Single-Cell Analysis of Whole PBMCs and Enriched B Cells

Following BCL conversion, fastq files were processed through CellRanger Pipeline (10X Genomics). This allowed demultiplexing, alignment, filtering, barcode counting, and UMI counting, and generating of cell x barcode matrices. These matrices were then input into SPRING¹⁵ , which is a tool for visualizing and analyzing single-cell data^{16 (link)}. Using this, we were able to visualize single-cell data obtained from whole PBMCs and enriched B cells. Using the gene-finder tool, cells expressing gene of interested were highlighted and compared across groups. Differential gene expression analysis (DEG) was performed with the R package Seurat^{17 (link)} (v3.0.0) with the FindMarkers function using the default settings. For BCR clonotype analysis, we used the CellRanger Pipeline. As per the definition by 10X Genomics: “Clonotypes are defined as a set of cells with the same CDR3 sequence in their V(D)J variable regions.”