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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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DNA methylation analysis by MeDIP-on-chip in mouse E3.5 blastocysts, E6.5 epiblasts and E9.5 whole embryos.

ABSTRACT: DNA methylation is extensively reprogrammed during early phases of mammalian development yet individual genomic targets of this process are largely unknown. We optimized MeDIP (Methylated DNA Immunoprecipitation) for low numbers of cells and profiled DNA methylation genome-wide during early development of the mouse embryonic lineage in vivo. We mapped DNA methylation at 3 consecutive stages of early development: E3.5 blastocysts, E6.5 epiblasts and E9.5 whole embryos. MeDIP and Input samples were hybridized to Nimblegen HD2 MM8 promoter deluxe arrays covering 12 kb of all gene promoters. Experiments were performed in duplicates for E3.5 blastocysts and triplicates for E6.5 epibalsts and E9.5 embryos. As a control we also hybridized pooled unamplified MeDIPs from E9.5 to Nimblegen 385K MM8 RefSeq promoter arrays.

ORGANISM(S): Mus musculus

SUBMITTER: Michael Weber

PROVIDER: E-GEOD-22831 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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DNA methylation analysis by MeDIP-on-chip in mouse E13.5 PGCs

Project description:Epigenetic reprogramming, characterized by loss of cytosine methylation and histone modifications, occurs during mammalian development in primordial germ cells (PGCs). Here we provide a detailed map of cytosine methylation on a large portion of the genome in developing male and female PGCs isolated from mouse embryos. We mapped DNA methylation in E13.5 PGCs isolated by FACS sorting from Oct4-GFP male and female embryos. As a control, we also mapped DNA methylation in E7.5 epiblasts from wich PGCs derive from. MeDIP and Input samples were hybridized to Nimblegen HD2 MM8 promoter deluxe arrays covering 12 kb of all gene promoters. Experiments were performed in duplicates for E7.5 epiblasts and triplicates for E13.5 PGCs.

2012-01-31 | E-GEOD-31572 | biostudies-arrayexpress

Epigenetic regulation and transcriptional repression by Tet1 in the early post-implantation mouse embryo: Methylation data.

Project description:The mammalian TET dioxygenases contribute to global waves of DNA demethylation in the zygote and in primordial germ cells, but their involvement during de novo DNA methylation at peri/post-implantation development is unknown. Here, we show novel physiological functions of Tet1 in the pre-primitive streak stage mouse embryo, where it is expressed not only in the primed-state epiblast, but also in the extra-embryonic ectoderm. In the epiblast, Tet1 contributes to DNA methylation patterning, which indirectly results in dominant transcriptional repression involving a Jumonji-family gene Jmjd8. In the extra-embryonic ectoderm, Tet1 suppresses expression of metabolic genes involved in oxidative phosphorylation. These lineage-specific gene repressive functions, involving distinct modes of regulation by DNA methylation, counteract precocious differentiation of the embryo prior to the onset of gastrulation. Such dysregulation in the absence of Tet1 are surprisingly tolerated in an inbred strain but results in full embryonic lethality in non-inbred mice, thus implicating a complex but essential role of Tet1 in normal gestational development.

2017-05-15 | E-MTAB-4581 | biostudies-arrayexpress

Mus musculus

Project description:DNA methylation analysis by MeDIP-on-chip in mouse E3.5 blastocysts, E6.5 epiblasts and E9.5 whole embryos.

| PRJNA127883 | ENA

Genome-wide Analysis Reveals Mecp2-dependent Regulation of MicroRNAs in a Mouse Model of Rett Syndrome

Project description:This SuperSeries is composed of the following subset Series: GSE24285: Genome-wide Analysis Reveals Mecp2-dependent Regulation of MicroRNAs in a Mouse Model of Rett Syndrome (mm8 chromosomal tiling arrays) GSE24286: Genome-wide Analysis Reveals Mecp2-dependent Regulation of MicroRNAs in a Mouse Model of Rett Syndrome (mm8 promoter tiling arrays) GSE24320: Genome-wide Analysis Reveals Mecp2-dependent Regulation of MicroRNAs in a Mouse Model of Rett Syndrome (high-throughput small RNA sequencing) Refer to individual Series

2010-09-29 | E-GEOD-24329 | biostudies-arrayexpress

Hypermethylation in the ZBTB20 gene is associated with major depressive disorder

Project description:Genome-wide MeDIP-Sequencing of 23 monozygotic twin pairs (n=46) from Australia discordant for major depressive disorder (MDD). MeDIP-seq of 23 monozygotic twin pairs discordant for major depressive disorder. MZ twin pairs were compared to identify significantly differently methylated sites associated with MDD.

