GEO series

Developmental gene expression patterns driving species-specific cortical features

GSE324846 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 17 samples Submitted 2026/03/18 Platform GPL24247Platform GPL24676

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 17 samples

What it is: ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism: Mus musculus (mouse)
Samples: 17 samples: 17 samples, each with a distinct title — no replicated groupsGroups 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: Developmental gene expression patterns driving species-specific cortical featuresNature · 2026

Summary (written by the submitters)

The cerebral cortex shows species-specific variations in size and organization, likely accounting for distinct behavioral abilities. These structural differences may reflect evolutionary changes in the developmental expression of shared genes. To investigate this possibility, we used machine vision to identify and compare cell-type-specific gene expression patterns in the developing mouse and human neocortex, and in human cortical organoids.

Read the full summary ↓

This identified genes with evolutionary conserved/divergent transcriptional regulation, revealing species-specific cyto-temporal gene expression patterns. Among such genes, the transcription factor JUNB showed mutually exclusive expression in human progenitors and mouse neurons. Through cell-type-specific gain- and loss-of-function experiments in mice and human organoids, we show that JUNB bidirectionally controls human cortical features, including progenitor proliferation rates, neuronal production timing, and total neuronal output. We identify IRF1 as a human RG-specific regulator that, when expressed in mouse RG, activates JUNB and recruits human-like gene regulatory networks, demonstrating cross-species activation of poised developmental programs. Together, these findings reveal how cyto-temporal regulation of shared genes drives species-specific cortical features and provides a molecular framework to understand and manipulate these evolutionary programs.

Published in

Developmental gene expression patterns driving species-specific cortical features

Javed A, Gómez L, Pravata V et al. · Nature 2026 · PMID 42129570 · doi:10.1038/s41586-026-10491-x

This dataset

Open GSE324846 in finder → Find more 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 GSE324846_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1437161 and SRA study SRP683562. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42129570) ↗

Study design

17 samples, each with a distinct title — no replicated groups

Supports a case/control comparison: 7 samples read as cases, 5 as controls.

How we read this: Read from 17 sample titles: 17 distinct titles with little repetition. 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

GSM9587288 P0 mouse cortex, Control, single cell RNA-seq
GSM9587289 P0 mouse cortex, JUNB overexpression, single cell RNA-seq
GSM9587290 P0 mouse cortex, Control, Trackerseq
GSM9587291 P0 mouse cortex, JUNB overexpression, Trackerseq
GSM9587292 E15+24h mouse cortex, Control, single nucleus RNA-seq
GSM9587293 E15+24h mouse cortex, JUNB overexpression, single nucleus RNA-seq
GSM9587294 E15+24h mouse cortex, Control, single cell RNA-seq
GSM9587295 E15+24h mouse cortex, IRF1 overexpression, single cell RNA-seq
GSM9587296 E15+24h mouse cortex, EGR1 overexpression, single cell RNA-seq
GSM9587297 E15+24h mouse cortex, IRF1+EGR1 overexpression, single cell RNA-seq
GSM9587298 E15+24h mouse cortex, Control, CUT&Tag, H3K27ac
GSM9587299 E15+24h mouse cortex, JUNB overexpression, CUT&Tag H3K27ac
GSM9587300 Day 40 human iPSC derived organoids, ,CUT&Tag, Rabbit IgG
GSM9587301 Day 40 human iPSC derived organoids, ,CUT&Tag, Junb
GSM9587302 Day 40 human iPSC derived organoids, ,CUT&RUN, Rabbit IgG
GSM9587303 Day 40 human iPSC derived organoids, ,CUT&RUN, Irf1
GSM9587304 Day 40 human iPSC derived organoids, ,CUT&RUN, H3K4me3

Datasets on a similar topic

GSE253852 Human and mouse adrenal glands are characterized by species-specific steroidogenic states and tissue turnover 31 samples shares species-specific
GSE270069 Species-specific progenitor domain extends neurogenesis and increases motor neuron production 3 samples shares species-specific
GSE289305 Alterations in chromatin architecture promote totipotent-like features in a DUX-dependent manner [RNA-Seq] 27 samples shares features
GSE245373 Mice are not men: scRNA-sequencing of the human atherosclerotic plaque identifies species-specific immune cell phenotypes that associate with clinical disease 11 samples shares species-specific
GSE276321 Chromodomain protein CDYL confers forebrain identity to human cortical organoids by inhibiting neuronatin [ChIP-seq] 9 samples shares cortical

Search all 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.