Expression data from human blastocyst stage embryo
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE180605 | GEO | 2021/07/23
REPOSITORIES: GEO
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Project description:Preimplantation Genetic Testing (PGT), which encompasses both Preimplantation Genetic Diagnosis (PGD) and Preimplantation Genetic Screening (PGS), is a form of prenatal screening done on embryos conceived through assisted reproduction techniques (ART) prior to the initiation of pregnancy to ensure that only select embryos are used for transfer. PGT is typically performed on 8-cell embryos derived from either in vitro fertilization or intracytoplasmic sperm injection (ICSI) followed by extended culture. PGT requires a highly invasive embryo biopsy procedure that involves 1) incubating embryos in divalent-cation-deficient medium to disrupt cell adhesion, 2) breaching the protective zona pellucida with acid Tyrodeâs, laser drilling, or mechanical force and 3) aspirating one or two blastomeres. In this study we developed a mouse model of the embryo biopsy procedure inherent to PGT to determine the effect of various aspects of the procedure (incubation in Ca2+/Mg2+-free medium (CMF), acid Tyrodeâs treatment, blastomere aspiration), performed individually or in combination, on global patterns of gene expression in the resulting blastocysts. Experiment Overall Design: The comprehensive embryo biopsy procedure was done as outlined below and was modified according to the specific experimental treatment being performed. Experiment Overall Design: Eight-cell embryos with rounded blastomeres and no fragmentation were initially incubated in CMF-Chatot-Ziomek-Brinster medium for 5 min at 37oC in a humidified atmosphere of 5% CO2 in air to loosen cell-cell contacts and then transferred to CMF-Dulbeccoâs Phosphate-Buffered Saline. The biopsies were done on the stage of a Nikon Eclipse TE2000 microscope equipped with Hoffman optics and motorized Eppendorf micromanipulators. No more than three embryos were manipulated outside of the incubator at any time. Embryos were held in place by gentle suction on an Eppendorf Sterile VacuTip holding pipette (15 μm diameter), and a dual-holder system was used to control the pipette containing acid Tyrodeâs (6 μm diameter) and the biopsy pipette (15 μm diameter). The zona pellucida was breached by gentle expulsion of a steady stream of acid Tyrodeâs solution (pH 1.6), and a single blastomere with a clear nucleus was removed by aspiration. Following each respective treatment, embryos were cultured individually in 10 μl drops of Potassium Simplex Optimization Medium supplemented with amino acids at 37oC in a humidified atmosphere of 5% CO2 in air until 96 h post-hCG injection. Four replicates of these five experimental groups, each containing 20 embryos, were generated for a total of 20 samples and 400 embryos. Experiment Overall Design: To determine the effect of the various aspects of the embryo biopsy procedure on global patterns of gene expression, total RNA was extracted from each set of 20 embryos in each treatment group at 96 h post-hCG injection. This total RNA was then used to prepare target cRNA by linear two-round amplification as described previously. The final yield of biotinylated cRNA/20 embryos ranged from 34 μg -78 μg, of which 20 μg was fragmented and submitted to the University of Pennsylvania Microarray Facility where the samples were serially hybridized to the MOE430v2 GeneChip. Quality control parameters for all samples were within the following ranges: scale factor: 0.27-0.47, percent of genes detected: 44-51%, actin 3â/5â signal ratio: 1.5-4.2, and GAPDH 3â/5â signal ratio: 3.1-4.3. The GC-RMA algorithm was used to quantify and normalize microarray signals using Stratagene Array Assist Lite, Version 3.4. The resulting .chp files were imported to GeneSpring (v7.31, Agilent Technologies) where probe sets were filtered to retain those that were flagged as P (present) in at least 3 of the 20 samples. The data was log2-transformed and subjected to analysis using Partek Genomics Suite (v6.3, Partek, Inc).
