GEO DataSets

(Submitter supplied) Maternal inactivation of genes encoding components of the sub-cortical maternal complex (SCMC) and its associated member PADI6 generally results in early embryo lethality. In humans, SCMC gene variants were found in the healthy mothers of children affected by multi-locus imprinting disturbances (MLID). However, how the SCMC controls the DNA methylation required to regulate imprinting remains poorly defined. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17021

96 Samples

Download data: COV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Other

Platforms:

GPL17021 GPL24247 GPL21626

193 Samples

Download data: COV, VCF

(Submitter supplied) Maternal inactivation of genes encoding components of the sub-cortical maternal complex (SCMC) and its associated member PADI6 generally results in early embryo lethality. In humans, SCMC gene variants were found in the healthy mothers of children affected by multi-locus imprinting disturbances (MLID). However, how the SCMC controls the DNA methylation required to regulate imprinting remains poorly defined. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL24247

1 Sample

Download data: VCF

(Submitter supplied) Maternal inactivation of genes encoding components of the sub-cortical maternal complex (SCMC) and its associated member PADI6 generally results in early embryo lethality. In humans, SCMC gene variants were found in the healthy mothers of children affected by multi-locus imprinting disturbances (MLID). However, how the SCMC controls the DNA methylation required to regulate imprinting remains poorly defined. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

96 Samples

Download data: TXT

(Submitter supplied) PADI6 is a component of the subcortical maternal complex (SCMC) which is a group of proteins that are abundantly expressed in the oocyte cytoplasm and essential for the proper development of the early embryo. The mutation(s) in the components of the subcortical maternal complex have been associated with reproductive failures, including formation of hydatidiform mole, female infertility and imprinting disorders with multi-locus imprinting disturbance (MLIDs).In the current study by using whole-exome sequencing analysis, we identified four cases of Beckwith-Wiedemann Syndrome with multi-locus imprinting disturbance while their mothers were carriers of variants in PADI6 gene. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

22 Samples

Download data: IDAT, TXT

(Submitter supplied) Multi-locus imprinting Disturbances (MLID) are methylation defects affecting germline-derived Differentially Methylated Regions (gDMRs) and they have been associated with maternal-effect variants causing imprinting disorders in the offspring. In a family with multiple pregnancy losses, a child with Beckwith-Wiedemann syndrome (BWS) and a further child without any features of imprinting disorders, novel compound heterozygous variants in the NLRP5 gene of the mother were found. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

10 Samples

Download data: IDAT, TXT

(Submitter supplied) Beckwith–Wiedemann syndrome (BWS) and Pseudohypoparathyroidism type 1B (PHP1B) are imprinting disorders (ID) caused by deregulation of the imprinted gene clusters located at 11p15.5 and 20q13.32, respectively. In both of these diseases a subset of the patients is affected by multi-locus imprinting disturbances (MLID). In several families, MLID is associated with damaging variants of maternal-effect genes encoding protein components of the subcortical maternal complex (SCMC). more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

18 Samples

Download data: IDAT, TXT

(Submitter supplied) Maternal-effect mutations in components of the subcortical maternal complex (SCMC) of the human oocyte can cause early embryonic failure, gestational abnormalities and recurrent pregnancy loss. Enigmatically, they are also associated with DNA methylation abnormalities at imprinted genes in conceptuses, in the devastating gestational abnormality biparental complete hydatidiform mole (BiCHM) or in multi-locus imprinting disease (MLID). more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

6 Samples

Download data: IDAT, TXT

(Submitter supplied) Mutations in components of the subcortical maternal complex (SMC) of the human oocyte are enigmatically associated with DNA methylation abnormalities specifically at imprinted genes in conceptuses, but the developmental timing, genomic extent and mechanistic details of these defects are unknown. Here, we show, by single-cell bisulphite sequencing, that mutation in human KHDC3L that causes recurrent hydatidiform mole results in a genome-wide deficit of de novo methylation in oocytes.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: COV

(Submitter supplied) One possible mechanism leading to the apparent polymorphic placenta-specific DMRs would be the failure to maintain allelic methylation during gestation. For a temporal comparison, we performed methylation profiling on first trimester chorionic villus sampling (CVS) and compared it with corresponding samples at term. This revealed that DNA methylation level at placenta-specific DMRs is highly stable between the two points. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array; Methylation profiling by array

Platforms:

