GEO DataSets

(Submitter supplied) Genome wide DNA methylation profiling of three normal (N) and eight ulcerative colitis (UC) samples as well as one human colon cancer cell (HCT116) . The Illumina Infinium 450k Human DNA methylation platform was used to obtain DNA methylation profiles across approximately 480,000 CpGs.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

12 Samples

Download data: IDAT, TXT

(Submitter supplied) Genome wide DNA methylation profiling of Crohn's disease, ulcerative colitis, and normal colon mucosa samples. The Illumina Infinium HumanMethylation450 BeadChip v1.1 was used to obtain DNA methylation profiles across 482,421 CpGs in colon mucosa samples. Samples came from 5 Crohn's disease affected, 5 ulcerative colitis affected, and 12 normal individuals. One ulcerative colitis sample was assayed before and after treatment with infliximab and mesalamine.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

23 Samples

Download data: TXT

(Submitter supplied) Genome wide expression profiling of ulcerative colitis, and normal colon mucosa samples. The GeneChip PrimeView Human Gene Expression Array was used to obtain expresion profiles across colon mucosa samples. Samples came from 5 ulcerative colitis affected, and 5 normal individuals.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL15207

10 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

73 Samples

Download data

(Submitter supplied) Genome wide DNA methylation profiling of Crohn's disease, ulcerative colitis, and normal colon mucosa samples. The Illumina Infinium HumanMethylation450 BeadChip v1.1 was used to obtain DNA methylation profiles across 482,421 CpGs in colon mucosa samples. Samples came from 10 Crohn's disease affected, 4 ulcerative colitis affected, and 10 normal individuals. One ulcerative colitis sample was assayed before and after treatment with 6-mercaptopurine and mesalamine.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

25 Samples

Download data: TXT

(Submitter supplied) In this research, 90 differential expression mRNAs (DEMs), 72 differential expression lncRNAs (DELs) and biological functions and pathway were identified in ulcerative colitisby (UC) integrated analysis. Potential therapeutic target for treatment was preliminary verified by qRT-PCR experiment and bioinformatics analysis.

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platform:

GPL20115

6 Samples

Download data: TXT

(Submitter supplied) Inflammatory bowel disease (IBD) is known to be caused by a genetic predisposition involving multiple genes; however, there is growing evidence that abnormal interaction with environmental, particularly epigenetic, factors can have a significant contribution during the development of IBD. Although many studies, particularly genome-wide association studies (GWAS), have been performed to identify the genetic changes underlying the pathogenesis of Crohn’s disease (CD), the role of epigenetic changes in the development of complications arising from CD is poorly understood. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

11 Samples

Download data: IDAT, TXT

(Submitter supplied) Genome wide DNA methylation profiling of Crohn's disease, ulcerative colitis, and normal peripheral blood samples. The Illumina Infinium HumanMethylation450 BeadChip v1.1 was used to obtain DNA methylation profiles across 482,421 CpGs in peripheral blood samples. Samples came from 17 Crohn's disease affected, 11 ulcerative colitis affected, and 20 normal individuals. Within these samples were three twin sets discordant for Crohn's disease and three twin sets discordant for ulcerative colitis.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

48 Samples

Download data: TXT

(Submitter supplied) Using the pools of DNA from squamous cervical carcinomas (SCC) and DNA from normal scraping cells discovered the abnormal changes of genomic wide methylation by methylation BeadChip. The 61 genes were selected to validate by quantitative methylation specific PCR (qMSP) and bisulfite pyrosequencing in further processes. A CpG islands methylator phenotype (CIMP) was confirmed at 14 candidates in an independent set contained a spectrum of scraping cells form abnormal cervical lesions. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

2 Samples

Download data: TXT

(Submitter supplied) We performed integrative methylation, gene dosage and expression profiling to explore the interplay between promoter methylation and loss in gene silencing at 3p11-p14 in cervical cancer. Totally 26 hypermethylated genes were identified by comparing the methylation level of individual CpG sites with corresponding data of normal cervical tissue. Candidate methylation regulated genes in tumors were proposed from the correlation between methylation and gene expression. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by array

