Next-generation Sequencing contributes to Quantitative Analysis of Transcriptomes in circBNC2-KO HK2 cells

Purpose: We idenficied a circRNA, circBNC2, that was downregulated during tubular epithelial cell (TEC) injury. To study the function of circBNC2, we performed CRISPR-Cas9 to knock out circBNC2 in HK2 (a well recognized TEC) cells. Next-generation Sequencing was used to identified the differentially expressed mRNA between circBNC2-KO HK2 cells and wild-type HK2 cells. Methods: mRNA profiles of circBNC2-KO cells or wild-type cells were generated by deep sequencing, in duplicate, using Illumina HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using SYBR Green assays.