ArticleNature communications2021
A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 146 papers, 1 of them a synthesis that pooled it.
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Who cites it
146 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Recent developments in omics studies and artificial intelligence in depression and suicide.Translational psychiatry · 2025Pooled it
- Targeted Mechanogenetics to Modulate Specific Deep Neural Circuits.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Review
- Single-cell splice isoform usage reveals distinct axes of cellular identity and senescence.bioRxiv : the preprint server for biology · 2026Article
- Systematic benchmarking and optimal strategy selection of cross-species integration methods.Briefings in bioinformatics · 2026Article
- Amplification bias in sequencing-based spatial transcriptomics: sources, mechanisms, impacts, and mitigation strategies.Briefings in bioinformatics · 2026Review
- Spatial isoform sequencing at single-cell resolution reveals cell-type-specific spatial isoform variability in multiple brain cell types.Nature methods · 2026Article
- Full-length single-cell spatial transcriptomics reveals spatial and cell-type-specific transcript isoforms in the primate brain.Nature methods · 2026Article
- Brain injury reactivates a developmental program driving genesis and integration of transient LGE-class interneurons.Stem cell reports · 2026Article
- Beyond the gene: isoform diversity as a key contributor to human brain disorders.Current opinion in genetics & development · 2026Review
- Encrypted immunity mediated by peptides.PLoS biology · 2026Review
- Combined single-cell profiling of chromatin-transcriptome and splicing across brain cell types, regions and disease state.Nature biotechnology · 2026Article
- Long-read transcriptomics of purified human cortical cell types exposes glial isoform complexity and disease-relevant transcript architecture.bioRxiv : the preprint server for biology · 2026Article
- SCOTCH: isoform-level characterization of gene expression through long-read single-cell RNA sequencing.Nature communications · 2026Article
- Current trends and challenges in deciphering single molecule resolution maps of single cell transcriptomes.Briefings in bioinformatics · 2026Review
- Single-Cell and Spatial Omics: Methods and Applications.MedComm · 2026Review
- ALDH2-mediated GABA biosynthesis regulates hippocampal LTP and learning adaptability.Nature chemical biology · 2026Article
- Decoding exon inclusion in the human brain reveals more divergent splicing mechanisms in neurons than glia.Genome biology · 2026Article
- SpaLSTF: Diffusion-based generative model with BiLSTM and XCA-Transformer for spatial transcriptomics imputation.PLoS computational biology · 2026Article
- FGF13 is not secreted from mouse neurons.JCI insight · 2026Article
86 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
30 authors.
Funding
Abstract
Splicing varies across brain regions, but the single-cell resolution of regional variation is unclear. We present a single-cell investigation of differential isoform expression (DIE) between brain regions using single-cell long-read sequencing in mouse hippocampus and prefrontal cortex in 45 cell types at postnatal day 7 ( www.isoformAtlas.com ). Isoform tests for DIE show better performance than exon tests. We detect hundreds of DIE events traceable to cell types, often corresponding to functionally distinct protein isoforms. Mostly, one cell type is responsible for brain-region specific DIE. However, for fewer genes, multiple cell types influence DIE. Thus, regional identity can, although rarely, override cell-type specificity. Cell types indigenous to one anatomic structure display distinctive DIE, e.g. the choroid plexus epithelium manifests distinct transcription-start-site usage. Spatial transcriptomics and long-read sequencing yield a spatially resolved splicing map. Our methods quantify isoform expression with cell-type and spatial resolution and it contributes to further our understanding of how the brain integrates molecular and cellular complexity.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.