title: GSM6599287: ko, ADT; Mus musculus; OTHER
library_construction_protocol: CITEseq samples from duplicate experiments were prepared as described above (scRNAseq section) and processed according to the CITE-seq protocol from the New York Center Technology Innovation Lab (https://cite-seq.com/protocols/). Briefly, enriched CD8 T cells were incubated for 10' at 4oC in Staining buffer (2%BSA/0.01% Tween in PBS) containing FcBlock (1/10 dilution ;TruStainTM FcX, Biolegend) followed by a 30' incubation in Staining Buffer containing TotalSeqB antibodies against Ly108, CD69, Tim-3, PD-1, CD127, CD122, Lag-3, CD38 and KLRG1 (BioLegend) previously titrated according to manufacturer's protocol using PE-conjugated version of each antibodies Samples were then washed, sorted as described above, down-sampled and equivalent number of cells (104) between samples were loaded onto the Chip (Chromium Next GEM Chip G) of a Chromium Next GEM Single Cell 3' Reagent Kit v3.1 (Dual Index, 10x Genomics) and run onto a Chromium Controller. Samples were then processed according to manufacturer's protocol. Gene expression and Cell surface Protein libraries were constructed using Dual Index TT Set A and Dual Index NT Set A (10x Genomics) respectively. Libraries were quantified by qPCR using a KAPA Library Quant Kit (KAPA Biosystems). Normalized libraries were pooled (0.23nM), diluted to 1.8pg/ml and loaded onto a NextSeq 500/550 High Output Kit v2.5 (150 cycles, Illumina) and paired-end sequencing was performed on a NextSeq 550 (Illumina).