Transcriptome-wide effect profile of HuR inhibitor KH-3

The purpose of this study is to generate mRNA effect profle of KH-3, an inhibitor of RNA-binding protein HuR, in human breast cancer cell line MDA-MB-231 cells by RNA sequencing. Total RNA from cells treated with DMSO or KH-3 was collected for library prepareation and deep sequencing, in duplicate, using Illumina Hiseq 2500 system. About 30 million sequence reads per sample were mapped against the transcript databases annotated in GENCODE v24 using STAR default parameters. The read counts for each transcript were calculated using eXpress. The differentially expressed transcripts were detected using DESeq2 with a q-value cutoff of 0.05. Overall design: mRNA effect profile of KH-3 in MDA-MB-231 cells was generated by RNA-seq, in duplicate, using Illumina Hiseq 2500 system.