Single cell RNA-seq of immune cells isolated from lymphoid organs of Aire-deficient and wild-type control mice

Autoimmune regulator (Aire) orchestrates the display of peripheral self-antigens to T cells developing in the thymus, thereby playing a crucial function in the induction of immune tolerance. Mice lacking Aire develop multiorgan autoimmunity, but how that reflects on immune cells in the major lymphoid organs is not well understood. Here we used single cell RNA-seq to characterize immune cells isolated from the thymus, bone marrow (BM) and lymph node (LN) of four Aire-deficient (B6.AireC313X-/-) and four wild-type (WT) mice with two male and two female mice per genotype. B6.AireC313X-/- mice were generated and kindly provided by Yael Goldfarb and Jakub Abramson (previously described in Goldfarb et.al 2021, DOI: 10.1084/jem.20201076). The mice were 6-9 weeks old at the time of sacrifice. A total of nine sample types per individual mouse were generated in this study; immune cells isolated from three tissues; thymus, lymph node and bone marrow, where each tissue was used for GEX, TCR and BCR-seq. Information about individual, tissue, library type and lane are indicated in the sample name as follows: Genotype_MouseID_tissue_librarytype_lane ex. AireC313X_1_thymus_GEX_lane1