Journal
NATURE COMMUNICATIONS
Volume 8, Issue -, Pages -Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/ncomms16027
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Funding
- NIH/NHGRI [HG006321, HG007827]
- NIH/NIDDK [R01DK100917]
- Alex's Lemonade Stand Foundation Innovation Award
- American Asthma Foundation
- CIRM Training grant [TG2-01157]
- NHLBI [K01HL130753-01A1]
- CIRM Shared Stem Cell Facilities [CL1-00506]
- CIRM Major Facilities awards [FA1-00617-1]
- California Institute for Regenerative Medicine (CIRM) New Faculty Award [RN1-00540]
- American Cancer Society Research Scholar Award [RSG-13-193-01-DDC]
- NHGRI/NIH training grant [1T32HG008345-01]
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Understanding gene regulation and function requires a genome-wide method capable of capturing both gene expression levels and isoform diversity at the single-cell level. Short-read RNAseq is limited in its ability to resolve complex isoforms because it fails to sequence full-length cDNA copies of RNA molecules. Here, we investigate whether RNAseq using the long-read single-molecule Oxford Nanopore MinION sequencer is able to identify and quantify complex isoforms without sacrificing accurate gene expression quantification. After bench-marking our approach, we analyse individual murine B1a cells using a custom multiplexing strategy. We identify thousands of unannotated transcription start and end sites, as well as hundreds of alternative splicing events in these B1a cells. We also identify hundreds of genes expressed across B1a cells that display multiple complex isoforms, including several B cell-specific surface receptors. Our results show that we can identify and quantify complex isoforms at the single cell level.
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