Single cell RNAseq data from A2058 cell line (Melanoma)

The goal of this study was to unlock the cellular diversity of A2058, a melanoma cell line known to be resistant to BRAF inhibition, by performing single cell RNAseq profiling using a 10X genomics platform. This approach allowed us to study the transcriptional programming of every single melanoma cell, particularly of those cells expressing ABCB5, a cell surface protein involved in invasiveness and resistance to BRAF inhibition. Findings from this study revelaed that ABCB5-expressing cells also expressed melanocytic genes (MITF) but with a distinct transcriptional program to those expressing AXL. We also used this data to identify the expresion of commonly studied drug efflux pumps in melanoma cells. Overall design: Viable A2058 cells were encapsulated and uniquely barcoded using Chromium Single Cell 3' Reagent Kit v2 on a Chromium platform (10X Genomics). Single cell libraries were prepared as recommended by 10X Genomics and sequenced at 30,000 raw reads per cell in a NextSeq500 High Output flow cell (2x150 bp reads). Bioinformatic analyses including alignment, transcript count and cell clustering were performed using the Cell Ranger™ 2.0 software (10X Genomics). Visualization of cell clustering and gene expression analyses were performed on Loupe Cell Browser (10X Genomics).