Effect of vitrification on global gene expression dynamics of bovine elongating embryos
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ABSTRACT:
PROVIDER: PRJNA670731 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12880550_1.fastq.gz | Fastqsanger.gz | |||
| SRR12880550_2.fastq.gz | Fastqsanger.gz | |||
| SRR12880551_1.fastq.gz | Fastqsanger.gz | |||
| SRR12880551_2.fastq.gz | Fastqsanger.gz | |||
| SRR12880552_1.fastq.gz | Fastqsanger.gz |
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Project description:Embryo vitrification involves exposure to high concentrations of cryoprotectants and osmotic stress during cooling and warming. A multitude of these factors have the potential of affecting gene expression. In this study, in vitro produced bovine embryos at the blastocyst stage were submitted to vitrification. Four recipients each were used for transferring non-vitrified (80) and vitrified (80) embryos. Twelve non-vitrified and nine vitrified viable day-14 (D14) embryos were recovered by uterine flushing. RNA-seq analysis of whole embryo or isolated trophectoderm (TE) from vitrified and fresh recovered D14 embryos revealed a total of 927 genes changed their expression as a result of vitrification, among them 782 and 145 genes were up- and down-regulated, respectively. In TE isolates, vitrification resulted in 4,096 and 280 up- and down-regulated genes, respectively. In addition, we found 671 and 61 genes commonly up- and down-regulated in both vitrified whole embryo and TE. Commonly up-regulated pathways by vitrification included epithelial adherens junctions, sirtuin signaling, germ cell-sertoli cell junction, ATM signaling, NER, and protein ubiquitination pathways. The commonly down-regulated pathways included EIF2 signaling, oxidative phosphorylation, mitochondrial dysfunction, regulation of eIF4 and p70S6K signaling, mTOR signaling, sirtuin singling, and NER pathways. Our analysis identified specific pathways and implicated specific gene expression patterns important to cryopreservation affecting embryo developmental competence.
2021-03-01 | GSE159891 | GEO
Project description:Embryo vitrification involves exposure to high concentrations of cryoprotectants and osmotic stress during cooling and warming in the cryopreservation process. Many of these factors can potentially affect gene expression. In this study, invitro-produced bovine embryos at the blastocyst stage were subjected to vitrification. Four recipients each were used for transferring non-vitrified (n=80) and vitrified (n=80) embryos. A total of 12 non-vitrified and 9 vitrified viable day-14 (D14) embryos were recovered by uterine flushing. RNA-seq analysis of the whole embryo or isolated trophectoderm (TE) from vitrified and fresh recovered D14 embryos revealed a total of 927 and 4376 genes with changed expression in embryos and TE isolates, respectively, as a result of vitrification. In addition, we found 671 and 61 genes commonly up- or downregulated in both vitrified whole embryos and TE. Commonly upregulated pathways by vitrification included epithelial adherens junctions, sirtuin signalling, germ cell-sertoli cell junction, ATM signalling, NER and protein ubiquitination pathways. The commonly downregulated pathways included EIF2 signalling, oxidative phosphorylation, mitochondrial dysfunction, regulation of eIF4 and p70S6K signalling and mTOR signalling pathways. Our analysis identified specific pathways and implicated specific gene expression patterns affecting embryo developmental competence that are important to cryopreservation.
| S-EPMC8049512 | biostudies-literature
Project description:Changes in gene expression induced by the Cryotop vitrification procedure in bovine blastocysts using Agilent EmbryoGENE microarray slides. Bovine in vitro-produced embryos at the blastocyst stage (144 to 156 hours post insemination) were vitrified using the Cryotop system and compared with non-vitrified (control) embryos. After vitrification, the embryos were warmed and cultured for an additional 4 hours. Embryos that re-expanded or developed to the expanded blastocyst stage were used for microarray analysis.
2015-08-03 | GSE65953 | GEO
Project description:Changes in gene expression induced by the Cryotop vitrification procedure in bovine blastocysts using Agilent EmbryoGENE microarray slides. Bovine in vitro-produced embryos at the blastocyst stage (144 to 156 hours post insemination) were vitrified using the Cryotop system and compared with non-vitrified (control) embryos. After vitrification, the embryos were warmed and cultured for an additional 4 hours. Embryos that re-expanded or developed to the expanded blastocyst stage were used for microarray analysis. Four pools of vitrified embryos were hybridized against four pools of control embryos in a dye-swap design.
