GSM8478610: CTCF CUTRUN  D3_Tex-eff_rep3; Mus musculus; OTHER
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 CTCF CUT&RUN analysis in live cells along with naive 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 CTCF CUT&RUN analysis. Additionally, WT naive P14 CD8+ T cells were adoptively transferred into CD45-disparate recipients, followed by infection with LCMV-Clone 13. At 72 hours (day 3) post-infection, Tim3+ Tex-eff P14 cells and GFP+ Tim3− Tex-prec P14 cells were sort-purified for CTCF CUT&RUN analysis. The DNA segments from CTCF Cut&Run were end-repaired and ligated to indexed Illumina adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina HiseqX platform.