Transcriptomic and V(D)J profiling at the single cell level of plasmablasts from lymph nodes of mice immunized with bMOG protein

Autoantibodies contribute to many autoimmune diseases, yet there is no therapy to neutralize them selectively. A popular mouse model, experimental autoimmune encephalomyelitis (EAE), could serve to develop such a therapy, provided we can better understand the nature and importance of the autoantibodies involved. In this study, we analyzed autoantibody-secreting extrafollicular plasmablasts in mice with EAE induced by immunization with a mutated myelin oligodendrocyte glycoprotein (MOG) antigen called bMOG. These CD138+ cells were enriched from lymph nodes at day 8 post-immunization and analyzed by single-cell RNA sequencing using 10× Genomics technologies. Here we provide the raw and processed data obtained from the gene expression (GEX) and VDJ cDNA libraries. Overall design: Single-cell suspensions were prepared from inguinal lymph nodes of mice at day 8 post-immunization with bMOG. CD138+ cells were enriched using the EasySep Mouse CD138 Positive Selection Kit (Stemcell Technologies). Cells were processed with the Chromium Single Cell Chip A and Chromium Controller (10× Genomics) with the goal of analyzing ~6,000 cells per mouse. RNA samples were pooled for reverse transcription and amplification to generate gene expression and V(D)J libraries using the Single Cell 5' Library Kit and Single Cell V(D)J Enrichment Kit (10× Genomics). Libraries were pooled and sequenced using both Illumina Hiseq 2500 PE100 technology (low pass) at the University Hospital Center of Quebec and Illumina NovaSeq 6000 S4 PE150 technology (high pass) at Genome Quebec. Sequencing results from both technologies were combined for bioinformatics analyses.