Project description:This SuperSeries is composed of the following subset Series: GSE11580: Time course RA-treatment of B16 mouse melanoma cells GSE11584: Melan-a mouse melanocytes vs. B16 mouse melanoma cells Keywords: SuperSeries Refer to individual Series
Project description:Gene expression profile of melan-a mouse melanocytes vs. B16 mouse melanoma cells. Experiment Overall Design: Balanced block design with dye swap. Six biological replicates, one replicate per array.
Project description:The melan-a cell line is derived from immortalized mouse melanocytes obtained from Ink4a-ARF-/- mice. RNA-seq was performed to assess the global nature of transcript and gene expression profiles in melan-a cells. These RNA-seq data, along with separate ChIP-seq performed in melan-a cells (GSE38498), were used to correlate gene expression patterns with the presence or absence of transcription factors of interest.
Project description:Using ChIP-seq for p300 and H3K4me1, we identified 2,489 putative melanocyte enhancer loci in the mouse genome. We demonstrated that these putative enhancers are evolutionarily constrained, enriched for sequence motifs predicted to bind key melanocyte transcription factors, located near genes relevant to melanocyte biology, and capable of driving reporter gene expression with high frequency in cultured melanocytes and in melanocytes of transgenic zebrafish. ChIP-seq for EP300 and H3K4me1 in the mouse melanocyte cell line melan-a.
Project description:We performed ChIP-Seq analysis of SOX10, histone H3 lysine 27 acetylation (H3K27ac) and H3K27 trimethylation (H3K27me3) in melanocytes to profile the genomic binding sites of SOX10 and the chromatin landscape. In parallel, we generated Sox10 haploinsufficient cell lines using gene knockout approaches and conducted microarray gene expression analysis to identify functional gene targets of SOX10 transcriptional regulation in melanocytes. We demonstrate that SOX10 predominantly engages “open” chromatin, binds to melanocyte enhancer elements and plays a central role in transcriptional activation and repression of functionally distinct classes of genes. Furthermore, we identified cis-regulatory sequence motifs of putative co-regulatory transcription factors that define SOX10-activated and SOX10-repressed target genes. Our results uncover novel mechanisms and roles of SOX10 in global transcriptional regulation of diverse regulatory pathways in the melanocyte lineage. ChIP-seq profiling of SOX10, H3K27ac, and H3K27me3 in the mouse melanocyte cell line melan-Ink4a-Arf-1 (melan-a).
Project description:With high genetic heterogeneity in melanoma, understanding epigenetic and transcriptional differences between melanocytes and melanoma cells will enable further understanding of the genes, pathways, and epigenetic regions influencing melanoma development. We performed RNA-seq and ATAC-seq on fluorescently-isolated melanocytes and melanoma cells from a zebrafish melanoma model.
Project description:The goal of this study is to compare the miRNA profiles of melanoma cells B16-derived exosomes with B16 cells and normal cells JB6-derived exosomes.
Project description:Analysis of gene expression patterns in cancer improved the understanding the mechanisms underlying the process of metastatic progression. Recent studies have attributed an important role to B-1 cells, a subset of B lymphocytes, in melanoma progression. It was already demonstrated that in vitro interaction between B16 melanoma cells and B-1 lymphocytes induced increase in metastatic potential of B16 lineage. In this study we used a microarray approach to assess gene expression profile in B16 melanoma cells after contacting B-1 lymphocytes (B16B1).
