GEO series

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

GSE291608 Mus musculus (mouse) Single-cell RNA-seq 28 samples Submitted 2025/11/28 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 28 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: 28 samples: 13 conditions, mostly in duplicateGroups 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 GSE291608 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 GSE291608_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 PRJNA1234490 and SRA study SRP569517. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41633977) ↗

Study design

13 conditions, mostly in duplicate

Camta1_EX_DIV7 ×2 Camta1_INC_DIV7 ×2 Clasp1-A_EX_DIV7 ×2 Clasp1-A_INC_DIV7 ×2 Ptk2-A_EX_DIV7 ×2 Ptk2-A_INC_DIV7 ×2 Ptprf-A_EX_DIV7 ×2 Ptprf-A_INC_DIV7 ×2 +7 more

Supports a between-group comparison across 26 samples.

How we read this: 13 replicated groups read from 28 sample titles; they account for 26 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

GSM8838407 Camta1_EX_DIV7_rep1 Camta1_EX_DIV7
GSM8838408 Camta1_EX_DIV7_rep2 Camta1_EX_DIV7
GSM8838409 Camta1_INC_DIV7_rep1 Camta1_INC_DIV7
GSM8838410 Camta1_INC_DIV7_rep2 Camta1_INC_DIV7
GSM8838411 Clasp1-A_EX_DIV7_rep1 Clasp1-A_EX_DIV7
GSM8838412 Clasp1-A_EX_DIV7_rep2 Clasp1-A_EX_DIV7
GSM8838413 Clasp1-A_INC_DIV7_rep1 Clasp1-A_INC_DIV7
GSM8838414 Clasp1-A_INC_DIV7_rep2 Clasp1-A_INC_DIV7
GSM8838415 Ptk2-A_EX_DIV7_rep1 Ptk2-A_EX_DIV7
GSM8838416 Ptk2-A_EX_DIV7_rep2 Ptk2-A_EX_DIV7
GSM8838417 Ptk2-A_INC_DIV7_rep1 Ptk2-A_INC_DIV7
GSM8838418 Ptk2-A_INC_DIV7_rep2 Ptk2-A_INC_DIV7
GSM8838419 Ptprf-A_EX_DIV7_rep1 Ptprf-A_EX_DIV7
GSM8838420 Ptprf-A_EX_DIV7_rep2 Ptprf-A_EX_DIV7
GSM8838421 Ptprf-A_INC_DIV7_rep1 Ptprf-A_INC_DIV7
GSM8838422 Ptprf-A_INC_DIV7_rep2 Ptprf-A_INC_DIV7
GSM8838423 Gfra1_Hom_DIV7_c5 Gfra1_Hom_DIV7_c
GSM8838424 Gfra1_Hom_DIV7_c13 Gfra1_Hom_DIV7_c
GSM8838425 WT_wt_DIV7_e5
GSM8838426 WT_wt_DIV7_b1
GSM8838427 Camta1_EX_ESC_rep1 Camta1_EX_ESC
GSM8838428 Camta1_EX_ESC_rep2 Camta1_EX_ESC
GSM8838429 Camta1_INC_ESC_rep1 Camta1_INC_ESC
GSM8838430 Camta1_INC_ESC_rep2 Camta1_INC_ESC
GSM8838431 Clasp1-A_EX_ESC_rep1 Clasp1-A_EX_ESC
GSM8838432 Clasp1-A_EX_ESC_rep2 Clasp1-A_EX_ESC
GSM8838433 Clasp1-A_INC_ESC_rep1 Clasp1-A_INC_ESC
GSM8838434 Clasp1-A_INC_ESC_rep2 Clasp1-A_INC_ESC

Datasets on a similar topic

GSE291610 Splice isoform-perturbation coupled to single cell transcriptome profiling reveals functions of microexons in neurogenesis and autism-linked pathways [snRNA-Seq] 96 samples shares isoform-perturbation, autism-linked, neurogenesis, microexons, functions, coupled, rna-seq, splice
GSE71485 Single-cell RNA-seq with Waterfall Reveals Molecular Cascades underlying Adult Hippocampal Neurogenesis 173 samples shares neurogenesis, rna-seq
GSE234316 The meninges host a unique compartment of regulatory T cells that bulwarks adult hippocampal neurogenesis [RNA-Seq] 87 samples shares neurogenesis, rna-seq
GSE281690 mRNA stability fine tunes gene expression in the developing cortex to control neurogenesis [RNA-Seq] 9 samples shares neurogenesis, rna-seq
GSE304355 A human-specific enhancer modulates chromosomal interactions to promote neurogenesis [mouse RNA-seq] 9 samples shares neurogenesis, rna-seq
GSE277737 Phf23 regulates embryonic neurogenesis by increasing the level of H3K27ac of Tcf4 [RNA-seq] 8 samples shares neurogenesis, rna-seq
GSE234315 The meninges host a unique compartment of regulatory T cells that bulwarks adult hippocampal neurogenesis [scRNA-Seq] 8 samples shares neurogenesis, rna-seq
GSE268332 GENERATION OF MOUSE NEOCORTICAL ORGANOIDS TO MODEL THE IMPACT OF CIS-REGULATORY VARIATION ON CORTICAL NEUROGENESIS ACROSS EVOLUTIONARY TIMESCALES (scRNA-Seq) 7 samples shares neurogenesis, rna-seq

Search all mouse 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.