Abstract
Droplet microfluidics has made high-throughput single-cell RNA sequencing accessible to more laboratories than ever before, but is restricted 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 the polyadenylated transcriptome in single cells, as well as enriched measurement of targeted RNA loci, including loci within non-A-tailed transcripts. 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.