Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

26 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DNA methylation anaylsis of placenta samples exposed to variable levels of arsenic during pregnancy

ABSTRACT: Genome-wide profiling of placental DNA methylation in relation to arsenic exposure. The Illumina 450k methylation array was used to profile 343 samples for which 3 different measurements of arsenic exposure were available during gestation. These samples have been collected from the New Hampshire Birth Cohort Study (NHBCS). Bisulfite converted DNA was hybridized to the 450k platform and processed at the University of Minnesota Genomic Core

ORGANISM(S): Homo sapiens

SUBMITTER: Carmen Marsit

PROVIDER: E-GEOD-71678 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

DNA methylation anaylsis of placenta samples exposed to variable levels of arsenic during pregnancy

Project description:Genome-wide profiling of placental DNA methylation in relation to arsenic exposure. The Illumina 450k methylation array was used to profile 343 samples for which 3 different measurements of arsenic exposure were available during gestation. These samples have been collected from the New Hampshire Birth Cohort Study (NHBCS).

2016-07-01 | GSE71678 | GEO

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

Genome-wide analysis of the isogenic embryonic and induced pluripotent stem cell lines revealed no traces of parental cell type or reprogramming process and provided the approach for the best clone selection [methylation]

Project description:Genome wide DNA methylation profiling of two parental human embryonic stem cell (ESC) lines (hESM01 and n5), three n5-derived somatic cell lines (N-neurons, F-fibroblasts, R-retinal pigment epithelium), and three pairs of induced pluripotent stem cell (iPSC) clones (iN, iF, iR). All lines are isogenic. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs. Bisulphite converted DNA from the 24 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip. For each line there are a biological (different passages) or technical (same passage) replicate.

2015-07-15 | E-GEOD-70737 | biostudies-arrayexpress

Genome wide methylation profliling of pediatric glioblastomas.

Project description:Genome wide DNA methylation profiling of WT, K27M, G34R and IDH1glioblastomas Bisulphite converted DNA from 38 WT, 28 K27M, 17 IDH1 AND 15 G34R samples hybridised to the Illumina 450k Human Methylation Beadchip

2014-03-09 | E-GEOD-55712 | biostudies-arrayexpress

Genome wide methylation profliling of ETMR tumours.

Project description:Genome wide DNA methylation profiling of normal, ETMR and PNET tumours Bisulphite converted DNA from 12 ETMR, 28 PNET and 34 control samples hybridised to the Illumina 450k Human Methylation Beadchip Please note that three of the 12 EMTR samples are tumor, cell line and xenograft sample derived from a single patient. Thus, there are 10 ETMR patients, 12 samples.

2013-11-21 | E-GEOD-52556 | biostudies-arrayexpress

DNA methylation and hydroxymethylation assessment through 450K analysis of paired bisulfite and oxidative-bisulfite conversion.

Project description:Analysis of genome-wide hydroxymethylation within infant placental tissue collected at term. These samples have been collected from the RhodeIsland Child Health Study (RICHS) cohort. Bisulfite and oxidative biulfite converted DNA was hybridized to the 450k platform and processed at the University of Minnesota Genomic Core

2016-07-01 | E-GEOD-71719 | biostudies-arrayexpress

Conversion of human fibroblasts into vascular cells (methylation)

Project description:We report a novel technique to reprogram human fibroblasts into endothelial and smooth muscle cells using partial iPSC reprogramming and chemically defined media. Using appropriate media conditions for differentiation of human pluripotent cells to CD34+ vascular progenitor cells, we show that temporary expression of pluripotent transcription factors and treatment with chemically-defined media, will induce differentiation of human fibroblasts to CD34+ vascular progenitor cells. Sorted CD34+ cells can then be directed to differentiate into vascular endothelial cells expressing a variety of smooth muscle markers. We have assessed the global DNA methylation (Illumina Infinium HD 450K DNA methylationBeadChips) and transcriptional (Illumina HT12v4 Gene Expression Bead Array) profiles of transdifferentiated endothelial cells and smooth muscle, human embryonic stem cell (hESC) and human induced pluripotent stem cell (hiPSC) differentiated CD34+ angioblasts, hESCs, hiPSC, primary smooth muscle and primary human umbilical vein endothelial cells using microarrays.

