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

ABSTRACT: 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.

ORGANISM(S): Bos taurus

PROVIDER: GSE131178 | GEO | 2019/08/31

REPOSITORIES: GEO

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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

Whole transcriptomic analysis of zebrafish embryos of dyrk1aakrb1, dyrk1aa knock out mutant and Wild Type (WT) (+/+) in the background of Tg(kdrl:egfp) [32 hpf]

Project description:Purpose: The goals of this experiments are to analyze the transcriptomic change in dyrk1aakrb1 mutants compared with WT embryos by mRNA-seq technique. Methods: Whole mRNA profiles of 32 hpf WT(+/+) and dyrk1aakrb1 mutants zebrafish embryos were generated by mRNA-seq techinque, in duplicate, using HiSeq 2500 (Illumina, Inc., USA). Results: This analysis identified 354 transcripts as differentially regulated genes (DEG), of which 125 were up-regulated and 229 were down-regulated in dyrk1aakrb1 mutant (more than 2 fold and less than 0.5 fold respectively,; p value< 0.05).

2019-05-20 | GSE123026 | GEO

Whole transcriptomic analysis of zebrafish embryos of dyrk1aakrb1, dyrk1aa knock out mutant and Wild Type (WT) (+/+) in the background of Tg(kdrl:egfp)

Project description:Purpose: The goals of this experiments are to analyze the transcriptomic change in dyrk1aakrb1 mutants compared with WT embryos by mRNA-seq technique. Methods: Whole mRNA profiles of 48 hpf WT(+/+) and dyrk1aakrb1 mutants zebrafish embryos were generated by mRNA-seq techinque, in duplicate, using HiSeq 2500 (Illumina, Inc., USA). Results: This analysis identified 222 transcripts as differentially regulated genes (DEG), of which 101 were up-regulated and 121 were down-regulated in dyrk1aakrb1 mutant (more than 2 fold and less than 0.5 fold respectively,; p value< 0.05).

2019-05-20 | GSE111280 | GEO

The use of a brief synchronization treatment after weaning, combined with superovulation, has moderate effects on the gene expression of surviving pig blastocysts

Project description:Use of combined estrus synchronization/superovulation treatments (SS) alters ovarian and en-dometrial gene expression patterns, impairing follicle and oocyte growth, fertilization, and em-bryo development. Since the impact of SS-treatments on the transcriptome of the surviving em-bryos remains undisclosed, we hereby examined gene expression changes in day 6 blastocysts that survived a brief regimen of synchronization treatment combined with superovulation. Embryos were surgically collection at day 6 after AI and transcriptome analysis performed on blas-tocyst-stage embryos with good morphology to disclose differentially expressed genes (DEGs) between groups at P-value < 0.05 and </> 1.5-fold change. Compared with the blastocysts from control (untreated) sows, the blastocysts from SS treated sows had moderate gene expression changes, with 7 pathways disrupted with a total of 10 transcripts affected, including metabolic RDH10 and SPTLC2 gene upregulation, and downregulation of oxidation related GSTK1 and GSTO1 genes. These gene expression alterations may suggest suboptimal embryo quality and could depress the embryos' response to oxidative stress, thereby impairing subsequent embryo development. These and previous findings call for avoidance of SS-treatments in embryo transfer programs.

2023-03-22 | E-MTAB-12820 | biostudies-arrayexpress

Decreased SATB1 expression promotes AML cell proliferation through NF-κB activation

Project description:Global gene expression profiles were analyzed in HL-60 cells with SATB1 knockdown to investigate the mechanisms underlying the regulation of AML cell growth by SATB1.Genes that displayed two-fold up-regulation or 0.5-fold down-regulation in expression in comparisons were selected for further analyses. Arrays with poor quality according to the manufacturer's recommendations were excluded from further analysis.We found the differentially expressed genes were involved in NF-κB, MAPK and PI3K/Akt signaling pathways. Nuclear NF-κB p65 levels were significantly increased in SATB1 depleted HL-60 cells.

