Single-cell Transcriptome and TCR Profiling

Two sequencing libraries were generated from each single cell cDNA preparation, one for the TRA/TRB repertoire and one for the 5′ ends of transcripts, and, subsequently, sequenced as described previously [39 (link)]. Briefly, for transcriptome analysis, 5′ end transcriptome libraries were extended from the purified cDNA by a 12 cycle PCR using the Nextera XT DNA library prep (Illumina) and sequenced according to the Illumina TruSeq Rapid v2 protocol on Illumina HiSeq2500 sequencer. Single reads were generated of 50 bp in length with a single 8 bp index sequence. For TRA/TRB profiling, TRA and TRB transcripts were amplified using specific PCR reactions which also added the Illumina adapter sequences. From the resulting TR sequencing libraries, paired-end reads of 300 bp in length were generated with an 8 bp index on an Illumina MiSeq sequencer per the manufacturer’s instructions (Illumina, San Diego, CA, USA).