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Histone deacetylase inhibitors target regulators of DNA replication and the cellular response to DNA replication stress in Ewing sarcoma cells

GSE280573 Homo sapiens (human) RNA-seq (gene expression) 15 samples Submitted 2025/06/03 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 15 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)
Topic
Ewing sarcomaThis series is part of our curated briefing on it.
Samples
15 samples: 5 conditions, mostly in triplicateGroups 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
Histone Deacetylase Inhibitors Target DNA Replication Regulators and Replication Stress in Ewing Sarcoma CellsCancer research communications · 2025
Summary (written by the submitters)
DNA replication stress is common feature of multiple tumor types. Histone deacetylases (HDAC) regulate diverse pathways in cancer cells and recent work has identified that HDAC inhibitors downregulate the expression of multiple proteins with critical roles in DNA replication and the cellular response to DNA replication stress, including the RRM1 and RRM2 subunits of ribonucleotide reductase (RNR), CHK1, and WEE1. RNA-seq analysis was performed on a Ewing sarcoma cell line to determine the effects of HDAC inhibitors on the transcriptome.
Published in
Histone Deacetylase Inhibitors Target DNA Replication Regulators and Replication Stress in Ewing Sarcoma Cells
Koppenhafer SL, Geary EL, Thomas MV et al. · Cancer research communications 2025 · PMID 40478628 · doi:10.1158/2767-9764.CRC-25-0058
This dataset
Open GSE280573 in finder → Find more human RNA-seq datasets → Ewing sarcoma landscape →
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 GSE280573_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 PRJNA1179425 and SRA study SRP541813. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40478628) ↗
Study design
5 conditions, mostly in triplicate
EW8 cells, DMSO, biol ×3 EW8 cells, Romidepsin 2.5 nM, biol ×3 EW8 cells, Romidepsin 5 nM, biol ×3 EW8 cells, Panobinostat 5 nM, biol ×3 EW8 cells, Panobinostat 10 nM, biol ×3

Supports a between-group comparison across 15 samples.

How we read this: 5 replicated groups read from 15 sample titles; they account for 15 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
More Ewing sarcoma datasets

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.