GEO series

CPSF73 activation and 3’ Pol II pausing are lost during read-through transcription after heat shock [RNA-seq]

GSE303856 Homo sapiens (human) RNA-seq (gene expression) 14 samples Submitted 2026/02/04 Platform GPL34281Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 14 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: 14 samples: 6 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: CPSF73 activation and 3' RNA polymerase II pausing are lost during readthrough transcription after heat shockCell reports · 2026

Summary (written by the submitters)

Multiple types of cellular stress induce RNA polymerase II (Pol II) to read through normal termination sites at mRNA genes, causing long downstream regions to be transcribed. We observed strong read-through transcription downstream of thousands of genes after heat shock. Additionally, the 3’ Pol II pause that normally occurs during termination was globally lost.

Read the full summary ↓

Heat shock also increased phosphorylation of Tyr1 and Ser2 residues in the Pol II C-terminal domain (CTD) at the 3’ ends of genes, with smaller increases observed at genes with read-through transcription. We found that 3’ RNA cleavage, a key step of transcription termination, was defective at read-through genes after heat shock; however, the CPSF73 endonuclease responsible for cleavage remained at the 3’ ends of genes. Over-expressing an activator of CPSF73 activity, RBBP6, during heat shock rescued the loss of cleavage and attenuated read-through transcription. Our data suggest that heat shock alters Pol II speed, CTD phosphorylation, and CPSF73 activity via RBBP6, contributing to a multifaceted mechanism that enables transcription to continue far downstream of normal termination sites during cellular stress.

Published in

CPSF73 activation and 3' RNA polymerase II pausing are lost during readthrough transcription after heat shock

Walsh KE, Goodrich JA, Kugel JF · Cell reports 2026 · PMID 41758649 · doi:10.1016/j.celrep.2026.117039

This dataset

Open GSE303856 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 GSE303856_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 PRJNA1297775 and SRA study SRP604061. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41758649) ↗

Study design

6 conditions, mostly in duplicate

no heat shock, 4sU RNA-seq, ×3 heat shock, 4sU RNA-seq, ×3 no heat shock, -Dox ctl, 4sU RNA-seq, ×2 no heat shock, +Dox N-RBBP6 exp, 4sU RNA-seq, ×2 heat shock, -Dox ctl, 4sU RNA-seq, ×2 heat shock, +Dox N-RBBP6 exp, 4sU RNA-seq, ×2

Supports a between-group comparison across 14 samples.

How we read this: 6 replicated groups read from 14 sample titles; they account for 14 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

GSM9137012 no heat shock, 4sU RNA-seq, R1 no heat shock, 4sU RNA-…
GSM9137013 heat shock, 4sU RNA-seq, R1 heat shock, 4sU RNA-seq,
GSM9137014 no heat shock, 4sU RNA-seq, R2 no heat shock, 4sU RNA-…
GSM9137015 heat shock, 4sU RNA-seq, R2 heat shock, 4sU RNA-seq,
GSM9137016 no heat shock, 4sU RNA-seq, R3 no heat shock, 4sU RNA-…
GSM9137017 heat shock, 4sU RNA-seq, R3 heat shock, 4sU RNA-seq,
GSM9137018 no heat shock, -Dox ctl, 4sU RNA-seq, R1 no heat shock, -Dox ctl…
GSM9137019 no heat shock, +Dox N-RBBP6 exp, 4sU RNA-seq, R1 no heat shock, +Dox N-R…
GSM9137020 heat shock, -Dox ctl, 4sU RNA-seq, R1 heat shock, -Dox ctl, 4…
GSM9137021 heat shock, +Dox N-RBBP6 exp, 4sU RNA-seq, R1 heat shock, +Dox N-RBBP…
GSM9137022 no heat shock, -Dox ctl, 4sU RNA-seq, R2 no heat shock, -Dox ctl…
GSM9137023 no heat shock, +Dox N-RBBP6 exp, 4sU RNA-seq, R2 no heat shock, +Dox N-R…
GSM9137024 heat shock, -Dox ctl, 4sU RNA-seq, R2 heat shock, -Dox ctl, 4…
GSM9137025 heat shock, +Dox N-RBBP6 exp, 4sU RNA-seq, R2 heat shock, +Dox N-RBBP…

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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.