WT and Aire-KO mouse MEChi RNAseq profiling

Aire-sensitive genes exhibit short 3'UTR transcript isoform preference in WT and Aire-KO mTEChi Overall design: ~100ng of total RNA isolated by Trizol extraction from MHC-II high mTECs (pool of 4 mice) was used to generate poly-A-selected transcriptome libraries using the non-directionnal TruSeq V3 RNA Sample Prep Kit (without additional pre-amplification) following the manufacturer's protocols. Enrichment of DNA fragment with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primer cocktail. Paired-end (2 × 100 bp) sequencing was performed using the Illumina HiSeq2000 machine.