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Links from GEO DataSets

Items: 20

1.

Genome-wide chromatin profiles of PBRM1 Drug treatment [ChIP-Seq]

(Submitter supplied) PBRM1 encodes an accessory subunit of the PBAF subclass of the SWI/SNF chromatin remodeler and the inactivation of PBRM1 is the second most frequent mutational event in kidney cancer. However, the impact of PBRM1 loss on chromatin remodeling, especially pertaining to kidney tumorigenesis, has not been well examined. Here we show that in VHL-deficient renal tumors, PBRM1 deficiency results in aberrant PBAF complexes that localize to de novo genomic loci and activate the pro-tumorigenic NF-κB pathway. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24676
32 Samples
Download data: NARROWPEAK
Series
Accession:
GSE222244
ID:
200222244
2.

Genome-wide chromatin profiles of PBRM1 Drug treatment [RNA-Seq]

(Submitter supplied) PBRM1 encodes an accessory subunit of the PBAF subclass of the SWI/SNF chromatin remodeler and the inactivation of PBRM1 is the second most frequent mutational event in kidney cancer. However, the impact of PBRM1 loss on chromatin remodeling, especially pertaining to kidney tumorigenesis, has not been well examined. Here we show that in VHL-deficient renal tumors, PBRM1 deficiency results in aberrant PBAF complexes that localize to de novo genomic loci and activate the pro-tumorigenic NF-κB pathway. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24676
20 Samples
Download data: TXT
Series
Accession:
GSE222245
ID:
200222245
3.

Genome-wide chromatin profiles of PBRM1

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
5 related Platforms
170 Samples
Download data: BED, NARROWPEAK
Series
Accession:
GSE152735
ID:
200152735
4.

Genome-wide chromatin profiles of PBRM1 [RNA-Seq]

(Submitter supplied) PBRM1 is an accessory subunit of the PBAF subclass of the SWI/SNF chromatin remodeler. The inactivation of PBRM1 is the second most frequent mutational event in kidney tumorigenesis. Here we show that in VHL-deficient ccRCC tumors, PBRM1 loss results in an altered PBAF complex that retains the association between SMARCA4 and ARID2 but disengages BRD7 from SMARCA4. The PBRM1-deficient PBAF complexes redistribute from promoter proxy regions to distal enhancer regions. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL11154 GPL20795 GPL24676
41 Samples
Download data: TXT
Series
Accession:
GSE152734
ID:
200152734
5.

Genome-wide chromatin profiles of PBRM1 [ChIP-Seq]

(Submitter supplied) PBRM1 encodes an accessory subunit of the PBAF subclass of the SWI/SNF chromatin remodeler and the inactivation of PBRM1 is the second most frequent mutational event in kidney cancer. However, the impact of PBRM1 loss on chromatin remodeling, especially pertaining to kidney tumorigenesis, has not been well examined. Here we show that in VHL-deficient renal tumors, PBRM1 deficiency results in aberrant PBAF complexes that localize to de novo genomic loci and activate the pro-tumorigenic NF-?B pathway. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL20301 GPL16791
77 Samples
Download data: BED
Series
Accession:
GSE152681
ID:
200152681
6.

The effects of PBRM1 loss on the ccRCC transcriptome

(Submitter supplied) Subunits of SWI/SNF chromatin remodeling complexes are frequently mutated in human malignancies. The PBAF complex is composed of multiple subunits, including the tumor suppressor protein PBRM1 (BAF180), as well as ARID2 (BAF200), that are unique to this SWI/SNF complex. PBRM1 is mutated in various cancers, with a high mutation frequency in clear cell renal cell carcinoma (ccRCC). In this study, we integrate RNA-seq, histone modification ChIP-seq, and ATAC-seq data to show that loss of PBRM1 results in de novo gains in H3K4me3 peaks throughout the epigenome including activation of a retinoic acid biosynthesis and signaling gene signature. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
18 Samples
Download data: SF
Series
Accession:
GSE196129
ID:
200196129
7.

