GEO DataSets

(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

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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

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(Submitter supplied) Testing the hypothesis that cytosine methylation and histone deacetylation regulate an overlapping set of genes. Keywords: other

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Datasets:

GDS919 GDS920

Platforms:

GPL1381 GPL1382

13 Samples

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Analysis of 16 day old Columbia plantlets grown in media with 7 ug/ml 5-aza-2'deoxycytosine (aza-dC) to block cytosine methylation (Cm) or 0.5 uM trichostatin A (TSA) to block histone deacetylation (HD) or both. Results provide insight into the interaction between Cm and HD in gene regulation.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array, log ratio, 3 agent sets

Platform:

GPL1382

Series:

GSE1612

5 Samples

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Analysis of 16 day old Columbia plantlets grown in media with 7 ug/ml 5-aza-2'deoxycytosine (aza-dC) to block cytosine methylation (Cm) or 0.5 uM trichostatin A (TSA) to block histone deacetylation (HD) or both. Results provide insight into the interaction between Cm and HD in gene regulation.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array, log ratio, 3 agent sets

Platform:

GPL1382

Series:

GSE1612

5 Samples

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(Submitter supplied) Tumor angiogenesis requires intricate regulation of gene expression in endothelial cells (EC). We recently showed that DNA methyltransferase (DNMT)- and histone deacetylase (HDAC) inhibitors directly repress EC growth and tumor angiogenesis, suggesting that epigenetic modifications mediated by DNMTs and HDACs are involved in regulation of EC gene expression during tumor angiogenesis. To understand the mechanisms behind the epigenetic regulation of tumor angiogenesis, we used microarray analysis to perform a comprehensive screen to identify genes downregulated in tumor-conditioned versus quiescent EC, and re-expressed by 5-aza-2’-deoxycytidine and trichostatin A. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL885

4 Samples

Download data: TXT, XML

(Submitter supplied) To understand the roles of DNA methylation and histone deacetylation in plant gene network that controls plant tolerance to freezing treatment, we used Affymetrix GeneChips ATH-121501 to analysis. For microarray analysis, Arabidopsis (ecotype Columbia) seedlings grew in four types of sterile growth medium: no any other modifying agents, added 7g/ml 0.5 M aza-dC in water (DNA methylation inhibitor), added TSA in methanol (histone deacetylation inhibitor), both aza-dC and TSA, all for 16 day in growth chamber (16-h day length at 70% relative humidity, 23 °C) , then all seedlings were cold treated at 0 °C for 24 h in growth chamber (16-h day length at 70% relative humidity). more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

10 Samples

Download data: CEL, TXT

(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) In order to dtermine the role of histone actylation in gene expresssion, E. histolytica 200:NIH trophozoites were treated with the HDAC inhibitor Trichostatin A, or grown in short chain fatty acids, which have been shown to alter histone actylation patterns in Entamoeba species. Keywords: Expression

Organism:

Entamoeba histolytica

Type:

Expression profiling by array

Platform:

GPL4622

8 Samples

Download data: CEL

(Submitter supplied) 61 human HCCs were analyzed for genome-wide gene expression. Samples were collected at two sites in Germany, Heidelberg (HD) and Hannover (N). The Heidelberg Collection include 40 independent HCC: 19 liver resections and 17 explant liver specimen (4 not determined); median age at surgery was 57 years (range, 16-78), and the male/female ratio was 3:1. All diagnoses were confirmed by histological reevaluation, and use of the samples was approved by the local ethics committee. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL14550

80 Samples

Download data: TXT

(Submitter supplied) Histone acetylation is involved in the regulation of gene expression in plants and eukaryotes. Histone deacetylases (HDACs) are enzymes that catalyze the removal of acetyl groups from histones, which is associated with the repression of gene expression. To study the role of histone acetylation in the regulation of gene expression during seed germination, trichostatin A (TSA), a specific inhibitor of histone deacetylase, was used to treat imbibing Arabidopsis thaliana seeds. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platforms:

GPL198 GPL71

7 Samples

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(Submitter supplied) Histone acetylation is involved in the regulation of gene expression in plants and eukaryotes. Histone deacetylases (HDACs) are enzymes that catalyze the removal of acetyl groups from histones, which is associated with the repression of gene expression. To study the role of histone acetylation in the regulation of gene expression during seed germination, trichostatin A (TSA), a specific inhibitor of histone deacetylase, was used to treat imbibing Arabidopsis thaliana seeds. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

3 Samples

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(Submitter supplied) Histone acetylation is involved in the regulation of gene expression in plants and eukaryotes. Histone deacetylases (HDACs) are enzymes that catalyze the removal of acetyl groups from histones, which is associated with the repression of gene expression. To study the role of histone acetylation in the regulation of gene expression during seed germination, trichostatin A (TSA), a specific inhibitor of histone deacetylase, was used to treat imbibing Arabidopsis thaliana seeds. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Dataset:

GDS2559

Platform:

GPL71

4 Samples

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Analysis of seeds imbibed for 3 days in the presence of trichostatin A, a specific inhibitor of histone deacetylase. Results provide insight into the role of histone acetylation in the regulation of gene expression during seed germination.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array, count, 2 agent sets

Platform:

GPL71

Series:

GSE3783

4 Samples

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(Submitter supplied) The innate immune signaling pathway plays a crucial role in the recognition and early response to pathogens associated with disease. Genetic analysis has been unable to completely account for individual variability in the strength of the innate immune response. The aim of this study was to determine the role of the epigenetic markers (DNA methylation or histone acetylation) in controlling bovine gene expression in relation to the response to lipopolysaccharide (LPS). more...

Organism:

Bos taurus

Type:

Expression profiling by array

Platform:

GPL17645

24 Samples

Download data: CEL

(Submitter supplied) In order to identify the specific DNA methylation pattern of different rhabdomyosarcoma (RMS) samples we performed a genome-wide study using Human DNA methylation platform (Agilent).

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL19930

15 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) The puropose of this experiment was to identify gene expression changes that result from 5-aza-2-deoxycytidine induced DNA demethylation of Swarm rat chondrosarcoma cells. The gene expression profiles of untreated Swarm rat chondrosarcoma cells were compared to the gene expression profiles of Swarm rat chondrosarcoma cells that were treated for 5 passages with a low dose of 5-aza-2-deoxycytidine (0.1uM).

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL8990

5 Samples

Download data: PAIR

(Submitter supplied) Fetal liver is predominately a hematopoietic organ, but shortly after birth transitions into the major site for xenobiotic (drug) metabolism. The epigenetic mechanisms controlling this developmental switch remain an open door for exploration. DNA methylation (meDNA) governs many diverse cellular functions and is essential for normal development. Histone H3 lysine 4 dimethylation (H3K4me2) is detected in active gene promoters and enhancers7. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array; Methylation profiling by genome tiling array

Platform:

GPL6448

13 Samples

Download data: BAR, BED, CEL