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Transcriptional programs of cell identity and p53-induced stress responses are associated with distinctive features of spatial genome organization [ChIP-seq]

GSE278977 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 80 samples Submitted 2025/07/10 Platform GPL20301
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 80 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
Homo sapiens (human)
Samples
80 samples: 40 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
Transcriptional programs of cell identity and p53-induced stress responses are associated with distinctive features of spatial genome organizationNucleic acids research · 2025
Summary (written by the submitters)
To date, most studies explored changes in 3D-genome organization between different tissues or during differentiation, which involve massive reprogramming of transcriptional programs. Much fewer studies examined alterations in genome organization in response to cellular stress, which involves less pervasive transcriptional modulation. Here, we examined associations between spatial chromatin organization and gene expression in two different biological contexts: transcriptional programs determining cell identity and transcriptional responses to stress, using p53 activation as a model.
Read the full summary ↓
We selected 10 cell lines of diverse tissues, and in each performed micro-C, RNA-seq, and p53 ChIP-seq, before and after p53 induction. In the comparison between cell types, we delineated marked correlations between gene expression and spatial genome organization and identified hundreds of active enhancer-promoter loops associated with the expression of cell-type marker genes. In contrast, within each cell type, no such links were observed for expression changes induced by p53 activation, even for enhancers and promoters activated by p53 binding. Our analysis points to a fundamental difference between chromatin interactions that define cell identity and those that are established in response to cellular stress. Our results on p53-induced transcriptional responses support the recently proposed TF activity gradient model, which speculated a contact-independent mechanism for enhancer-promoter communication.
Published in
Transcriptional programs of cell identity and p53-induced stress responses are associated with distinctive features of spatial genome organization
Shanel G, Hsieh TS, Cattoglio C et al. · Nucleic acids research 2025 · PMID 40626558 · doi:10.1093/nar/gkaf607
This dataset
Open GSE278977 in finder → Find more human 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 GSE278977_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 PRJNA1133054 and SRA study SRP518559. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40626558) ↗
Study design
40 conditions, mostly in duplicate
A549_CTRL_input ×2 A549_CTRL_p53 ×2 A549_NUT_input ×2 A549_NUT_p53 ×2 GM12878_CTRL_input ×2 GM12878_CTRL_p53 ×2 GM12878_NUT_input ×2 GM12878_NUT_p53 ×2 +32 more

Supports a between-group comparison across 80 samples.

How we read this: 40 replicated groups read from 80 sample titles; they account for 80 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

+ 40 more — browse all 80 samples with per-sample file links →

Datasets on a similar topic

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