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Molecular fingerprint of bovine embryos produced by superovulation with high competence to establish pregnancy

ABSTRACT: Molecular fingerprint of bovine embryos produced by superovulation with high competence to establish pregnancy

PROVIDER: PRJNA542821 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9052050.fastq.gz	Fastqsanger.gz
	SRR9052060.fastq.gz	Fastqsanger.gz
	SRR9052051.fastq.gz	Fastqsanger.gz
	SRR9052061.fastq.gz	Fastqsanger.gz
	SRR9052052.fastq.gz	Fastqsanger.gz

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Molecular fingerprint of bovine embryos produced by superovulation with high competence to establish pregnancy

Project description:The objective of the current experiment was to identify the transcriptome profile of in vivo-derived embryos with high competence to establish and maintain gestation. Using P < 0.01 and a fold change > 2-fold or < 0.5 fold as cut-off, there were 837 DEG (789 upregulated and 48 downregulated) between embryos that survived to day 60 versus those that did not. Using a more stringent criteria, a FDR < 0.05 and a fold-change of > 2-fold or < 0.5, there were 558 DEG (505 upregulated and 33 downregulated) between embryos that survived to day 60 versus those that did not.

2019-08-31 | GSE131178 | GEO

Molecular fingerprint of in vitro produced bovine embryos with high competence to establish pregnancy

Project description:Molecular fingerprint of in vitro produced bovine embryos with high competence to establish pregnancy

| PRJNA542094 | ENA

Molecular fingerprint of in vitro produced bovine embryos with high competence to establish pregnancy

Project description:The objective of the current experiment was to identify the transcriptome profile of in vitro-derived embryos with high competence to establish and maintain gestation and in vitro-derived embryos treated with CSF2. Using P < 0.01 and a fold change > 2-fold or < 0.5 fold as cut-offs, there were 617 differentially expressed genes (DEG) between embryos that survived to day 30 vs those that did not, 470 DEG between embryos that survived to day 60 and those that did not, 432 DEG between embryos that maintained pregnancy from day 30 to day 60 vs those where pregnancy failed after day 30, and 635 DEG regulated by CSF2, regardless of pregnancy outcome. For each comparison, pathways and ontologies in which DEG were overrepresented included many related to cellular responses to stress and cell survival.

2019-08-31 | GSE130954 | GEO

Molecular fingerprint of female bovine embryos produced in vitro with high competence to establish and maintain pregnancy†.

Project description:The objective was to identify the transcriptomic profile of in vitro-derived embryos with high competence to establish and maintain gestation. Embryos produced with X-sorted sperm were cultured from day 5 to day 7 in serum-free medium containing 10 ng/ml recombinant bovine colony-stimulating factor 2 (CSF2) or vehicle. The CSF2 was administered because this molecule can increase blastocyst competence for survival after embryo transfer. Blastocysts were harvested on day 7 of culture and manually bisected. One demi-embryo from a single blastocyst was transferred into a synchronized recipient and the other half was used for RNA-seq analysis. Using P < 0.01 and a fold change >2-fold or <0.5 fold as cutoffs, there were 617 differentially expressed genes (DEG) between embryos that survived to day 30 of gestation vs those that did not, 470 DEG between embryos that survived to day 60 and those that did not, 432 DEG between embryos that maintained pregnancy from day 30 to day 60 vs those where pregnancy failed after day 30, and 635 DEG regulated by CSF2. Pathways and ontologies in which DEG were overrepresented included many related to cellular responses to stress and cell survival. It was concluded that gene expression in the blastocyst is different between embryos that are competent to establish and maintain pregnancy vs those that are not. The relationship between expression of genes related to cell stress and subsequent embryonic survival probably reflects cellular perturbations caused by embryonic development taking place in the artificial environment associated with cell culture.

| S-EPMC7331872 | biostudies-literature

Embryo response to different progesterone concentrations during superovulation of Holstein heifers

Project description:Greater progesterone (P4) concentrations during the follicular growth have been associated with greater quality of embryos produced by superovulated cows and heifers. However, it is yet to be determined the mechanisms by which oocyte exposure to greater P4 concentrations improves early embryo quality. The objective of this study was to evaluate the impact of different P4 concentrations during superovulation on the transcriptome profile of early bovine embryos. A total of 63 post-puberty Holstein heifers were randomly assigned into two experimental groups: High P4 (n = 31) and Low P4 (n = 32). Heifers received a pre-synchronization protocol followed by a protocol of superovulation that included the allocated P4 treatment. Embryo collection was performed 7 days post artificial insemination and embryos were evaluated for stage of embryonic development and grades of quality. Embryos graded as good/excellent quality (High P4: n = 27; Low P4: n = 27) were randomly allocated in 3 biological replicates per treatment group, balanced for stage of embryonic development. Transcriptome analysis suggested that exposure to different concentrations of P4 during superovulation promote changes in gene expression of 7 days old embryos that may be related to their developmental competence. These modifications are associated with downregulation of beta-estradiol pathway, upregulation of trophoblast-related genes and downregulation of WNT signalling pathway. Our results suggest a potential sensitivity of future embryos to follicular P4 levels but do not allow to conclude if the effect is from the oocyte, the oviduct, or the uterus response to P4.

