Quantitative Analysis of Wild Type and miR-203 KO transcriptomes in the rat endometrial adenocarcinoma cell line RUCA-I. Rattus norvegicus

Purpose: identification of mRNAs that are potential targets of miR-203 in the endometrium and endometrial carcinoma Methods: mRNA profiles of three batches of wild-type (WT) and three independently generated miR-203 knockout (miR-203 KO) RUCA-I cells were produced by deep sequencing, using Illumina HiSeq 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Using an optimized data analysis workflow, we mapped between 30 and 50 million sequence reads per sample to the rat genome (build rn6) and identified 26751 transcripts of which 1591 are differentially expressed in WT and miR-203 KO cells (p<0.05). Overall design: mRNA profiles of three WT batches and three independently generated miR-203 KO RUCA-I rat endometrial adenocarcinoma cell lines were produced by deep sequencing, using Illumina HiSeq2500.