Isoform cell-type specificity in the mouse primary motor cortex.
IF: 69.504
Cited by: 37


Full-length SMART-seq1 single-cell RNA sequencing can be used to measure gene expression at isoform resolution, making possible the identification of specific isoform markers for different cell types. Used in conjunction with spatial RNA capture and gene-tagging methods, this enables the inference of spatially resolved isoform expression for different cell types. Here, in a comprehensive analysis of 6,160 mouse primary motor cortex cells assayed with SMART-seq, 280,327 cells assayed with MERFISH2 and 94,162 cells assayed with 10x Genomics sequencing3, we find examples of isoform specificity in cell types-including isoform shifts between cell types that are masked in gene-level analysis-as well as examples of transcriptional regulation. Additionally, we show that isoform specificity helps to refine cell types, and that a multi-platform analysis of single-cell transcriptomic data leveraging multiple measurements provides a comprehensive atlas of transcription in the mouse primary motor cortex that improves on the possibilities offered by any single technology.


Spatial Gene Expression
Spatial Omics
Spatial Transcriptomics

MeSH terms

Atlases as Topic
GABAergic Neurons
Gene Expression Profiling
In Situ Hybridization, Fluorescence
Mice, Inbred C57BL
Motor Cortex
Organ Specificity
Sequence Analysis
Single-Cell Analysis


Booeshaghi, A Sina
Yao, Zizhen
van Velthoven, Cindy
Smith, Kimberly
Tasic, Bosiljka
Zeng, Hongkui
Pachter, Lior

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