GSM6862391: TDLNDiv2_mouse_methylation; Mus musculus; Bisulfite-Seq
Cell sorting was performed by FACS Aria II (BD Biosciences). For RNA-seq of P14s in LCMV Arm or in TRAMPC1-GP bearing mice, Live, CD4-CD14-CD19-, CD45.1+CD8+CD44+PD1+ were sorted. For RNA-seq of endogenous CD8 T cells from tumor, Live, CD4-CD14-CD19-Ly6G-, CD8+CD44+PD1+ 127+ or TIM3+ were sorted. performed by FACS Aria II (BD Biosciences). For RNA-seq of P14s in LCMV Arm or in TRAMPC1-GP bearing mice, Live, CD4-CD14-CD19-, CD45.1+CD8+CD44+PD1+ were sorted. For RNA-seq of endogenous CD8 T cells from tumor, Live, CD4-CD14-CD19-Ly6G-, CD8+CD44+PD1+ 127+ or TIM3+ were sorted. Qiagen micro RNA/DNA all prep columns were used for RNA extraction. DNA was isolated using the AllPrep DNA/RNA Micro kit (Qiagen) and sonicated to generate random 300 to 500-bp fragments. DNA was end-repaired and A-tailed using the Hyper Prep Kit (KAPA Biosystems) following the manufacturer's protocol. Sequencing adapters that contained fully methylated cytosine residues (Integrated DNA Technologies) were ligated using the Hyper Prep Kit (KAPA Biosystems). Adapter-ligated DNA was bisulfite converted using the EpiTect Bisulfite Kit (Qiagen), with a denaturation time of 10 min. Final libraries were PCR amplified 8–11 times using Tru-seq (Illunima)-compatible custom index primers, as previously described in (Barwick et al., 2016), and HiFi Uracil (KAPA Biosystems). The resulting WGBS libraries were quality checked by Bioanalyzer, pooled at equimolar ratios and sequenced on a NovaSeq S4