GEO DataSets

Analysis of primary cutaneous melanomas derived from iMet (metastasis-capable) and iHRAS* (non-metastatic) models. Results provide insight into the molecular mechanisms underlying metastatic potential.

Organism:

Mus musculus

Type:

Expression profiling by array, transformed count, 3 cell type, 2 disease state, 3 genotype/variation sets

Platform:

GPL8321

Series:

GSE29074

16 Samples

Download data: CEL

(Submitter supplied) Clinical and genomic evidence support the view that the metastatic potential of a primary tumor may be dictated by transforming events acquired early in the tumorigenic process. It has been proposed that the presence of such pro-metastatic events in early-stage tumors reflects their additional capability to function as oncogenes. Here, to test this ‘deterministic’ hypothesis and identify potential pro-metastasis oncogenes, we adopted a comparative oncogenomics-guided functional genetic screening strategy involving (i) global transcriptomic data from two genetically engineered mouse models of melanoma with contrasting metastatic potential, (ii) genomic and transcriptomic profiles of human primary and metastatic melanoma and (iii) an invasion screen in TERT-immortalized human melanocytes and melanoma cells in vitro as well as (iv) evidence of expression selection in human melanoma tissues. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS4531

Platform:

GPL8321

16 Samples

Download data: CEL

(Submitter supplied) Melanoma can progress rapidly from a slow-growing surgically curable lesion to aggressive metastatic disease, with high mortality and poor response to current therapies. The mechanisms underlying melanoma progression and resistance to therapeutic agents are not well understood. There are few treatment options for melanoma once it has metastasized, and new biomarkers that aid diagnosis, predict clinical outcome, and suggest new therapies are required. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL8640

34 Samples

Download data: GPR

(Submitter supplied) We sought to identify genes and gene signatures which correlate with progression by sampling human melanomas from nevi, primary, and metastatic tumors. The large number of samples also permits analysis within groups.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

121 Samples

Download data: CEL

(Submitter supplied) Highly rearranged and mutated cancer genomes present major challenges in the identification of pathogenetic events driving the cancer process. Here, we engineered lymphoma-prone mice with chromosomal instability to assess the utility of mouse models in cancer gene discovery and the extent of cross-species overlap in cancer-associated copy number aberrations. Integrating with targeted re-sequencing, our comparative oncogenomic studies efficiently identified FBXW7 and PTEN as commonly deleted or mutated tumor suppressors in human T-cell acute lymphoblastic leukemia/lymphoma (T-ALL). more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL887

123 Samples

Download data: TXT

(Submitter supplied) Publication abstract: An incomplete view of the (epi)genetic events that drive melanoma initiation and progression has been a major barrier to rational development of effective therapeutics and prognostic diagnostics for melanoma patients. Recent approaches that integrate human melanoma genomic and transcriptomic data provide unprecedented opportunities to discover oncogenic melanoma drivers. One limitation, however, is that human melanoma genome exhibits a radically altered cytogenetic profile. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

10 Samples

Download data: TXT

(Submitter supplied) Expression was generated on tumors from 41 iBIP mice, which were previously described (Kwong, JCI, 2015).

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

41 Samples

Download data: CEL

(Submitter supplied) Malignant melanoma is the most fatal skin cancer with a high degree of genetic and epigenetic aberrations. To investigate the role of DNA methylation on melanoma heterogeneity, we performed methylated DNA immunoprecipitation (MeDIP) microarray analysis of 10 primary melanoma cell cultures.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platforms:

GPL17148 GPL15160

10 Samples

Download data: PAIR, TXT

(Submitter supplied) SOX9 is generally not expressed in melanomas with a high proliferative capacity but is expressed in melanomas with a high invasive capacity. Here we overexpress full length SOX9 in M010817, a melanoma cell culture with high proliferative capacity but low invasive capacity.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

6 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

synthetic construct; Homo sapiens

Type:

Non-coding RNA profiling by array

Platforms:

GPL19295 GPL19296

220 Samples

Download data: TXT

(Submitter supplied) We performed global microRNA expression profiling of a cohort of primary melanoma patient samples linked to a well-annotated clinical database. The goal of this study was to identify microRNA that are associated to or correlated with various clinical parameters and patient outcomes. Candidate microRNA were identified for building prognostic models and functional testing.

