GSE247544

Overall Design

P14 WT CD45.1 and P14 Foxo1f/f Cre-ERT2+/- CD45.1.2 CD8 T cells were adoptively co-transferred into congenically distinct recipient mice. The recipient mice were infected with 2x105 plaque forming units of lymphocytic choriomeningitis virus 30 minutes after transfer. 21 days post-infection, mice were treated with 0.5mg/g tamoxifen intraperitoneally daily for 5 days, and then sacrificed 2 weeks later. CD8 T cells were isolated from spleen, small intestines, and colon, and incubated in an antibody cocktail containing antibody-derived tags against cell surface markers and fluorescence-conjugated antibodies. The congenically distinct CD8 T cells were separated by fluorescence-activated cell sorting. About 20,000 cells for spleen, siIEL, and siLPL samples were loaded onto Chromium Next GEM Chip M (10x Genomics) and 2,000 cells for cIEL and cLPL were loaded onto Chromium Next Gem Chip G (10x Genomics), and partitioned into Gel Beads. CITE-seq was then performed using previously described protocol (Stoeckius et al., 2017).