Single-cell mRNA sequencing of embryonic and extra-embryonic mesoderm and extra-embryonic structures in mouse embryo during gastrulation.
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA705669 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We performed scRNAseq on embryonic and extra-embryonic mesoderm cells from mouse embryo at Mid/Late Streak stage (Embryonic day 7.25) as well as on Late Bud stage (Embryonic day 7.75) microdissected amnion, chorion and allantois. We used transgenic embryos (Brachyury-Cre; mTmG) in which all mesoderm cells are converted to membrane-GFP upon Cre-mediated recombination and the rest express membrane Tomato. For all the samples, we identified clusters related to the localization in the tissue or the structures. Those results provide an atlas of early stages of morphogenesis of the maternal-fetal interface.
2022-03-10 | GSE167958 | GEO
Project description:Single cell technologies hold promise for resolving complex early developmental phenotypes. Here we define a novel Hedgehog (Hh)-Fibroblast Growth Factor (FGF) signaling axis for the formation of anterior mesoderm lineages during gastrulation. Single-cell transcriptome analysis of Hh-deficient mesoderm revealed selective deficits in anterior mesoderm populations—culminating in defects to anterior embryonic structures including the pharyngeal arches, heart, and anterior somites. Transcriptional profiling of Hh-deficient mesoderm during gastrulation revealed disruptions to both transcriptional patterning of the mesoderm and FGF signaling for mesoderm migration. Mesoderm-specific Fgf4/Fgf8 double mutants recapitulated anterior mesoderm defects and Hh-dependent GLI transcription factors modulated enhancers at FGF gene loci. Cellular migration defects during gastrulation induced by Hh pathway antagonism were mitigated by FGF4 protein. These findings implicate a multicomponent signaling hierarchy activated by Hh ligands from the embryonic node and executed by FGF signals in nascent mesoderm to control anterior mesoderm patterning.
2020-06-23 | GSE149335 | GEO
Project description:Axis specification in mouse is determined by a sequence of reciprocal interactions between embryonic and extra-embryonic tissues so that a few extra-embryonic genes appear as ‘patterning’ the embryo. Considering these interactions as essential, but lacking in most mammals the genetically driven approaches used in mouse and the corresponding patterning mutants, we examined whether a molecular signature originating from extra-embryonic tissues could relate to the developmental stage of the embryo proper and predict it. To this end, we have profiled bovine extra-embryonic tissues at peri-implantation stages, when gastrulation and early neurulation occur, and analysed the subsequent expression profiles through the use of predictive methods as previously reported for tumour classification. A set of six genes (CALM1, CPA3, CITED1, DLD, HNRNPDL, and TGFB3), half of which had not been previously associated with any extra-embryonic feature, appeared significantly discriminative and mainly dependent on embryonic tissues for its faithful expression. The predictive value of this set of genes for gastrulation and early neurulation stages, as assessed on naive samples, was remarkably high (93%). In silico connected to the bovine orthologues of the mouse patterning genes, this gene set is proposed as a new trait for embryo staging. As such, this will allow saving the bovine embryo proper for molecular or cellular studies. To us, it offers as well new perspectives for developmental phenotyping and modelling of embryonic/extra-embryonic co-differentiation. 20 samples - Amplified material from each embryo (stage 2, stage3, stage4, stage5+) was indirectly labelled using "random" hexamers. One independent target per embryo was generated and hybridised onto one array. 5 measurements per embryonic stage were generated.
