Similar studies for GEO DataSets (Select 200130357) - GEO DataSets

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Items: 20

Select item 2001303571.

BAP1 loss triggers DNA methylomic repatterning in highly aggressive Class 2 uveal melanomas

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

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing; Methylation profiling by genome tiling array

Platforms:: GPL21145 GPL13534 GPL18573
26 Samples

Download data: IDAT, TAB

Series

Accession:: GSE130357

ID:: 200130357

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2001303562.

BAP1 loss triggers DNA methylomic repatterning in highly aggressive Class 2 uveal melanomas [RNA-Seq]

(Submitter supplied) The strong association between BAP1 mutations and highly aggressive Class 2 uveal melanoma (UM) suggests that epigenetic alterations may play a significant role in tumor progression. Thus, we characterized the impact of BAP1 loss on the DNA methylome in UM.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
6 Samples

Download data: TAB

Series

Accession:: GSE130356

ID:: 200130356

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Select item 2001303543.

BAP1 loss triggers DNA methylomic repatterning in highly aggressive Class 2 uveal melanomas [BeadChip 450K]

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

Platform:: GPL13534
12 Samples

Download data: IDAT, TXT

Series

Accession:: GSE130354

ID:: 200130354

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Select item 2001302954.

BAP1 loss triggers DNA methylomic repatterning in highly aggressive Class 2 uveal melanomas [MethylationEPIC]

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

Platform:: GPL21145
8 Samples

Download data: IDAT, TXT

Series

Accession:: GSE130295

ID:: 200130295

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Select item 2001101935.

RNA-seq analysis of BAP1-depleted uveal melanoma cells

(Submitter supplied) OCM-1A uveal melanoma cells were infected with lentivirus carrying shRNA expression constructs specific for BAP1 or GFP (control), and placed under selection for 6 days. RNA-seq was performed.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16791
6 Samples

Download data: TXT

Series

Accession:: GSE110193

ID:: 200110193

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Select item 2000736526.

Gene expression analysis of uveal melanoma Class 1 tumors with and without metastasis

(Submitter supplied) Uveal melanoma can be classified by gene expression profiling (GEP) into Class 1 (low metastatic risk) and Class 2 (high metastatic risk), the latter being strongly associated with mutational inactivation of the tumor suppressor BAP1. Nevertheless, a small percentage of Class 1 tumors give rise to metastatic disease, and the purpose of this study was to identify biomarkers of metastasis in Class 1 tumors.

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL10558
13 Samples

Download data: TXT

Series

Accession:: GSE73652

ID:: 200073652

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Select item 2000488637.

Gene expression changes resulting from the stable loss of BAP1 in uveal melanoma cell lines

(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

Series

Accession:: GSE48863

ID:: 200048863

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Select item 2001499208.

BAP1 mutant uveal melanoma is stratified by metabolic phenotypes with distinct vulnerability to metabolic inhibitors

(Submitter supplied) Inactivating mutations of BAP1 are linked with an increased risk of developing metastasis in UM, but the roles of BAP1 in UM progression is unclear. To characterize BAP1’s functions in UM, we performed RNA sequencing on BAP1 wild-type and mutant UM cell lines. Gene set enrichment analysis showed that there is metabolic heterogeneity in BAP1 mutant UM cells based on their oxidative phosphorylation gene signature.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
15 Samples

Download data: TXT

Series

Accession:: GSE149920

ID:: 200149920

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Select item 2001976569.

In uveal melanoma Gα-protein GNA11 mutations convey a shorter disease-specific survival and are more strongly associated with loss of BAP1 and chromosomal alterations than Gα-protein GNAQ mutations

(Submitter supplied) Mutations in the Gα-genes GNAQ and GNA11 are found in 85-90% of uveal melanomas (UMs). We analyzed the association between GNAQ and GNA11 mutations with disease-specific survival, gene expression profiles, and cytogenetic alterations in 219 UMs. Our analysis showed a shorter disease-specific survival of GNA11-mutated cases as compared to those carrying a GNAQ mutation (HR=1.97 [95%CI 1.12-3.46], p=0.02). more...

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL13158
8 Samples

Download data: CDF, CEL, CHP, CSV

Series

Accession:: GSE197656

ID:: 200197656

Select item 20002489610.

