GEO series

single-cell transcriptomic atlas of sensory-dependent gene expression in developing mouse visual cortex

GSE269482 Mus musculus (mouse) Single-cell RNA-seq 21 samples Submitted 2025/03/16 Platform GPL30172

At a glance

Single-cell RNA-seq · mouse · 21 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Mus musculus (mouse)
Samples: 21 samples: 6 conditions, mostly in triplicateGroups 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: A single-cell transcriptomic atlas of sensory-dependent gene expression in developing mouse visual cortexDevelopment (Cambridge, England) · 2025

Summary (written by the submitters)

Sensory experience drives the refinement and maturation of neural circuits during postnatal brain development through molecular mechanisms that remain to be fully elucidated. One likely mechanism involves the sensory-dependent expression of genes that encode mediators of circuit remodeling within developing cells. However, while studies in adult systems have begun to uncover crucial roles for sensory-induced genes in modifying circuit connectivity, the gene programs induced by brain cells in response to sensory experience during development remain to be fully characterized.

Read the full summary ↓

Here, we present a single-nucleus RNA-sequencing dataset describing the transcriptional responses of cells in mouse visual cortex to sensory deprivation or acute sensory stimulation during a developmental window when visual input is necessary for circuit refinement. We sequenced 118,529 individual nuclei across sixteen neuronal and non-neuronal cortical cell types isolated from control, sensory deprived, and sensory stimulated mice, identifying over 1268 unique sensory-induced genes within the dataset. To demonstrate the utility of this resource, we compared the architecture and ontology of sensory-induced gene programs between cell types, annotated transcriptional induction and repression events based upon RNA velocity, and discovered Neurexin and Neuregulin signaling networks that underlie cell-cell interactions in visual cortex. We find that excitatory neurons, especially pyramidal neurons in cortical layers two and three, are highly sensitive to sensory stimulation, and that the sensory-induced genes in these cells are poised to strengthen synapse-to-nucleus crosstalk by heightening protein serine/threonine kinase activity. Altogether, we expect this dataset to significantly broaden our understanding of the molecular mechanisms through which sensory experience shapes neural circuit wiring in the developing brain.

Published in

A single-cell transcriptomic atlas of sensory-dependent gene expression in developing mouse visual cortex

Xavier AM, Lin Q, Kang CJ et al. · Development (Cambridge, England) 2025 · PMID 40018816 · doi:10.1242/dev.204244

This dataset

Open GSE269482 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 GSE269482_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 PRJNA1114049 and SRA study SRP508943. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40018816) ↗

Study design

6 conditions, mostly in triplicate

P27 ×6 LDR0 ×3 LDR30 ×3 LDR2 ×3 LDR4 ×3 LDR6 ×3

Supports a between-group comparison across 21 samples.

How we read this: 6 replicated groups read from 21 sample titles; they account for 21 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

GSM8316309 P27_Biorep1 P27
GSM8316310 P27_Biorep2 P27
GSM8316311 P27_Biorep3 P27
GSM8316312 P27_Biorep4 P27
GSM8316313 P27_Biorep5 P27
GSM8316314 P27_Biorep6 P27
GSM8316315 LDR0_Biorep1 LDR0
GSM8316316 LDR0_Biorep2 LDR0
GSM8316317 LDR0_Biorep3 LDR0
GSM8316318 LDR30_Biorep1 LDR30
GSM8316319 LDR30_Biorep2 LDR30
GSM8316320 LDR30_Biorep3 LDR30
GSM8316321 LDR2_Biorep1 LDR2
GSM8316322 LDR2_Biorep2 LDR2
GSM8316323 LDR2_Biorep3 LDR2
GSM8316324 LDR4_Biorep1 LDR4
GSM8316325 LDR4_Biorep2 LDR4
GSM8316326 LDR4_Biorep3 LDR4
GSM8316327 LDR6_Biorep1 LDR6
GSM8316328 LDR6_Biorep2 LDR6
GSM8316329 LDR6_Biorep3 LDR6

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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.