GEO series

DNA replication fork speed Acts as A Pacer in Cortical Neurogenesis

GSE279962 Mus musculus (mouse) RNA-seq (gene expression) 22 samples Submitted 2025/09/27 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 22 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: Mus musculus (mouse)
Samples: 22 samples: 6 × ctrl vs 6 × cko vs 5 × dko vs 3 × ctrldGroups 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: DNA replication fork speed acts as a pacer in cortical neurogenesisNature communications · 2025

Summary (written by the submitters)

DNA replication fork speed, which controls the rate of genome duplication, has emerged as a key regulator of cellular plasticity. However, its role in neurogenesis remains unexplored. Mini-chromosome maintenance complex (MCMs)-binding protein (MCMBP) functions as a chaperone for newly synthesized MCMs, increasing chromatin coverage to restrain fork speed.

Read the full summary ↓

We demonstrate that selective deletion of MCMBP in neural progenitor radial glial cells (RGCs) accelerates fork speed, triggering widespread apoptosis, DNA damage, and micronuclei formation, ultimately activating p53 and causing microcephaly. Unexpectedly, concurrent deletion of Trp53 and Mcmbp further increased fork speed, leading to extensive RGC detachment from the ventricular zone and acquisition of outer-RGC characteristics. Mechanistically, we found that the MCM3 subunit coordinates DNA and centrosome duplication, thereby mediating RGC attachment. Behavioral analysis revealed that disruption of fork speed results in anxiety-like behavior in mice. These findings unveil a previously unrecognized role for replication fork speed in neurogenesis.

Published in

DNA replication fork speed acts as a pacer in cortical neurogenesis

Wang J, Kong Y, Li X et al. · Nature communications 2025 · PMID 41253827 · doi:10.1038/s41467-025-65269-y

This dataset

Open GSE279962 in finder → Find more mouse 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 GSE279962_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 PRJNA1175628 and SRA study SRP539892. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41253827) ↗

Study design

6 × ctrl vs 6 × cko vs 5 × dko vs 3 × ctrld

Supports a between-group comparison across 20 samples.

How we read this: 4 replicated groups read from 22 sample titles; they account for 20 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

GSM8584210 ctrl54 ctrl
GSM8584211 ctrl57 ctrl
GSM8584212 ctrl59 ctrl
GSM8584213 ctrl510 ctrl
GSM8584214 ctrl65 ctrl
GSM8584215 ctrl67 ctrl
GSM8584216 ctrld1 ctrld
GSM8584217 ctrld2 ctrld
GSM8584218 ctrld3 ctrld
GSM8584219 cko51 cko
GSM8584220 cko56 cko
GSM8584221 cko58 cko
GSM8584222 cko61 cko
GSM8584223 cko64 cko
GSM8584224 cko66 cko
GSM8584225 dko1 dko
GSM8584226 dko2 dko
GSM8584227 dko3 dko
GSM8584228 dko4 dko
GSM8584229 dko5 dko
GSM8783537 Ctrl
GSM8783538 dKO

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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.