SAKE (Single-cell RNA-Seq Analysis and Klustering Evaluation) Identifies Markers of Resistance to Targeted BRAF Inhibitors in Melanoma Cell Populations [10x]

The goal of this study is to apply the SAKE algorithms to identify drug-resistant cellular populations as human melanoma cells respond to targeted BRAF inhibitors. Single-cell RNA-Seq data from 10x Genomics platform was analyzed to dissect this problem at multiple scales. Data indicates that BRAF inhibitor resistant cells can emerge from rare populations already present before drug application, with SAKE identifying both novel and known markers of resistance Two Melanoma cell lines were treated with BRAF inhibitor for 6 weeks to derived a parental and resistant cell states. Bulk and single-cell RNA-Seq were generated using Illumina NextSeq to study cell response after drug treatment. UPDATE: [06-01-2023] The processed data files were replaced because the previous processed data files contained GEM barcodes that likely corresponded to background noise (e.g., GEMs with free-floating mRNA from lysed or dead cells). The updated processed data files now contain only barcodes that pass the filtering for missing cells/empty drops, and thus correspond to detected cell and feature counts that should be used for downstream analysis.