GEO series

CTCF is selectively required for maintaining chromatin accessibility and gene expression in human erythropoiesis [H2_HiC]

GSE201820 Homo sapiens (human) Other 8 samples Submitted 2025/01/27 Platform GPL24676

At a glance

human · 8 samples

Organism: Homo sapiens (human)
Samples: 8 samples: 8 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.
Paper: CTCF is selectively required for maintaining chromatin accessibility and gene expression in human erythropoiesisGenome biology · 2025

Summary (written by the submitters)

The three-dimensional chromatin niche provides a precise gene expression control of cell identity, differentiation, and disease development. CTCF is considered as the master transcription factor regulating chromatin architecture and gene expression. However, the genome-wide impact of CTCF has not been extensively investigated due to the lack of proper research tools.

Read the full summary ↓

Here, using a state-of-the-art auxin-inducible degron cellular model built up in human erythroid progenitors, we investigated the effects of acute CTCF loss on transcriptional programs and chromatin accessibility during human erythroid maturation. By integrating multi-omics datasets, we revealed that CTCF acute loss significantly disrupted genome-wide chromatin accessibility and transcription network. We further identified several direct novel target genes of CTCF in erythroid progenitor cells, including one master transcription factor GATA2 in hematopoiesis. Acute depletion of CTCF protein or disrupting CTCF binding sites in the topologically associated domains (TAD) boundary region of the GATA2 locus results in a significant transcriptional increase of GATA2. In summary, our results addressed a novel role of CTCF in regulating erythroid differentiation, which will undoubtedly extend our understanding of CTCF biology.

Published in

CTCF is selectively required for maintaining chromatin accessibility and gene expression in human erythropoiesis

Yang X, Cheng L, Xin Y et al. · Genome biology 2025 · PMID 40022213 · doi:10.1186/s13059-025-03510-z

This dataset

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Download · which file do I need?

Direct links to NCBI, 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.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE201820_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

Also filed as BioProject PRJNA833113. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40022213) ↗

Study design

8 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 8 sample titles: 8 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.

Samples in this study

GSM6072244 cloneC16noIAAdiff
GSM6072245 cloneC16noIAAundiff
GSM6072246 cloneC16withIAAdiff
GSM6072247 cloneC16withIAAundiff
GSM6072248 cloneC3noIAAdiff
GSM6072249 cloneC3noIAAundiff
GSM6072250 cloneC3withIAAdiff
GSM6072251 cloneC3withIAAundiff

Datasets on a similar topic

GSE201822 CTCF is selectively required for maintaining chromatin accessibility and gene expression in human erythropoiesis 60 samples shares ctcf, erythropoiesis, accessibility, selectively, maintaining, chromatin, required
GSE215328 Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [hESC_H9_d049_ChIP_Seq] 135 samples shares ctcf, maintaining, chromatin
GSE215323 Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [HEK293T_BPK25_ChIP_Seq] 53 samples shares ctcf, maintaining, chromatin
GSE278192 Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [HEK293T ChIP-seq] 45 samples shares ctcf, maintaining, chromatin
GSE253694 Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [HEK293T_siNURD_CTCF_ChIP_Seq] 36 samples shares ctcf, maintaining, chromatin
GSE253697 Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [HEK293T_siNURD_TET1_ChIP_Seq] 36 samples shares ctcf, maintaining, chromatin
GSE215326 Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [HEK293T_IAA72h_ChIP_Seq] 30 samples shares ctcf, maintaining, chromatin
GSE188175 Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [ChIP-Seq] 28 samples shares ctcf, maintaining, chromatin

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