September 22, 2019  |  

Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells.

Authors: Gupta, Ishaan and Collier, Paul G and Haase, Bettina and Mahfouz, Ahmed and Joglekar, Anoushka and Floyd, Taylor and Koopmans, Frank and Barres, Ben and Smit, August B and Sloan, Steven A and Luo, Wenjie and Fedrigo, Olivier and Ross, M Elizabeth and Tilgner, Hagen U

Full-length RNA sequencing (RNA-Seq) has been applied to bulk tissue, cell lines and sorted cells to characterize transcriptomes, but applying this technology to single cells has proven to be difficult, with less than ten single-cell transcriptomes having been analyzed thus far. Although single splicing events have been described for =200 single cells with statistical confidence, full-length mRNA analyses for hundreds of cells have not been reported. Single-cell short-read 3' sequencing enables the identification of cellular subtypes, but full-length mRNA isoforms for these cell types cannot be profiled. We developed a method that starts with bulk tissue and identifies single-cell types and their full-length RNA isoforms without fluorescence-activated cell sorting. Using single-cell isoform RNA-Seq (ScISOr-Seq), we identified RNA isoforms in neurons, astrocytes, microglia, and cell subtypes such as Purkinje and Granule cells, and cell-type-specific combination patterns of distant splice sites. We used ScISOr-Seq to improve genome annotation in mouse Gencode version 10 by determining the cell-type-specific expression of 18,173 known and 16,872 novel isoforms.

Journal: Nature biotechnology
DOI: 10.1038/nbt.4259
Year: 2018

Read publication

Talk with an expert

If you have a question, need to check the status of an order, or are interested in purchasing an instrument, we're here to help.