GEO DataSets

(Submitter supplied) DNA methylation, histone modifications, and nucleosomal occupancy collaborate to cause silencing of tumor related genes in cancer. The development of drugs that target these processes is therefore important for cancer therapy. Inhibitors of DNA methylation and histone deacetylation have already been approved by the FDA for the treatment of hematologic malignancies. However, drugs that target the other mechanisms still need to be developed. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6102

6 Samples

Download data: CSV

(Submitter supplied) DNA methylation, histone modifications, and nucleosomal occupancy collaborate to cause silencing of tumor related genes in cancer. The development of drugs that target these processes is therefore important for cancer therapy. Inhibitors of DNA methylation and histone deacetylation have already been approved by the FDA for the treatment of hematologic malignancies. However, drugs that target the other mechanisms still need to be developed. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6884

10 Samples

Download data: CSV

(Submitter supplied) Polycomb protein EZH2-mediated gene silencing is implicated in breast tumorigenesis through methylation of histone H3 on Lysine 27 (H3K27). We have previously shown that S-adenosylhomocysteine hydrolase (SAHH) inhibitor 3-Deazaneplanocin A (DZNep) can modulate histone methylation and disrupt EZH2 complex. Here, we used DZNep, together with other chromatin remodeling agents, as well as RNA interference-mediated EZH2 depletion, to probe the role of EZH2 in coordination with other epigenetic components in gene regulation in breast cancer cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL2700

24 Samples

Download data: TXT

(Submitter supplied) We demonstrated that 3-Deazaneplanocin A (DZNep), a histone methyltransferase inhibitor, induce robust apoptosis in AML cells through increased ROS production and ER stress. We identified a core gene signature including TXNIP, a major redox control molecule which is crucial in DZNep-induced apoptosis.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

4 Samples

Download data: CEL

(Submitter supplied) Background:Aberrant DNA methylation that silences tumor suppressor genes occurs frequently in patients with acute myeloid leukemia (AML). Treatment of AML patients with the inhibitor of DNA methylation, 5-aza-2'-deoxycytidine (5-AZA-CdR) can induce complete remissions, but most patients will relapse. The clinical efficacy of 5-AZA-CdR may be influenced by its limited capacity to activate tumor suppressor genes silenced by methylation of lysine 27 histone H3 (H3K27) by EZH2. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: FPKM_TRACKING

(Submitter supplied) Histone modifcations at the p15INK4b gene were compared in sample with p15INK4b DNA methylation vs. samples with no DNA methylation AML clinical samples without DNA methylation exhibit bivalent histone modifications at p15INK4b, while clinical samples with DNA methylation display lower H3K4me3 and retain H3K27me3

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL8754

40 Samples

Download data: TXT

(Submitter supplied) Expression profiling the response to inhibition of DNA methylation and histone deacetylation. Comparison of expression in HepG2 cells treated with 5-aza-dC, Trichostatin A, both, or none (control) to change methylation and acetylation status. Background:DNA methylation and histone deacetylation are epigenetic mechanisms that play major roles in eukaryotic gene regulation. We hypothesize that many genes in the human hepatoma cell line HepG2 are regulated by DNA methylation and histone deacetylation. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS2213

Platform:

GPL570

16 Samples

Download data

Analysis of HepG2 hepatoma cells following treatment with 5-aza-2'-deoxycytidine (5-aza-dC) to inhibit DNA methylation, or trichostatin A (TSA) to inhibit histone deacetylation, or both. Results identify epigentically regulated genes in hepatoma cells.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 4 agent sets

Platform:

GPL570

Series:

GSE5230

16 Samples

Download data

(Submitter supplied) 3-deazaneplanocin A (DZNeP) is a promising cancer drug affecting the methylation status of histone lysine residues. To investigate the specificity and mode of action of DZNeP, zebrafish embryos displaying high histone methyltransferase activity were cultured with DZNeP and histone methylation (H3K4me3, H3K9me3, H3K27me3) was mapped by ChIP-chip genome-wide promoter at post-MBT stage (5.3 hpf) . We used a custom 2.1M probe HD promoter array (Nimblegen) for ChIP and input DNA hybridization. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10835

