title: scTCR-seq of Homo sapiens- tumor tissue
design: For analysis of tumor samples, melanoma tumor biopsies acquired via core or punch biopsies were processed using the Miltenyi Tumor Dissociation kit (Miltenyi Biotec), with modifications for small sample size. Minced samples were digested in a thermomixer at 37C, with 42uL of enzyme H, 21uL of enzyme R, 5uL of enzyme A, and 932uL of R10 media in an Eppendorf tube, Samples were then passed through a 50μm filter, washed with R10, and resuspended in 1X PBS with 0.04% UltraPure BSA (Invitrogen) for downstream 10x analysis. Cells were loaded onto a 10x Genomics ChromiumTM instrument (10x Genomics) according to the manufacturer's recommendations. The scRNAseq libraries were processed using Chromium Next GEM Single Cell 5' Kit v2, and the scTCRseq libraries were made using Chromium Single Cell Human TCR Amplification Kit (10x Genomics). Quality controls for amplified cDNA libraries and final sequencing libraries were performed using Bioanalyzer High Sensitivity DNA Kit (Agilent). The sequencing libraries for scRNAseq and scTCRseq were normalized to 4nM concentration and pooled. The pooled sequencing libraries were sequenced on Illumina NovaSeq S4 300 cycle platform. The sequencing parameters were Read 1 of 26bp, Read 2 of 90bp, Index 1 of 10bp and Index 2 of 10bp.