GSM8478599: ATAC D8_Tex-prec_rep1; Mus musculus; ATAC-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 ATAC-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 ATAC-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 ATAC-seq analysis. Sort-purified cells were treated with TN5 transposase to generate tagged DNA fragments. TN5-tagged DNA fragements were purified, PCR amplified to build ATAC-seq libraries. The resulting libraries were seqeunced with Illumina HiseqX platform.