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Links from GEO DataSets

Items: 20

1.

A unique regulatory phase of DNA methylation in the early mammalian embryo

(Submitter supplied) DNA methylation is highly dynamic during mammalian embryogenesis. It is broadly accepted that the paternal genome is actively depleted of global cytosine methylation at fertilization, followed by passive depletion that reaches a minimum at the blastocyst stage. However, this model is based on limited data, and to date no base-resolution maps exist to support and refine it. Here, we generated genome-scale DNA methylation maps in mouse gametes and through post-implantation embryogenesis. more...
Organism:
Mus musculus
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL11002
76 Samples
Download data: TXT
Series
Accession:
GSE34864
ID:
200034864
2.

Allelic reprogramming of the histone modification H3K4me3 in early mammalian development

(Submitter supplied) Histone modifications are considered as fundamental epigenetic regulators that control many crucial cellular processes 1. However, whether these marks can be passed on from gametes to the next generation in mammals is a long-standing question that remains unclear. By developing a highly sensitive approach, STAR ChIP-seq, we provided a panoramic view of the landscape of H3K4me3, a histone hallmark for transcription initiation 2, from developing gametes to postimplantation embryos. more...
Organism:
Mus musculus; Danio rerio
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms:
GPL18171 GPL18480
57 Samples
Download data: BED, TXT
Series
Accession:
GSE71434
ID:
200071434
3.

Single cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed by reduced representation bisulfite sequencing

(Submitter supplied) We develop a single cell methylome analysis technique based on RRBS, which works robustly for mouse embryonic stem cells (mESCs), sperm, metaphase II oocytes, and zygotes.
Organism:
Escherichia virus Lambda; Mus musculus
Type:
Methylation profiling by high throughput sequencing
Platforms:
GPL17527 GPL13112
36 Samples
Download data: BED, TXT
Series
Accession:
GSE47343
ID:
200047343
4.

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

(Submitter supplied) 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.
Organism:
Mus musculus
Type:
Methylation profiling by genome tiling array
Platforms:
GPL8943 GPL9485
11 Samples
Download data: PAIR
Series
Accession:
GSE22831
ID:
200022831
5.

Preimplantation stage-specific effect of culture environment on the DNA methylome of bovine blastocysts

(Submitter supplied) The culture conditions of the early preimplantation embryos affects the DNA methylation landscape of the resulting blastocysts.
Organism:
Bos taurus
Type:
Methylation profiling by genome tiling array
Platform:
GPL18384
16 Samples
Download data: TXT
Series
Accession:
GSE69173
ID:
200069173
6.

Epigenetic profiling at mouse imprinted gene clusters

(Submitter supplied) Epigenetic profiling of DNA methylation, histone H3 lysine 4 trimethylation and histone H3 lysine 9 trimethylation at imprinted gene clusters in the mouse.
Organism:
Mus musculus
Type:
Methylation profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array
Platform:
GPL8714
18 Samples
Download data: TXT
Series
Accession:
GSE16588
ID:
200016588
7.

Highly sensitive sequencing reveals dynamic modifications and activities of small RNAs in mouse oocytes and early embryos

(Submitter supplied) Small RNAs play important roles in early embryonic development. However, their expression dynamics and modifications are poorly understood because of the scarcity of RNA that is obtainable for sequencing analysis. Using an improved deep sequencing method that requires as little as 10 ng of total RNA or 50 oocytes, we profile small RNAs in mouse oocytes and early embryos. We find that microRNA (miRNA) expression starts soon after fertilization, and the mature miRNAs carried into the zygote by sperm during fertilization are relatively rare compared to the oocyte miRNAs. more...
Organism:
Homo sapiens; Mus musculus
Type:
Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL13112 GPL11154
26 Samples
Download data: TXT
Series
Accession:
GSE83581
ID:
200083581
8.

