The cells were washed with PBS, trypsinized and labeled with cell hashing antibodies, TotalSeqTM-C0251 Hashtag 1 (BioLegend #394661) and TotalSeqTM-C0252 Hashtag 2 (BioLegend #394662). Viable cells were washed and resuspended in PBS with 0.04% BSA at a cell concentration of 1000 cells/µL About 17,000 viable mouse cells were loaded onto a 10× Genomics ChromiumTM instrument (10× Genomics) according to the manufacturer's recommendations. The scRNAseq libraries were processed using ChromiumTM single cell 5' library & gel bead kit (10× Genomics). Matched cell hashing libraries were prepared using single cell 5' feature barcode library kit. Quality controls for amplified cDNA libraries, cell hashing 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 using a volume ratio of 4:1. The pooled sequencing libraries were sequenced on Illumina NovaSeq S4 300 cycle platform. The sequencing parameters were: Read 1 of 150bp, Read 2 of 150bp and Index 1 of 8bp. The sequencing data were demultiplexed and aligned to mm10-3.0.0 using cell ranger version 3.1.0 pipeline (10× Genomics).