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Genome wide expression analysis of high passage growth arrested BJ fibroblasts maintained or withdrawn from rapamycin maintenance, in the presence or absence of various SMAD2/3 regulating molecules

GSE146579 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2025/05/30 Platform GPL16791
At a glance

RNA-seq (gene expression) · human · 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
Homo sapiens (human)
Samples
24 samples: 24 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 grown in the presence of rapamycin until reaching growth arrest at high passages, at which point cells were maintained in or withdrawn from rapamycin, while also being treated with control or SMAD2/3 regulating ligands. RNA was then harvested for RNA-seq
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 GSE146579 in finder → Find more human 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 GSE146579_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 PRJNA610886 and SRA study SRP251909. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40493192) ↗
Study design
24 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 24 sample titles: 24 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

Search all human RNA-seq datasets in GEO →

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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.