GEO DataSets

(Submitter supplied) Aberrant methylation of DNA is supposed to be a major and early driver of colonic adenoma development and may also lead to colorectal cancer (CRC) formation. While gene methylation assays are used already for CRC screening, differential epigenetic alterations of recurring and non-recurring colorectal adenomas have yet not been systematically investigated. Here, we collected a sample set (n=72) of formalin-fixed paraffin-embedded (FFPE) primary colorectal adenomas without recurrence (n=30), primary adenomas with recurrence at the same location (n=19), so-called “matched pair samples” (n=10; comprising the primary adenoma and the recurrent adenoma) and normal mucosa specimens (n=3). more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

72 Samples

Download data: IDAT, TXT

(Submitter supplied) Genetic and epigenetic alterations are a fundamental aspect of colorectal cancer formation. There is considerable heterogeneity between colorectal cancers regarding the mutations and methylated genes they carry, and this heterogeneity may arise early in the polyp-cancer sequence. However, our understanding of the epigenetic alterations and gene mutations in colon adenomas and their relation to colorectal cancer is incomplete. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

147 Samples

Download data: TXT

(Submitter supplied) DNA methylation was analysed using the Illumina Infinium HumanMethylation 450 Beadchip in 94 matched tissue pairs of colorectal cancer patients.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

192 Samples

Download data: TXT

(Submitter supplied) We explored the differential methylation patterns found in cfDNA between healthy controls (individuals with no colorectal findings, NCF) and patients with advanced neoplasia (advanced adenomas and colorectal cancer, AA andCRC) using pooled samples, to determine if pooled serum cfDNA samples can be used to search for non-invasive methylation biomarkers, as an affordable and efficient alternative to tissue biopsy. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

6 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:

GPL23126 GPL13534

31 Samples

Download data: CEL, IDAT

(Submitter supplied) Uveal melanoma (UM) is an aggressive malignancy, in which nearly 50% of the patients die from metastatic disease. Formalin-fixed paraffin-embedded (FFPE) samples represent a valuable source of tumor tissue. Our aim was to investigate differential DNA methylation correlated to gene expression in relation to survival data.We sought to identify aberrant DNA methylation of genes that could be linked to metastatic disease and poor survival. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL23126

8 Samples

Download data: CEL

(Submitter supplied) Uveal melanoma (UM) is an aggressive malignancy, in which nearly 50% of the patients die from metastatic disease. Formalin-fixed paraffin-embedded (FFPE) samples represent a valuable source of tumor tissue. Our aim was to investigate differential DNA methylation in relation to histopathological classification and survival data. In addition, we sought to identify aberrant DNA methylation of genes that could be linked to metastatic disease and poor survival. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

23 Samples

Download data: IDAT, TXT

(Submitter supplied) Genome wide DNA methylation profiling of normal and colon cancer and assosiation study between anti-cancer drug respond group and non-respond group. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in 118 paired anti-cancer drug response tested colon cancer and adjacent normal tissues

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

248 Samples

Download data: TXT

(Submitter supplied) Abnormal DNA methylation is a hallmark of human cancers and may be a promising biomarker for early diagnosis of human cancers1. However, the majority of DNA methylation biomarkers that have been identified are based on the hypothesis that early differential methylation regions (DMRs) are maintained throughout carcinogenesis and could be detected at all stages of cancer. In this study, we identified potential early biomarkers of colorectal cancer (CRC) development by genome-wide DNA methylation assay (Illumina infinium450, 450K) to normal (N=20) and pre-colorectal cancer samples including 18 low-grade adenoma (LGA) and 22 high-grade adenoma (HGA).

