Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

9 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Epigenome analysis of squamous cell carcinoma samples

ABSTRACT: Genome wide DNA methylation profiling of squamous cell carcinoma and location matched normal samples Bisulphite converted DNA from the 13 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip.

ORGANISM(S): Homo sapiens

SUBMITTER: Andrew Feinberg

PROVIDER: E-GEOD-67097 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin.

Vandiver Amy R AR Irizarry Rafael A RA Hansen Kasper D KD Garza Luis A LA Runarsson Arni A Li Xin X Chien Anna L AL Wang Timothy S TS Leung Sherry G SG Kang Sewon S Feinberg Andrew P AP

Genome biology 20150416

<h4>Background</h4>Aging and sun exposure are the leading causes of skin cancer. It has been shown that epigenetic changes, such as DNA methylation, are well established mechanisms for cancer, and also have emerging roles in aging and common disease. Here, we directly ask whether DNA methylation is altered following skin aging and/or chronic sun exposure in humans.<h4>Results</h4>We compare epidermis and dermis of both sun-protected and sun-exposed skin derived from younger subjects (under 35 ye ...[more]

PMID: 25886480

Similar Datasets

Epigenome analysis of human epidermal and dermal samples with aging and sun exposure

Project description:Genome wide DNA methylation profiling of epidermal and dermal samples obtained from sun-exposed and sun-protected body sites from younger (<35 years old) and older (>60 years old) individuals. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in dermal and epidermal samples. Samples included 10 younger sun protected dermal samples, 10 younger sun exposed dermal samples, 10 older sun protected dermal samples, 10 older sun exposed dermal samples, 9 younger sun protected epidermal samples, 9 younger sun exposed epidermal samples, 10 older sun protected epidermal sample, 10 older sun exposed epidermal samples. Bisulphite converted DNA from the 78 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip.

2015-03-23 | E-GEOD-51954 | biostudies-arrayexpress

Association of DNA Methylation with Acute Mania and Inflammatory Markers

Project description:Genome wide DNA methylation profiling of serum samples from 20 individuals hospitalized with acute mania and 20 unaffected controls using the Illumina 450K methylation arrays. Bisulphite converted DNA from the 40 samples were hybridised to the Illumina HumanMethylation450 BeadChip arrays

2015-06-22 | E-GEOD-68777 | biostudies-arrayexpress

BayMeth: improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach

Project description:Affinity capture of DNA methylation combined with high-throughput sequencing strikes a good balance between the high cost of whole genome bisulfite sequencing and the low coverage of methylation arrays. We present BayMeth, an empirical Bayes approach that uses a fully methylated control sample to transform observed read counts into regional methylation levels. In our model, inefficient capture can readily be distinguished from low methylation levels. BayMeth improves on existing methods, allows explicit modeling of copy number variation, and offers computationally-efficient analytical mean and variance estimators. BayMeth is available in the Repitools Bioconductor package. Benchmarking samples to compare MBD- and MeDIP-seq [GSE38679, GSE24546; PMID 21045081] datasets against 450k measurements

2014-01-25 | E-GEOD-54375 | biostudies-arrayexpress

Medulloblastoma Methylation Profiling

Project description:Genome wide DNA methylation profiling of human medulloblastoma. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 450,000 CpGs. Preprocessed data performed using Illumina normalization in the minfi package as described in Sturm et al, Cancer Cell, 2012. Bisulphite converted DNA from the 91 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.2

2015-11-19 | E-GEOD-75153 | biostudies-arrayexpress

Bisulphite sequencing of native LNCaP and PrEC DNA [methylation array]

Project description:As a reference dataset to compare BisChIP-seq and other methylated DNA capture experiments against, we have collected Illumina 450k to profile CpG methylation status on native DNA. Illumina 450k array for LNCaP and PrEC cell lines

2012-01-18 | E-GEOD-34340 | biostudies-arrayexpress

Epigenome analysis of Rett syndrome monozygotic twins samples

Project description:Genome wide DNA methylation profiling of Rett syndrome monozygotic twins. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles in primary skin fibroblast cells from Rett syndrome monozygotic twins. Bisulphite converted DNA from the 2 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

2012-12-27 | E-GEOD-43141 | biostudies-arrayexpress

Epigenome analysis of the effects of JQ1 on DNA methylation

Project description:Genome wide DNA methylation profiling of four female lymphoblastoid cell lines treated with DMSO control for 250 nM JQ1. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 485,000 CpGs. Bisulphite converted DNA from the 8 samples, which were hybridised to the Illumina Infinium 450k Human Methylation Beadchip.

2015-08-01 | E-GEOD-62111 | biostudies-arrayexpress

Epigenome analysis of normal lung tissue samples

Project description:Genome wide DNA methylation profiling of normal lung tissue samples. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in nor mal lung tissue samples. Samples included 244 normal lung tissue samples from lung cancer patients. Environment and Genetics in Lung Cancer Etiology EAGLE; Population-based case-control study Bisulphite converted DNA from 244 fresh-frozen primary human lung samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.2. This file has 60 samples.

2014-03-03 | E-GEOD-52401 | biostudies-arrayexpress

Epigenome analysis of the human muscle

Project description:Muscle tissue samples were obtained from severely obese individuals that underwent bariatric surgery. The goal of this study was to identify tissue specific methylation QTLs. Whole-transcriptome subcutaneous adipose tissue methylation levels were determined in 60 individuals with a BMI >35 kg/m2. Bisulphite converted DNA from the 60 muscle samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip.

2014-09-17 | E-GEOD-61452 | biostudies-arrayexpress

Epigenome analysis of the human liver

Project description:Liver tissue samples were obtained from severely obese individuals that underwent bariatric surgery. The goal of this study was to identify tissue specific methylation QTLs. Whole-transcriptome subcutaneous adipose tissue methylation levels were determined in 67 individuals with a BMI >35 kg/m2. Bisulphite converted DNA from the 67 Liver samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

2014-09-17 | E-GEOD-61446 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data