title: scRNA-Seq of Human RPTE cells (BKV infection) 2dpi donor1
design: Cells were infected with BKV, collected 2 days post infection and, together with hydrogel beads were encapsulated into droplets. Barcoding of single cells and preparation of sequencing libraries were performed according to previously reported inDrop protocols. In short, single-cell transcriptomes were first barcoded by reverse transcription in droplets. Next, emulsions were split into fractions containing <4,000 cells for inDrop library preparation using the inDrop single-cell RNA-seq kit from 1Cell-Bio. At the last PCR step, each library was indexed with a unique primer. Libraries were then pooled and sequenced on a NextSeq Illumina platform with a configuration of 36 bp on read 1, 6 bp on the index read, and 50 bp on read 2.