GEO DataSets

(Submitter supplied) we induced an energetic stress on in vitro embryos to observe the epigenetic response associated with metabolic stress. Embryos were created with slaughterhouse cows oocytes and then exposed to an elevated glucose concentration (5mM vs 0.2mM for the control embryos) for the first 3 days post fecundation and then cultivated in normal media until blastocyst stage. Blastocysts were collected from 4 different weeks of culture. more...

Organism:

Bos taurus

Type:

Methylation profiling by array

Platform:

GPL18384

4 Samples

Download data: TXT

(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

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

Organism:

Bos taurus

Type:

Expression profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL18384 GPL13226

12 Samples

Download data: TXT

(Submitter supplied) Metabolic stress associated with negative energy balance in high producing dairy cattle and obesity in women is a risk factor for decreased fertility. Non-esterified fatty acids (NEFA) are involved in this pathogenesis as they jeopardize oocyte and embryo development. Growing evidence indicates that maternal metabolic disorders can disturb epigenetic programming, and more specifically DNA methylation, in the offspring. more...

Organism:

Bos taurus

Type:

Expression profiling by array

Platform:

GPL13226

4 Samples

Download data: TXT

(Submitter supplied) Metabolic stress associated with negative energy balance in high producing dairy cattle and obesity in women is a risk factor for decreased fertility. Non-esterified fatty acids (NEFA) are involved in this pathogenesis as they jeopardize oocyte and embryo development. Growing evidence indicates that maternal metabolic disorders can disturb epigenetic programming, and more specifically DNA methylation, in the offspring. more...

Organism:

Bos taurus

Type:

Methylation profiling by genome tiling array

Platform:

GPL18384

8 Samples

Download data: TXT

(Submitter supplied) There is an inevitable need for combining in vitro and in vivo culture systems during specific developmental time points to facilitate a comprehensive understanding of early embryo development which would yield insights into the molecular pathways controlling early development and to improve our knowledge in regulation of embryonic development. In current study, we aimed to understand the influences of in vitro culture conditions on bovine blastocyst originated in vivo at 2- or 8-cell stagre. more...

Organism:

Bos taurus

Type:

Expression profiling by array

Platform:

GPL13226

12 Samples

Download data: TXT

(Submitter supplied) IVP blastocysts exposed to hyperglycaemia during early phase of development, i.e from zygote to 8-16 cells stages. Genes expression analysis is done at day 7.5 (7 days of embryo culture).

Organism:

Bos taurus

Type:

Expression profiling by array

Platform:

GPL13226

8 Samples

Download data: TXT

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

Organism:

Bos taurus

Type:

Methylation profiling by genome tiling array

Platform:

GPL18384

8 Samples

Download data: TXT

(Submitter supplied) The aim was to study the potential effect of hyperinsulinemia on gene expression and differential DNA-methylation of cow embryos by adding 0.1 µg/ml (INS0.1) during in vitro oocyte maturation.

Organism:

Bos taurus

Type:

Methylation profiling by genome tiling array

Platform:

GPL18384

4 Samples

Download data: TXT

(Submitter supplied) The aim was to study the potential effect of hyperinsulinemia on gene expression and differential DNA-methylation of cow embryos by adding 10 µg/ml (INS10) during in vitro oocyte maturation.

Organism:

Bos taurus

Type:

Methylation profiling by genome tiling array

Platform:

GPL18384

4 Samples

Download data: TXT

(Submitter supplied) There is an inevitable need for combining in vitro and in vivo culture systems during specific developmental time points to facilitate a comprehensive understanding of early embryo development which would yield insights into the molecular pathways controlling early development and to improve our knowledge in regulation of embryonic development. In current study, we aimed to understand the influences of alternative culture conditions (in vivo or in vitro) during EGA event on embryonic developmental rate, gene expression pattern and subsequent influences on pathways and biological functions controlling bovine embryo development.

