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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Ankyrin-3 as a Molecular Marker of Early Life Stress and Vulnerability to Psychiatric Disorders

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Rattus norvegicus

SUBMITTER: Moshe Szyf

PROVIDER: E-GEOD-84028 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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DNA methylation signatures of parental deprivation in peripheral tissues of male rhesus macaques

Project description:This study mapped the genome wide DNA methylation changes in whole blood and buccal swab samples of 2 year old male rhesus monkeys subjected to parental deprivation in their first months of life (surrogate peer-reared condition). Equal numbers of control mother-reared (MR) and surrogate peer-reared (SPR) male monkeys whole blood (5 vs 5) and buccal swab samples (3 vs 3) were analyzed by methylated DNA immunoprecipitation (MeDIP) coupled with promoter tiling arrays.

2016-07-06 | E-GEOD-84020 | biostudies-arrayexpress

Early life adversity alters normal sex-dependent developmental dynamics of DNA methylation in rhesus monkeys

Project description:This study mapped the genome wide DNA methylation changes in CD3+ T lymphocytes from rhesus monkeys from postnatal day 14 through two years of age in both males and females and determined the impact of maternal deprivation on the DNA methylation profile. We show here that DNA methylation profiles evolve from birth to adolescence and are sex dependent. DNA methylation changes accompany imposed weaning, attenuating the difference between males and females. Altogether 71 T cell DNA samples were used in 4 different groups (male control, male stress, female control, female stress) at 4 different developmental stage (1 month, before weaning at 6-7 months, after weaning at 9-10 months, and after 2 years at 26-30 months) having 3-6 samples per each group. The DNA samples were pooled in each group and then subjected to Whole Genome Amplification in triplicates.

2016-07-06 | E-GEOD-84024 | biostudies-arrayexpress

DNA methylation in CD34 positive cells derived from cord blood at birth following prenatal stress

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2016-07-06 | E-GEOD-84018 | biostudies-arrayexpress

Male Rat DNA methylation in the Prefrontal Cortex at postnatal day 62 following prenatal restraint stress

Project description:DNA methylation profiling of Prefrontal Cortex of male rats at postnatal day 62 whose mothers were exposed to restraint stress from gestation day 14 until delivery The groups consist of 1. Control rats (Ctrl) 2. Prenatally stressed rats (PNS)

2016-07-06 | E-GEOD-84021 | biostudies-arrayexpress

DNA methylation in the colon of Dnmt3b-induced and control mice

Project description:The methylation status of colon epithelial cells was profiled in wild type mice and mice expressing a Dnmt3b transgene. Genome-scale methylation profiles were generated using reduced representation bisulfite sequencing (RRBS), with CpG methylation scored by promoter and also summarized by gene. Dnmt3b expression is associated with a strong increase in de novo methylation of a discrete subset of "methylation sensitive" genes which show a strong concordance with genes methylated in human colon cancer. These results, together with further analysis, indicate that colon epithelial cell methylation in the Dnmt3b mouse model predicts DNA methylation of human colon cancer with high confidence. Three each of Dnmt3b-induced and control mice, each split into two fractions.

2011-10-25 | E-GEOD-26758 | biostudies-arrayexpress

Methylation profiling by array of subcutaneous fat derived from 856 TwinsUK participants

Project description:Epigenetic changes such as DNA methylation variation are known to play a role in gene regulation and common disease susceptibility. Little is known about the genome-wide frequency, localization and function of such changes and how they are regulated by genetic and environmental factors. We have utilized the MuTHER resource and generated methylation profiles across multiple tissues conducted in a large set of female individuals that allows systematic dissection of genetic and non-genetic effects on DNA methylation. DNA methylation was quantified in subcutaneous fat and skin derived from 648 TwinsUK participants using the Infinium HumanMethylation450 BeadChips. Data from transcription profiling of skin, adipose fat and lymphoblastoid cell lines (LCLs) from the same set of TwinsUK participants have been deposited in ArrayExpress under accession number E-TABM-1140 (https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-1140).

