GEO DataSets

(Submitter supplied) Solid tumors, including head and neck squamous cell carcinomas (HNSCC), arise as a result of genetic and epigenetic alterations in a sustained stress environment. Since it has been hypothesized that epigenetic alterations may act by providing the second carcinogenic hit in gene silencing, we sought to identify genome-wide DNA copy number alterations and CpG dinucleotide methylation events and examine the global/local relationships between these types of alterations in HNSCC. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL9183

30 Samples

Download data: TXT

(Submitter supplied) Solid tumors, including head and neck squamous cell carcinomas (HNSCC), arise as a result of genetic and epigenetic alterations in a sustained stress environment. Since it has been hypothesized that epigenetic alterations may act by providing the second carcinogenic hit in gene silencing, we sought to identify genome-wide DNA copy number alterations and CpG dinucleotide methylation events and examine the global/local relationships between these types of alterations in HNSCC. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platforms:

GPL3720 GPL3718

76 Samples

Download data: CEL, CHP, TXT

(Submitter supplied) Genome wide DNA methylation profiling of normal and adjacent OSCC samples. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 4,50,000 CpGs in tissue samples. Total 21 samples were taken including 10 paired and 1 unpaired tissues. 6 were HPV Positive and 5 were HPV negative.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

21 Samples

Download data: IDAT

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

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

322 Samples

Download data

(Submitter supplied) Genome-wide DNA methylation profiling of head and neck squamous cell carcinomas (HNSCCs). The Illumina Infinium 27k Human DNA methylation BeadChip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in fresh-frozen tumor tissues. Samples included 91 tumors from the oralpharynx and larynx, reflecting all stages of disease, 18 normal head and neck National Disease Research Interchange (NDRI) samples, and 213 normal control blood samples.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

213 Samples

Download data: TXT

(Submitter supplied) Genome-wide DNA methylation profiling of head and neck squamous cell carcinomas (HNSCCs). The Illumina Infinium 27k Human DNA methylation BeadChip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in fresh-frozen tumor tissues. Samples included 91 tumors from the oralpharynx and larynx, reflecting all stages of disease, 18 normal head and neck National Disease Research Interchange (NDRI) samples, and 213 normal control blood samples.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

91 Samples

Download data: TXT

(Submitter supplied) Genome-wide DNA methylation profiling of head and neck squamous cell carcinomas. The Illumina Infinium 27k Human DNA methylation BeadChip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in fresh-frozen tumor tissues. Samples included 91 tumors from the oralpharynx and larynx, reflecting all stages of disease, 18 normal head and neck National Disease Research Interchange (NDRI) samples, and 213 normal control blood samples.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

18 Samples

Download data: TXT

(Submitter supplied) DNA methylation in esophageal squamous cell carcinoma (ESCC)

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

10 Samples

Download data: CSV

(Submitter supplied) This study focused on global methylation changes between tumors, normal mucosa, primary tumor xenografts, and cell lines in order to determine epigenetic changes in cell cultures and xenografts derived from primary tumors.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

22 Samples

Download data: TXT

(Submitter supplied) Oncogene expressing human papillomavirus type 16 (HPV16) is found in a subset of head and neck squamous cell carcinomas (HNSCC). HPV16 drives carcinogenesis by inactivating p53 and pRb with the viral oncoproteins E6 and E7, reflected by a low level of mutations in TP53 and allelic loss at 3p, 9p and 17p, genetic changes frequently found in HNSCCs of non-viral etiology. We hypothesize that two pathways to HNSCC exist: one determined by HPV16 and one by environmental carcinogens. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL3441

24 Samples

Download data

(Submitter supplied) This study integrated Affymetrix SNPchip data for CNV estimation, Affymetrix HuEx1.0 data for gene expression estimation, and Illumina HumanMethylation27k BeadChip data for promoter methylation to estimate pathway activity

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5175

69 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by array; Genome variation profiling by SNP array

Platforms:

GPL6801 GPL6102 GPL8490

69 Samples

Download data: CEL, CHP

(Submitter supplied) Osteosarcomas are the most common primary malignant tumours of bone, and almost all conventional osteosarcomas are high-grade tumours showing complex genomic aberrations. We have integrated genome-wide genetic and epigenetic profiles from the EuroBoNeT panel of 19 human osteosarcoma cell lines based on microarray technologies. The cell lines showed complex patterns of DNA copy number changes, where copy number gains were significantly associated with gene-rich regions of the genome and losses with gene-poor areas. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL6801

19 Samples

Download data: CEL, CHP

(Submitter supplied) Osteosarcomas are the most common primary malignant tumours of bone, and almost all conventional osteosarcomas are high-grade tumours showing complex genomic aberrations. We have integrated genome-wide genetic and epigenetic profiles from the EuroBoNeT panel of 19 human osteosarcoma cell lines based on microarray technologies. The cell lines showed complex patterns of DNA copy number changes, where copy number gains were significantly associated with gene-rich regions of the genome and losses with gene-poor areas. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

25 Samples

Download data: TXT

(Submitter supplied) Osteosarcomas are the most common primary malignant tumours of bone, and almost all conventional osteosarcomas are high-grade tumours showing complex genomic aberrations. We have integrated genome-wide genetic and epigenetic profiles from the EuroBoNeT panel of 19 human osteosarcoma cell lines based on microarray technologies. The cell lines showed complex patterns of DNA copy number changes, where copy number gains were significantly associated with gene-rich regions of the genome and losses with gene-poor areas. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6102

25 Samples

Download data: TXT

(Submitter supplied) Epigenome-wide association study (EWAS) of blood samples from a case-control study of bladder cancer. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in peripheral blood. Samples included peripheral blood samples from 223 incident cases of bladder cancer and 205 control subjects.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

428 Samples

Download data: TXT

(Submitter supplied) The objective of the study was to identify differentially methylated regions of DNA (DMRs) that distinguish human leukocyte subtypes, and hence serve as biomarkers for those immune cell types. This file contains Illumina Infinium HumanMethylation27 BeadChip data for human leukocyte subtypes that were purified from whole blood samples via magnetic activated cell sorting (MACS) and purity confirmed by flourescence activated cell sorting (FACS).

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

73 Samples

Download data: TXT

(Submitter supplied) Genome wide DNA methylation profiling and semi-supervised classification of blood samples from a case-control study of head and neck squamous cell carcinoma (HNSCC). The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in peripheral blood. Samples included peripheral blood samples from 92 incident cases of HNSCC and 92 control subjects.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

184 Samples

Download data: TXT