RNAseq profiling of Ctr and CLP1 knockdown HEK293 cells

CLP1 promotes 3'UTR shortening and higher expression at Aire-sensitive genes in HEK293 cells Overall design: Specific knockdown of CLP1 and the control LacZ gene in HEK293 cells maintained in complemented DMEM high glucose medium, was performed by infection with lentivirus-expressing shRNAs. shRNA2 (sh2) and shRNA3 (sh3) were cloned into the lentivirus vector pLKO with an expression driven by the ubiquitously active U6 promoter. 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.