Abstract
High-throughput single-cell RNA sequencing technology has provided important insights into cellular complexity and transcriptome dynamics. However, current implementations of this technology are limited to capturing information from the ends of A-tailed messenger RNA (mRNA) transcripts. Here, we describe a versatile technology, Droplet Assisted RNA Targeting by single cell sequencing (DART-seq), that surmounts this limitation allowing investigation of all regions of the polyadenylated transcriptome, as well as measurement of other classes of RNA in the cell. We applied DART-seq to simultaneously measure transcripts of the segmented dsRNA genome of a reovirus strain, and the transcriptome of the infected cell. In a second application, we used DART-seq to simultaneously measure natively paired, variable region heavy and light chain (VH:VL) amplicons and the transcriptome of human B lymphocyte cells.