Organism:

synthetic construct; Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL19296

119 Samples

Download data: TXT

(Submitter supplied) We performed global microRNA expression profiling of a cohort of primary melanoma patient samples linked to a well-annotated clinical database. The goal of this study was to identify microRNA that are associated to or correlated with various clinical parameters and patient outcomes. Candidate microRNA were identified for building prognostic models and functional testing.

Organism:

synthetic construct; Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL19295

101 Samples

Download data: TXT

(Submitter supplied) Wild-type (WT) miR-378a-3p or edited miR-378a-3p were expressed in SB2 KD-ADAR1 cells to identify the genes regulated by edited miR-378a-3p vs WT miR-378a-3p. PARVA was one of the genes identified to be regulated by edited miR-378a-3p. We demonstrate that this regulation of PARVA is lost in highly metastatic melanoma cells. Microarray analysis was used to evaluate the robustness and reproducibility of the method used to generate the ex vivo tumor tissue model and confirm its ability to recapitulate the essential features of the original tumor.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

6 Samples

Download data: CEL

(Submitter supplied) T1C3 is a clonal cell line from a human melanoma tumor, expressing PNA lectin, and characterized by a high capacity of dermal invasion. IC8 is a clonal cell line from a human melanoma tumor, negative for PNA lectin, and non-invasive. To identify new gene markers involved in the mechanisms of early invasion, oligonuclotide microarrays were used to assess transcriptional chnages between the two cell lines.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4803

4 Samples

Download data: GPR

(Submitter supplied) Using 1 melanocyte and 6 melanoma cell line (3 pair of primary and metastatic), we generated base-resolution DNA methylation maps to document DNA methylation drivers of melanoma metastasis.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL16791

7 Samples

Download data: TXT

(Submitter supplied) Purpose: Asess the transcritpional changes induced upon RAB7 knock-down in melanoma (SK-Mel-28 and UACC-62) and in colon cancer (HCT-116) cell lines. Methods: mRNA profiles of tumor cell lines (SK-Mel-28, UACC-62, HCT-116) stably expressing scrambled shRNA or RAB7 shRNA (harvested at day 3 after lentiviral infection) were generated by deep sequencing, using three biological replicates per condition. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10999

18 Samples

Download data: TXT

(Submitter supplied) microRNA-7-5p (miR-7-5p) is an established tumor suppressor in multiple cancer types and inhibits growth and invasion by suppressing expression and activity of the epidermal growth factor receptor (EGFR) signaling pathway. While melanoma is not typically driven by EGFR signaling, expression of miR-7-5p is reduced in metastatic tumors compared to primary melanoma. Here, we investigated the biological and clinical significance of miR-7-5p in melanoma. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

6 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Methylation profiling by array; Expression profiling by array

Platforms:

GPL23126 GPL13534

31 Samples

Download data: CEL, IDAT

(Submitter supplied) Uveal melanoma (UM) is an aggressive malignancy, in which nearly 50% of the patients die from metastatic disease. Formalin-fixed paraffin-embedded (FFPE) samples represent a valuable source of tumor tissue. Our aim was to investigate differential DNA methylation correlated to gene expression in relation to survival data.We sought to identify aberrant DNA methylation of genes that could be linked to metastatic disease and poor survival. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL23126

8 Samples

Download data: CEL

(Submitter supplied) Uveal melanoma (UM) is an aggressive malignancy, in which nearly 50% of the patients die from metastatic disease. Formalin-fixed paraffin-embedded (FFPE) samples represent a valuable source of tumor tissue. Our aim was to investigate differential DNA methylation in relation to histopathological classification and survival data. In addition, we sought to identify aberrant DNA methylation of genes that could be linked to metastatic disease and poor survival. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

23 Samples

Download data: IDAT, TXT