Single cell isoform sequencing (scIso-Seq) identifies novel full-length mRNAs and cell type-specific expression

Author(s): Tseng, E. and Underwood, J. G. and Bhuduri, A. and Marrs, C. and Konopacki, F. and Wong, D. and Munson, K. M. and Lewis, A. and Pollen, A. A. and Eichler, E. E.

Single cell RNA-seq (scRNA-seq) is an emerging field for characterizing cell heterogeneity in complex tissues. However, most scRNA-seq methodologies are limited to gene count information due to short read lengths. Here, we combine the microfluidics scRNA-seq technique, Drop-Seq, with PacBio Single Molecule, Real-Time (SMRT) Sequencing to generate full-length transcript isoforms that can be confidently assigned to individual cells. We generated single cell Iso-Seq (scIso-Seq) libraries for chimp and human cerebral organoid samples on the Dolomite Nadia platform and sequenced each library with two SMRT Cells 8M on the PacBio Sequel II System. We developed a bioinformatics pipeline to identify, classify, and filter full-length isoforms at the single-cell level. We show that scIso-Seq reveals full-length isoform information not accessible using short reads that can reveal differences between cell types and amongst different species.

Organization: PacBio
Year: 2019

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