Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA341525 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We investigated the miRNAome in human melanocyte and melanoma cell lines using high-throughput RNA sequencing. We identified a group of dysregulated miRNAs by comparing the miRNA expression profiles among melanoma cell lines. Target genes of these miRNAs participate in functions associated with the cell cycle and apoptosis. Gene networks were built to investigate the interactions of genes during melanoma progression. We identified that the key genes that regulate melanoma cell proliferation were regulated by miRNAs. Our findings provide further knowledge regarding the mechanisms of melanoma development. miRNA profiles of melanocyte (HEMn-LP), low metastatic melanoma (A375) and high metastatic melanoma (A2058) cell line were generated using Illumina GA
2015-07-13 | E-GEOD-66823 | biostudies-arrayexpress
Project description:In most solid tumors, the Warburg effect, also known as aerobic glycolysis, represents a major biochemical alteration associated with malignant transformation. Although the exact molecular mechanisms underlying this metabolic change remain to be clarified, the biochemical alteration in cancer cell energy metabolism opens novel avenues for the development of therapeutic strategies to preferentially kill cancer cells by targeting the glycolytic pathway. We used microarrays to focus on differences among A375, M6 melanoma cells and normal melanocytes (HeMa cells) in terms of glucose metabolism- and invasion-related properties. The transcript analysis showed that melanoma cells exhibit typical transcriptional features of a glycolytic phenotype, matched with high invasive markers (including increased expression of several matrix metallo-proteinases)
2016-09-02 | GSE86373 | GEO
Project description:Aberrant DNA methylation and histone modifications both contribute to carcinogenesis, but how these two epigenetic factors interact to impact gene expression remain unclear. To address this issue, we studied gene expression profiles, DNA methylation and two key histone modifications (H3K4me3 and H3K27me3), in two types of normal melanocytes (HEMn and HEMa) and two melanoma cell lines SK-MEL-28 and LOXIMVI. Using these data, we analyzed the relationship between epigenetic factors and gene expression status in both normal and melanoma cells, and the impact of epigenetic switches on gene expression during melanomagenesis. ChIP-seq analysis of H3K4me3 and H3K27me3 in two types of normal melanocytes (HEMn and HEMa) and two melanoma cell lines (SK-MEL-28 and LOXIMVI).
2013-12-01 | E-GEOD-33930 | biostudies-arrayexpress
Project description:Aberrant DNA methylation and histone modifications both contribute to carcinogenesis, but how these two epigenetic factors interact to impact gene expression remain unclear. To address this issue, we studied gene expression profiles, DNA methylation and two key histone modifications (H3K4me3 and H3K27me3), in two normal melanocytes (HEMn and HEMa) and two melanoma cell lines SK-MEL-28 and LOXIMVI. Using these data, we analyzed the relationship between epigenetic factors and gene expression status in both normal and melanoma cells, and the impact of epigenetic switches on gene expression change during melanomagenesis. Each of the two normal melanocytes (HEMn and HEMa) and the two melanoma cell lines SK-MEL-28 and LOXIMVI was cultured in triplicate. For each cell line, the same culture conditions and cell density were applied to the triplicates. Total RNA was extracted and microarray analysis was performed for genome-wide gene expression profiling. Using the Sentrix Human-HT12 v4 Beadchip, all four cell samples, each in triplicate, were examined in 12 individual arrays on a same beadchip. Thus, together with the data on DNA methylation and histone modifications, we could not only analyze the epigenetic regulation of gene expression in each cell sample, but also investigate the expression change associated with epigenetic changes in melanoma when compared to normal melanocytes.
2013-09-04 | E-GEOD-31909 | biostudies-arrayexpress
Project description:Melanoma cell lines were genotyped to evaluate copy number differences between nodular melanoma (NM) and superficial spreading melanoma (SSM). Cell lines were also evaluated for copy number alterations in the SKP2/p27 axis. Affymetrix SNP arrays were performed according to manufacturer's instructions using DNA extracted from 18 melanoma cell lines and 4 melanocyte controls. Affymetrix SNP6.0 Array data for melanoma cell lines Copy number analysis of Affymetrix SNP 6.0 arrays was performed on 18 melanoma cell lines including 2 primary superficial spreading melanoma, 2 primary nodular melanoma, 2 metastatic nodular melanoma, and 12 metastatic cell lines. Four melanocyte control lines were also evaluated including 2 immortalized melanocyte cell lines (Hermes 1 and 2B) and 2 normal melanocyte lines cultured from neonatal foreskin (HEM-N and HEM-LP) that were used to construct the baseline for copy number analysis.
2010-10-21 | E-GEOD-22305 | biostudies-arrayexpress
Project description:The A375, human BRAFV600E mutant melanoma, cell line (wildtype), two PTEN-null, BRAFV600E cell lines (KO5 and KO11), and PI3K overexpression cells (WT and PI3K H1047R mutant) were treated with small molecule inhibitors (dabrafenib, BRAF inhibitor; trametinib, MEK inhibitor alone and in combination for 0, 1 and 7 days
2019-04-27 | GSE130396 | GEO
Project description:To generate drug signatures in human A375 melanoma cell lines. A375 cell line was plated at 4 x 105 cells/mL overnight and treated with ciclopirox or crizotinib at 75% inhibitory concentrations (IC75, determined previously at 72h of treatment) or DMSO (vehicle) for 8h or 24h before harvest.
2018-01-01 | GSE59340 | GEO
Project description:To generate drug signatures in human A375 melanoma cell lines. A375 cell line was plated at 4 x 105 cells/mL overnight and treated with trifluridine or lactimidomycin at 75% inhibitory concentrations (IC75, determined previously at 72h of treatment) or DMSO (vehicle) for 8h or 24h before harvest.
2018-01-01 | GSE59183 | GEO
Project description:The transcription factors PAX3 and MITF are required for the development of the neural crest and melanocyte lineage, and both proteins play important roles in melanoma cell growth and survival. PAX3 transcriptionally activates MITF expression during neural crest development, but the relationship between these transcription factors during melanocyte development and in melanoma cells is currently poorly understood. This study aimed to further our understanding of the interaction between transcriptional networks controlled by PAX3 and MITF by assessing the effect of siRNA-mediated knockdown of PAX3 and MITF in metastatic melanoma cell lines. The goals of this study were to determine (i) if PAX3 is required for maintaining expression of MITF in melanoma and melanocyte cell lines; (ii) whether PAX3 and MITF independently, or redundantly, influence growth and survival in melanoma cell lines; and (iii) to investigate the respective roles of PAX3 and MITF expression in melanoma cell differentiation. Microarrays were used to measure global changes in transcript expression in response to siRNA-mediated knockdown of PAX3 or MITF compared to non-targeting controls in two metastatic melanoma cells lines. RNA was isolated from two different metastatic melanoma cell lines 30 hours after one of four different treaments: (i) transfection with siRNA targeting PAX3; or (ii) transfection with siRNA targeting MITF; or (iii) or transfection with siRNA targeting luciferase (non-targeting negative control); or (iv) treatment with media only (control). Therefore, eight samples were used for gene expression profiling by using GeneChip arrays, with one replicate per cell line per treatment.
2010-01-01 | E-GEOD-16249 | biostudies-arrayexpress
Project description:We report the distribution of H3K27Ac histone marks in multiple human melanoma cell lines with the aim of identifying super-enhancer regions and regions of interest. Also performed ChipSeq for H3K4Me1 to identify active enhancers in a representative human melanoma cell line, A375.
2016-02-01 | GSE75352 | GEO