GEO series

Binding domain mutations provide insight into CTCF's relationship with chromatin and its contribution to gene regulation (RNA-seq)

GSE270619 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2025/02/20 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 24 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Mus musculus (mouse)
Samples: 24 samples: 12 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

Summary (written by the submitters)

Although only a fraction of CTCF motifs are bound in any cell type, and approximately half of the occupied sites overlap cohesin, the mechanisms underlying cell-type specific attachment and ability to function as a chromatin organizer remain unknown. To investigate the relationship between CTCF and chromatin we applied a combination of imaging, structural and molecular approaches, using a series of brain and cancer associated CTCF mutations that act as CTCF perturbations.

Read the full summary ↓

We demonstrate that binding and the functional impact of WT and mutant CTCF depend not only on the unique properties of each protein, but also on the genomic context of bound sites. Our studies also highlight the reciprocal relationship between CTCF and chromatin, demonstrating that the unique binding properties of WT and mutant proteins have a distinct impact on accessibility, TF binding, cohesin overlap, chromatin interactivity and gene expression programs, providing insight into their cancer and brain related effects.

Published in

Binding domain mutations provide insight into CTCF's relationship with chromatin and its contribution to gene regulation

Do C, Jiang G, Cova G et al. · Cell genomics 2025 · PMID 40118069 · doi:10.1016/j.xgen.2025.100813

This dataset

Open GSE270619 in finder → Find more mouse RNA-seq 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 GSE270619_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1127578 and SRA study SRP515708. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40118069) ↗

Study design

12 conditions, mostly in duplicate

totalRNASeq_H455R_ID ×2 totalRNASeq_K365T_ID ×2 totalRNASeq_Q418R_ID ×2 totalRNASeq_R339Q_ID ×2 totalRNASeq_R342C_ID ×2 totalRNASeq_R377C_ID ×2 totalRNASeq_R377H_ID ×2 totalRNASeq_R448Q_ID ×2 +4 more

Supports a between-group comparison across 24 samples.

How we read this: 12 replicated groups read from 24 sample titles; they account for 24 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

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
GSM8782661 totalRNASeq_WT_UN_rep1 totalRNASeq_WT_UN
GSM8782662 totalRNASeq_WT_UN_rep2 totalRNASeq_WT_UN

Datasets on a similar topic

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
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
GSE234248 Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF [RNA-seq] 24 samples shares ctcf, rna-seq
GSE253691 Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [mESC_d0246_RNA_Seq] 12 samples shares ctcf, chromatin
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

Search all mouse RNA-seq 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.