Genome-wide maps of histone modification and chromatin remodeler binding in mouse calvaria derived stromal cell line (OP9)

(Submitter supplied) We have used chromatin immunoprecipitation followed by high throughput sequencing to map regions of chromatin remodeler and histone modification state. We have used this data to understand the global distribution in stromal cell and probable mechanism of transcriptional regulation.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17021
14 Samples
Download data: BW
Series
Accession:
GSE139216
ID:
200139216
8.

MUC1-C Drives Lineage Plasticity in Progression to Neuroendocrine Prostate Cancer

(Submitter supplied) Neuroendocrine prostate cancer (NEPC) is a highly aggressive malignancy of increasing prevalence with an unmet need for targeted therapeutic approaches. The oncogenic MUC1-C protein is overexpressed in castration-resistant prostate cancer (CRPC) and NEPC; however, there is no known role for MUC1-C in driving lineage plasticity to these advanced PC phenotypes. The present studies demonstrate that upregulation of MUC1-C in androgen-independent (AI) PC cells suppresses androgen receptor (AR) axis signaling and induces the neural BRN2 transcription factor by a previously unrecognized MYC-mediated mechanism. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16791
12 Samples
Download data: CSV
9.

Transcriptome profiling of Caki2 cells re-expressing Polybromo-1 (PBRM1)

(Submitter supplied) PBRM1 is a component of the PBAF chromatin remodelling complex and has been observed to be deregulated in a significant proportion of patients with clear-cell Renal Cell Carcinoma (ccRCC). This study employs RNA-Seq to identify differentially expressed genes in cellular models of ccRCC by expressing PBRM1 in PBRM1-deficient Caki2 cells.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11154
6 Samples
Download data: TXT
10.

PBAF complex deficiency in melanoma mediates BAF occupancy and transcription factor dynamics

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18573
70 Samples
Download data: BW
Series
Accession:
GSE172386
ID:
200172386
11.

PBAF complex deficiency in melanoma mediates BAF occupancy and transcription factor dynamics (RNA-Seq)

(Submitter supplied) ARID2 is an essential subunit of the SWI/SNF PBAF chromatin remodeler and is highly mutate in melanoma. To elucidate the role of ARID2 in melanoma biology and chromatin structure we utilized CRISPR Cas9 methodology to generate isogenic ARID2 WT and KO melanoma clonal cell lines. We further map the genomic localization of several SWI/SNF subunits, open and repressed chromatin markers, and multiple transcription factors to characterize how loss of the PBAF subcomplex alters chromatin accessibility and the melanoma transcription factor network. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
18 Samples
Download data: CSV
12.

PBAF complex deficiency in melanoma mediates BAF occupancy and transcription factor dynamics (Chromatin)

(Submitter supplied) ARID2 is an essential subunit of the SWI/SNF PBAF chromatin remodeler and is highly mutate in melanoma. To elucidate the role of ARID2 in melanoma biology and chromatin structure we utilized CRISPR Cas9 methodology to generate isogenic ARID2 WT and KO melanoma clonal cell lines. We further map the genomic localization of several SWI/SNF subunits, open and repressed chromatin markers, and multiple transcription factors to characterize how loss of the PBAF subcomplex alters chromatin accessibility and the melanoma transcription factor network. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18573
52 Samples
Download data: BW
Series
Accession:
GSE172383
ID:
200172383
13.

PBRM1 bromodomains associate with RNA to facilitate chromatin association

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing; Other
Platform:
GPL24676
31 Samples
Download data: BW
Series
Accession:
GSE221620
ID:
200221620
14.

