Single cell RNA-seq of in vitro cultured human embryos
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB45572 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR6039560.fastq.gz | Fastqsanger.gz | |||
| ERR6039570.fastq.gz | Fastqsanger.gz | |||
| ERR6039561.fastq.gz | Fastqsanger.gz | |||
| ERR6039571.fastq.gz | Fastqsanger.gz | |||
| ERR6039562.fastq.gz | Fastqsanger.gz |
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Project description:scRNA-seq analysis of in vitro cultured monkey embryos
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Project description:Human embryogenesis is characterised by a series of coordinated cell fate specification events. Upon implantation on day 7, the three cell lineages forming the human blastocyst undergo major morphogenetic and transcriptomic changes. Using single-cell RNA sequencing, we reconstruct the molecular events driving post-implantation development of the human embryo at day 9 and 11. Our study provides the first molecular map of gene expression patterns in early post-implantation human embryos, unveiling how signalling interactions between embryonic and extra-embryonic tissues drive human embryogenesis.
2021-06-11 | E-MTAB-8060 | biostudies-arrayexpress
Project description:Primates embryo implants into the maternal uterus, forms three germ layers and begin early organogenesis, such as neurulation, heart formation, during the first 4 weeks of development. Although, this stage represents a milestone in early embryonic development of primate, our understanding remains limited. Here, we optimized our previously established in vitro culture system, which enable the ex-utero culture of cynomolgus monkey up to 25 days. Morphology histological, and single-cell RNA sequencing analyses confirm that the in vitro cultured embryos recapitulate key events of in vivo development. Using this platform, we delineate monkey early-stage lineage trajectory and genetic programs accompanying the neural, mesoderm and endoderm specification, as well as primordial germ cell–like cell (PGCLC). Thus, this culture system represents a valuable and easily accessible platform to study and manipulate early primate embryogenesis, which cannot easily accomplish in vivo.
2023-05-11 | GSE207534 | GEO
Project description:Study question: What is the relative effect of common environmental and biological factors on transcriptome changes during human preimplantation development? Summary answer: Developmental stage and maternal age had a larger effect on the global gene expression profile of human preimplantation embryos than the culture medium or oxygen concentration used in in vitro culture. What is known already: Studies on mouse and bovine embryos have shown that different conditions in the in vitro culture of embryos can lead to changes in transcriptome profiles. For humans, an effect of developmental stage on the transcriptome profile of embryos has been demonstrated, but studies on the effect of maternal age or culture conditions are lacking. Participants/materials, setting, methods: Embryos that developed to morula or blastocyst stage during these 2 days whose amplified mRNA passed our quality control criteria for microarray hybridization were individually examined for genome-wide gene expression (N = 37). Main results and the role of chance: Based on the number of differentially expressed genes (DEGs), developmental stage (3519 DEGs) and maternal age (1258 DEGs) had a larger effect on the global gene expression profile of human preimplantation embryos than either tested culture medium (596 DEGs) or oxygen concentration (492 DEGs) used during in vitro culture. Interactions between the factors were found, indicating that culture conditions might have a different effect depending on the developmental stage or the maternal age of the embryos. Affected pathways included metabolism, cell cycle processes and oxidative phosphorylation. Limitations, reasons for caution: Culture of embryos for only 2 days might have limited the effect on global gene expression by the investigated culture conditions. Earlier stages of development (Day 0 until Day 4) were not analyzed and these embryos might respond differently to the experimental conditions. The freezing and thawing procedures might have had an effect on gene expression. RTâPCR validation was not performed due to scarcity of the material. Wider implications of the findings: Our results show that when studying gene expression in single human preimplantation embryos under various experimental conditions, one should take into account the confounding effect of biological variables, such as developmental stage and maternal age. This makes these experiments different from gene expression experiments where these variables can be tightly controlled, for example when using cell lines. Study design, size, duration: Donated, good quality, day 4 cryopreserved human preimplantation embryos (N = 89) were randomized to be cultured in one of two culture media (G5 medium or HTF medium) and one of two oxygen concentrations (5% or 20%), with stratification for maternal age. Next to these variables, developmental stage after culture was taken into account in the analysis.