Genome-wide survey reveals dynamic widespread tissue-specific changes in DNA methylation during development

(Submitter supplied) To further our understanding of the role of DNA methylation in development, Methylated DNA Immunoprecipitation (MeDIP) was used in conjunction with a NimbleGen promoter plus CpG island array to identify Tissue and Developmental Stage specific Differentially Methylated DNA Regions (T-DMRs and DS-DMRs) on a genome-wide basis. Four tissues (brain, heart, liver, and testis) from C57BL/6J mice were analyzed at three developmental stages (15 day embryo, E15; new born, NB; 12 week adult, AD). more...
Organism:
Mus musculus
Type:
Methylation profiling by genome tiling array
Platform:
GPL7060
26 Samples
Download data: TXT
Series
Accession:
GSE21415
ID:
200021415
9.

Sperm but not oocyte DNA methylome is inherited by zebrafish early embyros

(Submitter supplied) 5-methylcytosine is a major epigenetic modification sometimes called "the fifth nucleotide". However, our knowledge of how offspring inherit the DNA methylome from parents is limited. We generated nine single-base resolution DNA methylomes including zebrafish gametes and early embryos. The oocyte methylome is significantly hypo-methylated compared to sperm. Strikingly, the paternal DNA methylation pattern is maintained throughout early embryogenesis. more...
Organism:
Danio rerio
Type:
Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform:
GPL14875
19 Samples
Download data: TXT, WIG
Series
Accession:
GSE44075
ID:
200044075
10.

The DNA methylation landscape of human early embryos

(Submitter supplied) Our data provided a genome-wide DNA methylation landscape of human early development embryos, including human MII oocytes, sperm, zygotes, 2-cell to 8-cell embryos, morula, blastocyst and postimplantation embryos at single base resolution.
Organism:
Homo sapiens
Type:
Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform:
GPL11154
87 Samples
Download data: TXT
Series
Accession:
GSE49828
ID:
200049828
11.

Comparison of the DNA methylation of bovine blastocysts and bovine sperm

(Submitter supplied) DNA from expanded bovine blastocysts and bovine sperm were extracted then subjected to methylation-sensitive enzymatic digestion and LM-PCR enrichment before being hybridized onto a microarray.
Organism:
Bos taurus
Type:
Methylation profiling by genome tiling array
Platform:
GPL18700
4 Samples
Download data: TXT
Series
Accession:
GSE57709
ID:
200057709
12.

Wax and Wane of genome-wide DNA methylation during monkey preimplantation embryogenesis

(Submitter supplied) This study reports, for the first time, the genome scale methylome of nonhuman primate preimplantation development and proposes a perspective of DNA methylation dynamic equilibrium involving both DNA demethylation and de novoremethylation during primate early embryogenesis.
Organism:
Macaca mulatta
Type:
Expression profiling by high throughput sequencing
Platform:
GPL14954
7 Samples
Download data: TXT
Series
Accession:
GSE60166
ID:
200060166
13.

DNA methylation dynamics of the human pre-implantation embryo

(Submitter supplied) We present genome-scale maps of DNA methylation in early human development and perform comparative analysis to mouse that confirm a conserved global erasure of the paternal genome. We find that while many global features of the early embryo are consistent between the two species, the target sequences in which DNA methylation is maintained are distinct. Repetitive elements show a broader range of class specific behaviors in the human embryo and a larger degree of methylation escape in human sperm. more...
Organism:
Homo sapiens; Mus musculus
Type:
Methylation profiling by high throughput sequencing
Platforms:
GPL11002 GPL10999
48 Samples
Download data: TXT
Series
Accession:
GSE51239
ID:
200051239
14.

Effects of Tdg deficiency on overall transcription in mouse embryonic fibroblasts and during cell differentiation

(Submitter supplied) Because it excises thymine from G•T mismatches, TDG was proposed to counter mutagenesis by 5-methylcytosine deamination. Yet, TDG was also observed to attack 5-methycytosine itself, making it a candidate DNA demethylase, and interactions with transcription factors implicated additional functions in gene regulation. Unlike other DNA glycosylases, TDG is essential for embryonic development. Fibroblasts from Tdg null embryos show massively impaired gene regulation, and this correlates with imbalanced histone modification and CpG methylation. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platforms:
GPL6887 GPL339
18 Samples
Download data: CEL, TXT
Series
Accession:
GSE20693
ID:
200020693
15.

