Preimplantation stage-specific effect of culture environment on the DNA methylome of bovine blastocysts
Ontology highlight
ABSTRACT:
ORGANISM(S): Bos taurus
PROVIDER: GSE69173 | GEO | 2015/10/07
SECONDARY ACCESSION(S): PRJNA284748
REPOSITORIES: GEO
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Project description:Blastocysts consist of cells that form the inner cell mass and the trophectoderm. The full transcriptome of bovine blastocyst embryos was examined in this study. Total RNA was isolated from three independent batches of blastocysts. Using Poly(A) capture mRNA was isolated and cDNA libraries prepared using Illumina TruSeq RNA sample Prep Kit. The libraries were sequenced using Illumina HiSeq 4000. This dataset should serve as a baseline for understanding bovine pluripotency and trophoblast stem cells providing a snapshot for functional interpretation of preimplantation embryo development.
2021-10-17 | GSE169674 | GEO
Project description:Maternal nutrition exclusively during the periconceptional period can induce remarkable effects on both oocyte maturation and early embryo development, which in turn can have lifelong consequences. The objective of this study was to evaluate the effect of maternal methionine supplementation on the transcriptome of bovine preimplantation embryos. Holstein cows were randomly assigned to one of two treatments differing in level of dietary methionine (1.89 Met vs. 2.43 Met % of metabolizable protein) from calving until embryo flushing. High quality preimplantation embryos from individual cows were pooled and then analyzed by RNA sequencing. A total of eight Holstein dairy cows were used in this study. Preimplantation embryos recovered from each cow were pooled in order to generate two replicates per cow assayed. Each pool consisted of 2-4 expanded blastocysts with excellent quality. Overall, a total of 16 embryo pools underwent RNA extraction, amplification, and subsequent sequencing.
2013-06-21 | E-GEOD-48147 | biostudies-arrayexpress
Project description:Upon fertilization, extensive chromatin reprogramming occurs during preimplantation development. Growing evidence reveals species-dependent regulations of this process in mammals. ATP-dependent chromatin remodeling factor SMARCA5 (also known as SNF2H) is required for peri-implantation development in mice. However, the specific functional role of SMARCA5 in preimplantation development and if it is conserved among species remain unclear. Herein, comparative analysis of public RNA-seq datasets reveals that SMARCA5 is universally expressed during oocyte maturation and preimplantation development in mice, cattle, humans and pigs with species-specific patterns. Immunostaining analysis further describes the temporal and spatial changes of SMARCA5 in both mouse and bovine models. siRNA-mediated SMARCA5 depletion reduces the developmental capability and compromises the specification and differentiation of inner cell mass in mouse preimplantation embryos. Indeed, OCT4 is not restricted into the inner cell mass and the formation of epiblast and primitive endoderm disturbed with reduced NANOG and SOX17 in SMARCA5-deficient blastocysts. RNA-seq analysis shows SMARCA5 depletion causes limited effects on the transcriptomics at the morula stage, however, dysregulates 402 genes, including genes involved in transcription regulation and cell proliferation at the blastocyst stage in mice. By comparison, SMARCA5 depletion does not affect the development through the blastocyst stage but significantly compromises the blastocyst quality in cattle. Primitive endoderm formation is greatly disrupted with reduced GATA6 in bovine blastocysts. Overall, our studies demonstrate the importance of SMARCA5 in fostering the preimplantation development in mice and cattle while there are species-specific effects.
2021-05-31 | GSE171760 | GEO
Project description:Sexual dimorphism in mammals is mostly attributable to sex-related hormonal differences in fetal and adult tissues; however, this may not be the sole determinant. Though genetically-identical for autosomal chromosomes, male and female preimplantation embryos could display sex-specific transcriptional regulation which can only be attributted to the differences in sexual chromosome dosage. We used microarrays to analyze sex-related transcriptional differences at the blastocyst stage. Day 7 bovine in vitro produced bovine blastocysts produced with sorted semen from 3 different bulls. Pooled RNA from 60 blastocysts of one sex and produced with one bull was used per chip. Three replicates of each sex per bull. In total, 18 Bovine GeneChip (Affymetrix) were used (3 replicates X 3 bulls X 2 sexes).