Organism:

Bos taurus

Type:

Expression profiling by array

Platform:

GPL13226

30 Samples

Download data: TXT

(Submitter supplied) A high incidence of pregnancy failures occurs in cattle during the second week of pregnancy as blastocysts transition into an elongated conceptus. This work explored whether interleukin-6 (IL6) supplementation during in vitro embryo production would improve subsequent conceptus development. Bovine embryos were treated with 0 or 100 ng/mL recombinant bovine IL6 beginning on day 5 post-fertilization. At day 7.5 post-fertilization, blastocysts were transferred into estrus synchronized beef cows (n=5 recipients/treatment, 10 embryos/recipient). Seven days after transfer (day 14.5), cows were euthanized to harvest reproductive tracts and collect conceptuses. Individual conceptus lengths and stages were recorded before processing for RNA-sequencing. Increases in conceptus recovery, length, and the proportion of tubular and filamentous conceptuses were detected in conceptuses derived from IL6-treated embryos. The IL6 treatment generated 591 differentially expressed genes (DEG) in conceptuses (n=9-10/treatment). Gene ontology enrichment analyses revealed changes in transcriptional regulation, DNA-binding, and antiviral actions. Only a few DEG were associated with extraembryonic development, but several DEG were associated with embryonic regulation of transcription, mesoderm and ectoderm development, organogenesis, limb formation, and somatogenesis. To conclude, this work provides evidence that IL6 treatment before embryo transfer promotes pre-implantation conceptus development and gene expression in ways that resemble the generation of a robust conceptus containing favorable abilities to survive this critical period of pregnancy.

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26012

20 Samples

Download data: TXT

(Submitter supplied) In vitro production of cattle embryos over the past two decades has revealed several negative impacts, which have been attributed to the artificial microenvironment. Studies of embryos produced in vitro clearly point to aberrant gene expression levels. So far, the causal association between phenotype and measured gene expression has not led to substantial improvement of in vitro production systems. The aim of the present study was to generate a unique dataset composed of microarray-derived relative transcript abundance values for blastocysts produced in ten in vitro systems differing primarily in culture medium formulation. Between-group comparisons allowed us to determine the level of overall similarity between systems relative to in vivo reference embryos. The use of the dataset to contrast all in vitro treatments with the in vivo blastocysts pointed to a single common gene network. The “boutique” array contained a panel of novel uncharacterized transcripts that were expressed variably depending on the medium in which the blastocysts were produced. These novel transcripts were expressed differentially in blastocysts even as carry-over from conditions encountered seven days earlier during oocyte maturation. All of the selected novel candidates that were thus expressed were from intergenic regions. The function of this long non-coding RNA remains unknown but points clearly to an additional level of complexity in early embryo development.

Organism:

Bos taurus

Type:

Expression profiling by array

Platform:

GPL13261

65 Samples

Download data: TXT

(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

(Submitter supplied) We aimed to study the effects of CSF2 treatment on the methylome of the Day 15 female and male embryo.

Organism:

Bos taurus

Type:

Methylation profiling by genome tiling array

Platform:

GPL18384

5 Samples

Download data: TXT

(Submitter supplied) We aimed to study the effects of CSF2 treatment on the transcriptome of the Day 15 female and male embryo. Within the raw files, channel 1= Cy3 and channel 2= Cy5

Organism:

Bos taurus

Type:

Expression profiling by array

Platform:

GPL13226

12 Samples

Download data: TXT

(Submitter supplied) Although the DNA methylome of human early embryos has been analyzed, some of the key features have not been addressed to date. Here, we performed single-cell DNA methylome sequencing for human preimplantation embryos and found that tens of thousands of genomic loci exhibited de novo DNA methylation. This finding indicates that genome-wide DNA methylation reprogramming during preimplantation development is a dynamic balance between strong global demethylation and significant focused re-methylation. more...

Organism:

Homo sapiens; Mus musculus

Type:

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

Platforms:

GPL16791 GPL17021

673 Samples

Download data: BED, FPKM_TRACKING, TXT

(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

(Submitter supplied) DNA methylation, chromatin states, and their interrelationships represent critical epigenetic information, but those are largely unknown in human early embryos. Here, we apply scCOOL-seq (Chromatin Overall Omic-scale Landscape Sequencing) to generate a genome-wide map of DNA methylation and chromatin accessibility at single-cell resolution during human preimplantation development. Unlike in mice, the chromatin of paternal genome is already more open than that of maternal genome at the mid-zygote stage in humans, and this state is maintained until the 4-cell stage. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL20301

288 Samples

Download data: BW