GEO DataSets

(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

(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

(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

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

(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

(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

(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

(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

(Submitter supplied) We assess whole-genome H3K9me3 distribution in cancer cells and find that H3K9me3 is largely enriched in long interspersed nuclear element-1 (LINE-1). A significant proportion of KDM4B-dependent H3K9me3 was located in evolutionarily young LINE-1 elements, which likely retain retrotransposition activity. Ectopic expression of KDM4B promoted LINE-1 expression, while depletion of KDM4B reduced it. Furthermore, KDM4B overexpression enhanced LINE-1 retrotransposition efficacy, copy number, and associated DNA damage, presumably via the histone demethylase activity of KDM4B. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20795

6 Samples

Download data: BED

(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

(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:

GPL9052

17 Samples

Download data: BED, TXT

(Submitter supplied) Endocrine resistance is a major obstacle in treating estrogen receptor α (ER)-positive (+) breast cancer. In order to better understand the mechanism of endocrine resistance, we established a stable tamoxifen-resistant (TamR) MCF7L cell model by culturing the parental (P) MCF7L cells in the presence of 100 nM of 4-hydroxytamoxifen (4HT) for over 6 months. To characterize the transcriptomic profiles in these cells, we performed an RNA-seq analysis.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9052

2 Samples

Download data: TXT

(Submitter supplied) Gene expression profiles (RNA seq of parental MCF7 cells and tamoxifen resistant cells after ER or FOXA1 knock down and after overexpression of FOXA1 in parenatl cells).

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9052

11 Samples

Download data: TXT

(Submitter supplied) ChIP sequencing of FOXA1 in MCF7 cells and tamoxifen resistant MCF7 cells

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9052

4 Samples

Download data: BED

(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

(Submitter supplied) Estrogen Receptor (ER) is a steroid hormone receptor that regulates epithelial genes in breast cancer. ER forms a regulatory network with the other transcription factors, FOXA1 and GATA3. GATA3 is known to be capable of specifying chromatin localization of FOXA1 and ER. GATA3 has been identified as one of the most frequently mutated genes in breast cancer. However, how GATA3 mutations impact this transcriptional network is unknown. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: BIGWIG

(Submitter supplied) A pioneer transcription factor, GATA3, is one of the most frequently mutated genes in breast cancer, yet the impact of these mutations is largely unknown. We generated a GATA3 mutant cell line (T47D wt/R330fs) by CRISPR. Mutation of one allele of GATA3 led to loss of binding and decreased expression at a subset of genes, including Progesterone Receptor. At other loci, associated with epithelial to mesenchymal transition, gain of binding at a novel sequence motif correlated with increased gene expression. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL18573 GPL11154

96 Samples

Download data: TXT

(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

Platforms:

GPL18573 GPL11154

22 Samples

Download data: BIGWIG, BW

(Submitter supplied) Forkhead box A1 (FOXA1) is a pioneer factor that facilitates chromatin binding and function of lineage-specific and oncogenic transcription factors. Here, we have demonstrated that FOXA1 overexpression in estrogen receptor-positive breast cancer cells drives genome-wide enhancer reprogramming to activate pro-metastatic transcriptional programs. We have identified the hypoxia-inducible transcription factor HIF-2α as the top FOXA1-engaged super-enhancer target induced by FOXA1 overexpression, activating pro-metastatic gene signatures associated with poor breast cancer outcome. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

9 Samples

Download data: TXT

(Submitter supplied) Forkhead box A1 (FOXA1) is a pioneer factor that facilitates chromatin binding and function of lineage-specific and oncogenic transcription factors. Here, we have demonstrated that FOXA1 overexpression in estrogen receptor-positive breast cancer cells drives genome-wide enhancer reprogramming to activate pro-metastatic transcriptional programs. Specifically, FOXA1 overexpression generated more gained chromatin binding regions than the lost regions with decreased FOXA1 binding. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

13 Samples

Download data: BIGWIG, BW