Single-cell RNA-sequencing of CD7 knockout CD8 T cells

The goal of this study is to identify transcriptional changes in antigen-specific CD8 T cells caused by CD7 deletion. CD7-/- mice were crossed to CD45.1+ P14 mice, which have a transgenic TCR specific for gp33, an epitope of lymphocytic choriomeningitis virus (LCMV). CD7 knockout (KO) and littermate wildtype (WT) P14 cells were co-transferred to C57BL/6J mice, which were subsequently infected with 2e6 PFU of LCMV clone 13 following transient CD4 T cell depletion. >45 days after infection, WT and KO P14 cells were isolated from liver and spleens of infected animals, and naive P14 WT and KO cells were isolated from the blood of the donor mice. Individual cell types were labeled with hashing antibodies, pooled, and subjected to the 10x Genomics Chromium scRNA-seq workflow. Mouse hashing antibody sequences: Naive WT: Totalseq-C hash 1 (ACCCACCAGTAAGAC); Naive KO: Totalseq-C hash 2 (GGTCGAGAGCATTCA); Spleen WT P14s from infected mice: Totalseq-C hash 3 (CTTGCCGCATGTCAT); Spleen KO P14s from infected mice: Totalseq-C hash 4 (AAAGCATTCTTCACG); Liver WT P14s from infected mice: Totalseq-C hash 5 (CTTTGTCTTTGTGAG); Liver KO P14s from infected mice: Totalseq-C hash 6 (TATGCTGCCACGGTA)