SRA

Purpose: The goals of this study are to identify differentially expressed genes between two groups of melanoma cell lines (Epgn1 and Epgn3) as compared to control melanocytes. Methods: Melanoma cell line profiles of control melanocytes and primary human cell lines were generated by deep sequencing 75bp paired end reads, in triplicate, using Illumina NextSeq500. Reads were aligned and counts called using STAR. The sequence reads that passed quality filters were analyzed at the transcript isoform level. Results: Using an optimized data analysis workflow, we mapped about 35 million reads per sample to the human genome (build hg37). We identified 4566 transcripts which showed differential expression between groups Epgn1 and Epgn2, with a log fold change =2 and p value <=0.005. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to melanoma progression. Conclusions: Our study allowed us to identify differentially expressed genes between two classes of melanoma cell lines as well as control melanocytes. Further in vitro and in vivo assays using some of the candidate genes identified will allow us to more fully understand primary melanoma progression. Overall design: mRNA profiles of control primary human melanocytes (n=2) and primary human melanoma cell lines (n=6) were generated by deep sequencing, in triplicate, using Illumina NextSeq500.