title: GSM8478638: hic D8_Tex-eff_rep2; Mus musculus; Hi-C
library_construction_protocol: 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 in situ Hi-C analysis. 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 in situ Hi-C 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 (day 3) post-infection, GFP+ P14 cells were sorted and purified for in situ Hi-C analysis. Sort-purified cells were crosslinked, digested with MboI restriction enzyme and underwent proximity ligation. The biotinylated DNA segments were captured, and ligated to the Illumina Paired End Adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina HiseqX platform.