2010-06-24 | E-GEOD-13013 | biostudies-arrayexpress
Project description:Axis specification in mouse is determined by a sequence of reciprocal interactions between embryonic and extra-embryonic tissues so that a few extra-embryonic genes appear as ‘patterning’ the embryo. Considering these interactions as essential, but lacking in most mammals the genetically driven approaches used in mouse and the corresponding patterning mutants, we examined whether a molecular signature originating from extra-embryonic tissues could relate to the developmental stage of the embryo proper and predict it. To this end, we have profiled bovine extra-embryonic tissues at peri-implantation stages, when gastrulation and early neurulation occur, and analysed the subsequent expression profiles through the use of predictive methods as previously reported for tumour classification. A set of six genes (CALM1, CPA3, CITED1, DLD, HNRNPDL, and TGFB3), half of which had not been previously associated with any extra-embryonic feature, appeared significantly discriminative and mainly dependent on embryonic tissues for its faithful expression. The predictive value of this set of genes for gastrulation and early neurulation stages, as assessed on naive samples, was remarkably high (93%). In silico connected to the bovine orthologues of the mouse patterning genes, this gene set is proposed as a new trait for embryo staging. As such, this will allow saving the bovine embryo proper for molecular or cellular studies. To us, it offers as well new perspectives for developmental phenotyping and modelling of embryonic/extra-embryonic co-differentiation.
2010-12-16 | GSE13013 | GEO
Project description:Evaluate the influence of maternal metabolism on gene expression profiles from extra-embryonic tissues at D18 Keyword: Holstein Heifers and Postpartum dairy cows, metabolism and energy status, elongation and gastrulation, extra-embryonic tissues, transcriptome, correlations between genes & metabolites?
2014-02-04 | GSE46940 | GEO
Project description:Evaluate the influence of maternal metabolism on gene expression profiles from extra-embryonic tissues at D18 Keyword: Holstein Heifers and Postpartum dairy cows, metabolism and energy status, elongation and gastrulation, extra-embryonic tissues, transcriptome, correlations between genes & metabolites? 8 replicates in GH, 11 replicates in ELC and 10 replicates in LLC (extra-embryonic tissues) per group of female (N=3) were hybridized (total N=29) against a placental reference that hybridized itself to 99% of the array. Hybridization design: 6 microarrays per experiment (N=5) were randomly hybridized to the EET from 2 conceptuses originating either from development in heifers, ELC or LLC. Extra-embryonic tissues were systematically labelled with Cy3 and Reference in Cy5.
2014-02-04 | E-GEOD-46940 | biostudies-arrayexpress
Project description:In addition to nourishing the embryo, extra-embryonic tissues (EETs) contribute to early embryonic patterning, primitive hematopoiesis, and fetal health. These tissues are of major importance for human medicine, as well as for efforts to improve livestock efficiency, but they remain incompletely understood. In bovines, EETs are accessible easily, in large amounts, and prior to implantation. We took advantage of this system to describe, in vitro and in vivo, the cell types present in bovine EETs at Day 18 of development. Specifically, we characterized the gene expression patterns and phenotypes of bovine extra-embryonic ectoderm (or trophoblast; bTC), endoderm (bXEC), and mesoderm (bXMC) cells in culture and compared them to their respective in vivo micro-dissected cells. After a week of culture, certain characteristics (e.g., gene expression) of the in vitro cells were altered with respect to the in vivo cells, but we were able to identify “cores” of cell-type-specific (and substrate-independent) genes that were shared between in vitro and in vivo samples. In addition, many cellular phenotypes were cell-type-specific with regard to extracellular adhesion. We evaluated the ability of individual bXMCs to migrate and spread on micro-patterns, and observed that they easily adapted to diverse environments, similar to in vivo EE mesoderm cells, which encounter different EE epithelia to form chorion, yolk sac, and allantois. With these tissue interactions, different functions arose that were detected in silico and corroborated in vivo at D21-D25. Moreover, analysis of bXMCs allowed us to identify the EE cell ring surrounding the embryonic disc (ED) at D14-15 as mesoderm cells, which had been hypothesized but not shown prior to this study. We envision these data will serve as a major resource for the future in the analysis of peri-implanting phenotypes in response to the maternal metabolism and contribute to subsequent studies of placental/fetal development in eutherians. Amplified material was indirectly labelled using "random" hexamers. One independent target was generated and hybridised onto one array. 1-3 measurements per cell type were generated.
