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Comprehensive mass spectrometry screening-derived atlas of HDAC inhibitors revelas histone specific acetylation chnages [RNA-seq]

GSE308262 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2026/03/18 Platform GPL34284
At a glance

RNA-seq (gene expression) · human · 12 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
12 samples: 3 × HeLa cells, DMSO-control, 24h, biol vs 3 × HeLa cells, Entinostat-treatment, 24h, biol vs 3 × MDA-MB-231 cells, DMSO-control, 24h, vs 3 × MDA-MB-231 cells, Entinostat-treatment, 24h,Groups 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
Comprehensive mass spectrometry screening-derived atlas of HDAC inhibitors reveals histone-specific acetylation changesCell reports · 2026
Summary (written by the submitters)
Histone deacetylases inhibitors (HDACi) have emerged as valuable therapeutics in cancer and other diseases, yet their effect on histone post-translational modification remains incompletely characterized. Here, we applied quantitative mass spectrometry and high throughput sequencing to systematically profile site-specific histone modification changes in response to a panel of HDAC inhibitors.
Read the full summary ↓
This platform enabled mapping of histone modification changes across hundreds of sites including low abundant histone marks. Furthermore, integrative analysis of ChIP-seq and RNA-seq identified genome wide binding site for a low-abundant histone mark H2A.Z acetylation in HeLa cells and MDA-MB-231 breast cancer cells, highlighting the role of H2A.Z acetylation in regulating gene expression through various biological pathways and specific genes involved in tumor suppressor pathways. Our findings provide a functional resource for identification and quantification of epigenetic changes and transcriptional regulation of histone H2A.Z acetylation upon pharmacological perturbation
Published in
Comprehensive mass spectrometry screening-derived atlas of HDAC inhibitors reveals histone-specific acetylation changes
Karki R, Vitorino FNL, Searfoss RM et al. · Cell reports 2026 · PMID 42030158 · doi:10.1016/j.celrep.2026.117289
This dataset
Open GSE308262 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 GSE308262_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 PRJNA1329323 and SRA study SRP620871. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42030158) ↗
Study design
3 × HeLa cells, DMSO-control, 24h, biol vs 3 × HeLa cells, Entinostat-treatment, 24h, biol vs 3 × MDA-MB-231 cells, DMSO-control, 24h, vs 3 × MDA-MB-231 cells, Entinostat-treatment, 24h,

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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
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