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MM in murine models: WES

ABSTRACT: MM in murine models: WES

PROVIDER: PRJEB18119 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1742980_1.fastq.gz	Fastqsanger.gz
	ERR1742980_2.fastq.gz	Fastqsanger.gz
	ERR1742990_1.fastq.gz	Fastqsanger.gz
	ERR1742990_2.fastq.gz	Fastqsanger.gz
	ERR1742981_1.fastq.gz	Fastqsanger.gz

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MM in murine models: WES

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Project description:Blood samples from patients with myeloid malignancies were analyzed using whole exome sequencing (WES). Data set from genotyping by microarray of the same samples has been deposited in ArrayExpress under accession number E-MTAB-1845 (https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1845/).

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Project description:WES of murine syngeneic models

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RNA/WES/ATAC/scRNA sequencing of murine melanoma primary and LN metastases

Project description: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.

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