Sorted cells were washed and counted according to the 10x Genomics Cell Preparation Guide. Shortly, cells were washed three times in 1 ml 1X PBS 0.5% BSA, 2 mmol EDTA using wide-bore pipette tips for low-shear mixing and centrifuged at 300 rcf for 5 min. After final centrifugation step, cells were resuspended in 50 µl 1X PBS 0.5% BSA, 2 mmol EDTA and cell numbers were obtained by using a Neubauer chamber. Cells were adjusted to a final stock concentration of 1000 cells/µl and 10000 cells were loaded to the Chromium Next GEM Chip for each sample. Library construction was performed according to the manufacture's protocol (single cell 5' v2 (dual index) + human TCR amplification). To generate gel beads-in-emulsion (GEMs), cells were loaded to Chromium Next GEM Chip K together with master mix, gel beads and partitioning oil. After GEM generation, poly-A RNA was retrotranscripted to cDNA and Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and a 10x Barcode were included. For final library construction, pooled cDNA was cleaned up with Silane DynaBeads, further amplified by PCR and size-restricted by using SPRIselect reagent. To generate TCR libraries, a part of the amplified cDNA was used for V(D)J amplification followed by SPRIselect cleanup steps. During final libarary construction and V(D)J amplification, Illumina R2 primer, paired-end constructs and induvidual sample indeces were included. scRNA-seq and TCR seq