GPL13534 GPL21145

12 Samples

Download data: CSV

(Submitter supplied) Zygotic genomic activation (ZGA) is a landmark event in the maternal-to-zygotic transition (MZT), and the regulation of ZGA by maternal factors remains to be elucidated. In this study, the depletion of maternal RNF114 led to 2-cell embryos developmental arrest in mice. RNF114 was proven to play an important role in major ZGA using ethynyl uridine (EU) incorporation and transcriptome analysis. To study the underlying mechanism, we performed protein profiling in mature oocytes and found a potential substrate for RNF114, Chromobox protein CBX5, whose ubiquitination and degradation was regulated by RNF114. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

29 Samples

Download data: BW

(Submitter supplied) Oocyte acquires developmental competence during its maturation. This stage is accompanied with large-scale alteration in transcription, and series of genome-wide epigenetic reprogramming, including de novo establishment of DNA methylation. However, our understanding of mechanisms regulating this process is limited. To investigate the role of Stella (Dppa3) in de novo methylation during mouse oogenesis, here we measured DNA methylation by RRBS and expression profiles by RNA-seq in PGCs and oocytes at serveral development stages, including genotypes of both Stella (Dppa3) +/- and Stella -/-.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

4 related Platforms

83 Samples

Download data: TXT

(Submitter supplied) A conserved event of the maternal-to-zygotic transition (MZT) in animal embryos is the elimination of a subset of the maternal transcripts that accumulated during oogenesis. In invertebrates and lower vertebrates, a maternally encoded mRNA decay pathway (M-decay) acts before zygotic genome activation (ZGA) while a second pathway, which requires zygotic transcription, subsequently clears additional mRNAs (Z-decay). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

9 Samples

Download data: TXT

(Submitter supplied) Embryos were collected at 2 cell stage. cRNA from four biological replicates of each were generated and the expression profiles were determined using Affymetrix MOE430 v2. Keywords: repeat

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS2156

Platform:

GPL1261

8 Samples

Download data

Analysis of two-cell stage embryos maternally depleted for BRG1, a catalytic subunit of SWI/SNF-related chromatin remodeling complexes. After fertilization, the embryo shifts from maternal to zygotic genome expression. Results provide insight into the role of Brg1 in this transition.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 genotype/variation sets

Platform:

GPL1261

Series:

GSE5371

8 Samples

Download data

(Submitter supplied) An embryo starts its life with maternal mRNA clearance, which is crucial for embryonic development. The elimination of maternal transcripts occurs by the joint action of two pathways: the first is a maternally encoded mRNA decay pathway (M-decay), while the second is zygotic genome activation (ZGA)-dependent pathway (Z-decay). However, the zygotic factors triggering maternal mRNA decay in early mammalian embryos remain largely unknown. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

15 Samples

Download data: TXT

(Submitter supplied) Good quality standard adult blood samples and cord blood samples hybridized to the Illumina Infinium HumanMethylation450 BeadChip and used as methylation controls.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array; Methylation profiling by SNP array

Platform:

GPL13534

23 Samples

Download data: TXT

(Submitter supplied) We previously reported a child with transient neonatal diabetes mellitus (TNDM), who upon molecular diagnosis was homozygous for a one base-pair deletion in ZFP57, inheriting the mutations from both heterozygous parents. Methylation profiling at diagnosis revealed severe hypomethylation at PLAGL1 and mosaic loss-of-methylation (LOM) at GRB10, NAP1L5 and GNAS-XL DMRs. Some years after the first child, a second sibling was born with a comparable clinical presentation. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array; Methylation profiling by SNP array

Platforms:

GPL13534 GPL21145

6 Samples

Download data: TXT

(Submitter supplied) Bisulphite (BS) converted DNA from 2 paternal uniparental diploidies (pUPDs), one maternal (mUPD) and 5 control leukocytes samples were hybridized to the Infinium HumanMethylationEPIC BeadChip (Illumina), obtaining the BS DNA methylation profiles across approximately 850,000 CpGs. In addition, the 5 control leukocyte samples were also coverted using oxidative bisulphite (oxBS) treatment. The selective chemical oxidation of 5-hydroxymethylcytosine (5hmC) to 5-formylcytosine (5fC) and the deamination of the latter to uracil during the BS conversion allowed the quantification of independent 5-methylcytosine (5mC) and 5hmC methylation levels at every single CpG.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

13 Samples

Download data: TXT

(Submitter supplied) Faithful maintenance of genomic imprinting is essential for mammalian development. While germline DNA methylation-dependent (canonical) imprinting is relatively stable during development, the recently discovered oocyte-derived H3K27me3-mediated noncanonical imprinting is mostly transient in early embryos with only a few genes maintain imprinted expression in the extraembryonic lineage. How these few noncanonical imprinted genes maintain their extraembryonic-specific imprinting is unknown. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

31 Samples

Download data: BW