone2, CTCF, rep2, ChIP-seq
- GSM8705146 N2A, WT, RAD21, rep1, ChIP-seq
- GSM8705147 N2A, WT, RAD21, rep2, ChIP-seq
- GSM8705148 N2A, ADA-Clone1, RAD21, rep1, ChIP-seq
- GSM8705149 N2A, ADA-Clone1, RAD21, rep2, ChIP-seq
- GSM8705150 N2A, ADA-Clone2, RAD21, rep1, ChIP-seq
- GSM8705151 N2A, ADA-Clone2, RAD21, rep2, ChIP-seq
- GSE285577 CCCTC-binding Factor N-terminal Domain Regulates Clustered Protocadherin Gene Expression by Enhancing Cohesin Processivity [RNA-Seq] 47 samples shares protocadherin, processivity, n-terminal, clustered, enhancing, cohesin
- GSE277289 Cohesin-mediated chromatin remodeling controls the differentiation and function of conventional dendritic cells (RAD21 and CTCF ChIP-seq of Hoxb8-FL differentiation) 9 samples shares ctcf, chip-seq, cohesin
- GSE249430 Cohesin trajectories shape the epigenetic and transcriptional landscape of clustered Protocadherin genes for single neuron identities 80 samples shares protocadherin, clustered, cohesin
- GSE287375 CTCF-RNA interactions orchestrate cell-specific chromatin loop organization [ChIP-seq] 54 samples shares ctcf, chip-seq
- 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, chip-seq
- GSE270620 Binding domain mutations provide insight into CTCF's relationship with chromatin and its contribution to gene regulation (chip-seq) 48 samples shares ctcf, chip-seq
- GSE243710 Analysis of three-dimensional enhancer network regulated by CTCF in CD4+ T cells [ChIP-seq] 33 samples shares ctcf, chip-seq
- GSE234273 Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF [ChIP-seq] 32 samples shares ctcf, chip-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.