Splicing factor SF3B1 promotes endometrial cancer progression via regulating KSR2 RNA maturation

The goal of this study is to compare transcriptome profiling of SF3B1 depleted Ishikawa endometrial cancer cells by RNA-sequencing Methods: SF3B1 depleted mRNA profiles of control siRNA treated and SF3B1 siRNA treated Ishikawa endometrial cancer cells were generated by deep sequencing, in triplicate using Illumina HiSeq 3000 sequencers with 2×150 paired-end reads. Basecalls and demultiplexing were performed with Illumina's RTA version 1.9 and bcl2fastq2 software with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.0.4b. qRT–PCR validation was performed using TaqMan assays Results: Using a 2.5-fold cutoff and Benjamini-Hochberg false discovery rate (FDR) of <0.01 threshold for inclusion, we identified 1,992 differentially expressed genes (DEGs) between Control and SF3B1 depleted Ishikawa cells Conclusions: Our study represents the first detailed analysis of SF3B1 depleted Ishikawa endometrial cancer cells transcriptomes, with biologic replicates, generated by RNA-seq technology. Overall design: Transcriptome profiling of Control siRNA and SF3B1 siRNA depleted Ishikawa cells