A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain
Dataset ID: STDS0000004
3,024 Spots
31,053 Genes


Dataset information
Alternative RNA splicing varies across brain regions, but the single-cell resolution of such regional variation is unknown. Here we present the first single-cell investigation of differential isoform expression (DIE) between brain regions, by performing single cell long-read transcriptome sequencing in the mouse hippocampus and prefrontal cortex in 45 cell types at postnatal day 7. Using isoform tests for brain-region specific DIE, which outperform exon-based tests, we detect hundreds of brain-region specific DIE events traceable to specific cell-types. Many DIE events correspond to functionally distinct protein isoforms, some with just a 6-nucleotide exon variant. In most instances, one cell type is responsible for brain-region specific DIE. Cell types indigenous to only one anatomic structure display distinctive DIE, where for example, the choroid plexus epithelium manifest unique transcription start sites. However, for some genes, multiple cell-types are responsible for DIE in bulk data, indicating that regional identity can, although less frequently, override cell-type specificity. We validated our findings with spatial transcriptomics and long-read sequencing, yielding the first spatially resolved splicing map in the postnatal mouse brain (www.isoformAtlas.com). Our methods are highly generalizable. They provide a robust means of quantifying isoform expression with cell-type and spatial resolution, and reveal how the brain integrates molecular and cellular complexity to serve function.
Overall design
10x single-cell sequencing done on two replicates of Hippocampus and Prefrontal Cortex (PFC) samples. PacBio sequencing done on the same cDNA to get long read expression data in single cells. Spatial sequencing was conducted using 10x visium sequencing on brain slices, followed by PacBio and Oxford Nanopore sequencing on the same cDNA
10x Visium, scRNA-seq
Illumina HiSeq 4000, Illumina NovaSeq 6000, PromethION
Mus musculus
Cell types
astrocytes, oligodendrocytes, populations of vascular and immune cells, neuronal types
Joglekar A, Prjibelski A, Mahfouz A, Collier P et al. A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal Mus musculus brain. Nat Commun 2021 Jan 19;12(1):463.
Submission date: 2020-09-23Update date: 2021-02-01
Sample number: 11Section number: 1

Joglekar A; Collier P; Tilgner H

GEO Series Accessions: GSE158450