title: scRNASeq of antigen-specific B cells in Rheumatoid Arthritis
design: Template-switching reverse transcription of messenger RNA was primed using the STRT-oligo, and cDNAs were barcoded using template-switched oligos containing cell and molecular identifiers. Barcoded cDNA libraries were pooled and amplified using PCR1-FWD and PCR1-REV primers and then sonicated. We purified fragments of cDNA molecules using MyOne C1 streptavidin dynabeads and uncoupled them by restriction digest. Libraries were constructed using TruSeq-V2 kits and sequenced using a HiSeq 2000 Sequencing System, 100 bp read length. Custom R scripts extracted cell and molecule barcodes from raw sequencing reads in order to de-multiplex the libraries for submission to the SRA.  The extracted cell and molecular barcode for each read were specified in the form '!cellular barcode!molecular barcode' after the Illumina X/Y coordinates of the read in the sequence identifer line of the FASTQ.