2008-06-11 | E-GEOD-11206 | biostudies-arrayexpress
Project description:Studies on embryo cryopreservation efficiency had been focused mainly on technical and embryo factors. While structural damages can be easily evaluated, physiological damages only can be estimated by analyzing their in vitro and in vivo development to later stages. In order to determine how cryopreservation process affect embryo pre-implantory development, a transcriptional microarray study has been performed comparing gene expression of 6 days old rabbit embryos, previously vitrified or frozen and transferred into recipients rabbit females, to their in vivo counterparts. For each experimental group, control, vitrified and frozen late blastocysts, total RNA was extracted from 3 pools of approximately 10 embryos and labeled with Cy3 or Cy5 dyes. Then, six competitive hybridizations were carried out including two dye-swaps to compensate dye-bias. A specifically microarray designed to study rabbit gene expression profiling, the Rabbit 44K oligonucleotide array (Agilent Technologies), was used in this study. Identification of differentially expressed transcripts from 6 day old blastocysts was achieved using the Limma algorithm, and functional annotation was performed by Blast2GO software. Compared to 6 day old in vivo derived embryos, viable vitrified embryos only present 3 differentially expressed genes, in contrast to frozen viable embryos with 24 genes upregulated and 46 genes downregulated. These results reveal that effects of cryopreservation still remain in late blastocyst pre-implantatory gene expression, and potential damage and alterations produced by vitrification and slow-freezing procedures are differentially resolved after 3 days of in vivo development. Transcriptional microarray study that compares gene expression of viable 6 day old rabbit embryos, previosly vitrified or frozen and tranferred into recipient rabbit females, to their in vivo counterparts. Experiment 1: Control embryos vs. Vitrified embryos and Experiment 2: Control embryos vs. Frozen embryos. Biological replicates used: 3 replicates for control embryos, 3 replicates for vitrified embryos and 3 replicates for frozen embryos.
2011-09-22 | E-GEOD-32263 | biostudies-arrayexpress
Project description:Studies on embryo cryopreservation efficiency had been focused mainly on technical and embryo factors. While structural damages can be easily evaluated, physiological damages only can be estimated by analyzing their in vitro and in vivo development to later stages. In order to determine how cryopreservation process affect embryo pre-implantory development, a transcriptional microarray study has been performed comparing gene expression of 6 days old rabbit embryos, previously vitrified or frozen and transferred into recipients rabbit females, to their in vivo counterparts. For each experimental group, control, vitrified and frozen late blastocysts, total RNA was extracted from 3 pools of approximately 10 embryos and labeled with Cy3 or Cy5 dyes. Then, six competitive hybridizations were carried out including two dye-swaps to compensate dye-bias. A specifically microarray designed to study rabbit gene expression profiling, the Rabbit 44K oligonucleotide array (Agilent Technologies), was used in this study. Identification of differentially expressed transcripts from 6 day old blastocysts was achieved using the Limma algorithm, and functional annotation was performed by Blast2GO software. Compared to 6 day old in vivo derived embryos, viable vitrified embryos only present 3 differentially expressed genes, in contrast to frozen viable embryos with 24 genes upregulated and 46 genes downregulated. These results reveal that effects of cryopreservation still remain in late blastocyst pre-implantatory gene expression, and potential damage and alterations produced by vitrification and slow-freezing procedures are differentially resolved after 3 days of in vivo development.
2011-09-23 | GSE32263 | GEO
Project description:The functional role of the maternal protein during early embryo development remains to be elucidated. Here we show that the maternal protein, Rbpms2, is highly expressed in mouse oocytes and that knockdown of Rbpms2 inhibits development from the morula to blastocyst stage. To study the underlying mechanism, we firstly analysed the differential expressed genes after Rbpms2 knockdown through single-cell sequencing. Combined the bioinformatics analysis of sequencing data, we then identify the impaired location of E-cadherin after knockdown of Rbpms2 may leading to the morula arrested development . Furthermore, Rbpms2 is important for development of mouse early embryos, most likely because it activates the BMP pathway. Taken together, our study uncovers that Rbpms2 activate the BMP pathway, and thus adjust the location of E-cadherin which is important for mouse early embryos development.
