ABSTRACT: We performed a targeted scRNA-seq approach using the BD Rhapsody™ Single Cell Analysis Systems (BD Biosciences). Peripheral blood mononuclear cells (PBMCs) were labeled with sample tags (BD Human Single Cell Multiplexing Kit) and AbSeq antibodies (CD1c, CD3, CD4, CD5, CD8, CD11c, CD14, CD16, CD18, CD19, CD20, CD21, CD23, CD24, CD25, CD27, CD28, CD31, CD38, CD40, CD44, CD45RA, CD45RO, CD56, CD62L, CD123, CD127, CD134, CD137, CD161, CD183, CD185, CD186, CD196, CD197, CD272, CD278, CD279, CD303, CD314, CD337, CD357, CD366, HLA-DR, IgD, IgM, TCRαβ, TCRγ8, Vα24-Jα18) and counted. Single-cell capture was performed using the BD Rhapsody Express following manufacturer’s instructions. The libraries were pooled and sequenced on NovaSeq 6000 S2 as a dual index pair-end run. Fastq files were processed using BD's Rhapsody analysis pipeline on the Seven Bridges Platform using default parameters, the GRCh38-PhiX-gencodev29 reference genome and the gencodev29-20181205 transcriptome annotation. Data (molecules per gene per cell based on DBEC error correction) were analyzed using BD SeqGeq v1.8 and the Seurat plug-in to perform dimensionality reduction (UMAP) and differential analysis output for selected cell subsets (CD4+ T cells, CD8+ T cells, NK cells, NKT cells, classical monocytes, intermediate monocytes, non-classical monocytes).
