GEO DataSets

(Submitter supplied) A complex network of inflammation succeeds somatic cell transformation and malignant disease. Immune cells and their associated molecules are responsible for detecting and eliminating cancer cells as they establish themselves as the precursors of a tumour. By the time a patient has a detectable solid tumour, cancer cells have escaped the initial immune response mechanisms. To date, no model exists to allow us to study the underlying mechanisms that govern the initial phase of the immune response as cells are transformed to become the precursors of cancer. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

4 Samples

Download data: TXT

(Submitter supplied) The most common mutation in human melanoma, BRAF(V600E), activates the serine/threonine kinase BRAF and causes excessive activity in the mitogen-activated protein kinase pathway. BRAF(V600E) mutations are also present in benign melanocytic naevi, highlighting the importance of additional genetic alterations in the genesis of malignant tumours. Such changes include recurrent copy number variations that result in the amplification of oncogenes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9115

5 Samples

Download data: WIG, YLF

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

Organism:

Danio rerio; Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL6244 GPL10392 GPL9115

19 Samples

Download data: CEL, CHP, TXT, WIG, YLF

(Submitter supplied) Investigation of expression differences induced by expression of the histone methyltransferase SETDB1 in human melanoma short-term culture WM451-Lu.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

6 Samples

Download data: CEL, CHP

(Submitter supplied) Investigation of expression differences between melanomas harvested from MiniCoopR-GFP versus MiniCoopR-SETDB1 transgenic zebrafish.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL10392

8 Samples

Download data: TXT

(Submitter supplied) We compared the transformation efficiencies of mutant NRAS and KRAS in immortal, non-transformed Ink4a/Arf-deficient melanocytes. NRAS mutation leads to increased cellular proliferation and is potently tumorigenic. In contrast, KRAS mutation does not enhance melanocyte proliferation and is only weakly tumorigenic on its own. While both NRAS and KRAS activate MAPK signaling, only NRAS enhances MYC activity in these cells. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL4487

12 Samples

Download data: GPR

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

Organism:

Danio rerio

Type:

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

Platform:

GPL18413

23 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) 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.

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18413

12 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) 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.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

11 Samples

Download data: TXT, XLSX

(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) 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) OIS is characterized by a stable proliferation arrest and secretion of pro-inflammatory cytokines and chemokines, the senescence-associated secretory phenotype (SASP). Proliferation arrest and the SASP collaborate to enact tumor suppression, the former by blocking cell proliferation and the latter by recruiting immune cells to clear damaged cells. However, the interactions of OIS cells with the immune system are still poorly defined. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11002

9 Samples

Download data: CSV, DIFF

(Submitter supplied) To explore the roles of cell-type specific methylation QTL (meQTL) for melanoma GWAS annotation, we generated DNA methylation data from the same sample set as our previouse eQTL study including 106 primary melanocyte cultures. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 480,000 CpGs in 106 primary melanocyte cultures. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13534

106 Samples

Download data: IDAT, TXT

(Submitter supplied) Interrogation of gene regulatory circuits in complex organisms requires precise tools for the selection of individual cell types, as well as robust methods for tissue-specific labeling and biochemical profiling of target proteins. By exploiting multiple transgenesis strategies, we have developed a tissue-specific binary in vivo biotinylation system in zebrafish termed "biotagging", a versatile methodology that uses genetically-encoded components to biotinylate target proteins, enabling in-depth genome-wide analyses of their molecular interactions. more...

Organism:

Danio rerio

Type:

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

Platforms:

GPL14875 GPL18413 GPL20828

18 Samples

Download data: BW

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

Organism:

Danio rerio; Homo sapiens

Type:

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

4 related Platforms

48 Samples

Download data: BW, NARROWPEAK