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Links from GEO DataSets

Items: 20

1.
Full record GDS5662

Histone demethylase KDM3A-deficiency effect on estrogen-stimulated breast cancer cells in vitro

Analysis of estrogen receptor (ER)-positive breast cancer cell line MCF-7 depleted for KDM3A (histone lysine demethylase 3A) then treated with estrogen. Histone lysine methylation is an important regulator of transcription. Results provide insight into role of KDM3A in ER signaling in breast cancer.
Organism:
Homo sapiens
Type:
Expression profiling by array, transformed count, 2 agent, 2 genotype/variation sets
Platform:
GPL10558
Series:
GSE68918
11 Samples
Download data
2.

Identification of KDM3A regulated genes in the ER positive breast cancer cell line MCF-7

(Submitter supplied) Using a siRNA screen we identified the histone demethylase enzyme KDM3A as a potential positive regulator of ER signalling in breast cancer. To interrogate the full extent of KDM3A regulation on ER signalling we assessed basal and estrogen (E2)- stimulated global gene expression changes in KDM3A-depleted MCF-7 cells by microarray analysis using the Illumina Human HT12 Version 4 BeadChip array. We identified ER regulated genes affected by KDM3A knockdown and determined that KDM3A is required for ER recruitment to estrogen response elements in the promotors of ER regulated genes. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Dataset:
GDS5662
Platform:
GPL10558
11 Samples
Download data: TXT
Series
Accession:
GSE68918
ID:
200068918
3.

Identification of the KDM4B regulated transcriptome in the ER positive breast cancer cell line MCF-7

(Submitter supplied) To elucidate the KDM4B regulated transcriptomes in ER-positive breast cancer cells we assessed global gene expression changes in KDM4B-depleted MCF-7 cells by microarray analysis using the Illumina Human HT12 Version 4 BeadChip array. Differentially expressed genes were compared with KDM3A and FOXA1 regulated transcriptomes. We identified 229 genes co-regulated by all three enzymes and that co-regulated genes were involved in cell cycle processes. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL10558
4 Samples
Download data: TXT
Series
Accession:
GSE135427
ID:
200135427
4.

Identification of overlap between KDM3A and FOXA1 regulated transcriptome in the ER positive breast cancer cell line MCF-7

(Submitter supplied) To interrogate the extent of overlap between KDM3A and FOXA1 regulated transcriptomes in ER-positive breast cancer cells we assessed global gene expression changes in KDM3A-depleted and FOXA1-depleted MCF-7 cells by microarray analysis using the Illumina Human HT12 Version 4 BeadChip array. We identified that 43% of the KDM3A regulated transcriptome was also regulated by FOXA1 and that 43% of the FOXA1 regulated transcriptome was also regulated by KDM3A. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL10558
9 Samples
Download data: TXT
Series
Accession:
GSE124270
ID:
200124270
5.

The histone demethylase KDM3A regulates the transcriptional program of the androgen receptor in prostate cancer cells

(Submitter supplied) To identify the genes regulated by androgen receptor (AR), we performed the profiling array analysis on the CWR22Rv1 cells and determined the differentially expressed genes upon the knockdown of AR.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL16686
4 Samples
Download data: CEL
Series
Accession:
GSE86547
ID:
200086547
6.

Epigenomic profiling reveals the key function of histone H3K9 methylation during tumor transformation process

(Submitter supplied) To understand transcriptome and epigenome profilings alteration during breast cancer initiation and development, we constructed a in vitro breast cancer transformation model. And then, we use mRNA-Seq to uncover differential expression genes during breast cancer transformation process. For epigenomic profilings, we specificly analysis genome wide H3K9me2, H3K9me3,H3K4me3 and H3K27me3 modifications using ChIP-Seq. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL11154
34 Samples
Download data: TXT, WIG
Series
Accession:
GSE64367
ID:
200064367
7.

Specific phosphorylation of histone demethylase KDM3A determines target gene expression in response to heat shock

(Submitter supplied) Histone lysine (K) residues, which are modified by methyl- and acetyl-transferases, diversely regulate RNA synthesis. Unlike the ubiquitously activating effect of histone K acetylation, the effects of histone K methylation vary with the number of methyl groups added and with the position of these groups in the histone tails. Histone K demethylases (KDMs) counteract the activity of methyl-transferases and remove methyl group(s) from specific K residues in histones.KDM3A (also known as JHDM2A or JMJD1A) is an H3K9me2/1 demethylase. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL10999
4 Samples
Download data: BED, WIG
Series
Accession:
GSE62309
ID:
200062309
8.

