Figure S3.
The diagram starts with dissociated islet cells from four pools: WT pool 1, WT pool 2, KO pool 1, and KO pool 2. These cells are stained with cell hashing antibodies and combined. The sorting strategy involves flow cytometry plots to sort cells into CD45.1 positive CD4 positive T cells and non-CD4 T cells. The sorted cells undergo 10X Genomics library preparation and sequencing. The results are shown in two main clusters: Non-CD4 T cells combined from all pools and CD4 T cells combined from all pools. Each cluster is further analyzed for specific cell markers. The Non-CD4 T cells are categorized into various types such as B cells, CD8 T cells, CD8 T cells, NK/T cells, Acinar contaminant, Myeloid cells, ILC/gd T cells, pDC, and Undefined. The CD4 T cells are categorized into different types such as Memory, Naïve, Treg, early effector/Tfh-like, Th1, Effector memory, Proliferating, Acinar contamination, and Naïve. Violin plots show the expression levels of various markers for T cell, B cell, NK/ILC, and DC/macrophage/pDC markers.
Study design and cell sorting strategy for scRNA-seq analysis, related to Figs. 3, 4, and 5. Two pools of islet cells combined from two Cre+-Tnfrsf9+/+ (WT) or Cre+-Tnfrsf9fl/fl (KO) female mice were labeled with anti-CD45.1, anti-CD4, and a unique hashtag antibody for each cell pool. Stained cells were combined and sorted into CD45.1+ CD4+ T cells and non-CD4 T cells. Transcriptomic, V(D)J, and hashtag libraries were prepared for both cell populations and sequenced. Cell identities for unique clusters were identified by their corresponding marker genes.