← BioTransfer GEO Dataset Finder
GEO series

CTCF-RNA interactions orchestrate cell-specific chromatin loop organization [ChIP-seq]

GSE287375 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 54 samples Submitted 2025/03/19 Platform GPL34328
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 54 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
54 samples: 21 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-RNA interactions orchestrate cell-specific chromatin loop organizationbioRxiv : the preprint server for biology · 2025
Summary (written by the submitters)
CCCTC-binding factor (CTCF) is essential for chromatin organization, but its role in dynamically shaping chromatin loops during cellular differentiation is not fully understood. We previously demonstrated that CTCF interacts with endogenous RNAs, and deletion of its ZF1 RNA-binding region disrupts chromatin loops in mouse embryonic stem cells (ESCs).
Read the full summary ↓
Using an ESC-to-neural progenitor cell (NPC) differentiation model, we show that the ZF1 RNA-binding region of CTCF is crucial for maintaining cell-type specific chromatin loops. Expression of CTCF-∆ZF1 leads to dysregulation of genes within these disrupted loops, particularly those involved in neuronal development and function. We identified NPC-specific, CTCF-interacting RNAs and chose Podxl and Grb10 for further study. We found that CRISPR-Cas9-mediated truncation of Podxl and Grb10 disrupts chromatin loops in cis, similar to the disruption seen in the NPC-∆ZF1 mutant. Our study underscores the importance of CTCF-ZF1 RNA interactions in preserving cell-specific genome structure and cellular identity.
Published in
CTCF-RNA interactions orchestrate cell-specific chromatin loop organization
Lucero K, Han S, Huang PY et al. · bioRxiv : the preprint server for biology 2025 · PMID 40166279 · doi:10.1101/2025.03.19.643339
This dataset
Open GSE287375 in finder → Find more mouse ChIP / ATAC / CUT&Tag datasets →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE287375_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA1212515 and SRA study SRP558248. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40166279) ↗
Study design
21 conditions, mostly in duplicate
CTCF ChIP, ESC, CTCF-WT rescue, ×4 CTCF ChIP, ESC, CTCF-ZF1 mutant rescue, ×4 CTCF ChIP, NPC, CTCF-WT rescue, ×4 CTCF ChIP, NPC, CTCF-ZF1 mutant rescue, ×4 Input, ESC, CTCF-WT rescue, ×4 Input, NPC, CTCF-WT rescue, ×4 Rad21 ChIP, ESC, CTCF-WT rescue, ×2 Rad21 ChIP, ESC, CTCF-ZF1 mutant rescue, ×2 +13 more

Supports a case/control comparison: 24 samples read as cases, 6 as controls.

How we read this: 21 replicated groups read from 54 sample titles; they account for 54 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.

Samples in this study

+ 14 more — browse all 54 samples with per-sample file links →

Datasets on a similar topic

Search all mouse ChIP / ATAC / CUT&Tag datasets in GEO →

Share this dataset

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.