GEO DataSets

(Submitter supplied) We demonstrated that loss of Histone 2A Ubiquitination and PRC1 activity drives uveal melanoma progression

Organism:

Homo sapiens

Type:

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

Platforms:

GPL20301 GPL24676

62 Samples

Download data: TXT

(Submitter supplied) Chromosomal instability (CIN) and epigenetic alterations have been implicated in tumor progression and metastasis. Yet, how these two hallmarks of cancer are related remains poorly understood. By integrating genetic, epigenetic, and functional analyses at the single cell level, we show that the progression of uveal melanoma (UM), the most common intraocular primary cancer, is driven by loss of Polycomb Repressive Complex 1 (PRC1) in a subpopulation of tumor cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

7 Samples

Download data: CSV, H5AD

(Submitter supplied) Uveal melanoma is an aggressive cancer that metastasizes to the liver in about half of patients, being at that time almost always fatal. Identification of patients at high risk of metastases may provide indication for a frequent follow-up for early detection of metastases and treatment. The analysis of the gene expression profiling of primary human uveal melanomas showed high expression of SDCBP (encoding for syndecan-binding protein-1 or syntenin-1), which appeared higher in patients with recurrence, whereas expression of syndecans was lower and unrelated to progression. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4281

Platform:

GPL570

29 Samples

Download data: CEL, CHP

Analysis of 29 uveal melanomas isolated from male and female patients. Uveal melanoma is an aggressive intraocular tumor cancer that metastasizes to the liver in ~50% of patients, with high lethality. Results provide insight into molecular pathways involved in uveal melanoma metastatic progression.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 gender, 2 tissue sets

Platform:

GPL570

Series:

GSE27831

29 Samples

Download data: CEL, CHP

(Submitter supplied) Lats1/2 kinases are the core Hippo pathway kinases. In this study, we use RNAseq to analyze the gene expression profiles of adult mouse uveal tract cells and mouse uveal melanoma generated by Lats1/2 deletion induced by AAV-based Cre injection into mouse uveal tract.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

5 Samples

Download data: DIFF, 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

(Submitter supplied) Development of liver metastasis remains the most common cause of mortality in uveal melanoma (UM). Although advances in genomics allowed the direct evaluation of clinical samples of this eye cancer, there is still a need for reliable preclinical models to progress from correlative studies to mechanistic investigations. A few UM cell lines have been characterized, but so far the translation of basic knowledge to the clinic for the treatment of metastatic disease has been incremental at best. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13607

8 Samples

Download data: TXT

(Submitter supplied) Chromosomal instability (CIN) is a driver of cancer metastasis and immune evasion. Yet, the extent to which this effect depends on the immune system remains unknown. Here we show that CIN-induced chronic activation of the cGAS-STING pathway in cancer cells induces signal re-wiring downstream of STING, promoting a pro-metastatic tumor microenvironment (TME). Using ContactTracing, a newly developed, validated, and benchmarked tool to infer conditionally-dependent cell-cell interactions from single cell transcriptomic data, we identify a cancer cell-derived STING-dependent ER stress response that remodels a TME replete with immune suppressive myeloid cells and dysfunctional T cells. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

13 Samples

Download data: H5, H5AD

(Submitter supplied) Uveal melanoma is a highly aggressive cancer with a strong propensity for metastasis, yet little is known about the biological mechanisms underlying this metastatic potential. We recently showed that most metastasizing uveal melanomas, which exhibit a class 2 gene expression profile, contain inactivating mutations in the tumor suppressor BAP1. The aim of this study was to investigate the role of BAP1 in uveal melanoma progression. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

12 Samples

Download data: TXT

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

Organism:

Xenopus laevis

Type:

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

Platform:

GPL21248

29 Samples

Download data: BW

(Submitter supplied) We performed morpholino-mediated knockdown of Bap1 protein expression in Xenopus laevis developing embryos, and analyzed inhibiting and activating histone marks . We find that inhibition of Bap1 leads to decrease in H3K27AC activating makrs around lineage commitment genes, and increased global methylation.

Organism:

Xenopus laevis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21248

20 Samples

Download data: BW

(Submitter supplied) We performed morpholino-mediated knockdown of Bap1 protein expression in Xenopus laevis developing embryos, and analyzed gene expression at stage 12. We find that inhibition of Bap1 leads to decrease in lineage specific commitment genes, and increased expression of pluripotency genes.

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21248

9 Samples

Download data: BW

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL570 GPL11154

8 Samples

Download data: CEL, WIG

(Submitter supplied) Epigenetic regulators have emerged as critical factors governing the biology of cancer. Here, in the context of melanoma, we show that RNF2 is prognostic, exhibiting progression-correlated expression in human melanocytic neoplasms. Through a series of gain of function and loss of function studies, we establish that RNF2 is oncogenic and pro-metastatic. Mechanistically, RNF2-mediated invasive behavior is dependent on its ability to mono-ubiquitinate H2AK119 at the promoter of LTBP2, resulting in silencing of this negative regulator of TGFβ signaling. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: WIG

(Submitter supplied) Epigenetic regulators have emerged as critical factors governing the biology of cancer. Here, in the context of melanoma, we show that RNF2 is prognostic, exhibiting progression-correlated expression in human melanocytic neoplasms. Through a series of gain of function and loss of function studies, we establish that RNF2 is oncogenic and pro-metastatic. Mechanistically, RNF2-mediated invasive behavior is dependent on its ability to mono-ubiquitinate H2AK119 at the promoter of LTBP2, resulting in silencing of this negative regulator of TGFβ signaling. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

4 Samples

Download data: CEL

(Submitter supplied) Gene expression profiling of ABCB1 positive and ABCB1 negative OCM1A cells. ABCB1 is an ATP-dependent transporter efflux pump. OCM1A cell line is derived from uveal melanomas.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6883

6 Samples

Download data: TXT

(Submitter supplied) We analyzed RING1B binding regions in 3T3-L1 cell lines transduced with the retroviral vector for V5-tagged Fbxl10 or its dF-box mutant.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9185

7 Samples

Download data: BAR

(Submitter supplied) Target genes of Fbxl10 during 3T3-L1 adipogenesis was analyzed

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

2 Samples

Download data: CEL, TXT