Ontology highlight
ABSTRACT:
PROVIDER: PRJNA880895 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21607309_1.fastq.gz | Fastqsanger.gz | |||
| SRR21607309_2.fastq.gz | Fastqsanger.gz | |||
| SRR21607310_1.fastq.gz | Fastqsanger.gz | |||
| SRR21607310_2.fastq.gz | Fastqsanger.gz | |||
| SRR21607311_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
Similar Datasets
Project description:Loss of tight junctions disrupts gastrulation patterning and increases differentiation towards the germ cell lineage in human pluripotent stem cells
| PRJNA883000 | ENA
Project description:The blueprint of embryonic development is first visualized in the context of regionalization of cell fates of germ layer tissues in the post-implantation mouse embryo. Knowledge of the genetic and signaling activities that underpin gastrulation, lineage specification and tissue patterning has been gleaned from embryological experimentation and phenotypic analysis of loss- and gain-of-function genetic models. However, a comprehensive genome-wide molecular annotation of the mechanism of gastrulation has yet to be undertaken. Here, we reported the findings of a transcriptome study of cell populations at defined positions in the epiblast, ectoderm, mesoderm and endoderm of the pre-gastrulation and gastrulation stage embryos. This developmental and spatial transcriptome has defined the genealogy of sub-populations of cells in the germ layers. The transcriptome further identifies the molecular determinants such as the transcriptional factors and epigenetic entities, and the activity of signaling pathway and the transcriptional networks that drive the lineage commitment of the pluripotent epiblast cells and the germ layer precursors.
2023-02-07 | GSE110284 | GEO
Project description:During postimplantation development of the mouse embryo, descendants of the inner cell mass cells in the early epiblast transit from the naïve pluripotent state to the primed pluripotent state. Concurrent with the transition of the pluripotency states is the specification of cell lineages and formation of germ layers in the embryos that serves as the blueprint for embryogenesis. Fate mapping and lineage analysis studies have revealed that cells in different regions of the germ layers acquire location-specific cell fates during gastrulation. The regionalization of cell fates heralding the formation of the basic body plan is conserved in vertebrate embryos at a common phylotypic stage of development. Knowledge of the molecular regulation that underpin the lineage specification and tissue patterning is instrumental for understanding embryonic programming and stem cell-based translational study. However, a genome-wide molecular annotation of lineage segregation and tissue architecture of post-implantation embryo has yet to be undertaken. Here, we reported a spatially resolved transcriptome of cell populations at defined positions in the germ layers over the period of pre- to late gastrulation development. This spatio-temporal transcriptome provides high resolution digitized gene expression profiles and defines the molecular attribute of the genealogy of lineages and continuum of pluripotency states in time and space. The transcriptome further identifies the networks of molecular determinants that drive lineage specification and tissue patterning in the early postimplantation mouse embryo.
2019-08-08 | GSE120963 | GEO
Project description:The ability of the pluripotent epiblast to contribute progeny to all three germ layers is thought to be lost after gastrulation. The later-forming neural crest (NC) rises from ectoderm and it remains poorly understood how its exceptionally high stem-cell potential to generate mesodermal- and endodermal-like cells is obtained. We monitored transcriptional changes from gastrulation to neurulation using single-cell-Multiplex-Spatial-Transcriptomics (scMST) complemented with RNA-sequencing. Unexpectedly, we find maintenance of undecided Nanog/Oct4-PouV/Klf4-positive pluripotent-like pan-ectodermal stem-cells spanning the entire ectoderm late in the neurulation process with ectodermal patterning completed only at the end of neurulation when pluripotency becomes restricted to NC, challenging our understanding of gastrulation. Furthermore, broad ectodermal pluripotency is found at all axial levels unrelated to the NC lineage the cells later commit to, suggesting a general role in stemness enhancement and proposing a mechanism by which the NC acquires its ability to form derivatives beyond “ectodermal-capacity” in chick and mouse embryos.
