GEO DataSets

(Submitter supplied) The MITF-low melanoma transcriptional signature is predictive of poor outcome for patients but little is known about its biological signature. We used genetic models of zebrafish with low expression of mitfa (MITF-low) to study this biological subtype. We performed whole bulk RNA-seq to classify zebrafish MITF-low melanoma that cluster mainly by their directionality of growth and assess their resemblance to patients’ MITF-low subgroups. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20828 GPL18413

140 Samples

Download data: TXT

(Submitter supplied) The MITF-low melanoma transcriptional signature is predictive of poor outcome for patients but little is known about its biological signature. We used genetic models of zebrafish with low expression of mitfa (MITF-low) to study this biological subtype. Using genetic inhibition of MITF activity we discover minimal residual disease at the site of regression. We performed single cell RNA-seq (Smart-seq2) to characterise cells at the site of residual disease, and put in relation with primary tumours and recurring disease.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

332 Samples

Download data: TXT

(Submitter supplied) Investigation of expression differences between melanomas harvested from MiniCoopR-GFP versus MiniCoopR-SETDB1 transgenic zebrafish The embryos described in this study are further analyzed in a manuscript submitted for publication by White, et al.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL1319

12 Samples

Download data: CEL

(Submitter supplied) Investigation of expression differences between skin and melanomas from a transgenic BRAFV600E zebrafish model of melanoma The embryos described in this study are further analyzed in a manuscript submitted for publication by White, et al.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL1319

15 Samples

Download data: CEL

(Submitter supplied) Identification of genes differentially regulated after treatment of zebrafish embryos from 50% epiboly to 24hpf with 6.5uM leflunomide

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL1319

6 Samples

Download data: CEL

(Submitter supplied) Human A375 melanoma cells were treated with leflunomide 25uM for 3 days, then RNA harvested

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6884

6 Samples

Download data: TXT

(Submitter supplied) 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.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

3 Samples

Download data: TXT

(Submitter supplied) Damage to the gene regulatory network governing terminal differentiation of melanocytes leads to pigmentation phenotypes and increases the risk for melanoma. Microphthalmia-associated transcription factor (MITF) directly activates expression of melanocyte differentiation effectors, and levels of MITF have been proposed to govern the melanoma phenotype. Mutations in the gene encoding Transcription Factor Activator Protein 2 alpha (TFAP2A) cause reduced pigmentation in model organisms and premature hair graying in humans, and TFAP2A expression tends to be lower in advanced melanoma tumors than in benign nevi. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11002

3 Samples

Download data: BIGWIG, NARROWPEAK

(Submitter supplied) Mutations in the gene encoding transcription factor TFAP2A result in pigmentation anomalies in model organisms and premature hair graying in humans. However, the pleiotropic functions of TFAP2A and its redundantly-acting paralogs have made the precise contribution of TFAP2-type activity to melanocyte differentiation unclear. Defining this contribution may help to explain why TFAP2A expression is reduced in advanced-stage melanoma compared to benign nevi. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9442

2 Samples

Download data: BED

(Submitter supplied) The primary cause of cancer deaths is metastasis. While studies have identified multiple signals that drive invasiveness, the first step in metastatic colonisation, the reason for cells to move away from the primary tumor is less well understood. Salubrinal inhibits an eIF2-alpha phosphatase and consequently leads to increase eIF2-alpha phosphorylation and inhibition of the eIF2B translation initiation factor, leading to reprogramming of translation. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

15 Samples

Download data: TXT

(Submitter supplied) The primary cause of cancer deaths is metastasis. While studies have identified multiple signals that drive invasiveness, the first step in metastatic colonization, the reason for cells to move away from the primary tumor is less well understood. The dataset presented here examines the effect of different culture conditions on gene expression by comparing expression of a melanoma cell line in nutrient rich DMEM to MEM. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

12 Samples

Download data: TXT

(Submitter supplied) Adoptive cell therapies (ACT) with cytotoxic T-cell targeting melanocytic antigens can achieve remissions in metastatic melanoma patients, but tumours frequently relapse. To study the underlying mechanisms of resistance we have generated a genetically engineered mouse melanoma model that faithfully recapitulates tumour regression, remission and relapse as seen in patients. HCmel3 mouse melanoma cells were injected into syngneic C57/BL6 (H-2b) mice. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

21 Samples

Download data: TXT

(Submitter supplied) Uveal melanoma (UM) is the most common primary malignancy of the eye in adults, but lacks any FDA-approved therapy for the deadly metastatic disease. Thus, there is great need to dissect the driving mechanisms for UM, and develop strategies to evaluate potential therapeutics. Using a zebrafish model, we previously identified MITF, the master melanocyte transcription factor, as a tumor suppressor in GNAQQ209L-driven UM. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

37 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL21103

22 Samples

Download data: WIG

(Submitter supplied) We have used a mouse model where melanoma can be induced by Tamoxifen treatment that induces expression of oncogenic Braf and deletion of Pten in the melanocyte lineage using a Tyr::Cre-ER-T2 transgene to mediate recombination. Cells from these melanoma tumours were cultured in vitro and the effects of siRNA mediated silencing of transcription factors Mitf and Sox10 was performed and analysed by RNA-seq. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

18 Samples

Download data: XLS

(Submitter supplied) Somatic oncogenic mutation of BRAF coupled with inactivation of PTEN constitute a frequent combination of genomic alterations driving development of human melanoma. Mice genetically engineered to conditionally express oncogenic BrafV600E and inactivate Pten in melanocytes following tamoxifen treatment rapidly develop melanoma. While early stage melanomas comprised melanin-pigmented Mitf and Dct-expressing cells, expression of these and other melanocyte identity genes was lost in later stage tumours that showed histological and molecular characteristics of de-differentiated neural crest type cells. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

4 Samples

Download data: WIG

(Submitter supplied) Recent studies revealed trajectories of mutational events in early melanomagenesis, but the accompanying changes in gene expression are far less understood. Therefore, we performed a comprehensive RNA-Seq analysis of laser-microdissected melanocytic nevi (n=23) and primary melanoma samples (n=57) and characterized the molecular mechanisms of early melanoma development. Using self-organizing maps, unsupervised clustering and analysis of pseudotime (PT) dynamics to identify evolutionary trajectories, we describe here two transcriptomic types of melanocytic nevi (N1 and N2) and primary melanomas (M1 and M2). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

80 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; SNP genotyping by SNP array; Genome variation profiling by SNP array

Platforms:

GPL570 GPL13135

126 Samples

Download data: CEL, IDAT

(Submitter supplied) eQTL is a powerful method to detect genotype-expression correlation. To be able to identify the genes whose expression levels are correlated with melanoma-associated common variants, eQTL analysis was performed in 59 early passage melanoma cell lines

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array; Genome variation profiling by SNP array

Platform:

GPL13135

67 Samples

Download data: IDAT, TXT

(Submitter supplied) eQTL is a powerful method to detect genotype-expression correlation. To be able to identify the genes whose expression levels are correlated with melanoma-associated common variants, eQTL analysis was performed in 59 early passage melanoma cell lines

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

59 Samples

Download data: CEL