C57Bl/6 mouse splenocytes were obtained by 10x Genomics from C&M Lab Pro.
Gene Expression, BCR Enriched, and TCR Enriched libraries were generated from 16,124 cells (87% viable, expected cell recovery 8,417) as described in the Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) (CG000331 Rev A) and sequenced on an Illumina NovaSeq 6000.
Sequencing Configuration:
- Gene Expression: Paired-end (26X90), dual-indexed sequencing. Read 1: 26 cycles, i7 index: 10 cycles, i5 index: 10 cycles, Read 2: 90 cycles
- BCR Enriched: Paired-end (28X90), dual-indexed sequencing. Read 1: 28 cycles, i7 index: 10 cycles, i5 index: 10 cycles, Read 2: 90 cycles. Note: Read 1 requirement is 26 bp; 28 bp Read 1 is trimmed by Cell Ranger pipeline.
- TCR Enriched: Paired-end (26X90), dual-indexed sequencing. Read 1: 26 cycles, i7 index: 10 cycles, i5 index: 10 cycles, Read 2: 90 cycles
Analysis Settings:
- Gene Expression: --expect-cells=10000