GEO series

Splice isoform-perturbation coupled to single cell transcriptome profiling reveals functions of microexons in neurogenesis and autism-linked pathways [snRNA-Seq]

GSE291610 Mus musculus (mouse) Single-nucleus RNA-seq 96 samples Submitted 2025/11/28 Platform GPL24247

At a glance

Single-nucleus RNA-seq · mouse · 96 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: 96 samples: 8 conditions, mostly with about 12 replicates eachGroups 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: Splice isoform-perturbation coupled to single cell transcriptome profiling reveals functions of microexons in neurogenesis and autism-linked pathwaysNature communications · 2026

Summary (written by the submitters)

A major challenge of biomedical research is to assign functions to the myriad alternative RNA and protein isoforms. This challenge is particularly relevant to the mammalian nervous system, which produces complex repertoires of alternative splicing events. Here, we describe CHyMErA-seq, a platform that couples systematic deletion of exons to a single cell transcriptomics read-out, and apply this method to investigate a critical program of brain-specific microexons.

Read the full summary ↓

Perturbation of microexons during neurogenesis reveals convergent roles in the temporal regulation of gene expression programs that direct signalling pathways and morphogenesis. We further observe microexons, including those in the Bin1, Clasp1, Gfra1, Med23, Ptprf and Ralgapb genes, that are required for the correct timing of autism-linked gene expression. Collectively, we describe a flexible system for isoform-resolution perturbation at a single cell level, together with insights into the roles of microexons in the developmental timing of neurogenesis transcriptomic signatures linked to brain disorders.

Published in

Splice isoform-perturbation coupled to single cell transcriptome profiling reveals functions of microexons in neurogenesis and autism-linked pathways

Dupas SJ, Parada GE, Li JD et al. · Nature communications 2026 · PMID 41633977 · doi:10.1038/s41467-025-67931-x

This dataset

Open GSE291610 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 GSE291610_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 PRJNA1234491 and SRA study SRP569523. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41633977) ↗

Study design

8 conditions, mostly with about 12 replicates each

P1-A ×12 P1-B ×12 P1-C ×12 P1-D ×12 P1-E ×12 P1-F ×12 P1-G ×12 P1-H ×12

Supports a between-group comparison across 96 samples.

How we read this: 8 replicated groups read from 96 sample titles; they account for 96 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

GSM8838435 P1-A01 P1-A
GSM8838436 P1-A02 P1-A
GSM8838437 P1-A03 P1-A
GSM8838438 P1-A04 P1-A
GSM8838439 P1-A05 P1-A
GSM8838440 P1-A06 P1-A
GSM8838441 P1-A07 P1-A
GSM8838442 P1-A08 P1-A
GSM8838443 P1-A09 P1-A
GSM8838444 P1-A10 P1-A
GSM8838445 P1-A11 P1-A
GSM8838446 P1-A12 P1-A
GSM8838447 P1-B01 P1-B
GSM8838448 P1-B02 P1-B
GSM8838449 P1-B03 P1-B
GSM8838450 P1-B04 P1-B
GSM8838451 P1-B05 P1-B
GSM8838452 P1-B06 P1-B
GSM8838453 P1-B07 P1-B
GSM8838454 P1-B08 P1-B
GSM8838455 P1-B09 P1-B
GSM8838456 P1-B10 P1-B
GSM8838457 P1-B11 P1-B
GSM8838458 P1-B12 P1-B
GSM8838459 P1-C01 P1-C
GSM8838460 P1-C02 P1-C
GSM8838461 P1-C03 P1-C
GSM8838462 P1-C04 P1-C
GSM8838468 P1-C05 P1-C
GSM8838476 P1-C06 P1-C
GSM8838477 P1-C07 P1-C
GSM8838478 P1-C08 P1-C
GSM8838479 P1-C09 P1-C
GSM8838480 P1-C10 P1-C
GSM8838481 P1-C11 P1-C
GSM8838482 P1-C12 P1-C
GSM8838483 P1-D01 P1-D
GSM8838484 P1-D02 P1-D
GSM8838485 P1-D03 P1-D
GSM8838486 P1-D04 P1-D

+ 56 more — browse all 96 samples with per-sample file links →

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GSE291608 Splice isoform-perturbation coupled to single cell transcriptome profiling reveals functions of microexons in neurogenesis and autism-linked pathways [RNA-seq] 28 samples shares isoform-perturbation, autism-linked, neurogenesis, microexons, functions, coupled, splice
GSE71485 Single-cell RNA-seq with Waterfall Reveals Molecular Cascades underlying Adult Hippocampal Neurogenesis 173 samples shares neurogenesis
GSE248250 Multimodal perspectives on the upper layer neurogenesis in the murine cerebral cortex 137 samples shares neurogenesis
GSE312790 Aberrant mRNA Splicing and Impaired Hippocampal Neurogenesis in Grin2b Mutant Mice 133 samples shares neurogenesis
GSE234317 The meninges host a unique compartment of regulatory T cells that bulwarks adult hippocampal neurogenesis 95 samples shares neurogenesis
GSE234316 The meninges host a unique compartment of regulatory T cells that bulwarks adult hippocampal neurogenesis [RNA-Seq] 87 samples shares neurogenesis
GSE312325 Aberrant mRNA Splicing and Impaired Hippocampal Neurogenesis in Grin2b Mutant Mice [RNAseq] 63 samples shares neurogenesis
GSE306924 Aberrant mRNA Splicing and Impaired Hippocampal Neurogenesis in Grin2b Mutant Mice [grin2b_bulkRNAseq] 38 samples shares neurogenesis

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.