2015-12-31 | E-GEOD-49374 | biostudies-arrayexpress
Project description:Chromosomal instability (CIN) occurs at high frequency during early in vitro embryogenesis and is known to be associated with early embryonic loss in humans. The chromosomal stability of in vivo-conceived cleavage stage embryos largely remains unknown. Here, we applied haplotyping and copy number profiling to investigate genomic architecture of 171 single bovine blastomeres and to compare the nature and frequency of CIN between in vivo embryos, in vitro embryos produced from ovum pick up with ovarian stimulation (OPU-IVF), and in vitro produced embryos from in vitro matured oocytes without ovarian stimulation (IVM-IVF). Our data shows that CIN is significantly lower in in vivo conceived cleavage stage embryos when compared to in vitro cultured embryos, as genomic stability of single blastomeres in both IVF embryos was severely compromised (P<0.0001)
2017-09-24 | GSE95358 | GEO
Project description:Study question: What is the relative effect of common environmental and biological factors on transcriptome changes during human preimplantation development? Summary answer: Developmental stage and maternal age had a larger effect on the global gene expression profile of human preimplantation embryos than the culture medium or oxygen concentration used in in vitro culture. What is known already: Studies on mouse and bovine embryos have shown that different conditions in the in vitro culture of embryos can lead to changes in transcriptome profiles. For humans, an effect of developmental stage on the transcriptome profile of embryos has been demonstrated, but studies on the effect of maternal age or culture conditions are lacking. Participants/materials, setting, methods: Embryos that developed to morula or blastocyst stage during these 2 days whose amplified mRNA passed our quality control criteria for microarray hybridization were individually examined for genome-wide gene expression (N = 37). Main results and the role of chance: Based on the number of differentially expressed genes (DEGs), developmental stage (3519 DEGs) and maternal age (1258 DEGs) had a larger effect on the global gene expression profile of human preimplantation embryos than either tested culture medium (596 DEGs) or oxygen concentration (492 DEGs) used during in vitro culture. Interactions between the factors were found, indicating that culture conditions might have a different effect depending on the developmental stage or the maternal age of the embryos. Affected pathways included metabolism, cell cycle processes and oxidative phosphorylation. Limitations, reasons for caution: Culture of embryos for only 2 days might have limited the effect on global gene expression by the investigated culture conditions. Earlier stages of development (Day 0 until Day 4) were not analyzed and these embryos might respond differently to the experimental conditions. The freezing and thawing procedures might have had an effect on gene expression. RT–PCR validation was not performed due to scarcity of the material. Wider implications of the findings: Our results show that when studying gene expression in single human preimplantation embryos under various experimental conditions, one should take into account the confounding effect of biological variables, such as developmental stage and maternal age. This makes these experiments different from gene expression experiments where these variables can be tightly controlled, for example when using cell lines.
2015-12-31 | GSE49374 | GEO
Project description:It is often overlooked that human ESCs are generated from in vitro cultured, often surplus/‘discard’, embryos considered unsuitable for transfer in infertility clinics. In vitro culture of preimplantation embryos has been associated with a number of perturbations, including ultrastructure, gene expression, metabolism and post-transfer development. We report here the transcriptional profiles characteristic of ESC lines generated from either in vitro cultured or in vivo derived embryos. Embryonic stem cell RNAs were prepared from samples collected from 8 different lines. Four lines were generated from preimplantation embryos derived in vivo (R series; Thomson et al 1995) and four lines were generated from in vitro cultured preimplantation embryos (Ormes series; Mitalipov et al 2003). ChipInspector carries out significance analysis on the single probe level. Normalized probe set level data not provided for individual Sample records. Processed data is available on Series record.
2010-11-09 | E-GEOD-25198 | biostudies-arrayexpress
Project description:Single-cell RNA-sequencing of in vitro fertilized and nuclear transfer embryos
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Project description:In mammalian preimplantation development, pluripotent cells are set aside from cells that contribute to extra-embryonic tissues. Although the pluripotent cell population of mouse and human embryos can be cultured as embryonic stem cells, little is known about the pathways involved in formation of a bovine pluripotent cell population, nor how to maintain these cells in vitro. The objective of this study was to determine the transcriptomic profile related to bovine pluripotency. Therefore, in vitro derived embryos were cultured in various culture media that recently have been reported capable of maintaining the naïve pluripotent state of human embryonic cells. Gene expression profiles of embryos cultured in these media were compared using microarray analysis and quantitative RT-PCR. Compared to standard culture conditions, embryo culture in 'naïve' media reduced mRNA expression levels of the key pluripotency markers NANOG and POU5F1. A relatively high percentage of genes with differential expression levels were located on the X-chromosome. In addition, reduced XIST expression was detected in embryos cultured in naïve media and female embryos contained fewer cells with H3K27me3 foci, indicating a delay in X-chromosome inactivation. Whole embryos cultured in one of the media, 5iLA, could be maintained until 23 days post fertilization. Together these data indicate that 'naïve' conditions do not lead to altered expression of known genes involved in pluripotency. Interestingly, X-chromosome inactivation and development of bovine embryos were dependent on the culture conditions.
2017-05-02 | GSE69399 | GEO
Project description:Background: Production of functional sperms from spermatogonial stem cells in vitro is important for understanding of biological mechanisms underlying physiological spermatogenesis and for treatment of male infertility. However, comparing with the in vivo testes, in vitro spermatogenesis is severely lower efficiency. Here we describe abnormalities occurring in early stage of in vitro spermatogenesis at single cell resolution. Results: While spermatogenesis was similarly progressed between in vivo and in vitro-cultured testes, noticeable acute inflammatory response occurred right after in vitro culture of neonatal testes not only in immune cells but also non-immune testicular somatic cells. Inhibitor treatment revealed NLRP3 inflammasome signaling is key to the inflammation occurring in in vitro cultured testes We also found accumulation of damaged/dead germ cells in in vitro cultured testes, which may be due to dysfunction of sertoli cell phagocytosis. Conclusion: Our data revealed tissue-wide sterile inflammation occurring in in vitro cultured testes, in which DAMPs - NLRP3 inflammasome axis may key element. Thus, these abnormal testicular microenvironments may be a cause of low spermatogenesis efficiency of in vitro spermatogenesis.
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