Sequencing

scRNAseq 5′ gene expression libraries and BCR V(D)J enriched libraries were sequenced on an Illumina NovaSeq 6000 instrument using the S2, or S4 reagent kits (300 cycles). Libraries were balanced to allow for ~150,000 reads/cell for 5′ gene expression libraries. Sequencing parameters were set for 150 cycles for Read1, 8 cycles for Index1, and 150 cycles for Read2. Prior to sequencing, library quality and concentration were assessed using an Agilent 4200 TapeStation with High Sensitivity D5000 ScreenTape Assay and Qubit Fluorometer (Thermo Fisher Scientific) with dsDNA BR assay kit according to the manufacturer’s recommendations.