GEO DataSets

(Submitter supplied) DNA Methylation profiles were generated for retrospective cases to support work into investigation of the immune environment in pediatric ependymoma. Samples were analyzed using the Illumina 450k beadchip and processed using the Heidelberg classifier (v11.2b and subsequently v12.3 for subgrouping/subtyping). The aim of the study was to better understand the immune-tumor microenvironment in pediatric ependymoma and the methylation profiles support the diagnoses of each case.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

74 Samples

Download data: IDAT, TXT

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

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platforms:

GPL21145 GPL13534

33 Samples

Download data

(Submitter supplied) Comprehensive DNA methylation analysis of each histological LUAD subtype. Infinium HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across 485,577 CpG sites. Samples included 6 Micropapillary subtype, 5 Papillary subtype, 5 Lepidic subype and 3 normal lung tissues.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

19 Samples

Download data: TXT

(Submitter supplied) Meningiomas are common intracranial tumors in adults. Abnormal miRNA expression plays a role in their pathogenesis. Change in miRNA expression level can be caused by impaired epigenetic regulation of miRNA-encoding genes. We found genomic region covering MIR193B gene as DNA hypermethylated in meningiomas based on analysis of genome-wide methylation (HM450k Illumina arrays). Hypermethylation of MIR193B was as also confirmed by bisulfite pyrosequencing. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

27 Samples

Download data: IDAT, TXT

(Submitter supplied) The purpose of this data set was to identify the affects of somatic cell introduction of the methylation results of the sperm samples. This data was then used to help build a computational tool to properly identify somatic cell contamination within a sperm sample.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

48 Samples

Download data: IDAT

(Submitter supplied) Accurate pathological diagnosis is crucial for optimal management of cancer patients. For a number of hematolymphoid tumor entities, standardization of the diagnostic process has been shown to be particularly challenging - with substantial inter-observer variability in the histopathological diagnosis of many tumor types. Genome-wide DNA methylation profiling has been shown to contribute to accurate and precise tumor classification and diagnosis in several tumor types, including central nervous system neoplasms. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array; Third-party reanalysis

Platforms:

GPL13534 GPL23976

989 Samples

Download data: CSV, IDAT, TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL13534 GPL23976 GPL13158

188 Samples

Download data: CEL, IDAT

(Submitter supplied) The tubular adenoma sample cohort (accrued by Janssen Pharmaceuticals) consisted of 127 high-risk baseline adenoma samples acquired retrospectively by Avaden Biosciences. High risk patients are defined here as presenting a tubular adenoma ? 10mm, 3 or more adenomas, adenomas with villous histology or adenomas showing high-grade dysplasia based on Lieberman et al. Patients with familial adenomatous polyposis (FAP) and Lynch syndrome were excluded. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

61 Samples

Download data: IDAT, TXT

(Submitter supplied) Risk of hepatocellular carcinoma (HCC) remains after sustained virological response (SVR) in patients with chronic hepatitis C (CHC). Epigenetic abnormalities might be key regulators in the development of HCC. This study aimed to identify the genes involved in hepatocarcinogenesis after SVR. DNA methylation in liver tissues was compared between 21 CHC patients without HCC and 28 CHC patients with HCC, all of whom had achieved SVR. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

82 Samples

Download data: TXT

(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 genome tiling array

Platforms:

GPL18573 GPL21145 GPL13534

82 Samples

Download data: IDAT

(Submitter supplied) Here, we investigated tumor tissue from 26 patients affected by AT/RT to identify signatures of recurrences in comparison to matched primary tumor samples.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platforms:

GPL21145 GPL13534

56 Samples

Download data: IDAT, TXT

(Submitter supplied) The data contains Illumina 450k array methylation files from 380 patients with diffuse IDH wild-type glioma from the EORTC-26101 trial

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

380 Samples

Download data: CSV, IDAT

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

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array; Methylation profiling by genome tiling array; Other

Platforms:

GPL13534 GPL18900

43 Samples

Download data: IDAT

(Submitter supplied) Meningiomas are the most common primary brain tumor. Though typically benign with a low mutational burden, histopathologic analysis has poor predictive value for malignant behavior and there are no proven chemotherapies. Although DNA methylation patterns distinguish subgroups of meningiomas and have higher predictive value for tumor behavior than histologic classification, little is known about differences in DNA methylation between meningiomas and surrounding normal dura tissue. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array; Third-party reanalysis

Platform:

GPL13534

24 Samples

Download data: IDAT, TXT

(Submitter supplied) Osteosarcomas (OS) arise more commonly during the rapid bone growth and remodeling, thus it is plausible to infer the relationship between their tumorigenesis and cell cycle disruption by genetic and epigenetic factors. Methylation data of 28 primary OS was obtained using the HM450K microarray, and compared with nine normal bone tissues. The tumor mutational burden was analyzed using data from the TruSight One sequencing panel. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

37 Samples

Download data: IDAT

(Submitter supplied) Tobacco smoking alters DNA methylation profiles of immune cells which may underpin some of the pathogenesis of smoking-associated diseases. However, approaches linking smoking-driven epigenetic effects in specific immune cell types with disease risk are limited. We isolated six leukocyte subtypes, CD14+ monocytes, CD15+ granulocytes, CD19+ B cells, CD4+ T cells, CD8+ T cells, and CD56+ natural killer cells, from whole blood of healthy adult smokers and nonsmokers for epigenome-wide association study (EWAS).

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platforms:

GPL13534 GPL29753

876 Samples

Download data: IDAT, TXT

(Submitter supplied) DNA methylation analysis was perfomed using Infinium 450K Methylation BeadChip platform on 140 PFA ependymoma patient samples. Resulting .idat files were then uploaded to the molecularneuropathology.org classifier to obtain molecular subgroup and copy number variance. Idat files were batch normalized and background corrected using default settings of the R package ChAMP to obtain GpG methylation beta values for analysis of differentially methylated GpG regions.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

140 Samples

Download data: IDAT, TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Methylation profiling by array

4 related Platforms

291 Samples

Download data: IDAT

(Submitter supplied) Oesophageal adenocarcinoma (OAC) is a poor prognosis cancer and the molecular features underpinning response to treatment remain unclear. We investigated whole genome, and where possible transcriptomic and methylation data from 115 OAC patients mostly from the DOCTOR phase II clinical trial (ANZCTR-ACTRN12609000665235). We identified genomic features associated with poorer overall survival, such as the APOBEC mutational and RS3-like rearrangement signatures. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platforms:

GPL21145 GPL13534

72 Samples

Download data: IDAT

(Submitter supplied) The therapeutic effect of DNA-hypomethylating agents (HMAs) in AML/MDS is discussed to be via its effects on aberrant gene silencing by reactivation (e.g. through promoter demethylation). While this has been broadly studied in cell line models, only very few studies have addressed the global effects of HMAs in primary blasts serially isolated from AML patients (pts) undergoing HMA treatment (Claus et al., Leuk. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

132 Samples

Download data: IDAT, TXT