Platforms:

GPL13534 GPL10558

391 Samples

Download data: TXT, XLS

(Submitter supplied) Ulcerative colitis is heritable disorder with variable clinical outcome but to date only less than 10% of the disease susceptibility and the disease outcome is explained by IBD (inflammatory bowel disease) associated genetic loci. This missing heritability lay fertile grounds for investigating epigenetics as possible explanation. The aims of the study were to investigate genome-wide DNA methylation of the rectal tissue in an inception cohort of UC at two time points, once at baseline (treatment naïve) and at follow-up to explore how longitudinal DNA methylation influences the disease onset, disease progression and outcome. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

369 Samples

Download data: IDAT, TXT

(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) Methylation of CpG islands is associated with transcriptional repression and, in cancer, leads to the abnormal silencing of tumor-suppressor genes. We developed a novel and robust technique that allows the unbiased, genome wide detection of CpG-methylation in limited DNA samples, without applying methylation-sensitive restriction endonucleases or bisulfite-treatment. The approach is based on a recombinant, methyl-CpG binding protein that efficiently binds CpG-methylated DNA depending on its degree of CpG methylation. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL2040

10 Samples

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(Submitter supplied) Methylation of CpG islands is associated with transcriptional repression and, in cancer, leads to the abnormal silencing of tumor-suppressor genes. Genome wide methylation profiling of myeloid leukemia cell lines identified a large number of genes with aberrantly methylated CpG islands. Comparative mRNA expression analysis suggests that more than half of these genes show extremely low or absent expression in normal cells, suggesting that hypermethylation in cancer may be independent of the transcriptional status of the affected gene. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by array

Dataset:

GDS2251

Platform:

GPL570

4 Samples

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Comparison of myeloid leukemia cells to normal monocytes. Transcriptional status of each gene compared to its CpG methylation state. The methylation of CpG islands is associated with transcriptional repression and, in cancer, leads to the abnormal silencing of tumor suppressor genes.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 4 cell line, 2 disease state sets

Platform:

GPL570

Series:

GSE3280

4 Samples

Download data

(Submitter supplied) Due to the lack of clinical, immunologic, genetic and laboratory markers to predict remission without relapse, there is no clear recommendation regarding withdrawal of therapy. Therefore, this study was to investigate if transcriptional analysis together with Cox survival analysis might be able to reveal molecular markers that are specific for remission duration and outcome. Mucosal biopsies from patients in remission, with active treatment-naïve ulcerative colitis and healthy control subjects underwent whole-transcriptome RNA-seq. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

56 Samples

Download data: TXT

(Submitter supplied) Background: This study addresses whether existing specific transcriptional profiles can improve and support the current status of the definition of ulcerative colitis (UC) remission apart from the existing endoscopic, histologic, and laboratory scoring systems. For that purpose, a well-stratified UC patient population in remission was compared to active UC and control patients and was investigated by applying the next-generation technology RNA-Seq. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

44 Samples

Download data: TAB, TXT

(Submitter supplied) Ulcerative colitis (UC) is a chronic inflammatory disease of the colon with preiods of active disease followed by remission. We performed a whole-genome transcriptional analysis of colonic biopsies from patients with histologically active and inactive UC, as well as non-inflammatory controls.

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4365

Platform:

GPL570

43 Samples

Download data: CEL

Analysis of colonic biopsies from patients with histologically active or inactive UC and from healthy, non-inflammatory controls. UC is a chronic inflammatory disease with periods of active disease followed by remission. Results provide insight into molecular events associated with UC remission.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 5 agent, 4 disease state sets

Platform:

GPL570

Series:

GSE38713

43 Samples

Download data: CEL

(Submitter supplied) Genome wide DNA methylation profiling of normal adrenocortical tissue, adrenocortical adenomas and adrenocortical carcinomas. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles. Samples included 6 normal adrenocortical tissue samples, 27 adenomas and 15 carcinomas.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

48 Samples

Download data: TXT