2013-10-01 | E-MTAB-1866 | biostudies-arrayexpress

Maternal folate depletion during early development and high fat feeding from weaning elicit similar changes in gene expression, but not in DNA methylation, in adult offspring (DNA methylation data)

Project description:Abstract Scope: The âPredictive Adaptive Responseâ hypothesis suggests the in utero environment when mismatched with the post-natal environment can influence later life health. Underlying mechanisms are poorly understood, but may involve gene transcription changes, regulated via epigenetic mechanisms. Methods and Results: In a 2x2 factorial design, female C57Bl/6 mice were randomised to low or normal folate diets (0.4mg/2mg folic acid/kg diet) prior to and during pregnancy and lactation with, offspring randomised to high or low fat diets at weaning. Genome-wide gene expression and promoter DNA methylation were measured using microarrays in adult male livers. Maternal folate depletion and high fat intake post-weaning influenced gene expression (1959 and 1612 genes respectively) and promoter DNA methylation (208 and 344 loci respectively) but changes in expression and methylation were poorly matched for both dietary interventions. Expression of 667 genes was altered in response to both maternal folate depletion and post-weaning high fat feeding. In addition, there was evidence that the combined dietary insult (i.e. maternal folate depletion followed by high fat post-weaning) exerted the largest expression change for most of these genes. Conclusion: Our observations align with, and provide evidence in support of a potential underlying mechanism for, the âPredictive Adaptive Responseâ hypothesis. Elucidation of these mechanisms may identify targets for interventions to mitigate effects of adverse nutrition exposures during early development on disease risk in later life.

2017-05-22 | E-MTAB-4990 | biostudies-arrayexpress

Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution

Project description:We report the application of DNA sequencing technology for high-throughput sequencing of mix bis-PCR products totally 38 based on bisulfate treated DNA from human, chimpanzee, gibbon, macaque and crab eating macaque profrontal cortex tissues. Mix bisulfate PCR products from 1 tissues, 23 individula humans, 2 individual chimpanzees, 1 individual gibbons, 7 individual rhesus macaques and 5 crab eating macaques were sequenced by using MiSeq

2016-08-16 | E-GEOD-76788 | biostudies-arrayexpress

Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-08-20 | E-GEOD-85868 | biostudies-arrayexpress

Retroviral Integration Mutagenesis in Mice and Comparative Analysis in Human AML Identify Reduced PTP4A3 Expression as a Prognostic Indicator

Project description:Acute myeloid leukemia (AML) results from multiple genetic and epigenetic aberrations, many of which remain unidentified. Frequent loss of large chromosomal regions marks haplo-insufficiency as one of the major mechanisms contributing to leukemogenesis. However, which haplo-insufficient genes (HIGs) are involved in leukemogenesis is largely unknown and powerful experimental strategies aimed at their identification are currently lacking. Here, we present a new approach to discover HIGs, using retroviral integration mutagenesis in mice in which methylated viral integration sites and neighbouring genes were identified. In total we mapped 6 genes which are flanked by methylated viral integration sites (mVIS). Three of these, i.e., Lrmp, Hcls1 and Prkrir, were up regulated and one, i.e., Ptp4a3, was down regulated in the affected tumor. Next, we investigated the role of PTP4A3 in human AML and we show that PTP4A3 expression is a negative prognostic indicator, independent of other prognostic parameters. In conclusion, our novel strategy has identified PTP4A3 to potentially have a role in AML, on one hand as a candidate HIG contributing to leukemogenesis in mice and on the other hand as a prognostic indicator in human AML. We designed a new strategy to specifically identify DNA methylated proviral integrations on a large scale by combining methylated DNA immunoprecipitation (MeDIP), inverse PCR and promoter array hybridization. We used 6 murine leukemia samples from a previous screen that were induced by injecting Gr 1.4 MLV into newborn mice.

2011-10-26 | E-GEOD-19706 | biostudies-arrayexpress

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