Transcriptomics revealed the putative mechanism underlying the impact of HFL1 fibroblasts with overexpression of GALC on LoVo cell

ABSTRACT: Purpose:To elucidate the mechanism by which overexpression of GALC senescent fibroblasts promote the tumor properties of LoVo CRC cells Methods: LoVo cell which co-cultured with LV-GALC HFL1 fibroblasts cells and LoVo cell which co-cultured with LV-NC HFL1 fibroblasts cells using Transwell chamber were generated by deep sequencing, in triplicate, 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 Conclusions: Our study represents the first detailed analysis of the impact of LV-GALC HFL1 fibroblasts and LV-NC HFL1 fibroblasts on LoVo cell with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles.We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.Fibroblasts regulate the tumorigenicity of CRC cells and play important roles in tumor biology.

ORGANISM(S): Homo sapiens

PROVIDER: GSE145662 | GEO | 2020/02/25

REPOSITORIES: GEO