2014-01-25 | E-GEOD-54370 | biostudies-arrayexpress

miRNA profiling in male and female chicken embryonic gonads during sexual differentiation

Project description:MicroRNAs (miRNAs) are a highly conserved class of small RNAs which function in a sequence-specific manner to post-transcriptionally regulate expression of target genes. Tissue-specific miRNA expression studies have discovered numerous functions for miRNAs in various aspects of embryonic development, but a role for miRNAs in gonadal development and sex differentiation has not yet been reported. Using the chicken embryo as a vertebrate model, differential miRNA expression between male and female embryonic gonads, was analysed at three developmental stages (embryonic days (E) 5.5, E6.5 and E9.5), using custom-designed 4x2K CombiMatrix miRNA microarray. The aims of this study were to: 1-identify miRNAs differentialy expressed by sex; 2-identify sex-specific miRNAs; 3-analyse global changes in miRNA up-regulation in male versus female gonads before, during and after the histological onset of sexual differentiation. This study provides a basis for establishing whetehr miRNAs are involved in either initiating or regulating vertebrate gonadal sex differentiation. Keywords: miRNA, sex comparison, developmental stage comparison. miRNA samples from male and female embryonic chicken gonads from three developmental stages: embryonic day (E) 5.5 (Hamilton & Hamburger (HH) stage 27-28), E6.5 (HH stage 29-30) & E9.5 (HH stage 35-36). Samples are listed with biological replicates used for analysis in brackets following: 1 - Male E5.5 (5); 2 - Female E5.5 (4); 3 - Male E6.5 (5); 4 - Female E6.5 (3); 5 - Male E9.5 (4); 6 - Female E9.5 (4).

2010-05-18 | E-GEOD-13154 | biostudies-arrayexpress

5-hydroxymethylcytosine: the sixth DNA base

Project description:We performed a meta analysis of publicly available TET1, 5mC, 5hmC and genome wide bisulfite profiling data mostly from mouse embryonic stem cells (ESC). Genome wide chromatin immunoprecipitation combined with deep sequencing (ChIP-seq) has revealed binding of the TET1 protein at CpG-island (CGI) promoters and at bivalent promoters. We show that TET1 also coincides with DNAseI hypersensitive sites (HS). Presence of TET1 at these THREE locations suggests that it may play a dual role: an active role at CpG-islands and DNAseI hypersensitive sites and a repressive role at bivalent loci. In line with the presence of TET1, significant enrichment of 5hmC but not 5mC is detected at bivalent promoters and DNaseI HS. Surprisingly, 5hmC is not detected or present at very low levels at CGI promoters notwithstanding the presence of TET1 at these loci. Our meta analysis suggest that asymmetric methylation is present at CA- and CT-repeats in the genome of some human ESC. Examination of the distribution of 5-methylcytosine and 5-hydroxymethylcytosine in the genome of mouse embryonic stem cells.

2011-11-24 | E-GEOD-31343 | biostudies-arrayexpress

Analysis of age-associated transcriptome changes in uterus and decidua

Project description:We use RNA-sequencing to measure global transcription in uteri of young and aged (~1yr old) C57BL/6 females at day 3.5 (E3.5) of pregnancy, and of the decidual part of E11.5 placentas developed in young and aged (~1yr old) females. We report dys-regulation of gene expression in the E3.5 uteri and E11.5 deciduae of aged mice. We compare the transcriptome of young and aged E11.5 deciduae with that of young deciduae from E9.5-E12.5 of pregnancy, and report that aged E11.5 deciduae are developmentally retarded in comparison to young deciduae.

2017-09-14 | GSE98901 | GEO

Differentiation time course of trophoblast stem cells

Project description:To characterized the changes in gene expression during the differentiation of TS cells. TS cells can be derived from two time point during embryogenesis, cell lines tested were from each of these time points. Keywords: time course TS cells derived from either E3.5 or E6.5 embryos were differentiated over 6 days by withdrawal of FGF4 and feeder conditioned medium. Cell were sampled every 24 hrs and assayed by microarray.

2010-02-21 | E-GEOD-12985 | biostudies-arrayexpress

MeDIP analysis of 5mC and 5hmC marks in human ataxia-telangiectasia cerebellum

Project description:Genomic DNA was prepared, fragmented, and immunoprecipitated with antibodies specific for 5mC or 5hmC prior to standard sequencing. The neurodegenerative disease known as ataxia-telangiectasia (A-T) is caused by the absence of the ATM (A-T mutated) protein. A long-standing mystery surrounding A-T is why cerebellar Purkinje cells (PCs) appear uniquely vulnerable to ATM-deficiency. Here, we present that 5-hydroxymethylcytosine (5hmC), a newly recognized epigenetic marker found at high levels in neurons, is substantially reduced in human A-T and Atm-/- mouse cerebellar PCs. TET1, an enzyme that converts 5mC to 5hmC, responds to DNA damage. Manipulation of TET1 activity directly affects neuronal cell cycle reentry and cell death after the induction of DNA damage. Quantitative, genome-wide analysis of 5hmC of samples from human cerebellum showed that in ATM-deficiency there is a remarkable genome-wide reduction of 5hmC enrichment at both proximal and distal regulatory elements. These results reveal a role of TET1-mediated 5hmC in DNA damage response, and provide insights into the basis of a PC-specific DNA demethylation alteration in ATM-deficiency. There are two groups, A-T and Control. For each group, cerebellar DNA samples were immunoprecipitated with anti-5mC (n=1) or anti-5hmC (n=3). There were also two replicates of input control for each group.

2015-10-30 | E-GEOD-61133 | biostudies-arrayexpress

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