GSE117529
RNA/WES/ATAC/scRNA sequencing of murine melanoma primary and LN metastases
The purpose of this study is to identify transcriptional, mutational, andepigenetic differences between LN metastases from primary tumors. Using in vivo serial passaging of the minimally metastatic syngeneic murine melanoma cell line B16-F0, we have generated nearly 300 unique cell lines spanning nine generations of in vivo passaging, derived from LNs, and exhibiting varying degrees of metastatic potential to LNs. Here, we perform mRNAseq on 30 of the lines representing a range of anatomical locations (distinct LNs), generations, and phylogenetic lineages. The subsequent differential expression analysis reveals a marked upregulation of immune-related genes. Additionally, we perform WES to identify differences in particular mutations, total mutational burden, and predicted neoantigen burden. Additionally, we perform ATAC-seq to assess changes in chromatin accessibility hat correlate with LN metastasis. We also perform scRNA-seq on dissociated LNs from mice with and without LN metastases. Overall design: mRNA profiles were generated from 30 cell lines derived from the various LN lines and parental. The parental was sequenced in triplicate where each replicate was harvested at distinct passage numbers to account for variability in the profile due to culture. Samples were sequenced on an Illumina HiSeq 2500 to a depth of 50M reads. Following quality filtering, transcript abundance was quantified using Salmon and differential gene expression analysis was performed using DESeq2. LN lines from later generations were compared to the parental or early generation lines. For WES, 10 cell lines were analyzed. These data are accessible directly from SRA at Accession PRJNA820881. For ATAC-seq, 3 samples each from parental, LN3, and LN7 generations were analyzed. For scRNAseq, a LN from tumor naive, parental (non-metastatic) tumor, and LN6 (LN-metastatic) tumor mice each were analyzed.