2023-08-28 | GSE232432 | GEO
Project description:Zic3 regulates early embryonic patterning in vertebrates. Its loss-of-function disrupts gastrulation, left-right patterning, and neurogenesis. We use the zebrafish as a model to study the developmental role of Zic3 in vivo. Using a combination of two genomics approaches – ChIP-seq and microarray, we identified Zic3 targets, which include genes from the Nodal and Wnt pathways, and show for the first time cis-regulation of these genes by Zic3 using in vivo enhancer assay. We uncovered a previously unrecognized link between Zic3 and the non-canonical Wnt pathway in gastrulation and left-right patterning, and identified neural pre-pattern genes as Zic3 targets during the early steps of neural induction. Zic3 preferably binds to distal intergenic regions, some of which contain evolutionarily conserved functional enhancers. Our study establishes the zebrafish as an excellent model for genome-wide study of a transcription factor in vivo. Zic3 ChIP of wild type and sqet33 transgenic
2014-02-27 | E-GEOD-41458 | biostudies-arrayexpress
Project description:The ability of the pluripotent epiblast to contribute progeny to all three germ layers is thought to be lost after gastrulation. The later-forming neural crest (NC) rises from ectoderm and it remains poorly understood how its exceptionally high stem-cell potential to generate mesodermal- and endodermal-like cells is obtained. We monitored transcriptional changes from gastrulation to neurulation using single-cell-Multiplex-Spatial-Transcriptomics (scMST) complemented with RNA-sequencing. Here we show maintenance of pluripotency-signature (Nanog/Oct4-PouV/Klf4-positive) in undecided pan-ectodermal stem-cells spanning the entire ectoderm late during neurulation with ectodermal patterning completed only at the end of neurulation when the pluripotency-signature becomes restricted to NC, challenging our understanding of gastrulation. Furthermore, broad ectodermal pluripotency-signature is found at all axial levels unrelated to the NC lineage the cells later commit to, suggesting a general role in stemness enhancement and proposing a mechanism by which the NC acquires its ability to form derivatives beyond “ectodermal-capacity” in chick and mouse embryos.
2023-03-02 | GSE221188 | GEO
Project description:The ability of the pluripotent epiblast to contribute progeny to all three germ layers is thought to be lost after gastrulation. The later-forming neural crest (NC) rises from ectoderm and it remains poorly understood how its exceptionally high stem-cell potential to generate mesodermal- and endodermal-like cells is obtained. We monitored transcriptional changes from gastrulation to neurulation using single-cell-Multiplex-Spatial-Transcriptomics (scMST) complemented with RNA-sequencing. Here we show maintenance of pluripotency-signature (Nanog/Oct4-PouV/Klf4-positive) in undecided pan-ectodermal stem-cells spanning the entire ectoderm late during neurulation with ectodermal patterning completed only at the end of neurulation when the pluripotency-signature becomes restricted to NC, challenging our understanding of gastrulation. Furthermore, broad ectodermal pluripotency-signature is found at all axial levels unrelated to the NC lineage the cells later commit to, suggesting a general role in stemness enhancement and proposing a mechanism by which the NC acquires its ability to form derivatives beyond “ectodermal-capacity” in chick and mouse embryos.
2023-03-02 | GSE221125 | GEO
Project description:The germ cell lineage ensures reproduction, heredity and evolution. However, the mechanism for germ cell specification in primates, including humans, has been unknown. In primates, the pluripotent epiblast segregates the amnion upon implantation and thereafter initiates gastrulation to generate three germ layers. Here, we show that in cynomolgus monkeys, the SOX17/BLIMP1/TFAP2C-positive primordial germ cells (cyPGCs) arise from the dorsal amnion at embryonic day (E) 11. cyPGCs then migrate down beneath the epiblast and expand their numbers, through proliferation and continuous recruitment from the posterior amnion, around posterior yolk sac endoderm by E17. Remarkably, the amnion itself expresses BMP4, a cytokine potentially critical for PGC specification, thereby inducing cyPGCs in an autocrine fashion. Consistently, the amnion expresses T, a key mesodermal factor, prior to the onset of gastrulation. Our study demonstrates the origin of cyPGCs in the amnion, which undergoes a unique morphogenetic event prior to and independent from the gastrulation.
2016-10-12 | GSE76267 | GEO
Project description:Generating properly organized and differentiated embryonic structures in vitro from aggregates of pluripotent cells remains a major challenge. In a living embryo, the interplay in between signaling molecules known as morphogens and their antagonists lead to gradients of activity that instruct cells about their fate, leading to patterning and morphogenesis. Here we show that experimentally engineering a morphogen signaling center within an aggregate of mouse pluripotent stem cells is sufficient to mimic the function of an embryo organizer and to trigger embryonic development. The resulting embryoids are remarkably well patterned along anterior-posterior and dorsal-ventral axes, generate three germ layers through a process of gastrulation and differentiate germ layer derivatives (including notochord, vasculature, neural tube, neural crest, endoderm) similar to an authentic embryo at E9-E9.5.
2021-04-25 | GSE142309 | GEO
Project description:Generating properly organized and differentiated embryonic structures in vitro from aggregates of pluripotent cells remains a major challenge to overcome. In the living embryo, the interplay between morphogens and their antagonists set up gradients of activity that instruct cells about their fate, leading to patterning and morphogenesis. Here we show that experimentally engineering a morphogen signaling center within an aggregate of mouse pluripotent stem cells is sufficient to mimic in vitro the function of an embryo organizer and to trigger embryonic development. The resulting embryoids are extensively patterned along their anterior-posterior and dorsal-ventral axes, with formation of three germ layers through a process of gastrulation and differentiation of germ layer derivatives similar to those of a neurula-stage mouse embryo.
2021-04-22 | GSE168539 | GEO