Stability of Aire-upregulated and Aire-neutral transcripts in medullary thymic epithelial cells

Aire-upregulated transcripts exhibit higher stability than the transcripts neutral to Aire's action in mTEChi Total RNA isolated by Trizol extraction from MHC-II high or low mTECs (from pooled thymi of B6 mice) was used to generate poly-A-selected transcriptome libraries using the non-directionnal TruSeq V3 RNA Sample Prep Kit (without additional pre-amplification) for WT and Aire-KO mTEChi, as well as for mTEChi used as the reference timepoint (ActinoD 0h) or for mTEChi and lo from the same mice. Paired-end sequencing (2x100bp) was performed for these samples. 1h30, 3h, 6h and 12h-ActinoD-treated mTEChi libraries were generated using the Smarter Ultra Low Input RNA kit (Clontech) combined to the Nextera library preparation kit (Illumina). Single-end sequencing was performed for these ActinoD-treated samples. Sequencing was performed on the Illumina HiSeq2000 machine.