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Developmental dynamics of the cortical cellular and molecular landscapes in autism spectrum disorder models

GSE328363 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 135 samples Submitted 2026/06/16 Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 135 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
135 samples: 135 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
Cortical development dynamics across autism spectrum disorder mouse modelsNature · 2026
Summary (written by the submitters)
Recent research has identified over 100 causal genes in autism spectrum disorder (ASD), raising the question of how mutations in genes with diverse functions result in similar clinical presentations. Here, we profiled 251 samples from eleven monogenic ASD mouse models using single-nucleus multi-omic sequencing across three developmental stages, both sexes, and two brain regions.
Read the full summary ↓
We discovered that, despite wide genetic heterogeneity, ASD-linked mutations converged on perturbations of the radial glial cell lineage. This converging alteration primarily reflects a transient developmental delay rather than a lasting lineage misspecification and resolves by postnatal stages. Molecularly, the largest transcriptional differences emerged in neurons at early postnatal stages. These changes included downregulation of synaptic and ion channel-related genes, consistent with homeostatic adaptation or delayed maturation. Network analysis indicated that molecular convergence is strong across models within each developmental stage, suggesting that diverse ASD mutations impinge on common, stage-specific processes. Convergence becomes less pronounced by postnatal day 14, highlighting the dynamic nature of ASD-associated changes. Cross-genotype heterogeneity is superimposed on stage-specific effects. Electrophysiology corroborated this pattern: mutants generally showed altered neuronal excitability and synaptic properties with model-specific nuances. Our study also highlighted sex-specific gene expression alterations, with females often displaying larger effect sizes than males. Altogether, our findings provide a comprehensive view of the developmental cellular and molecular dynamics across ASD models.
Published in
Cortical development dynamics across autism spectrum disorder mouse models
Schwarz LA, Dotter CP, Isaev S et al. · Nature 2026 · PMID 42310454 · doi:10.1038/s41586-026-10679-1
This dataset
Open GSE328363 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 GSE328363_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 PRJNA1454847 and SRA study SRP692757. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42310454) ↗
Study design
135 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 135 sample titles: 135 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

+ 95 more — browse all 135 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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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.