RNAseq profiling of Aire and Ctr-transfected HEK293 cells

Aire-sensitive genes exhibit short 3'UTR transcript isoform preference in Aire and Ctr-transfected HEK293 cells HEK293 cells were transfected with the pCMV-Aire-Flag plasmid (or the control empty plasmid) using the TransIT-293 transfection reagent (Mirus) for 48 hours. CLP1 knockdown was performed by lentivirus infection of CLP1-specific shRNAs (sh2 and sh3). Total RNA isolated by Trizol extraction 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. Single-end (50 bp) sequencing was performed using the Illumina HiSeq2000 machine. Single-end (75bp) reads generated by the Illumina NextSeq 500 machine (lentivirus infected samples) were truncated to 50 bp.