GSM8478619: RNAseq D3_WT_Tex-prec_rep1; Mus musculus; RNA-Seq
Naive P14 TCR transgenic CD8+ T cells, carrying a Tcf7-GFP reporter to mark Tcf1-expressing cells, were adoptively transferred into CD45-disparate recipients and subsequently infected with either LCMV Armstrong or LCMV-Clone 13 to induce acute or chronic viral infection, respectively. On day 8 post-infection in the acute infection model, KLRG1+IL-7Rα- P14 cells were sorted and purified as effector CD8+ T (Teff) cells for RNA-seq analysis along with Naive P14 cells.  In the chronic infection model, on day 8 post-infection, Tim3+Slamf6-GFP- P14 cells were sorted and purified as effector exhausted CD8+ T (Tex-eff) cells, while Tim3−Slamf6+GFP+ P14 cells were sorted and purified as  precursors to stem-like exhausted CD8+ T (Tex-prec) cells, both for RNA-seq analysis.  Additionally, hCD2-Cre, Rosa26-lsl-GFP, and CTCF wild-type or floxed CD8+ T cells were adoptively transferred into CD45-disparate recipients, followed by infection with LCMV-Clone 13. At 72 hours post-infection, GFP+ Tim3+ Tex-eff P14 cells and GFP+ Tim3− Tex-prec P14 cells from both the WT and CTCF-KO groups were sorted and purified for RNA-seq analysis. Sort-purified cells were used for total RNA extraction using standard Qiagen RNeasy columns, and RNA libraries were prepared for sequencing using stardard Illumina protocol. The resulting libraries were seqeunced with Illumina HiseqX platform.