2015-04-18 | E-GEOD-52967 | biostudies-arrayexpress
Project description:Different types of in vitro expanded stem cells can contribute to embryonic or extra-embryonic compartments after microinjection into blastocysts. However, whether stem cells could give rise to advanced gastrulating whole embryo-like structures with both embryonic and extra-embryonic compartments, without relying on a micro-injected host embryo, remains to be achieved. Thus far, in vitro aggregated stem cells have failed to generate post-gastrulation embryos ex utero or in utero, which partially resulted from the lack of methods for prolonged expansion of embryos until advanced developmental stages ex utero. Here we adapt recently optimized platform and conditions for ex utero growth of natural embryos, to generate complete mouse synthetic embryos, with both embryonic and extra-embryonic compartments, and by starting solely from naïve ESCs. The latter is achieved following co-aggregating non-transduced naïve ESCs, with Cdx2- and Gata4- transiently pulsed naïve ESCs, to promote their trophoblast and primitive endoderm lineage induction, respectively. The obtained synthetic embryos adequately advance in this platform through developmental milestones and accomplish gastrulation and develop organs progenitors within normally developed extra-embryonic compartments. Our findings highlight the plastic developmental potential of the naïve pluripotent state to functionally self-organize and reconstitute the entire early mammalian embryo.
2022-07-31 | GSE208680 | GEO
Project description:Different types of in vitro expanded stem cells can contribute to embryonic or extra-embryonic compartments after microinjection into blastocysts. However, whether stem cells could give rise to advanced gastrulating whole embryo-like structures with both embryonic and extra-embryonic compartments, without relying on a micro-injected host embryo, remains to be achieved. Thus far, in vitro aggregated stem cells have failed to generate post-gastrulation embryos ex utero or in utero, which partially resulted from the lack of methods for prolonged expansion of embryos until advanced developmental stages ex utero. Here we adapt recently optimized platform and conditions for ex utero growth of natural embryos, to generate complete mouse synthetic embryos, with both embryonic and extra-embryonic compartments, and by starting solely from naïve ESCs. The latter is achieved following co-aggregating non-transduced naïve ESCs, with Cdx2- and Gata4- transiently pulsed naïve ESCs, to promote their trophoblast and primitive endoderm lineage induction, respectively. The obtained synthetic embryos adequately advance in this platform through developmental milestones and accomplish gastrulation and develop organs progenitors within normally developed extra-embryonic compartments. Our findings highlight the plastic developmental potential of the naïve pluripotent state to functionally self-organize and reconstitute the entire early mammalian embryo.
2022-07-31 | GSE205634 | GEO
Project description:During mammalian pre-implantation development, the cells of the blastocyst’s inner cell mass differentiate into the epiblast and primitive endoderm lineages, which give rise to the fetus and extra-embryonic tissues, respectively. Extra-embryonic endoderm differentiation can be modeled in vitro by induced expression of GATA transcription factors in mouse embryonic stem cells. Here we use this GATA-inducible system to quantitatively monitor the dynamics of global proteomic changes during the early stages of this differentiation event and also investigate the fully differentiated phenotype, as represented by embryo-derived extra-embryonic endoderm (XEN) cells. Using mass spectrometry-based quantitative proteomic profiling with multivariate data analysis tools, we reproducibly quantified 2,336 proteins across three biological replicates and have identified clusters of proteins characterized by distinct, dynamic temporal abundance profiles. We first used this approach to highlight novel marker candidates of the pluripotent state and extra-embryonic endoderm differentiation. Through functional annotation enrichment analysis, we have shown that the downregulation of chromatin-modifying enzymes, the re-organization of membrane trafficking machinery and the breakdown of cell-cell adhesion are successive steps of the extra-embryonic differentiation process. Thus, applying a range of sophisticated clustering approaches to a time-resolved proteomic dataset has allowed the elucidation of complex biological processes which characterize stem cell differentiation and could establish a general paradigm for the investigation of these processes.
2015-06-13 | PXD001901 | Pride