Global expression analysis of BAP1 knockdown in transfected 92.1 cells

(Submitter supplied) Analysis of the effect that reduced BAP1 levels have on global gene expression.The hypothesis tested was that reduction in BAP1 levels would produce changes in gene expression similar to changes observed in class 2 uveal melanomas. Data provided insight into genes that are disrupted with reduced BAP1 levels.

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL10558
6 Samples

Download data: TXT

Series

Accession:: GSE24896

ID:: 200024896

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Select item 20014578211.

Transcriptomic analysis of BAP1 negative primary and metastatic uveal melanoma tumors

(Submitter supplied) Individualized immune transcriptome analysis were successfully constructed through expression profiling of a total of immune genes in uveal melanoma tumors.

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL25262
11 Samples

Download data: RCC

Series

Accession:: GSE145782

ID:: 200145782

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Select item 20007803312.

Expression Data from Uveal Melanoma patient-derived xenograft and tumor of origin

(Submitter supplied) We compare the genetic profiles of the primary tumors of uveal melanoma or metastasis to their corresponding xenografts that have been passaged over time. The study included patient tumors and corresponding xenografts at very early (P1), early (P4), and late (P9) in vivo passages

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL21472
45 Samples

Download data: CEL

Series

Accession:: GSE78033

ID:: 200078033

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Select item 20016064513.

Integrated differential DNA methylation and gene expression of formalin-fixed paraffin-embedded uveal melanoma specimens identifies genes associated with early metastasis and poor prognosis

(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

Series

Accession:: GSE160645

ID:: 200160645

Select item 20015687714.

Gene expression data from formalin-fixed paraffin-embedded (FFPE) human uveal melanoma tumors; subset early metastasis vs subset no metastasis

(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

Series

Accession:: GSE156877

ID:: 200156877

Select item 20015687615.

llumina 450k array was used to identify DNA methylation data from formalin-fixed paraffine-embedded (FFPE) human uveal melanoma correlated to gene expression, metastasis and poor prognosis

(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

Series

Accession:: GSE156876

ID:: 200156876

Select item 20012659916.

Loss of Bap1 in Xenopus laevis embryos

(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

Series

Accession:: GSE126599

ID:: 200126599

PubMed Full text in PMC Similar studies

Select item 20012659817.

Loss of Bap1 leads to an increased global methylation and decrease in H3K27AC enhancer marks around key lineage commitment genes in Xenopus laevis embryos [ChIP-seq]

(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

Series

Accession:: GSE126598

ID:: 200126598

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20012659718.

Bap1 loss leads to decreased expression of lineage specific commitment genes, and increased expression of pluripotency genes [RNA-seq]

(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

Series

Accession:: GSE126597

ID:: 200126597

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20018119419.

RNA-seq analysis of BAP1 mutant and wild-type uveal melanoma cell lines

(Submitter supplied) Inactivating mutations of BAP1 are associated with an increased risk of developing metastasis in uveal melanoma (UM), but the roles of BAP1 in UM progression is unclear. To characterize BAP1’s functions in UM, we performed RNA sequencing on BAP1 wild-type and mutant UM cell lines. Differential analysis revealed that BAP1 loss is associated with an upregulated gene expression profile of multiple cell adhesion molecules (CAMs), including E-cadherin (CDH1), cell adhesion molecule 1 (CADM1), and syndecan-2 (SDC2).

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
9 Samples

Download data: TXT

Series

Accession:: GSE181194

ID:: 200181194

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Select item 20007457320.

Combined Genetic and Genealogic Studies Uncover a Large BAP1 Cancer Syndrome Kindred Tracing Back Nine Generations to a Common Ancestor from the 1700s.

(Submitter supplied) We recently discovered an inherited cancer syndrome caused by BRCA1-Associated Protein 1 (BAP1) germline mutations with high incidence of mesothelioma, uveal melanoma and other cancers and very high penetrance by age 55. To identify families with the BAP1 cancer syndrome, we screened patients with family histories of multiple mesotheliomas and melanomas and/or multiple cancers. We identified four families that shared an identical BAP1 mutation: they lived across the US and did not appear to be related. more...

Organism:: Homo sapiens

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

Platform:: GPL13135
8 Samples

Download data: IDAT, TXT

Series

Accession:: GSE74573

ID:: 200074573

PubMed Full text in PMC Similar studies

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