Pkd2-dependent transcriptome profile in a newly estabilshed mouse Pkd2 knockout cell line

Purpose: The goal of this study is to explore early changes of gene expression in the new mouse kidney Pkd2 knockout cell model. To identify compreshensive expressional changes of genes by Pkd2 knockout, transcriptomic changes by Pkd2 knockout induced by doxycycline treatment for 6 days at two different passages were profiled and analyzed. Methods: Total RNAs were isolated from cells treated with or without doxycycline for 6 days. Four replicates of each group were generated. cDNA libraries were prepared and sequenced on Illumina HiSeq4000 platform and then sequence reads were qualified and quantified. Differential expression analysis were performed using edgeR. Results: mRNA profiles of the new mouse kidney Pkd2 knockout cell model treated with doxycycline for 6 days were generated using an optimized RNA-Seq workflow. Transcript level quantification using the STAR quant mode was performed to calculate transcript abundance in each sample. Then differential expression analysis identified the differentially expressed genes at different passages of cell culture. Conclusions: This study revealed early transcriptomic changes dependent on Pkd2 in a new in vitro Pkd2 knockout cell model of the mouse kidney. Overall design: Early transcriptomic responses to Pkd2 knockout was studied using a doxycycline-inducible Pkd2 knockout cell line newly established from the Pkd2 knockout mouse.