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Transcriptional profiling of cumulus cells differentiation throughout oocyte competence acquisition in the murine ovarian follicles.

Project description:Cumulus cells surrounding the oocyte were sampled at the following stages: developmentally incompetent or poorly competent prophase I oocytes (NC1 oocytes), developmentally competent prophase I oocytes (C1 oocytes), and developmentally competent metaphase II oocytes (C2 oocytes). NC1 samples were collected from immature, unexpanded cumulus-oocytes complexes (COC) from prepubertal (3-week-old) mice, C1 samples from immature, unexpanded cumulus-oocytes complexes (COC) from adult (8-week-old) and C2 samples from mature, expanded COCs obtained from the oviduct from 8-week-old mice after standard superovulation protocol. Global transcriptional profiling was performed using cumulus cells collected from murine ovarian follicles during in vivo oocyte developmental competence acquisition. Cumulus cells were collected at 3 stages: early stage follicles (prophase I arrested oocytes, meiotically competent but developmentally incompetent, n=5), late stage follicles (prophase I arrested oocytes, meiotically competent and developmentally competent, n=5) and ovulatory follicles collected in vivo (metaphase II arrested oocytes, developmentally fully competent, n=5).

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SoxC transcription factors shape the epigenetic landscape to establish competence for sensory differentiation in the mammalian organ of Corti

Project description:Understanding the molecular basis of competence acquisition by the lineage-specific progenitor cells can provide mechanistic insights into tissue development and regeneration. The sensory epithelium of the inner ear represents a convenient model to study this process, as only two cell types – the mechanosensory hair cells and their associated supporting cells – are specified from a single pool of progenitors in this lineage. Here we show that competence to respond to Atoh1, a transcriptional master regulator both necessary and sufficient for induction of mechanosensory hair cells, is established in the organ of Corti progenitor cells between E12.0 and 13.5. The transition to the competent state is rapid and is associated with extensive remodeling of the epigenetic landscape controlled by the SoxC group of transcription factors. Conditional loss of Sox4 and Sox11 – the two homologous family members transiently expressed in the inner ear at the time of competence establishment – blocks the ability of sensory progenitors to differentiate into hair cells. Mechanistically, we show that Sox4 binds to and establishes accessibility of early sensory lineage-specific regulatory elements, including ones associated with Atoh1 itself and its direct downstream targets. Consistent with these observations, overexpression of Sox4 or Sox11 prior to developmental establishment of competence precociously induces hair cell differentiation in the cochlear progenitors. Further, reintroducing Sox4 or Sox11 expression restores the ability of postnatal supporting cells to differentiate as hair cells in vitro and in vivo. Our findings demonstrate the pivotal role of SoxC family members as agents of epigenetic and transcriptional changes necessary for establishing competence for sensory receptor differentiation in the inner ear.

2023-08-01 | GSE215171 | GEO

SoxC transcription factors shape the epigenetic landscape to establish competence for sensory differentiation in the mammalian organ of Corti

Project description:SoxC transcription factors shape the epigenetic landscape to establish competence for sensory differentiation in the mammalian organ of Corti

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RNA-seq of paired oocytes and granulosa cells from 3M and 12M old mice after natural and superovulation

Project description:Oocytes and granulosa cells were collected after natural and superovulation in young (3 month-old) and old (12 month-old) mice while conserving pairing information between oocyte and granulosa cells from each cumulus-oocyte-complex (COC). This experimental design allows for the analysis of the effects of ageing and / or superovulation on the transcriptome of COCs. The naming convention for samples is as follows: [ovulation, NO/SO][age, 3M/12M][cell, OC/GC][COC number], meaning that NO12MOC01 and NO12MGC01 are from the same COC. Oocyte and granulosa cell samples were processed for full-length cytoplasmic RNA amplification using slightly modified SMART-seq2 protocol. After amplification of cDNA and library preparation, samples were sequenced on NextSeq 550 using Single-Ended 75bp High-Output kit.

2024-09-22 | E-MTAB-13479 | biostudies-arrayexpress

Effect of superovulation treatment on oocyte´s DNA methylation

Project description:Effect of superovulation treatment on oocyte´s DNA methylation

| PRJNA699313 | ENA