Single-cell RNA-sequencing of CD4+ T cells from lung and draining lymph node of flu-infected mice

We performed a single-cell transcriptome analysis of pooled samples from lung and lymph node of 4-12 mice per time point in days post infection (d9, d14, d30) sorted for I-Ab NP311-325 specific CD4 T cells. Additionally we include mRNA counts from liver cells from LCMV infected mice day 37 post-infection, which were sequenced simultaneously with spleen cells from GSE134157. Cells negative for dump and positive for CD4, CD44 and I-Ab NP311-325 were sorted for lung and lymph node at each time point and used for single cell RNA Seq (10x genomics platform). Liver cells were negative for dump and positive for CD4, CD44 and GP66.