Genome-wide maps of chromatin state and Gene Expression Profiling in HCT116 cells

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform:
GPL11154
74 Samples
Download data: BW, TXT
Series
Accession:
GSE108922
ID:
200108922
9.

Gene Expression Profiling of WT and KDM3A Knocked out Cell

(Submitter supplied) We identified KDM3A, a demethylase of histone H3K9me1/2, as a positive regulator for hippo target genes. We found that H3K27ac upregulation is highly correlated with gene activation, but not H3K4me3; and transcription repression of certain TEAD1 target genes, such as BBC3, is important for the pathway function. KDM3A knockout caused upregulation of H3K9me2 mainly on TEAD1-binding enhancers rather than gene bodies, leading to decrease of H3K27ac and TEAD1 binding on enhancers and impaired transcription.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11154
12 Samples
Download data: TXT
Series
Accession:
GSE108921
ID:
200108921
10.

Genome-wide maps of chromatin state in HCT116 cells.

(Submitter supplied) We identified KDM3A, a demethylase of histone H3K9me1/2, as a positive regulator for hippo target genes. We found that H3K27ac upregulation is highly correlated with gene activation, but not H3K4me3; and transcription repression of certain TEAD1 target genes, such as BBC3, is important for the pathway function. KDM3A knockout caused upregulation of H3K9me2 mainly on TEAD1-binding enhancers rather than gene bodies, leading to decrease of H3K27ac and TEAD1 binding on enhancers and impaired transcription. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL11154
62 Samples
Download data: BW
Series
Accession:
GSE108920
ID:
200108920
11.

Effect of Fbxo22 on ER and SRC-3 recruitment to the genomic loci

(Submitter supplied) The agonistic/antagonistic bio-character of selective estrogen receptor modulators (SERMs) can have therapeutic advantages, particularly in the case of premenopausal breast cancers. Although the contradictory effects of these modulators have been studied in terms of cross-talk between estrogen receptor (ER)-coactivator dynamics and growth factor signaling, the molecular basis of these mechanisms is still obscure. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL9052
8 Samples
Download data: TXT
Series
Accession:
GSE119702
ID:
200119702
12.

The histone demethylase Kdm3a is essential to progression through differentiation

(Submitter supplied) Histone demethylation has important roles in regulating gene expression and forms part of the epigenetic memory system that regulates cell fate and identity, by still poorly understood mechanisms. Here we examined the role played by the histone demethylase Kdm3a, which demethylates lysine 9 of histone H3, during cellular differentiation. Using F9 mouse embryonal carcinoma cells as a model for progression through terminal differentiation, we showed that Kdm3a is essential to differentiation into parietal endoderm-like (PE) cells. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6887
12 Samples
Download data: TXT
Series
Accession:
GSE33841
ID:
200033841
13.

Expression data from precancerous mouse liver under PI3K signaling activation with or without Kdm3a defficiency

(Submitter supplied) Epigenetic gene regulation in various oncogenic pathways is currently an important focus of cancer research. The PI3K pathway plays a pivotal role in hepatocellular carcinoma, but the significance of histone modification in the PI3K pathway-dependent hepatotumorigenesis remains unknown. We used microarrays to investigate the oncogenic gene regulation by histone demethylase Kdm3a under PI3K signaling activation in the liver.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL1261
2 Samples
Download data: CEL, CHP
Series
Accession:
GSE87765
ID:
200087765
14.

Cholesterol biosynthesis pathway as a novel mechanism of resistance to estrogen deprivation in estrogen receptor positive breast cancer

(Submitter supplied) Therapies targeting estrogenic stimulation in estrogen receptor positive (ER+) breast cancer (BC) reduce mortality, but resistance remains a major clinical problem. Molecular studies have shown few high frequency mutations to be associated with endocrine resistance. In contrast, expression profiling of primary ER+ BC samples has identified several promising signatures/networks for targeting. In this study, the cholesterol biosynthesis pathway was the common upregulated pathway in the ER+ LTED but not ER- LTED cell lines, suggesting a potential mechanism dependent on continued ER expression. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL10558
54 Samples
Download data: TXT
Series
Accession:
GSE75971
ID:
200075971
15.

