Single cell RNA-seq of hemagglutinin specific B cells after influenza virus infection: gene expression data

Understanding dynamics of antigen specific B cell responses and link between BCR and B cell differentiation is crucial for our ability to direct immune responses and to generate memory and plasma cells responses to protective targets. Here we have infected mice with IAV-PR8 and sacrificed them at different days after infection (7-14-28). 2 naive mice were used as controls (spleen and lungs). From individual spleen, lungs and mediastinal lymph nodes we have sorted Hemagglutinin (HA)-specific IgD- B cells and single cell sequenced RNA and BCR. We identify several known and novel B cell subpopulations forming after infection and find organ-specific difference that persist over the course of the response. We found important transcriptional differences between memory cells in lungs and immune organs and describe organ-restricted clonal expansion. Strikingly, by combining BCR mutational analysis, monoclonal antibody expression and affinity measurements we found no differences between germinal center (GC)-derived memory and plasma cells, at odds with an affinity-based selection model. These finding provide the most comprehensive picture to date of organ specific antiviral B cell responses, differentiation, clonal-proliferation and dynamics.