GEO series

HSF1 and YTHDC1 facilitate DNA damage repair upon heat stress by promoting the expressions of repair related genes

GSE291973 Homo sapiens (human) RNA-seq (gene expression) 10 samples Submitted 2026/05/05 Platform GPL24676Platform GPL29480

At a glance

RNA-seq (gene expression) · human · 10 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: 10 samples: 5 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: HSF1 and YTHDC1 enhance DNA repair under heat stress by promoting repair-associated gene expressionNucleic acids research · 2026

Summary (written by the submitters)

External stressors, especially heat stress, always lead to DNA damage and genome instability in cells. However, how cells rapidly response to these DNA damage remains largely unknown. In this study, we found that the major transcription factor in heat shock response, HSF1, activated several NHEJ pathway related genes, especially NHEJ1, through the puncta it formed, thereby promoting the NHEJ pathway, reducing the DNA double-strand break upon heat stress.

Read the full summary ↓

Furthermore, RNA m6A modification and its reader YTHDC1 were also found to play a role in this process, promoting the splicing of the NHEJ1 gene. Depletion of HSF1 or YTHDC1 led to increased nuclear γH2AX intensities in the heat shocked cells, which was rescued by overexpression of NHEJ1. Besides, overexpression of HSF1 or YTHDC1 both caused increased NHEJ pathway level in the heat shocked cells, indicating the HSF1/YTHDC1 – NHEJ1 – DNA double-strand repair axis. Our findings investigate an approach through which cells repair their damaged DNAs in the heat shock response, offering a new insight of how cells maintain a bare-minimum genome stability when exposed to external stressors.

Published in

HSF1 and YTHDC1 enhance DNA repair under heat stress by promoting repair-associated gene expression

Ding W, Deng Q, Wang T et al. · Nucleic acids research 2026 · PMID 42055551 · doi:10.1093/nar/gkag418

This dataset

Open GSE291973 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 GSE291973_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 PRJNA1236276 and SRA study SRP570508. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42055551) ↗

Study design

5 conditions, mostly in duplicate

U2OS cells, Total RNA-seq, shCtrl, NHS, ×2 U2OS cells, Total RNA-seq, shCtrl, HS, ×2 U2OS cells, Total RNA-seq, shYTHDC1, HS, ×2 U2OS cells, Total MeRIP-seq, WT, Input, ×2 U2OS cells, Total MeRIP-seq, WT, IP, ×2

Supports a between-group comparison across 10 samples.

How we read this: 5 replicated groups read from 10 sample titles; they account for 10 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

GSM8845931 U2OS cells, Total RNA-seq, shCtrl, NHS, rep1 U2OS cells, Total RNA-s…
GSM8845932 U2OS cells, Total RNA-seq, shCtrl, NHS, rep2 U2OS cells, Total RNA-s…
GSM8845933 U2OS cells, Total RNA-seq, shCtrl, HS, rep1 U2OS cells, Total RNA-s…
GSM8845934 U2OS cells, Total RNA-seq, shCtrl, HS, rep2 U2OS cells, Total RNA-s…
GSM8845935 U2OS cells, Total RNA-seq, shYTHDC1, HS, rep1 U2OS cells, Total RNA-s…
GSM8845936 U2OS cells, Total RNA-seq, shYTHDC1, HS, rep2 U2OS cells, Total RNA-s…
GSM8845937 U2OS cells, Total MeRIP-seq, WT, Input, rep1 U2OS cells, Total MeRIP…
GSM8845938 U2OS cells, Total MeRIP-seq, WT, Input, rep2 U2OS cells, Total MeRIP…
GSM8845939 U2OS cells, Total MeRIP-seq, WT, IP, rep1 U2OS cells, Total MeRIP…
GSM8845940 U2OS cells, Total MeRIP-seq, WT, IP, rep2 U2OS cells, Total MeRIP…

Datasets on a similar topic

GSE294470 NSUN2 Facilitates Dicer Cleavage of DNA Damage-Associated R-Loops to Promote Repair [ChIP-Seq] 12 samples shares facilitate, damage, repair
GSE283317 YTHDC1 cooperates with the THO complex to prevent RNA damage-induced DNA breaks 30 samples shares ythdc1, damage
GSE239333 YTHDC1 m6A-dependent and m6A-independent functions converge to preserve DNA damage response 21 samples shares ythdc1, damage
GSE251729 JMJD1C facilitates long distance genomic interactions by promoting condensates formation of key leukemic transcription factors in multiple AML cells 28 samples shares facilitate, promoting
GSE251726 JMJD1C facilitates long distance genomic interactions by promoting condensates formation of key leukemic transcription factors in multiple AML cells [ChIP-seq] 18 samples shares facilitate, promoting
GSE285696 High Mobility Group Box protein 3 (HMGB3) facilitates DNA interstrand crosslink processing and double-strand break repair in human cells 16 samples shares facilitate, repair
GSE288071 Sequential histone H1 N76/77 deamidation and K75 acetylation facilitate chromatin relaxation and genome stability by DNA repair 16 samples shares facilitate, repair
GSE288972 Limosilactobacillus reuteri-derived exopolysaccharides facilitate the repair of intestinal epithelium barrier compromised by chemotherapy exposure 15 samples shares facilitate, repair

Search all human RNA-seq datasets in GEO →

Share this dataset

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.