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

60 Samples

Download data: IDAT

(Submitter supplied) Samples from 72 AD patients and 62 age-matched cognitively normal controls were assayed using Illumina© Infinium MethylationEPIC BeadChip. We performed an epigenome-wide association study (EWAS) to evaluate the epigenetic differences using post-mortem superior temporal gyrus (STG) and inferior frontal gyrus (IFG) samples. We performed an epigenome-wide association study (EWAS) to evaluate the epigenetic differences using post-mortem superior temporal gyrus (STG) and inferior frontal gyrus (IFG) samples.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

244 Samples

Download data: TXT

(Submitter supplied) To clarify the role of diacylglycerol kinase gamma (DGKG) in colorectal cancer, we carried out a gene expression microarray analysis using HCT116 cells infected with adenoviral vectors which express LacZ, kinase-dead mutant of DGKG (DGKG-KD) or constitutively active form of DGKG (DGKG-CA).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13607

3 Samples

Download data: TXT

(Submitter supplied) Genome-wide DNA methylation profiles were obtained from colon adenocarcinoma samples (22), corresponding normal colon tissue (22) and cancer-unrelated normal colon tissue using Illumina HumanMethylation450 BeadChips. Approximately 485000 CpG sites were measured in every sample.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

63 Samples

Download data: TXT

(Submitter supplied) The pathophysiology of intervertebral disc (IVD) degeneration is not entirely understood; however, environmental and endogenous factors under genetic predisposition are considered to initiate the degenerative changes of human IVDs. Aberrant epigenetic alterations play a pivotal role in several diseases, including osteoarthritis. However, epigenetic alternations, including DNA methylation, in IVD degeneration have not been evaluated. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

16 Samples

Download data: IDAT, TXT

(Submitter supplied) Aberrant DNA methylation is frequently observed in breast cancer. However, the relationship between methylation patterns and the heterogeneity of breast cancer has not been comprehensively characterized. Whole-genome DNA methylation analysis using 450K Illumina BeadArrays was performed on 188 human breast tumors. Unsupervised bootstrap consensus clustering was performed to identify DNA methylation epigenetic subgroups (epitypes). more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

188 Samples

Download data: TXT

(Submitter supplied) We performed whole-genome methylation analysis using 450K Illumina BeadArrays on different human cell types. In total 24 experiments were performed. Dermal fibroblasts, three different epidermal melanocytes (dark, medium and light pigmentation), epidermal keratinocytes, mammary fibroblasts, mammary epithelial cells, mammary endothelial cells and mesenchymal stem cells were analyzed in technical duplicates. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

24 Samples

Download data: IDAT, TXT

(Submitter supplied) Genome-wide DNA methylation screening was performed using the Infinium HumanMethylation450 BeadChip in 34 samples of non-cancerous pancreatic tissue and 82 samples of cancerous tissue samples obtained from 82 patients with pancreatic ductal adenocarcinoma.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

116 Samples

Download data: IDAT

(Submitter supplied) Whole genomic microarray analysis was performed in order to identify gene expression profile alterations focusing on the dysplastic adenoma-carcinoma transition. Our aims were to determinate characteristic transcript sets for developing diagnostic mRNA expression patterns for objective classification of benign and malignant colorectal diseases and to test the classificatory power of these markers on an independent sample set.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

94 Samples

Download data: CEL

(Submitter supplied) By characterizing at the genome-wide level the DNA methylation patterns of the largest series of well-differentiated thyroid tumors described to date, we provide novel insights into the biology underlying on the one hand the histological heterogeneity, and on the other differential patient outcomes of this disease. We describe distinct subtype- and mutational-specific methylation profiles as well as novel markers associated with recurrence-free survival, which could provide an improved classification of patients.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

91 Samples

Download data: TXT

(Submitter supplied) In our study we applied a genome-wide DNA methylation analysis approach, MethylCap-seq, to map the differentially methylated regions in 24 tumor and matched normal colon samples. In total, 2687 frequently hypermethylated and 468 frequently hypomethylated regions were identified, which include potential biomarkers for CRC diagnosis. Hypermethylation in the tumor samples was enriched at CpG islands and gene promoters, while hypomethylation was distributed throughout the genome. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL10999

68 Samples

Download data: BED, TXT, WIG

(Submitter supplied) Background: Colorectal cancer (CRC) remains a major concern with high morbidity and mortality worldwide. DNA methylation alteration plays a pivotal role in cancer development. We aimed to screen novel biomarkers for CRC diagnosis and chemotherapy-related adverse event (CRAE) prediction using the advanced Illumina Infinium MethylationEPIC (850K) BeadChip. Methods: We analyzed the methylation profiles of paired tumor and normal tissues from 21 Chinese CRC patients. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

44 Samples

Download data: TXT