RNA-seq of patient-derived melanoma cells depleted for GLI1 and SOX2

We report the RNA-seq of melanoma cells depleted for SOX2 and GLI1. Three pairs of total RNAs from each condition were generated for library preparations and subsequent RNA-seq. All samples had over 50 million reads with over 93% of the reads mapping to the human genome (obtained from the UCSC Genome Browser assembly ID:hg19). Using differential expression analysis (fold change (FC)>1.5, false discovery rate (FDR)<0.1 as standard cut-offs), we identified 1104 entities commonly altered in both SOX2- and GLI1-knocked down cells. We grouped genes into enrichment clusters revealed by DAVID functional annotation tool (https://david.ncifcrf.gov/). Overall design: Examination of the top pathways significantly downregulated in both SOX2-and GLI1-depleted melanoma cells and identification of SOX2/GLI1 commonly regulated genes