GEO series

Global stabilization of the transcriptome in mitotic cells [RNA-Seq]

GSE314020 Homo sapiens (human) RNA-seq (gene expression) 48 samples Submitted 2025/12/23 Platform GPL34295Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 48 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: 48 samples: 15 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: Global stabilization of the transcriptome in mitotic cellsThe EMBO journal · 2026

Summary (written by the submitters)

In the presence of cell division errors, mammalian cells can pause in mitosis for tens of hours with little to no transcription, while still requiring continued translation for viability. These unique aspects of mitosis require substantial adaptations to the core gene expression programs. During interphase, the homeostatic control of mRNA levels involves a constant balance of transcription and degradation, with a median mRNA half-life of ~2–4 hours.

Read the full summary ↓

If such short mRNA half-lives persisted in mitosis, cells would be expected to rapidly deplete their transcriptome in the absence of new transcription. Here, we report that the transcriptome is globally stabilized during prolonged mitotic delays. Median mRNA half-lives are increased >4-fold in mitosis compared to interphase, thereby buffering mRNA levels in the absence of new synthesis. Moreover, the poly(A)-tail-length profile of mRNAs changes in mitosis, strongly suggesting a partial mitotic repression of deadenylation. In contrast, the machinery required for siRNA-mediated mRNA degradation remains active. We further show that mitotic mRNA stabilization is dependent on cytoplasmic poly(A)-binding proteins PABPC1&4. Depletion of PABPC1&4 and consequently reduced mRNA stability disrupts the maintenance of mitotic arrest, highlighting the critical physiological role of mitotic transcriptome buffering.

Published in

Global stabilization of the transcriptome in mitotic cells

Khalizeva E, Latifkar A, Xiang K et al. · The EMBO journal 2026 · PMID 41957211 · doi:10.1038/s44318-026-00765-5

This dataset

Open GSE314020 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 GSE314020_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 PRJNA1389473 and SRA study SRP655781. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41957211) ↗

Study design

15 conditions, mostly in duplicate

HeLa, STLC 0 h, ×2 HeLa, STLC 6 h, ×2 HeLa, STLC 24 h, ×2 HeLa, RO3306, actD, 0 h, ×2 HeLa, RO3306, actD, 1 h, ×2 HeLa, RO3306, actD, 3 h, ×2 HeLa, RO3306, actD, 6 h, ×2 HeLa, STLC, actD, 0 h, ×2 +25 more

Supports a between-group comparison across 30 samples.

How we read this: 15 replicated groups read from 48 sample titles; they account for 30 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

GSM9380025 HeLa, STLC 0 h, bio rep 1 HeLa, STLC 0 h,
GSM9380026 HeLa, STLC 0 h, bio rep 2 HeLa, STLC 0 h,
GSM9380027 HeLa, STLC 6 h, bio rep 1 HeLa, STLC 6 h,
GSM9380028 HeLa, STLC 6 h, bio rep 2 HeLa, STLC 6 h,
GSM9380029 HeLa, STLC 24 h, bio rep 1 HeLa, STLC 24 h,
GSM9380030 HeLa, STLC 24 h, bio rep 2 HeLa, STLC 24 h,
GSM9380031 HeLa, RO3306, actD, 0 h, bio rep 1 HeLa, RO3306, actD, 0 h,
GSM9380032 HeLa, RO3306, actD, 0 h, bio rep 2 HeLa, RO3306, actD, 0 h,
GSM9380033 HeLa, RO3306, actD, 1 h, bio rep 1 HeLa, RO3306, actD, 1 h,
GSM9380034 HeLa, RO3306, actD, 1 h, bio rep 2 HeLa, RO3306, actD, 1 h,
GSM9380035 HeLa, RO3306, actD, 3 h, bio rep 1 HeLa, RO3306, actD, 3 h,
GSM9380036 HeLa, RO3306, actD, 3 h, bio rep 2 HeLa, RO3306, actD, 3 h,
GSM9380037 HeLa, RO3306, actD, 6 h, bio rep 1 HeLa, RO3306, actD, 6 h,
GSM9380038 HeLa, RO3306, actD, 6 h, bio rep 2 HeLa, RO3306, actD, 6 h,
GSM9380039 HeLa, STLC, actD, 0 h, bio rep 1 HeLa, STLC, actD, 0 h,
GSM9380040 HeLa, STLC, actD, 0 h, bio rep 2 HeLa, STLC, actD, 0 h,
GSM9380041 HeLa, STLC, actD, 1 h, bio rep 1 HeLa, STLC, actD, 1 h,
GSM9380042 HeLa, STLC, actD, 1 h, bio rep 2 HeLa, STLC, actD, 1 h,
GSM9380043 HeLa, STLC, actD, 3 h, bio rep 1 HeLa, STLC, actD, 3 h,
GSM9380044 HeLa, STLC, actD, 3 h, bio rep 2 HeLa, STLC, actD, 3 h,
GSM9380045 HeLa, STLC, actD, 6 h, bio rep 1 HeLa, STLC, actD, 6 h,
GSM9380046 HeLa, STLC, actD, 6 h, bio rep 2 HeLa, STLC, actD, 6 h,
GSM9380047 HeLa, RO3306, THZ1, 0 h
GSM9380048 HeLa, RO3306, THZ1, 1 h
GSM9380049 HeLa, RO3306, THZ1, 2 h
GSM9380050 HeLa, RO3306, THZ1, 4 h
GSM9380051 HeLa, RO3306, THZ1, 6 h
GSM9380052 HeLa, STLC, THZ1, 0 h
GSM9380053 HeLa, STLC, THZ1, 1 h
GSM9380054 HeLa, STLC, THZ1, 2 h
GSM9380055 HeLa, STLC, THZ1, 4 h
GSM9380056 HeLa, STLC, THZ1, 6 h
GSM9380057 HeLa, G1, actD, 0 h
GSM9380058 HeLa, G1, actD, 1 h
GSM9380059 HeLa, G1, actD, 3 h
GSM9380060 HeLa, G1, actD, 6 h
GSM9380061 HeLa, M, actD, 0 h
GSM9380062 HeLa, M, actD, 1 h
GSM9380063 HeLa, M, actD, 3 h
GSM9380064 HeLa, M, actD, 6 h

+ 8 more — browse all 48 samples with per-sample file links →

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