Gene expression profile of murine thymic B cells in the presence or absence of CD40 signaling

The thymus contains some B cells that are located at the corticomedullary junction. We found that these thymic B cells express and present the water channel protein AQP4 and are necessary and sufficient to mediate the negative selection of AQP4-reactive thymocytes. In order to express and present AQP4, thymic B cells need to be licensed through a CD40 signal. Here, we tested the significance of CD40 signaling in thymic B cells for the expression and presentation of distinct autoantigens (besides AQP4) to orchestrate thymocyte selection for these autoantigens. 2000 B cells per sample were sorted from the thymus of naive, untreated wild type (WT, C57BL/6, Charles River) or CD40KO (JAX strain 002927) mice aged 6-8 weeks (5 mice per genotype) and then subjected to bulk RNAseq. After the initial run, the same libraries were sequenced again to increase overall sequencing depth.