6 Samples

Download data: PAIR

(Submitter supplied) The 3-Deazaneplanocin A (DZNep), one of S-adenosylhomocysteine (AdoHcy) hydrolase inhibitors, has shown antitumor activities in a broad range of solid tumors and acute myeloid leukemia. Here, we examined its effects on multiple myeloma (MM) cells and found that, at 500 nM, it potently inhibited growth and induced apoptosis in 2 of 8 MM cell lines. RNA from un-treated and DZNep treated cells was profiled by Affymetrix HG-U133 Plus 2.0 microarray and genes with a significant change in gene expression were determined by significance analysis of microarray (SAM) testing. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4288

Platform:

GPL570

8 Samples

Download data: CEL, CHP

Analysis of MM cell lines (KMS18, MM.1S, NCI-H929, OPM-2) exposed to 500nM 3-Deazaneplanocin A (DZNep). DZNep potently inhibited growth and induced apoptosis in the NCI-H929 and MM.1S cell lines. Results provide insight into the molecular mechanisms underlying DZNep-induced apoptosis in MM cells.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 agent, 4 cell line sets

Platform:

GPL570

Series:

GSE26921

8 Samples

Download data: CEL, CHP

(Submitter supplied) Genetic and epigenetic defects in Wnt/?-catenin signaling play important roles in colorectal cancer progression. Here we identify DACT3, a member of the DACT (Dpr/Frodo) gene family, as a negative regulator of Wnt/ß-catenin signaling that is transcriptionally repressed in colorectal cancer. Unlike other Wnt signaling inhibitors that are silenced by DNA methylation, DACT3 repression is associated with bivalent histone modifications. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6104

60 Samples

Download data: TXT

(Submitter supplied) Genetic and epigenetic defects in Wnt/ß-catenin signaling play important roles in colorectal cancer progression. Here we identify DACT3, a member of the DACT (Dpr/Frodo) gene family, as a negative regulator of Wnt/ß-catenin signaling that is transcriptionally repressed in colorectal cancer. Unlike other Wnt signaling inhibitors that are silenced by DNA methylation, DACT3 repression is associated with bivalent histone modifications. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6104

12 Samples

Download data: TXT

(Submitter supplied) 24 colon normal and tumor pairs using Illumina BeadChip Human Ref8-v2. Genetic and epigenetic defects in Wnt/ß-catenin signaling play important roles in colorectal cancer progression. Here we identify DACT3, a member of the DACT (Dpr/Frodo) gene family, as a negative regulator of Wnt/ß-catenin signaling that is transcriptionally repressed in colorectal cancer. Unlike other Wnt signaling inhibitors that are silenced by DNA methylation, DACT3 repression is associated with bivalent histone modifications. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6104

48 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by array

Platforms:

GPL10558 GPL13534

32 Samples

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(Submitter supplied) A combinatorial treatment consisting of a DNMTi and a LSD1i shows synergistic effects in reactivating aberrantly silenced genes by enriching H3K4me2 and H3K4me.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

24 Samples

Download data

(Submitter supplied) A combinatorial treatment consisting of a DNMTi and a LSD1i shows synergistic effects in reactivating aberrantly silenced genes by enriching H3K4me2 and H3K4me.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

8 Samples

Download data: TXT

(Submitter supplied) A characteristic feature of anaplastic large cell lymphoma (ALCL) is the significant reduction of the T-cell expression program despite its T-cell origin, a finding very similar to the loss of B-cell identity of classical Hodgkin lymphoma (cHL). Previously we demonstrated that epigenetic mechanisms are active in cHL to induce this peculiar phenotype. The results show that combined DNA demethylation and histone acetylation of T-cell lines induce an almost complete extinction of the T-cell phenotype, including the down-regulation of essential T-cell receptor signalling pathway genes such as CD3, LCK and ZAP70, as well as an up-regulation of ALCL-characteristic genes. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

16 Samples

Download data: CEL

(Submitter supplied) mRNA expression after Ezh2 knock down was analyzed to identify genes regulated by Ezh2.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

3 Samples

Download data: TXT

(Submitter supplied) Very little is known on the nature of epigenetic states in developing zebrafish despite its growing importance as a model organism in developmental biology. We report histone modifications on promoters of pluripotency genes in zebrafish embryos at the mid-late blastula transition (MBT+) stage. We identify three classes of expressed genes based on these profiles: (1) those with a promoter occupied by marks of active genes without any repressive marks; (2) those co-occupied by both activating and repressive modifications; of these genes, klf4 was notably found to be mosaically expressed in the embryo, possibly accounting for this epigenetic pattern; (3) those occupied by repressive marks with, surprisingly, little not acetylated H3K9 or H4. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL9998

7 Samples

Download data: TXT