GEO DataSets

(Submitter supplied) Analysis of nucleosome positioning and chromatin state by using CpG methyltransferase M.SssI to methylate nuclei. Unmethylated regions that gain methylation (low to high beta value) are known to be accessible and nucleosome depleted. Method used to study changes after epigenetic drug treatments identified that majority of demethylation events are not accompanied by chromatin accessibility changes.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

20 Samples

Download data: TXT

(Submitter supplied) Analysis of nucleosome positioning and chromatin state by using CpG methyltransferase M.SssI to methylate nuclei. Unmethylated regions that gain methylation (low to high beta value) are known to be accessible and nucleosome depleted. Method used to study changes after epigenetic drug treatments identified that majority of demethylation events are not accompanied by chromatin accessibility changes.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10904

12 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Methylation profiling by array; Expression profiling by array

Platforms:

GPL10904 GPL13534

42 Samples

Download data

(Submitter supplied) Analysis of nucleosome positioning and chromatin state by using CpG methyltransferase M.SssI to methylate nuclei. Unmethylated regions that gain methylation (low to high beta value) are known to be accessible and nucleosome depleted.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

10 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:

GPL6884 GPL8490

12 Samples

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(Submitter supplied) Genome wide gene expression profiling of RKO cells with combination treatments of non-target siRNA or SRCAP siRNA and PBS or 1uM 5-Aza-CdR treatment. The sample treated with non target siRNA and PBS serves as control sample.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6884

8 Samples

Download data: TXT

(Submitter supplied) Genome wide DNA methylation profiling of RKO cells with combination treatments of non-target siRNA or SRCAP siRNA and PBS or 1uM 5-Aza-CdR treatment. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across 27,578 CpGs in treated RKO cells. Samples included cells under 4 different treatments. The sample treated with non target siRNA and PBS serves as control sample.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

4 Samples

Download data: TXT

(Submitter supplied) Esophageal cancers (ECs) are highly aggressive tumors with poor prognosis and few treatment options. This study investigated the possibility of treating esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC) cells by inhibitors of broad and specific histone deacetylases (HDACi; SAHA, MS-275, FK228) and/or of DNMT (Azacytidine, AZA). Drug targets (HDAC1,2,3 and DNMT1) were present in non-neoplastic (HET-1A), ESCC (OE21) and EAC (OE33) cell lines. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

36 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:

GPL13534 GPL10558

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) 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) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by array

Platforms:

GPL10558 GPL6947 GPL8490

36 Samples

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(Submitter supplied) Human embryonal carcinoma (EC) cells are the stem cells of nonseminoma testicular germ cells tumors (TGCTs) and share remarkable similarities to human embryonic stem (ES) cells. In prior work we found that EC cells are hypersensitive to low nanomolar doses of 5-aza deoxycytidine (5-aza) and that this hypersensitivity partially depended on unusually high levels of the DNA methyltransferase, DNMT3B. We show here that low-dose 5-aza treatment results in DNA damage and induction of p53 in NT2/D1 cells. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

12 Samples

Download data: TXT

(Submitter supplied) Human embryonal carcinoma (EC) cells are the stem cells of nonseminoma testicular germ cells tumors (TGCTs) and share remarkable similarities to human embryonic stem (ES) cells. In prior work we found that EC cells are hypersensitive to low nanomolar doses of 5-aza deoxycytidine (5-aza) and that this hypersensitivity partially depended on unusually high levels of the DNA methyltransferase, DNMT3B. We show here that low-dose 5-aza treatment results in DNA damage and induction of p53 in NT2/D1 cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

12 Samples

Download data: TXT

(Submitter supplied) Human embryonal carcinoma (EC) cells are the stem cells of nonseminoma testicular germ cells tumors (TGCTs) and share remarkable similarities to human embryonic stem (ES) cells. In prior work we found that EC cells are hypersensitive to low nanomolar doses of 5-aza deoxycytidine (5-aza) and that this hypersensitivity partially depended on unusually high levels of the DNA methyltransferase, DNMT3B. We show here that low-dose 5-aza treatment results in DNA damage and induction of p53 in NT2/D1 cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6947

12 Samples

Download data: TXT

(Submitter supplied) To establish a miRNA expression profile for DPCs undergoing epigenetically-mediated mineralisation, rodent DPCs were induced to mineralise and treated with a HDAC inhibitor, SAHA, and a DNMT inhibitor, 5-AZA-CdR. RNA was then isolated from DPCs at day 4 of culture and subjected to RNA sequencing. Subsequent bioinformatic analysis identified differentially expressed miRNAs compared with untreated mineralising DPCs.

Organism:

Rattus norvegicus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18694

12 Samples

Download data: XLSX

(Submitter supplied) Mutations in chromatin-modifying proteins and transcription factors are commonly associated with a wide variety of cancers. Through gain- or loss-of-function, these mutations may result in characteristic alterations of accessible chromatin, indicative of shifts in the landscape of regulatory elements genome-wide. The identification of compounds that reverse a specific chromatin signature could lead to chemical probes or potential therapies. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

2 Samples

Download data: BED