GEO DataSets

Analysis of U2OS osteosarcoma cells depleted for the ubiquitin carboxyl hydrolase BAP1. BAP1 is a deubiquitinating enzyme. Results provide insight into the role of BAP1 in transcriptional regulation.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 3 other, 2 protocol sets

Platform:

GPL570

Series:

GSE23035

9 Samples

Download data: CEL

(Submitter supplied) The deubiquitinase BAP1 is a candidate tumor suppressor regulating cell proliferation in human and is required for development in Drosophila. BAP1 is assembled into high molecular weight transcriptional multi-protein complexes. In order to identify potential BAP1 target genes, global mRNA expression profiling using microarrays was conducted.

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS5238

Platform:

GPL570

9 Samples

Download data: CEL

(Submitter supplied) We report the genome wide binding sites of BAP1, HCF1 and OGT in bone marrow derived macrophages. De-ubiquitinating enzyme BAP1 is mutated in a hereditary cancer syndrome with increased risk of mesothelioma and uveal melanoma. Somatic BAP1 mutations occur in various malignancies. We show that mouse Bap1 gene deletion is lethal during embryogenesis, but systemic or hematopoietic-restricted deletion in adults recapitulates features of human myelodysplastic syndrome (MDS). more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9250

4 Samples

Download data: BED

(Submitter supplied) BAP1 has been studied as a tumor suppressor. Our aim was to characterize genes that were altered in various hematopoietic cell types upon deletion of BAP1.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL13692

24 Samples

Download data: GPR

(Submitter supplied) Renal cell carcinoma (RCC) exhibits some unusual features and genes commonly mutated in cancer are rarely mutated in clear-cell RCC (ccRCC), the most common type. The most prevalent genetic alteration in ccRCC is the inactivation of the tumor suppressor gene VHL. Using whole-genome and exome sequencing we discovered BAP1 as a novel tumor suppressor in ccRCC that shows little overlap with mutations in PBRM1, another recent tumor suppressor. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4282

Platform:

GPL570

76 Samples

Download data: CEL

(Submitter supplied) Renal cell carcinoma (RCC) exhibits some unusual features and genes commonly mutated in cancer are rarely mutated in clear-cell RCC (ccRCC), the most common type. The most prevalent genetic alteration in ccRCC is the inactivation of the tumor suppressor gene VHL. Using whole-genome and exome sequencing we discovered BAP1 as a novel tumor suppressor in ccRCC that shows little overlap with mutations in PBRM1, another recent tumor suppressor. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platforms:

GPL6801 GPL6984

82 Samples

Download data: CEL, CHP, TXT

Analysis of BAP1- and PBRM1-deficient ccRCC primary tumors, tumors growing in immunodeficient mice (tumorgrafts), and matched normal kidney cortices. BAP1 loss, but not PBRM1 loss, is associated with high-grade tumors. Results provide insight into molecular classification of RCC subtypes.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 3 genotype/variation, 29 individual, 11 tissue sets

Platform:

GPL570

Series:

GSE36895

76 Samples

Download data: CEL

(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

(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

30 Samples

Download data: BW, TXT

(Submitter supplied) BAP1 is a deubiquitinase (DUB) of the Ubiquitin C-terminal Hydrolase (UCH) family that regulates gene expression and other cellular processes, via deubiquitination of histone H2AK119ub and other substrates. BAP1 is an important tumour suppressor in human, expressed and functional across many cell-types and tissues, including those of the immune system. B lymphocytes are the mediators of humoral immune response, however the role of BAP1 in B cell development and physiology remains poorly understood. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

21 Samples

Download data: TXT

(Submitter supplied) BAP1 is a deubiquitinase (DUB) of the Ubiquitin C-terminal Hydrolase (UCH) family that regulates gene expression and other cellular processes, via deubiquitination of histone H2AK119ub and other substrates. BAP1 is an important tumour suppressor in human, expressed and functional across many cell-types and tissues, including those of the immune system. B lymphocytes are the mediators of humoral immune response, however the role of BAP1 in B cell development and physiology remains poorly understood. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

