Next Generation Sequencing Facilitates Quantitative Analysis of shNC/sh337/ and EV/337 Transcriptomes

Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare PDAC cell silencing or overexpressing linc00337 with control cells transcriptomse profiling (RNA-seq) Methods: Retinal mRNA profiles of PANC1 stable cells(shNC and sh337) and AsPC1 stable cells (EV and 337) were generated by deep sequencing, using Illumina GAIIx. 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 TaqMan and SYBR Green assays Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample and identified more than 20000 transcripts in each stable cell lines. Conclusions: Our study illustrated the biological significance of linc00337 in PDAC progression. PDAC stable cell lines' mRNA profiles by deep sequencing, in triplicate, using Illumina Hiseq2000.