2010-03-09 | E-GEOD-17921 | biostudies-arrayexpress
Project description:Study question: Is gene expression in human preimplantation embryos affected by medium used for culturing embryos during an IVF treatment? Summary answer: Six days of in vitro culture of human preimplantation embryos resulted in a medium-dependent expression level of genes involved in apoptosis, protein degradation, metabolism and cell cycle regulation. What is known already: Several human studies have shown an effect of culture medium on embryo development, pregnancy outcome and birthweight. However, the underlying mechanisms in human embryos are still unknown. In animal blastocysts, it has been demonstrated that culture of preimplantation embryos affects gene expression. In humans, it has been found that culture medium affects gene expression of cryopreserved embryos that, after thawing, were cultured in two different media for 2 more days. Study design, size, duration: In a multicenter trial, women were randomly assigned to two culture media groups (G5 and HTF). Data on embryonic development were collected for all embryos. In one center, embryos originating from 2PN zygotes that were not selected for transfer or cryopreservation on day 2 or 3, were further cultured until day 6 and collected for this study, if couples consented. Participants/materials, setting, methods: Ten blastocysts from each study group, matched for fertilization method, maternal age and blastocyst quality, were selected and their mRNA was isolated and amplified. Embryos were individually examined for genome-wide gene expression using Agilent microarrays and PathVisio was used to identify the pathways that showed a culture medium-dependent activity. Main results and the role of chance: Expression of 951 genes differed significantly (P < 0.01) between the two study groups. Eighteen pathways, involved in apoptosis, metabolism, protein processing and cell cycle regulation, showed a significant overrepresentation of differentially expressed genes (DEGs). The DNA replication, G1 to S cell cycle control and oxidative phosphorylation pathways were upregulated in the G5 group compared with the HTF group. This is in agreement with the higher number of cells seen in G5 embryos on day 2 and 3. Limitations, reasons for caution: Despite careful matching of the embryos, it cannot be ruled out that differences observed between the study groups are affected by factors not investigated. Extrapolation of these results to embryos used for transfer demands caution as in the present study embryos that were not selected for either embryo transfer or cryopreservation have been used for the culture experiment until day 6. Wider implications of the findings: This study shows that gene expression in human preimplantation embryos is affected by the culture medium used during an IVF treatment. Furthermore, it provides insight into the biological mechanisms that are affected. The increased cell cycle regulation is reflected by a higher number of blastomeres. Whether these results are also connected to long-term effects remains unknown. However, it is not unlikely that early adaptations of the preimplantation embryo to its environment persist during fetal and post-natal development. Note: this study has been conducted using the Agilent-028004 SurePrint G3 Human GE 4x180K Microarray. This array contains the same reporters as the Agilent-028004 SurePrint G3 Human GE 8x60K Microarray. As such we have linked this entry to the A-GEOD-14550 array design, belonging to the latter.
2015-07-08 | E-MTAB-3405 | biostudies-arrayexpress
Project description:The objective of this study was to identify changes on the CSF2 embryo transcriptome that make them more able to become a blastocyst and more likely to survive after transfer. Embryos were treated with CSF2 at day 5 after fertilization and at day 6 morulae and blastocysts were select for the microarray analysis. A total of 160 genes that had a 1.5-fold difference in expression and a significance of P M-bM-^IM-$ 0.05 could be annotated. Analysis of the data identified 13 biological process ontologies that could be grouped into four functional groups (development and differentiation process, cell communication, apoptosis and cell adhesion). Experimental conditions: CSF2 treated vs. CSF2 nontreated bovine in vitro produced preimplantation embryos. Biological replicates: CSF2 treated vs. nontreated bovine preimplantation embryos were used in a dye switch two-color microarray experimental design. Ratio data was not used in these experiments.
2011-03-30 | E-GEOD-22579 | biostudies-arrayexpress
Project description:EtOH-Lipid form serum have been added in BSA-supplemented SOF during post-compaction development of IVP bovine embryos. Lipid-treated blastocysts were compared with control treated blastocysts (no lipid addition to BSA, EtOH balanced).
2014-01-09 | GSE53905 | GEO
Project description:In vitro culture of preimplantation mouse embryos is associated with changes in gene expression. It is however not known if the method of fertilization affects the global pattern of gene expression. We compared gene expression and development of mouse blastocysts produced in vitro (IVF), vs. blastocysts fertilized in vivo and cultured in vitro from the zygote stage (IVC), vs. control blastocysts flushed out of the uterus on post coital day 3.5. The global pattern of gene expression was assessed using the Affymetrix 430 2.0 chip.
2007-05-06 | E-MEXP-1030 | biostudies-arrayexpress
Project description:Transcriptomic analysis of 5 IVF-derived bovine blastocysts using Illumina sequencing technology
2013-02-03 | GSE44023 | GEO
Project description:Epigenetics (DNA methylation) profiling of bovine in vitro cultured expanded blastocysts (EB) comparing control non-treated expanded blastocysts with SAM-treated expanded blastocysts. S-Adenosyl methionine (SAM) is the global methyl donor providing methyl
2016-02-02 | GSE74081 | GEO