2019-05-16 | GSE131247 | GEO

Kinetic of gene expression signatures on ischemia porcine kidney

Project description:Using an oligonucleotide microarray we performed differential transcriptomic analysis of porcine kidneys subjected to intense ischemic stress which could be observed in donors deceased after circulatory death situation (60 min warm ischemia then 0h, 6h or 24h of cold storage in University of Wisconsin solution) compared to healthy kidneys (n=5 per group). Microarray analysis identified genes which were differentially expressed in different ischemic times versus healthy kidneys (adjusted p value <0.05 + log2 fold change >0.5 or <-0.5).

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2014-05-14 | E-MTAB-2219 | biostudies-arrayexpress

Effect of SOPS and Cryotop vitrification of porcine blastocysts produced in vivo on their transcriptome profile

Project description:The objective of this study was therefore to evaluate the impact of simultaneous vitrification of large numbers of embryos with the OC (20 embryos per device) system on gene expression patterns of in vivo-derived blastocysts when compared to the Superfine Open Pulled Straw (SOPS) system (5-7 embryos per device) through a microarray approach. In vivo-developed embryos were surgically retrieved from 16 sows in 4 replicates. Embryos at the blastocyst stage (n=180) were selected for the experiment and divided into three experimental groups: blastocysts vitrified with the OC system (n=60), blastocysts vitrified with the SOPS system (n=60), and a control group consisting of fresh, nonvitrified blastocysts (n=60). After in vitro culture for 24 h, six pools of 8 viable embryos (n=48 embryos per group) were prepared for transcriptome analysis. Embryos were placed in sterile tubes with 5 µL of PBS, immediately immersed in LN2 and stored at -80 °C until microarray analysis. After microarray analysis, a list of DEGs was generated for comparison of each vitrification system (OC and SOPS) with the control. Then, the two DEG lists were compared to determine the specific genes altered in each vitrification system and the DEGs shared by both systems. In addition, a list of DEGs was obtained by direct comparison of both vitrification systems. Pathway enrichment analysis was performed for each obtained list of DEGs.

2023-03-06 | E-MTAB-12772 | biostudies-arrayexpress

Transcriptomic differences in bovine blastocysts following vitrification and slow freezing at morula stage [EmbryoCryoSF]

Project description:This study aimed to compare the transcriptome of vitrified and slow frozen embryos with the untreated control. Bovine embryos (compact morulae) were vitrified or slow frozen and post-warm embryos were cultured to expanded blastocyst stage. The vitrified- and slow frozen-derived were subjected to microarray analysis and compared with untreated control embryos for differential gene expression. Morula to blastocyst conversion rate was higher (P<0.05) in control (72%) and vitrified (77%) embryos compared to slow frozen (34%) embryos. Total 20 genes were upregulated and 44 genes were downregulated in the vitrified embryos (fold change ≥ +-2, P<0.05). In slow frozen embryos, 102 genes were upregulated and 63 genes were downregulated (fold change ≥ +-1.5, P<0.05) in comparison with untreated embryos. Vitrified embryos exhibited significant changes in gene expression mainly involving embryo implantation (PTGS2, CALB1), lipid peroxidation and ROS generation (HSD3B1, AKR1B1, APOA1) and cell differentiation (KRT19, CLDN23). The slow frozen embryos, however, showed significant changes in the expression of genes related to cell signaling (SPP1), cell structure and differentiation (DCLK2, JAM2 and VIM), and lipid metabolism (PLA2R1 and SMPD3). In silico comparison between vitrified and slow-frozen (reference) embryos revealed similar changes in gene expression as between vitrified and untreated embryos. In conclusion, the vitrified bovine embryos demonstrated better post-warming embryo development than slow-frozen bovine embryos but their gene expression related to lipid metabolism, steroidogenesis, cell differentiation and placentation changed significantly. Slow freezing killed more embryos than vitrification, and the survived embryos did not express significant change in their gene expression.

2017-03-31 | GSE95381 | GEO

Transcriptomic differences in bovine blastocysts following vitrification and slow freezing at morula stage [EmbryocryoVit]

2017-03-31 | GSE95380 | GEO

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