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Single-nucleus RNA-seq atlas of 17 ASD-risk mouse lines under early-postnatal fluoxetine or lithium exposure (4-plex On-Chip Multiplexed)

GSE330728 Mus musculus (mouse) Single-nucleus RNA-seq 53 samples Submitted 2026/07/28 Platform GPL34328
At a glance

Single-nucleus RNA-seq · mouse · 53 samples

What it is
Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue).
Organism
Mus musculus (mouse)
Samples
53 samples: 53 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.
Summary (written by the submitters)
Autism spectrum disorder (ASD) involves more than 1,000 risk genes, complicating mechanistic subtyping. To resolve the cellular basis of transcriptomic stratification, we generated single-nucleus RNA-seq (snRNA-seq) profiles from the prefrontal cortex of 17 mouse lines carrying ASD-associated synaptic, chromatin-regulatory, and signaling mutations, together with C57BL/6J wild-type controls.
Read the full summary ↓
Both sexes were profiled under baseline and early-postnatal (P3-P25) fluoxetine or lithium exposure. Four mice were multiplexed per 10x Genomics GEM-X v4 4-plex On-Chip Multiplexing (OCM) library, yielding 53 sequencing libraries (tubes) covering 212 individual mice. After downstream QC, approximately 1,016,895 nuclei from 205 mice were retained at postnatal day 25.
This dataset
Open GSE330728 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 GSE330728_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1465349 and SRA study SRP699801. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
53 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 53 sample titles: 53 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

+ 13 more — browse all 53 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.