Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

58 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Early life Lead exposure causes distinct gender specific changes in the DNA methylation profile of DNA extracted from dried blood spots

ABSTRACT: Study of influence of gender and Lead(Pb) exposure on DNA methylation for whole blood measured in dried blood spots for a Detroit cohort of child between the age of 3 months to 5years DNA methylation profiling of dried blood spots for a Detroit cohort of child between the ages of 3 months to 5 years Differential methylation study

ORGANISM(S): Homo sapiens

SUBMITTER: Douglas Ruden

PROVIDER: E-GEOD-60598 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Gender-specific post-natal demethylation and establishment of epigenetic memory

Project description:DNA methylation patterns are set up in a relatively fixed programmed manner during normal embryonic development and are then stably maintained. Using genome-wide analysis, we have discovered a postnatal pathway involving gender-specific demethylation that occurs exclusively in the male liver. This demodification is programmed to take place at tissue-specific enhancer sequences, and our data show that the methylation state at these loci is associated with and appears to play a role in the transcriptional regulation of nearby genes. This process is mediated by the secretion of testosterone at the time of sexual maturity, but the resulting methylation profile is stable and therefore can serve as an epigenetic memory even in the absence of this inducer. These findings add a new dimension to our understanding of the role of DNA methylation in vivo and provide the foundations for deciphering how environment can impact on the epigenetic regulation of genes, in general. DNA methylation profile of male and female mouse and Human tissues was generated using the RRBS protocol followed by deep sequncing. Whole genome DNA methylation profile using deep sequencing was genereted for male and female mouse tissues. RNAseq was performed on male and female mouse tissues.

2015-05-03 | E-GEOD-60012 | biostudies-arrayexpress

Early life Lead exposure causes distinct gender specific changes in the DNA methylation profile of DNA extracted from dried blood spots

Project description:Study of influence of gender and Lead(Pb) exposure on DNA methylation for whole blood measured in dried blood spots for a Detroit cohort of child between the age of 3 months to 5years

2014-09-01 | GSE60598 | GEO

Genome-wide DNA methylation patterns in pancreatic ductal adenocarcinoma (PDAC)

Project description:Determine methylation pattern in PDAC a genome-wide analysis was performed in a cohort of 167 PDAC and 29 adjacent pancreatic tissues samples using the Infinium 450k methylation arrays (Illumina). 167 pancreatic tumors (PDAC) x 29 adjacent -non tumor samples.

2014-07-08 | E-GEOD-49149 | biostudies-arrayexpress

Ceratitis capitata gene expression

Project description:This SuperSeries is composed of the following subset Series: GSE19571: Ceratitis capitata gene expression related to sexual maturation in females GSE19572: Ceratitis capitata gene expression related to sexual maturation in males GSE19573: Ceratitis capitata gene expression related to mating status in mature females (mated vs virgin) GSE19608: Ceratitis capitata gene expression related to mating status in mature males (mated vs virgin) Refer to individual Series

2011-12-25 | E-GEOD-19614 | biostudies-arrayexpress

Methylation profiling by array of 108 clear cell renal cell carcinoma

Project description:A Cartes d'Identite des Tumeurs (CIT) project from the French Ligue Nationale Contre le Cancer (<a href=\\ttp://cit.ligue-cancer.net/\\ target=\\_blank\\>http://cit.ligue-cancer.net</a>). Selecting patients with metastatic clear-cell renal cell carcinoma (m-ccRCC) who might benefit from treatment with targeted tyrosine kinase inhibitors (TKIs) is a challenge. Our aim was to identify molecular markers associated with outcome in m-ccRCC patients treated with sunitinib.\

2016-02-26 | E-MTAB-3274 | biostudies-arrayexpress

Gender differences in hepatic gene expression

Project description:Gene expression differences between mal and female rat livers (female/male).