2015-08-03 | E-GEOD-65953 | biostudies-arrayexpress
Project description:Very limited information about the post-implantatory effects of vitrification has been published till now. In a previous study, we observed that vitrification procedure introduced transcriptomic and proteomic modifications in the rabbit foetal placenta at the middle of gestation. In addition, a reduction in maternal placenta and foetal weight was also detected. In order to know if these alterations were temporary or not, the aim of the current study was to analyse the proteomic profile of rabbit foetal placenta at two different times of gestation: Day 14 and Day 24. We performed a comparative 2D-DIGE analysis and found that placentas from vitrified embryos expressed eleven different proteins at Day 14 and thirteen at Day 24. The alteration of serum albumin, isocitrate dehydrogenase 1 [NADP+] and phosphoglycerate mutase 1 were maintained both Day 14 and Day 24. Our results demonstrate that vitrification is not neutral, and induce a substantial alteration of placental protein expression, even at the end of gestation. But, apart from short-term effects observed on embryos, could vitrification entail long-term consequences in those foetuses that are going to be born? Further studies will determine if alterations observed could be the set point of future modifications to manifest into adulthood
2015-08-11 | PXD001836 | Pride
Project description:Very limited information about the post-implantatory effects of vitrification has been published till now. In a previous study, we observed that vitrification procedure introduced transcriptomic and proteomic modifications in the rabbit foetal placenta at the middle of gestation. In addition, a reduction in maternal placenta and foetal weight was also detected. In order to know if these alterations were temporary or not, the aim of the current study was to analyse the proteomic profile of rabbit foetal placenta at two different times of gestation: Day 14 and Day 24. We performed a comparative 2D-DIGE analysis and found that placentas from vitrified embryos expressed eleven different proteins at Day 14 and thirteen at Day 24. The alteration of serum albumin, isocitrate dehydrogenase 1 [NADP+] and phosphoglycerate mutase 1 were maintained both Day 14 and Day 24. Our results demonstrate that vitrification is not neutral, and induce a substantial alteration of placental protein expression, even at the end of gestation. But, apart from short-term effects observed on embryos, could vitrification entail long-term consequences in those foetuses that are going to be born? Further studies will determine if alterations observed could be the set point of future modifications to manifest into adulthood
2015-07-17 | PXD001840 | Pride
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
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 | GSE95380 | GEO
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 | GSE95379 | GEO
Project description:The present study mainly aimed to investigate the effect of vitrification temperature (VT) and cryoprotective agent concentrations (CPAs) on the mRNA transcriptome of bovine immature oocytes (BIOs). Cumulus oocyte complexes (COCs) were randomly divided into the following five groups: fresh oocytes (control), oocytes vitrified in liquid helium (LHe; -269℃) with 5.6 M CPAs (LHe 5.6 M), oocytes vitrified in LHe with 6.6 M CPAs (LHe 6.6 M), oocytes vitrified in liquid nitrogen (LN; -196℃) with 5.6 M CPAs (LN 5.6 M), and oocytes vitrified in LN with 6.6 M CPAs (LN 6.6 M). mRNA transcriptomes of each sample were analyzed by Smart-seq4, and the differentially expressed genes (DGEs) were detected by edgeR (p≤0.05; fold-change≥2). Compared with the control group, 505 DGEs were detected with 342 up-regulated and 163 down-regulated genes in LHe 5.6 M; 609 DGEs were detected with 493 up-regulated and 116 down-regulated gene in LHe 6.6 M; 218 DGEs were determined with 101 up-regulated and 117 down-regulated genes in LN 5.6 M; and 221 DGEs were detected with 104 up-regulated and 117 down-regulated genes in LN 6.6 M. LHe vitrification affected the mRNA transcriptome of vitrified BIOs mainly by up-regulating gene expression. Reduced CPAs (5.6 M) decreased the effect of vitrification on mRNA transcriptome when LHe vitrification was used. Among all the DGEs closely related to bovine immature oocytes, the genes possibly related to VT were ND2, MPV17L2, PIF1, LPIN1, IMP3, BRD1, DCTN3, DERA, ATP7B, NEK5, HVCN1 and MARK2. The gene that may be associated with CPAs is CC2D2A. Genes that may be affected by both VT and CPAs were PGK1, SLC7A3, FITM2, NPM3, ISCU, CWC15 and PSAP. DERA was up-regulated when reduced VT (-269 °C) was used, which may have contributed to the recovery and stress prevention of vitrified oocyte.
2022-04-02 | GSE133550 | GEO