JMJD2B knockdown treatment in normoxia and hypoxia

(Submitter supplied) Estrogen receptor alpha plays a critical role in breast cancer and is a major target in endocrine therapy. HIF-1 alpha have been associated with ER alpha and predict a worse outcome. Recent studies indicate that histone demethylase JMJD2B is a HIF-1 alpha target. However, little is known about the biological functions of JMJD2B, especially in breast cancer. To elucidate the mechanism by which JMJD2B reguates gene expression in normoxia and hypoxia, MCF-7 breast cancer cells were depleted forJMJD2B in normoxia and hypoxia. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL6884
8 Samples
Download data: TXT
Series
Accession:
GSE18384
ID:
200018384
16.

The histone demethylase KDM3A, and its downstream target MCAM, promote Ewing Sarcoma cell migration and metastasis

(Submitter supplied) Ewing Sarcoma is the second most common solid pediatric malignant neoplasm of the bone and soft tissue. Driven by EWS/Ets, or rarely variant, oncogenic fusions, Ewing Sarcoma is a biologically and clinically aggressive disease with a high propensity for metastasis. Our laboratory has previously identified the Jumonji-domain H3K9 me 1/2 histone demethylase KDM3A as a novel oncogene downstream of EWS/Fli1, the most common oncofusion in Ewing Sarcoma. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL11532
9 Samples
Download data: CEL
Series
Accession:
GSE94619
ID:
200094619
17.

Vitamin C Induces Specific Demethylation of H3K9me2 in Mouse Embryonic Stem Cells via Kdm3a/b

(Submitter supplied) Histone methylation patterns regulate gene expression and are highly dynamic during development. The erasure of histone methylation is carried out by histone demethylase enzymes. We had previously shown that vitamin C enhances the activity of Tet enzymes in embryonic stem (ES) cells, leading to DNA demethylation and activation of germline genes. We report here that vitamin C induces a remarkably specific demethylation of histone H3 lysine 9 dimethylation (H3K9me2) in ES cells. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13112
4 Samples
Download data: WIG
Series
Accession:
GSE84009
ID:
200084009
18.

EPRS is a Critical Regulator of Cell Proliferation and Estrogen Signaling in ER+ Breast Cancer

(Submitter supplied) Aminoacyl tRNA synthetases (ARSs) are a class of enzymes with well-conserved housekeeping functions in cellular translation. Recent evidence suggests that ARS genes may participate in a wide array of cellular processes, and may contribute to the pathology of autoimmune disease, cancer, and other diseases. Several studies have suggested a role for the glutamyl prolyl tRNA synthetase (EPRS) in breast cancers, although none has demonstrated any underlying mechanism about how EPRS contributes to carcinogenesis. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11154
12 Samples
Download data: TXT
Series
Accession:
GSE81162
ID:
200081162
19.

ER ChIP-seq of Androstenedione treated Letrozole Resistant Breast Cancer Cell line

(Submitter supplied) Acquired resistance to aromatase inhibitor (AI) therapy is a major clinical problem in the treatment of breast cancer. The detailed mechanisms of how tumour cells develop this resistance remain unclear. Here estrogen receptor ChIPseq analysis identifies adaptations of the ER in response to prolonged letrozole treatment.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL9115 GPL11154 GPL10999
8 Samples
Download data: BED, BEDGRAPH
Series
Accession:
GSE54592
ID:
200054592
20.

Effect of RBP2 on MCF7 breast cancer cells (RNA-seq)

(Submitter supplied) RNA-sequencing analysis of RBP2 overexpressing MCF7 cell lines. RBP2 (also known as JARID1A), a member of the JARID1 family of histone H3 lysine K4 demethylases, has been considered to have an oncogenic potential in several cancer including breast cancer. Results provide insight into the transcriptional regulation of RBP2 in estrogen receptor positve breast cancer.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
6 Samples
Download data: TXT
Series
Accession:
GSE92943
ID:
200092943
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