Long-read mRNA isoform atlas of human cortical cell types
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The human brain expresses a highly complex transcriptome shaped by extensive alternative splicing, yet the full-length isoform landscape across cortical cell types remains largely uncharacterized. By integrating fluorescence-activated nuclei sorting with long-read (PacBio Iso-Seq) and short-read (Illumina) RNA sequencing, we generated isoform-resolved transcriptomes across five major cortical lineages, including MGE-derived GABAergic neurons, glutamatergic neurons, oligodendrocytes, astrocytes, and microglia from adult human prefrontal and orbitofrontal cortex. Breif overivew of methods: raw long reads generated on the PacBio Sequel II platform were processsed with IsoSeq3 to generate high-quality full-length transcripts, which were aligned to the GRCh38 genome (GENCODE v38) using minimap2. Transcript models were collapsed and merged across samples within each cell type in the DLPFC and OFC using TAMA to generate nonredundant transcript annotations, followed by classification and QC filtering with SQANTI3. Transcript abundance was quantified using Salmon. This resources houses the input data and R scripts (GitHub) to generate all of the main figures (preprint), along with the cell type-resolved transcriptomes (BED and GTF files) generated via SQANTI3. Correspondence: michael.breen@mssm.edu (Lead contact)
