Browse
Submit Data
Databases
API
Help

Dataset Information

40 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Whole-genome gene expression profiling of normal melanocytes and melanoma cell lines

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

SUBMITTER: LONG HAI

PROVIDER: S-ECPF-GEOD-31909 | biostudies-other |

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

miRNA profiling of Melanoma Cell lines and Normal Melanocytes

Project description:To identify microRNAs potentially involved in melanomagenesis we compared microRNA transcription profiles between melanoma cell lines and cultured melanocytes. miRNA microarrays were manufactured by Agilent Technologies (Santa Clara, CA), and contain 20-40 features targeting each of 470 human miRNAs (Agilent design ID 016436). Sequences of the 470 miRNAs were obtained from the Sanger miRBase, release 9.1. Labeling and hybridization of total RNA samples were performed according to the manufacturer’s protocol. 100ng total RNA was used as input into the labeling reaction, and the entire reaction was hybridized to the array for 20 hours at 55°C. The labeling and hybridizations of the nine human tissues were done 4-5 times using the same starting RNA sample for each tissue. Total RNA was extracted from 51 melanoma cells and 2 pools of melanocytes using the QIAGEN miRNA kits.

| S-ECPF-GEOD-25653 | biostudies-other

Whole-genome gene expression profiling of normal melanocytes and melanoma cell lines

2013-09-04 | GSE31909 | GEO

Whole-genome gene expression profiling of normal melanocytes and melanoma cell lines

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

Transcription profiling of normal human melanocytes and melanoma cell lines from advanced lesions

Project description:Affymetrix oligonucleotide microarrays were used to assess global differential gene expression comparing normal human melanocytes with six independent melanoma cell strains from advanced lesions. The data, validated at the protein level for selected genes, confirmed the overexpression in melanoma cells relative to normal melanocytes of several genes in the growth factor/receptor family that confer growth advantage and metastasis. In addition, novel pathways and patterns of associated expression in melanoma cells not reported before emerged.

| S-ECPF-GEOD-4570 | biostudies-other

Transcription profiling of human normal melanocytes and melamoma cell lines reveal defective cell cycle checkpoint functions in melanoma are associated with altered patterns of gene expression

Project description:Defects in DNA damage responses may underlie genetic instability and malignant progression in melanoma. Cultures of normal human melanocytes (NHMs) and melanoma lines were analyzed to determine whether global patterns of gene expression could predict the efficacy of DNA damage cell cycle checkpoints that arrest growth and suppress genetic instability. NHMs displayed effective G1 and G2 checkpoint responses to ionizing radiation-induced DNA damage. A majority of melanoma cell lines (11/16) displayed significant quantitative defects in one or both checkpoints. Melanomas with B-RAF mutations as a class displayed a significant defect in DNA damage G2 checkpoint function. In contrast the epithelial-like subtype of melanomas with wildtype N-RAS and B-RAF alleles displayed an effective G2 checkpoint but a significant defect in G1 checkpoint function. RNA expression profiling revealed that melanoma lines with defects in the DNA damage G1 checkpoint displayed reduced expression of p53 transcriptional targets, such as CDKN1A and DDB2, and enhanced expression of proliferation-associated genes, such as CDC7 and GEMININ. A Bayesian analysis tool was more accurate than significance analysis of microarrays for predicting checkpoint function using a leave-one-out method. The results suggest that defects in DNA damage checkpoints may be recognized in melanomas through analysis of gene expression. Experiment Overall Design: Normal human melanocyte and melanoma cell lines w/wo mutations in B-raf or N-ras were treated with 1.5 Gy IR irridiartion for G1 and G2 checkpoint determination. RNA was isolated from exponentially growing cultures and applied for microarray hybridizaton with Agilent 44 K (G4112A) array.

| S-ECPF-GEOD-7469 | biostudies-other

Genome-wide gene expression analysis of primary uveal melanoma cells, normal uveal melanocytes, neural crest stem cells, embryonic stem cells and uveal melanoma cell lines MUM2B and OCM1A

Project description:Gene expression in primary uveal melanoma cells and normal cell controls The HumanHT-12 v3 gene expression microarray (Illumina) was used to analyze RNA isolated from snap-frozen primary uveal melanoma tissue isolated from enucleated eyes and from normal cell controls.

| S-ECPF-GEOD-44295 | biostudies-other

gene expression profiling of brain metastatic melanoma cell lines

Project description:Cerebral metastases occur in a majority of metastatic melanoma patients and are a major cause of mortality. Despite this, there is a poor understanding of the molecules/pathways that lead to the brain-metastatic phenotype. Studies designed to address this deficiency and test novel therapeutic approaches have until recently been slowed by an absence of preclinical models of spontaneous CNS metastatic melanoma disease. To address this, we isolated two variants of the human melanoma cell line WM239 (named 131/4-5B1 and 131/4-5B2) which can metastasize spontaneously to brain parenchyma from an orthotopic primary transplant. We have performed gene expression profiling on both brain metastatic cell lines (131/4-5B1 and 131/4-5B2) and compared to the poorly metastatic parental cell line WM239A and a derived highly metastatic variant 113/6-4L in order to examine the mechanisms that influence the progression of malignant melanoma to a brain-metastatic phenotype. Two-condition experiment, brain metastatic cell lines (131/4-5B1 and 131/4-5B2) and compared to the poorly metastatic parental cell line WM239A and a derived highly metastatic variant 113/6-4L. Biological replicates: 4 independently grown and harvested cell line passages. Two technical replicate per condition (including dye swap).

| S-ECPF-GEOD-23601 | biostudies-other

Comparison of growth factor signalling pathway utilisation in cultured normal melanocytes and melanoma cell lines.

Project description:The phosphatidylinositol-3-kinase (PI3K-PKB), mitogen activated protein kinase (MEK-ERK) and the mammalian target of rapamycin (mTOR- p70S6K), are thought to regulate many aspects of tumour cell proliferation and survival. We have examined the utilisation of these three signalling pathways in a number of cell lines derived from patients with metastatic malignant melanoma of known PIK3CA, PTEN, NRAS and BRAF mutational status.Western blotting was used to compare the phosphorylation status of components of the PI3K-PKB, MEK-ERK and mTOR-p70S6K signalling pathways, as indices of pathway utilisation.Normal melanocytes could not be distinguished from melanoma cells on the basis of pathway utilisation when grown in the presence of serum, but could be distinguished upon serum starvation, where signalling protein phosphorylation was generally abrogated. Surprisingly, the differential utilisation of individual pathways was not consistently associated with the presence of an oncogenic or tumour suppressor mutation of genes in these pathways.Utilisation of the PI3K-PKB, MEK-ERK and mTOR-p70S6K signalling pathways in melanoma, as determined by phosphorylation of signalling components, varies widely across a series of cell lines, and does not directly reflect mutation of genes coding these components. The main difference between cultured normal melanocytes and melanoma cells is not the pathway utilisation itself, but rather in the serum dependence of pathway utilisation.

| S-EPMC3352269 | biostudies-literature

miRNA profiling of Melanoma Cell lines and Normal Melanocytes

Project description:To identify microRNAs potentially involved in melanomagenesis we compared microRNA transcription profiles between melanoma cell lines and cultured melanocytes.

2011-10-17 | GSE25653 | GEO

miRNA profiling of Melanoma Cell lines and Normal Melanocytes

2011-10-16 | E-GEOD-25653 | biostudies-arrayexpress