Key U2 spliceosomal proteins and their interactors were knocked down in Huh-7 cells and the subsequent changes in pre-mRNA splicing were detected by RNASeq

Through a genome-wide siRNA screening we discovered that the knockdown of U2-spliceosomal proteins and some of their interactors is associated with a decrease in LDL endocytosis in Huh-7 human hepatocarcinoma cells. In order to elucidate the underlying molecular mechanism, we performed RNASeq (Illumina) upon knockdown of the aforementioned spliceosomal proteins and analyzed the data at the exon / intron level in order to detect changes in splicing patterns. Each gene was tested in three replicate experiments. 3 experimental runs were performed, each containing different target spliceosomal genes. Target genes were compared to scrambled siRNA controls within each run. The fastq files are labelled as follows: TARGETGENE_Replicate_Run.fastq.gz SCR = scrambled (non-targeting) siRNA