RNA-seq of HeLa cells and RPE1 cells after USP39 KD using RNAi
We used HeLa cells and RPE1 cells after knockdown (KD) of USP39 using siRNAs. We compared differential expression and alternative splicing between Control and KD cells. Overall design: We used 3 biological replicates for ctrl siRNAs and 3 biological replicates for the KD siRNAs. PolyA-selected RNA was sequenced with 150-bp paired end reads with 50 Million reads per replicate.