GEO DataSets

(Submitter supplied) Promoter hypermethylation and transcriptional silencing is a common epigenetic mechanism of tumour suppressor inactivation in cancer, including malignant brain tumours. To identify targets of epigenetic silencing mediated by CpG island methylation in paediatric ependymoma, we used a pharmacological unmasking approach through treatment with the demethylating agent 5-Aza-2’-deoxycytidine followed by global expression microarray analysis.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

12 Samples

Download data: CEL

(Submitter supplied) To genome-wide screening for the genes whose expression are responsible for the promoter DNA methylation, we performed the cDNA microarray with oral cancer cells before and after a DNA methyltransferase inhibitor, 5-aza-2’-deoxycytidine (AzC), treatment.

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS5625

Platform:

GPL6883

16 Samples

Download data: TXT

(Submitter supplied) According to epidemiological studies, a vast majority, approximately 80%~90% of male OSCC patients in Taiwan habitually drink alcohol (A), and chew betel quid (B), and use cigarette (C). To assess the impact of these dietary factors on the transcriptom, we conduct a high-throughput screen survey in an oral cancer cohort with exposure of A, B, and C. Results indicate several potential oncogenes and tumor suppressor genes are dysregulated in OSCC patients with ABC risk factors.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6883

80 Samples

Download data: TXT

Analysis of oral squamous cell carcinoma (OSCC) cell lines: OC3, SAS, SCC-15, and HSC3, treated with 5-aza-2’-deoxycytidine (AzC), an inhibitor of DNA methyltransferase. Results provide insight into potential tumor suppressor genes silenced by DNA hypermethylation in OSCC.

Organism:

Homo sapiens

Type:

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

Platform:

GPL6883

Series:

GSE38823

16 Samples

Download data

(Submitter supplied) Efficient and sustained knockdown of DNMT1 transcript and protein was achieved using a consecutive transfection protocol in the mouse pituitary adenoma cell line, AtT-20. Genome wide microarray analysis identified 91 transcripts that were significantly differentially expressed relative to cells treated with a non-targeting control. Keywords: Differential expression

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

6 Samples

Download data: CEL, CHP

(Submitter supplied) Cancers are characterized by non-random, chromosome copy number variations that presumably contain oncogenes and tumor suppressor genes (TSGs). The affected loci are often large, making it difficult to pinpoint which genes are driving the cancer. Here, we report a cross-species, in vivo screen of 84 candidate oncogenes and 39 candidate TSGs, located within 28 recurrent chromosomal alterations in ependymoma. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL11180

24 Samples

Download data: CEL

(Submitter supplied) Background: Neuroblastoma is a childhood cancer in which many children still have poor outcomes, emphasising the need to better understand its pathogenesis. Despite recent genome-wide mutation analyses, most neuroblastomas do not contain recognisable driver mutations, suggesting that epigenetic changes could underlie many cases. Methods: To discover genes that become epigenetically deregulated during neuroblastoma tumorigenesis, we compared neuroblastomas to their neural crest precursor cells, using genome-wide DNA methylation analysis; probing CpG island promoter microarrays with methyl CpG-immunoprecipitated DNA. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL16062

5 Samples

Download data: PAIR

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

Organism:

Mus musculus

Type:

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

Platform:

GPL19057

34 Samples

Download data: BW

(Submitter supplied) To profile H3K4me3Q5Ser (5HT-H3) distribution in mouse ZFTA-RELA ependymoma tumors Furthermore, we also sought to examine H3K27ac and H3K27me3 distribution in mouse ZFTA-RELA ependymoma versus ETV5 overexpressing tumors

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

23 Samples

Download data: BIGWIG, BW

(Submitter supplied) To profile gene expression differences between mouse non-tumor cortex versus ZFTA-RELA ependymoma versus ETV5 overexpressing tumors Furthermore, we also sought to profile gene expression differences between ZFTA-RELA ependymoma versus NPY overexpressing tumor

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

12 Samples

Download data: TXT

(Submitter supplied) Background: Epigenetic modifications have been shown to play an important role in the classification and pathogenesis of the pediatric brain tumor ependymoma, suggesting they are a potential therapeutic target. Methods: The effects of agents targeting epigenetic modifications on the growth and death of a panel of ependymoma cell lines was investigated, as well as toxicity to normal fetal neural stem cells. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platforms:

GPL21145 GPL13534

16 Samples

Download data: IDAT, TXT

(Submitter supplied) DNA methylation profiling using Illumina Infinium HumanMethylation450 BeadChip arrays was used to assign cell lines to previously defined subgroups.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

6 Samples

Download data: CSV, IDAT