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Genome wide mapping of the effect of SMAD2/3 regulating treatments upon the epigenomic landscape in high passage growth arrested cells being withdrawn from rapamycin

GSE146568 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 33 samples Submitted 2025/05/30 Platform GPL16791
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 33 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
33 samples: 33 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
Ligand-specific regulation of a binary enhancer code dictating cellular senescenceProceedings of the National Academy of Sciences of the United States of America · 2025
Summary (written by the submitters)
BJ Fibroblasts were maintained in rapamycin and were passaged until reaching growth arrest at very high passages. These cells were then maintained in or withdrawn from rapamycin, during which time they were given either control treatments or treatments with factors regulating SMAD2/3 activity.
Published in
Ligand-specific regulation of a binary enhancer code dictating cellular senescence
Suter T, Friedman MJ, Tazearslan C et al. · Proceedings of the National Academy of Sciences of the United States of America 2025 · PMID 40493192 · doi:10.1073/pnas.2506321122
This dataset
Open GSE146568 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 GSE146568_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 PRJNA610866 and SRA study SRP251897. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40493192) ↗
Study design
33 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 33 sample titles: 33 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
Datasets on a similar topic

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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.