Next Generation Sequencing Profiles Transcriptomes of Control and shDANCR HCT116 Cell Lines

Purpose: The goal of this study is to compare Next Generation Sequencing-derived transcriptome profiling (RNA-seq) of a negative control cell line to two independent shDANCR cell lines. Methods: mRNA profiles of HCT116 colorectal cancer cell lines transfected with lentiviruses containing a negative control vector and two independent shRNA vectors for DANCR knockdown were generated by deep sequencing using Illumina HiSeq2000. The sequence reads that passed quality filters were analyzed at the transcript level with the method of HISAT2, and StringTie followed by FPKM calculation. Results: Using the described data analysis workflow, we mapped about 40 million sequence reads per sample to the human genome (GRCh38) and identified about 130,000 transcripts (transcribed from about 40,000 genes) per sample with StringTie. Approximately 2.5% of the genes showed differential expression between the Control and shDANCR cell lines, with a fold change ≥1.5 and p value <0.05. Conclusions: Our study represents a detailed analysis of gene expression changes affected by DANCR knockdown in colorectal cancer cell line HCT116. mRNA profiles of HCT116 Colorectal Cancer cell lines with a negative control vector and two independent shDANCR vectors were generated by deep sequencing using Illumina HiSeq2000.