Doxycycline-responsive transcriptome in the mouse inner medullary collecting duct cell line (mIMCD3)

Purpose: The goal of this study is to identify doxycycle-responsive genes in mouse kidney inner medullary collecting duct cell line mIMCD3. To explore compreshensive profile of doxycycline-mediated gene expression, transcriptomes of doxycycline-responsive genes at two different time points (3 days and 6 days) were profiled and analyzed. Methods: Total RNAs were isolated from mIMCD3 cells treated with doxycycline or vehicle at different time points (3 days and 6 days). Four replicates for vehicle- or doxycycline-treated group were generated at each tested time point. cDNA libraries were prepared using a Nextera DNA library preparation protocol. The sequence reads from Illumina HiSeq3000 platform were qualified and quantified at the transcript level using Salmon (0.14.1). Differential expression analysis were performed using edgeR. Results: mRNA profiles of mouse kidney inner medullary collecting duct mIMCD3 cells treated with doxycycline or vehicle (DMSO) for 3 days and 6 days were generated using an optimized RNA-Seq workflow. Transcript level quantification using a pseudo-alignment quantification method (Salmon) was performed to calculate transcript abundance in each sample. Then differential expression analysis identified the differentially expressed genes at each time point comparison (DOX vs vehicle). Conclusions: This study revealed comprehensive transcriptomic changes of doxycycline-responsive gene expression in mouse kidney inner medullary collecting duct cells. Doxycycline-responsive transcriptome in mouse kidney inner medullary collecting duct cell line mIMCD3