2010-06-10 | E-GEOD-2497 | biostudies-arrayexpress

Identification of Hnf6 binding sites in male and female mouse liver

Project description:∼40,000 HNF6 binding sites were identified in mouse liver chromatin, including several thousand sites showing significant differences in level of HNF6 binding between male and female mouse liver. These sex-biased HNF6 binding sites showed strong enrichment for sex-biased DNase hypersensitive sites and for proximity to genes showing local sex-biased chromatin marks and a corresponding sex-biased expression. ~90% of genome-wide CUX2 binding sites identified previously in female mouse liver (Conforto TL, Zhang Y, Sherman J, Waxman DJ., Mol Cell Biol. 2012;32(22):4611-4627) were also bound by HNF6, giving evidence for genome-wide competition between HNF6 and CUX2 for chromatin binding in female mouse liver. These HNF6/CUX2 common binding sites were enriched for genomic regions more accessible in male than in female mouse liver chromatin, and showed strongest enrichment for male-biased genes, suggesting HNF6 displacement by CUX2 as a mechanism to explain the observed CUX2 repression of male-biased genes in female liver. However, HNF6 binding was sex-independent at a majority of its binding sites, and peak regions of HNF6 binding were frequently associated with co-binding by multiple other liver transcription factors, consistent with HNF6 playing a global regulatory role in both male and female liver. Livers were excised from individual male and female mice, cross-linked and sonicated, then used to identify HNF6 binding sites by ChIP-Seq using antibody specific to HNF6 (sc-13050; Santa Cruz Biotechnology, Inc).

2015-07-28 | E-GEOD-60014 | biostudies-arrayexpress

Whole-genome methylation analysis (450k) of school aged children prenatally exposed to alcohol vs controls

Project description:We tested a hypothesis that prenatal alcohol exposure may lead to epigenetic alterations to the DNA resulting in attentional and cognitive alterations of the children. 6-9 year old children school children of the Franconian Cognition and Emotion Studies (FRANCES) cohort which were tested for an objective marker of PAE, ethyl glucuronide (EtG) in meconium at birth. 32 newborns were found to be exposed to alcohol with a threshold above 30 ng/g (EtG+) but without a FAS diagnosis. DNA for methylation analysis was extracted from buccal cells, DNA methylation was analyzed using the Infinium Human Methylation 450K BeadChip array (Illumina).

2018-05-12 | E-MTAB-6730 | biostudies-arrayexpress

BAC CGH array profiling using Phi29-amplified microdissected samples

Project description:Details of the experiment are available within the Nucleic Acid Research, 2004 manuscript "Genomic profiling by DNA amplification of laser capture microdissected tissues and array CGH", by Cardoso J. et al.

2010-06-05 | E-GEOD-1841 | biostudies-arrayexpress

Multigenerational epigenetic inheritance in humans: DNA methylation changes associated with maternal exposure to lead can be transmitted to the grandchildren

Project description:We report that the DNA methylation profile of a child’s neonatal whole blood can be significantly influenced by his or her mother’s neonatal blood lead levels (BLL). We recruited 35 mother-infant pairs in Detroit and measured the whole blood lead (Pb) levels and DNA methylation levels at over 450,000 loci from current blood and neonatal blood from both the mother and the child. We found that mothers with high neonatal BLL correlate with altered DNA methylation at 564 loci in their children’s neonatal blood. Our results suggest that Pb exposure during pregnancy affects the DNA methylation status of the fetal germ cells, which leads to altered DNA methylation in grandchildren’s neonatal dried blood spots. This is the first demonstration that an environmental exposure in pregnant mothers can have an epigenetic effect on the DNA methylation pattern in the grandchildren. For the study, we selected 35 dried blood spots (DBS) collected from mother-infant pairs from Health Fairs ran in three Detroit communities, because they have a high prevalence (8-11%) of high BLL in children. The sample set consisted of 25 male children and 18 female children. We also collected the neonatal DBS and mother neonatal DBS for these mother-infant pairs from the Michigan Neonatal Biobank. Then we measured a blood lead levels in dried blood spots using using atomic absorbtion spectrophotometry. Finally we measured the DNA methylation levels using human methylation 450K array from Illumina. Then we normalized the data for technical biases and tried to infer the the locus specific DNA methylation changes due to Pb exposure which was carried over from the grandmothers to the grandchildren by the Pb –exposed fetal germ cells of the mother using statistical model proposed by Sofer et al, 2012.

2015-04-01 | E-GEOD-67444 | 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