2023-06-21 | GSE202359 | GEO
Project description:Following intracytoplasmic sperm injection (ICSI), in vitro culture (IVC) in ART media causes imbalance in the blastocyst's inner cell mass (ICM)with reduction of the primitive endoderm compartment compared to non-IVC blastocystsFollowing embryo transfer (ET), these imbalances do not influence birth rates, and the postnatal effects are inconspicuous. ICSI alters gene expression in mouse embryos. Choice of embryo culture media has been correlated with birth and body growth rates in human studies. No analysis has yet been made combining ICSI and IVC in the mouse. We produced mouse concepti by ICSI followed by IVC and ET so as to mimic,at least in part, the way human embryos are produced and handled in the clinical practice. Fertilized oocytes were cultured in two sets of sequential ART media, compared with an optimized mouse medium and with the mouse oviduct. Embryos were analyzed or implanted to produce newborns. In total, 3706 fertilized mouse oocytes, 1672 blastocysts and 78 newborns were examined during the course of the study. Mice of the B6C3F1, C57Bl/6 and CD1 strains were used as oocyte donors, sperm donors and embryo recipients, respectively. B6C3F1 oocytes were fertilized by intracytoplasmic C57Bl/6 sperm injection and were allowed to cleave in HTF/MultiBlast and in ISM1/ISM2 sequential culture protocols as well as in optimized mouse medium (KSOM(aa)) and in vivo in the CD1 mouse oviduct. Cleavage and blastocyst rates were analyzed by Wilcoxon / Kruskal-Wallis test and the blastocysts were split in two subgroups:one subgroup was analyzed for cell lineage allocation and for transcriptome, the other subgroup was transferred to genital tract, allowed to develop to term and characterized for birth rate, litter size, neonatal bodyweight and behavior using ANOVA F-test and t-test. The effects of ART media on blastocyst rates exceed those of ICSI. Protein and mRNA analysis reveal that IVC has a marked effect on the primitive endoderm lineage of ICSI blastocysts. In contrast to preimplantation, birth rates after ET are indistinguishable not only among ICSI but also in comparison to non-injected controls. At birth, ICSI-IVC-ET concepti are outwardly normal and weigh the same as non-ICSI controls. Confounding effects of subfertility, lifestyle and genetic heterogeneity are reduced to a minimum in the hybrid inbred mouse model compared to human patients. Confounding effects of polyspermy and parthenogenetic activation are prevented by ICSI. There is more to ART than ICSI, IVC and ET, and only a small number of ART media were examined. Preimplantation effects of ART culture media can effectively be modeled in the mouse because the in vitro environment is suboptimal for both mouse and human. However, in the optimal uterine environment of their own species, mouse and human ART blastocysts may be supported and selected for differently, depending on species-specific features such as the kinetics of implantation and the endometrium. 14 samples were analyzed. HTF/MultiBlast: Mouse multiblastocysts in HTF medium, 3 biological rep ISM1/ISM2: Mouse blastocysts in ISM1 and ISM2 medium, 3 biological rep KSOM(aa): Mouse blastocysts in KSOM(aa) medium, 2 biological rep oviduct: Mouse oviduct, 3 biological rep micromanipulation control: Mouse micromanipulation control, 3 biological rep
2016-08-25 | E-GEOD-50193 | biostudies-arrayexpress
Project description:Thallium (Tl) is a trace metal element used in the electronics, semiconductor and electro-optical industries. With the development of high-tech industries, thallium severely pollutes the aquatic environment. The purpose of this study was to evaluate the cardiotoxicity and developmental toxicity of Tl by using vertebrate model zebrafish embryos. RNA-seq was performed on wild type zebrafish embryos exposed to 0, 200, and 800 ppb Tl from 6 to 48 hpf. The transcriptomic profile revealed molecular understanding regarding the cardiovascular and developmental toxicity of Tl, providing valuable information for risk assessment of the emerging contaminant thallium.
2022-09-21 | GSE213589 | GEO
Project description:Results suggest that the observed differences in morphometric parameters between the studied varieties have a background in differently expressed genes involved in different biochemical pathways.