Genome-wide bisulfite sequencing in zygotes identifies demethylation targets and maps the contribution of TET3 oxidation

(Submitter supplied) Fertilization triggers a global erasure of 5-methylcytosine from paternal DNA as part of extensive epigenetic reprogramming during the transition from gametic specialization to totipotency. This active removal has been shown to involve oxidation by TET3, but the targeting of this pathway and the wider context of demethylation remain poorly understood. We optimized a novel technique for whole-genome bisulfite sequencing and applied it to wild-type and TET3-deficient zygotes, using SNPs to access paternal alleles. more...
Organism:
Mus musculus
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL13112
2 Samples
Download data: TXT
Series
Accession:
GSE63417
ID:
200063417
16.

Single-Cell Whole-Genome Bisulfite Sequencing for Analysis of Epigenetic Heterogeneity

(Submitter supplied) We report a single-cell whole-genome bisulfite sequencing method (scBS-Seq) capable of accurately measuring DNA methylation at up to 36% of CpGs. We observed that ESCs grown in serum/LIF or 2i/LIF both display epigenetic heterogeneity, with “2i-like” cells present in serum cultures. In silico integration of 12 individual MII oocytes datasets  recapitulates the whole DNA methylome, making scBS-Seq a versatile tool to explore DNA methylation in rare cells and heterogeneous populations.
Organism:
Mus musculus
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL13112
56 Samples
Download data: TXT, ZIP
Series
Accession:
GSE56879
ID:
200056879
17.

Unique Broad Histone Lysine 4 Methylation Domains in Mouse Oocytes and Dynamic Regulation during Maternal to Zygotic Transition

(Submitter supplied) The maternal to zygotic transition (MZT) involves the transfer of genome regulation from the oocyte to the embryo and is essential for the formation of totipotent embryos. However, regulatory mechanisms are still poorly understood despite recent progress in mapping the dynamics in RNA transcripts and DNA methylation1-9. Previous studies suggest that dynamic histone modifications may play important roles in MZT10-12, however direct measurements of chromatin states has been hindered by technical difficulties in profiling histone modifications from small quantities of cells. more...
Organism:
Homo sapiens; Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms:
GPL17021 GPL16791
65 Samples
Download data: BW, TXT
Series
Accession:
GSE72784
ID:
200072784
18.

Resetting epigenetic memory by reprogramming of histone modifications in mammals

(Submitter supplied) Polycomb group proteins and the related histone modification H3K27me3 can maintain the silencing of key developmental regulators and provide cellular memory. However, how such epigenetic state is reprogrammed and inherited between generations is poorly understood. Using an ultra-sensitive approach STAR ChIP-seq, we investigated H3K27me3 across 14 developmental stages along mouse gametogenesis and early development. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform:
GPL18480
27 Samples
Download data: BED, TXT
Series
Accession:
GSE76687
ID:
200076687
19.

Identification of maternal imprinting control regions (ICRs) in the post-implantation mouse embryo.

(Submitter supplied) Genomewide DNA methylation profiles, generated by MeDIP-seq, for 8.5dpc wildtype and Dnmt3l-/+ mouse embryos were compared to identify differentially methylated regions (DMRs) that depend on the activity of the de novo DNA methyltransferase cofactor Dnmt3l in the oocyte. These DMRs were further characterised by their methylation state in mature mouse sperm and in the livers of inter-subspecies newborn mice. more...
Organism:
Mus musculus
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL11002
19 Samples
Download data: BAM
Series
Accession:
GSE32687
ID:
200032687
20.

DNA methylation analysis and expression profiling during murine embryogenesis and in embryos deficient for DNMT3A or DNMT3B

(Submitter supplied) We quantified the targets and kinetics of DNA methylation acquisition in mouse embryos, and determined the contribution of the de novo methyltransferases DNMT3A and DNMT3B to this process. We provide single-base maps of cytosine methylation by RRBS from the blastocysts to post-implantation stages and in embryos lacking DNMT3A or DNMT3B activity, and performed RNA-Seq in embryos lacking DNMT3B activity.
Organism:
Mus musculus
Type:
Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform:
GPL13112
27 Samples
Download data: IGV, TXT
Series
Accession:
GSE60334
ID:
200060334
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