Next Generation Sequencing Facilitates Quantitative Analysis of a circRNA, hsa_circ_0005505 regulated Transcriptomes in breast cancer cells (MDA-MB-231 lung metastatic cells LM2)

Purpose: hsa_circ_0005505 stably knockdown cells (circ-sh1 and circ-sh2) and its corresponing control cells (con-sh) were constructed using its specific shRNAs. Next-generation sequencing (NGS) has used to examine hsa_circ_0005505 regulated transcripts. Methods: mRNA profiles of circsh1, circsh2 and con-sh were generated by deep sequencing using IlluminaI 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 Results: We found 816 and 909 transcripts downregulated in circ-sh1 and circ-sh2 cells compared with con-sh cells, respectively. But 712 and 723 transcripts upregulated in circ-sh1 and circ-sh2 cells compared with con-sh cells, respectively. The differential expression with a fold change ≥1.5 and p value <0.05. Conclusions: Our study represents the first detailed analysis of hsa_circ_0005505-regulated transcripts in breast cancer cells. Next Generation Sequencing Facilitates Quantitative Analysis of a circRNA, hsa_circ_0005505 regulated Transcriptomes in breast cancer cells