RNA sequencing (RNA-seq) was performed using map analysis and plotting server (MAPS), as previously described (99). Briefly, total RNA was extracted from iNKT cells using TRIzol reagent (Invitrogen) and was reverse-transcribed using a biotinylated oligo (dT) primer and SuperScript III (Invitrogen). Terminal transferase was used to block 3′ end of complementary DNA (cDNA) in the presence of dideoxynucleotides (ddNTP). After second-strand cDNA synthesis, 23 cycles of PCR were performed to amplify cDNAs. PCR products with lengths of 200 to 400 nt were subjected to deep sequencing on a HiSeq 2500 (Illumina). The reads of RNA-seq were mapped to the mouse reference genome using Bowtie (v1.1.1).

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