PBRM1 bromodomains associate with RNA to facilitate chromatin association (CLIP-seq)

(Submitter supplied) PBRM1 is a subunit of the PBAF chromatin remodeling complex, which is mutated in 40-50% of clear cell renal cell carcinoma patients. It is thought to largely function as a chromatin binding subunit of the PBAF complex, but the molecular mechanism underlying this activity is not fully known. PBRM1 contains six tandem bromodomains which are known to cooperate in binding of nucleosomes acetylated at histone H3 lysine 14 (H3K14ac). more...
Organism:
Homo sapiens
Type:
Other
Platform:
GPL24676
7 Samples
Download data: BW
Series
Accession:
GSE221619
ID:
200221619
15.

PBRM1 bromodomains associate with RNA to facilitate chromatin association (ChIP-seq)

(Submitter supplied) PBRM1 is a subunit of the PBAF chromatin remodeling complex, which is mutated in 40-50% of clear cell renal cell carcinoma patients. It is thought to largely function as a chromatin binding subunit of the PBAF complex, but the molecular mechanism underlying this activity is not fully known. PBRM1 contains six tandem bromodomains which are known to cooperate in binding of nucleosomes acetylated at histone H3 lysine 14 (H3K14ac). more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24676
24 Samples
Download data: BW
Series
Accession:
GSE221618
ID:
200221618
16.

The ATPase module of mammalian SWI/SNF family complexes mediates subcomplex identity and catalytic activity-independent genomic targeting

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18573
63 Samples
Download data: BW, TXT
Series
Accession:
GSE117735
ID:
200117735
17.

The mSWI/SNF ATPase module mediates subcomplex identity and non-catalytic targeting in SCCOHT [ChIP-seq]

(Submitter supplied) Perturbations to mammalian SWI/SNF (mSWI/SNF) chromatin remodeling complexes have been widely implicated as driving events across cancers1. One such perturbation is the dual loss of the SMARCA4 and SMARCA2 ATPase subunits, which has recently been implicated in rare cancers such as small cell carcinoma of the ovary, hypercalcemic type (SCCOHT)2-5, SMARCA4-deficient thoracic sarcomas6 and dedifferentiated endometrial carcinomas7. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18573
44 Samples
Download data: BW
Series
Accession:
GSE117734
ID:
200117734
18.

The mSWI/SNF ATPase module mediates subcomplex identity and non-catalytic targeting in SCCOHT [RNA-seq]

(Submitter supplied) Perturbations to mammalian SWI/SNF (mSWI/SNF) chromatin remodeling complexes have been widely implicated as driving events across cancers1. One such perturbation is the dual loss of the SMARCA4 and SMARCA2 ATPase subunits, which has recently been implicated in rare cancers such as small cell carcinoma of the ovary, hypercalcemic type (SCCOHT)2-5, SMARCA4-deficient thoracic sarcomas6 and dedifferentiated endometrial carcinomas7. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
11 Samples
Download data: TXT
19.

The mSWI/SNF ATPase module mediates subcomplex identity and non-catalytic targeting in SCCOHT [ATAC-seq]

(Submitter supplied) Perturbations to mammalian SWI/SNF (mSWI/SNF) chromatin remodeling complexes have been widely implicated as driving events across cancers1. One such perturbation is the dual loss of the SMARCA4 and SMARCA2 ATPase subunits, which has recently been implicated in rare cancers such as small cell carcinoma of the ovary, hypercalcemic type (SCCOHT)2-5, SMARCA4-deficient thoracic sarcomas6 and dedifferentiated endometrial carcinomas7. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18573
8 Samples
Download data: BW
Series
Accession:
GSE117301
ID:
200117301
20.

Transcriptional profiling of 2 SCCOHT PDX models and the SCCOHT cell lines BIN67 and SCCOHT1

(Submitter supplied) Transcriptional profiling of 2 SCCOHT patient-derived xenograft (PDX) models and 2 SCCOHT cell lines compared to normal ovary to investigate underlying biology of SCCOHT.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL4133
4 Samples
Download data: TXT
Series
Accession:
GSE66434
ID:
200066434
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