Divergent molecular networks program functionally distinct CD8+ skin-resident memory T cells

scRNA CITE-seq with paired TCR from mouse CD8+ T cells in skin and spleen after Staphylococcus epidermidis association Polyclonal CD8+ T cells were sort-purified from skin (CD44hiCD69+CD103+) or spleen (CD44hi) of bone marrow chimeras reconstituted with WT (B6 or CD4-cre), Hobit KO or cMaf CD4-cre cKO cells 14-18d after Staphylococcus epidermidis association. Sort-purified cells were barcoded with hashtag oligos and pooled for sequencing. Libraries were prepared using 10x Genomics kits. Naïve transgenic CD8+ gBT-I cells (CD44lo) were also sorted from the spleen and included as a control. the citeseq_reference file contains the HTO sequences for the demultiplexing.