2023-07-12 | GSE222066 | GEO
Project description:Following intracytoplasmic sperm injection (ICSI), in vitro culture (IVC) in ART media causes imbalance in the blastocyst's inner cell mass (ICM)with reduction of the primitive endoderm compartment compared to non-IVC blastocystsFollowing embryo transfer (ET), these imbalances do not influence birth rates, and the postnatal effects are inconspicuous. ICSI alters gene expression in mouse embryos. Choice of embryo culture media has been correlated with birth and body growth rates in human studies. No analysis has yet been made combining ICSI and IVC in the mouse. We produced mouse concepti by ICSI followed by IVC and ET so as to mimic,at least in part, the way human embryos are produced and handled in the clinical practice. Fertilized oocytes were cultured in two sets of sequential ART media, compared with an optimized mouse medium and with the mouse oviduct. Embryos were analyzed or implanted to produce newborns. In total, 3706 fertilized mouse oocytes, 1672 blastocysts and 78 newborns were examined during the course of the study. Mice of the B6C3F1, C57Bl/6 and CD1 strains were used as oocyte donors, sperm donors and embryo recipients, respectively. B6C3F1 oocytes were fertilized by intracytoplasmic C57Bl/6 sperm injection and were allowed to cleave in HTF/MultiBlast and in ISM1/ISM2 sequential culture protocols as well as in optimized mouse medium (KSOM(aa)) and in vivo in the CD1 mouse oviduct. Cleavage and blastocyst rates were analyzed by Wilcoxon / Kruskal-Wallis test and the blastocysts were split in two subgroups:one subgroup was analyzed for cell lineage allocation and for transcriptome, the other subgroup was transferred to genital tract, allowed to develop to term and characterized for birth rate, litter size, neonatal bodyweight and behavior using ANOVA F-test and t-test. The effects of ART media on blastocyst rates exceed those of ICSI. Protein and mRNA analysis reveal that IVC has a marked effect on the primitive endoderm lineage of ICSI blastocysts. In contrast to preimplantation, birth rates after ET are indistinguishable not only among ICSI but also in comparison to non-injected controls. At birth, ICSI-IVC-ET concepti are outwardly normal and weigh the same as non-ICSI controls. Confounding effects of subfertility, lifestyle and genetic heterogeneity are reduced to a minimum in the hybrid inbred mouse model compared to human patients. Confounding effects of polyspermy and parthenogenetic activation are prevented by ICSI. There is more to ART than ICSI, IVC and ET, and only a small number of ART media were examined. Preimplantation effects of ART culture media can effectively be modeled in the mouse because the in vitro environment is suboptimal for both mouse and human. However, in the optimal uterine environment of their own species, mouse and human ART blastocysts may be supported and selected for differently, depending on species-specific features such as the kinetics of implantation and the endometrium.
2016-08-25 | GSE50193 | GEO
Project description:Preimplantation Genetic Testing (PGT), which encompasses both Preimplantation Genetic Diagnosis (PGD) and Preimplantation Genetic Screening (PGS), is a form of prenatal screening done on embryos conceived through assisted reproduction techniques (ART) prior to the initiation of pregnancy to ensure that only select embryos are used for transfer. PGT is typically performed on 8-cell embryos derived from either in vitro fertilization or intracytoplasmic sperm injection (ICSI) followed by extended culture. PGT requires a highly invasive embryo biopsy procedure that involves 1) incubating embryos in divalent-cation-deficient medium to disrupt cell adhesion, 2) breaching the protective zona pellucida with acid Tyrode’s, laser drilling, or mechanical force and 3) aspirating one or two blastomeres. In this study we developed a mouse model of the embryo biopsy procedure inherent to PGT to determine the effect of various aspects of the procedure (incubation in Ca2+/Mg2+-free medium (CMF), acid Tyrode’s treatment, blastomere aspiration), performed individually or in combination, on global patterns of gene expression in the resulting blastocysts. Keywords: embryo biopsy, preimplantation genetic diagnosis, blastocyst
2008-04-22 | GSE11206 | GEO
Project description:Mechanisms of implantation such as determination of the attachment pole, fetal-maternal communication, as well as underlying causes of implantation failure are largely unexplored. Here we performed single-cell RNA sequencing (scRNA-seq) on peri-implantation embryos from both humans and mice to explore trophectoderm development and embryo–endometrium crosstalk. We found that the transcriptomes of polar and mural trophectoderm (TE) diverged after embryos hatched from the zona pellucida in both species, with polar TE being more mature than mural TE. The implantation poles show similarities in cell cycle activities, as well as in expression of genes critical for implantation and placentation. Embryos that either fail to attach in vitro or fail to implant in vivo, show abnormalities in pathways related to energy production, protein metabolism and 18S rRNA m6A methylation. These findings uncover the gene expression characteristics of humans and mice TE differentiation during the peri-implantation period and provide new insights into embryo implantation.
2022-08-01 | GSE133200 | GEO