2012-09-18 | E-GEOD-40909 | biostudies-arrayexpress

Recurrent Variations in DNA Methylation in Human Pluripotent Stem Cells and their Differentiated Derivatives

Project description:This SuperSeries is composed of the following subset Series: GSE30652: Recurrent Variations in DNA Methylation in Human Pluripotent Stem Cells and their Differentiated Derivatives [Illumina HT12v3 Gene Expression] GSE30653: Recurrent Variations in DNA Methylation in Human Pluripotent Stem Cells and their Differentiated Derivatives [Illumina Infinium 27K DNA Methylation] GSE31848: Recurrent Variations in DNA Methylation in Human Pluripotent Stem Cells and their Differentiated Derivatives [Illumina Infinium 450K DNA Methylation] Refer to individual Series

2012-05-13 | E-GEOD-30654 | biostudies-arrayexpress

A Composite Framework for the Statistical Analysis of Epidemiological DNA Methylation Data with the Infinium Human Methylation 450K BeadChip

Project description:High-throughput DNA methylation profiling exploits microarray technologies thus providing a wealth of data, which however solicits rigorous, generic and analytical pipelines for an efficient systems level analysis and interpretation. In the present study, we utilize the Illumina's Infinium Human Methylation 450K BeadChip platform in an epidemiological cohort, targeting to associate interesting methylation patterns with breast cancer predisposition. The computational framework proposed here extends the -established in transcriptomic microarrays- logarithmic ratio of the Methylated versus the Unmethylated signal intensities, quoted as M-value. Moreover, intensity-based correction of the M-signal distribution is introduced in order to correct for batch effects and probe-specific errors in intensity measurements. This is accomplished through the estimation of intensity-related error measures from quality control samples included in each chip. Moreover, robust statistical measures based on coefficient variation measurements of DNA methylation between control and case samples alleviate the impact of technical variation. The results presented here are juxtaposed to those derived by applying classical pre-processing and statistical selection methodologies. Overall, in comparison to traditional approaches, the introduced framework's superior performance in terms of technical bias correction, along with its generic character, support its suitability for various microarray technologies. Bisulphite converted DNA from the samples were hybridized to the Illumina Infinium HumanMethylation450 BeadChip

2016-07-03 | E-GEOD-52635 | biostudies-arrayexpress

Recurrent Variations in DNA Methylation in Human Pluripotent Stem Cells and their Differentiated Derivatives [Illumina Infinium 450K DNA Methylation]

Project description:Human pluripotent stem cells (hPSCs) are potential sources of cells for modeling disease and development, drug discovery, and regenerative medicine. However, it is important to identify factors that may impact the utility of hPSCs for these applications. In an unbiased analysis of 205 hPSC and 130 somatic samples, we identified hPSC-specific epigenetic and transcriptional aberrations in genes subject to X chromosome inactivation (XCI) and genomic imprinting, which were not corrected during directed differentiation. We also found that specific tissue types were distinguished by unique patterns of DNA hypomethylation, which were recapitulated by DNA demethylation during in vitro directed differentiation. Our results suggest that verification of baseline epigenetic status is critical for hPSC-based disease models in which the observed phenotype depends on proper XCI or imprinting, and that tissue-specific DNA methylation patterns can be accurately modeled during directed differentiation of hPSCs, even in the presence of variations in XCI or imprinting. To obtain a comprehensive view of hPSC-specific epigenomic patterns, we collected 136 hESC and 69 hiPSC samples representing more than 100 cell lines for analysis. In order to establish expected variation in human tissues, we collected 80 high-quality and well-replicated samples representing 17 distinct tissue types from multiple individuals. Finally, we selected 50 additional samples from primary cell lines of diverse origin to control for any aberrations that may arise as a general, non-hPSC-specific, consequence of in vitro manipulation. With these samples, we performed genome-wide DNA methylation and mRNA expression profiling using the Illumina Infinium 27K and 450K DNA Methylation BeadChips as well as the Illumina HT12v3 Gene Expression BeadArray.

2012-05-13 | E-GEOD-31848 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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