Sorted cells were resuspended in TRIzol (Invitrogen). RNA was purified using Direct-Zol RNA Microprep (Zymo Research) kit with on-column DNase digestion. Protocol is adapted from Mamedov et al. (2013) and Turchaninova et al. (2016). Tcra transcripts were amplified by 5' rapid amplification of cDNA ends. 5 ng of total RNA was reverse transcribed using template switch oligo and Trac specific primer. cDNA was amplified, dual-indexing of amplified cDNA was performed, indexed samples were pooled at equal concentration and final library preparation carried out using NEBNext Ultra II DNA library preparation kit (NEB). Sequencing performed on MiSeq sequencer (Illumina) (300 x 300 bp).