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Nat Biotechnol. 2018 Oct 15. doi: 10.1038/nbt.4259. [Epub ahead of print]

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

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Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York, New York, USA.
The Rockefeller University, New York, New York, USA.
Leiden Computational Biology Center, Leiden University Medical Center, Leiden, the Netherlands.
Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands.
Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, Amsterdam, the Netherlands.
Department of Neurobiology, Stanford University, Stanford, California, USA.
Brain and Mind Research Institute and Appel Alzheimer's Research Institute, Weill Cornell Medicine, New York, New York, USA.


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.


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