9 Samples

Download data: BED, BW

(Submitter supplied) Nuclear deubiquitinase BAP1 (BRCA1-Associated Protein 1) is a core component of multiprotein complexes that promote transcription by reversing the ubiquitination of histone 2A (H2A). BAP1 is a tumor suppressor gene whose germline loss-of-function variants predispose to cancer. To our knowledge, there are very rare examples of different germline variants in the same gene causing either a NDD or a tumor predisposition syndrome. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

10 Samples

Download data: TXT

(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:

GPL9115 GPL570

18 Samples

Download data: BED, BEDGRAPH, CEL

(Submitter supplied) Analysis of transcriptional regulation in human cells has implicated a large number of promoter-specific DNA-binding proteins that regulate transcription via diverse mechanisms. In some cases, these DNA-sequence-specific factors associate with intermediaries that orchestrate interactions with the chromatin-modifying enzymes. One such intermediary is HCF-1 (host-cell factor-1; HCFC1). HCF-1, first identified for its involvement in herpes-simplex virus transcription and subsequently shown to be an important cell-cycle regulator, has a poorly defined role in genome-wide transcriptional regulation. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9115

12 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) We compared in triplicate mRNA levels from cells treated with siRNA against either HCF-1 or, as a negative control, luciferase. We observed that 19% of Refseq annotated genes are differentially expressed (either up or down regulated with a multiple testing corrected p value of ≤ 0.05) upon depletion of HCF-1. This large number of differentially expressed genes upon HCF-1 depletion demonstrates a broad role of HCF-1 in the regulation of gene expression.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL570 GPL9115

18 Samples

Download data: BED, BEDGRAPH, CEL, TXT

(Submitter supplied) The bromodomain and extra-terminal (BET) protein BRD4 functions as a transcriptional activator and is a therapeutic target for different human cancers. Here, we report a critical link between Polycomb repressive deubiquitinase-BAP1 (PR-DUB) complex and BRD4, which is bridged by the physical interaction between additional sex combs-like protein 3 (ASXL3) in small cell lung cancer (SCLC). We further showed that ASXL3 functions as an adaptor protein, which directly interacts with BRD4-extra-terminal (ET) domain via a novel BRD4 binding motif (BBM), and maintains chromatin occupancy of BRD4 at active enhancers. more...

Organism:

Mus musculus; Homo sapiens

Type:

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

Platforms:

GPL16791 GPL17021

37 Samples

Download data: BW

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

Organism:

Homo sapiens

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

3 Samples

Download data: BIGWIG

(Submitter supplied) Yin Yang 1 (YY1) is a multifunctional transcription factor shown to be critical in a variety of biological processes. Although it has been reported to be regulated by multiple types of post-translational modifications (PTMs), whether YY1 is methylated, which enzyme methylates YY1, and hence the functional significance of YY1 methylation remain completely unknown. Here we reported the first methyltransferase, SET7/9 (KMT7), capable of methylating YY1 in vitro and in vivo at two highly conserved lysine (K) residues, K173 and K411, located in two distinct domains, one in the central glycine-rich region and the other in the very carboxyl-terminus. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

1 Sample

Download data: BIGWIG

(Submitter supplied) Yin Yang 1 (YY1) is a multifunctional transcription factor shown to be critical in a variety of biological processes. Although it has been reported to be regulated by multiple types of post-translational modifications (PTMs), whether YY1 is methylated, which enzyme methylates YY1, and hence the functional significance of YY1 methylation remain completely unknown. Here we reported the first methyltransferase, SET7/9 (KMT7), capable of methylating YY1 in vitro and in vivo at two highly conserved lysine (K) residues, K173 and K411, located in two distinct domains, one in the central glycine-rich region and the other in the very carboxyl-terminus. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

2 Samples

Download data: BIGWIG

(Submitter supplied) Compared to the well-established roles of apoptosis in tumor suppression, the roles and regulatory mechanisms of ferroptosis, a non-apoptotic form of cell death, in tumor biology remain much less understood. BRCA1-associated protein 1 (BAP1) encodes a nuclear de-ubiquitinating (DUB) enzyme to reduce histone 2A ubiquitination (H2Aub) on chromatin, and is a tumor suppressor in several human cancers. Here, integrated transcriptomic, epigenomic, and cancer genomic analyses link BAP1 to metabolism-related biological processes, including oxidative stress response, and identify cystine transporter SLC7A11 as a BAP1-repressed target gene with high relevance to BAP1-mediated tumor suppression in human cancers. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: BW