Spatial Embryo Profiling of primate gastrulation
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB47607 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We investigated marmoset gastrulation using SpaTial Embryo Profiling (STEP) to generate 3D-transcriptomes based on the physical location of samples within the implanted embryo. Samples were isolated from unfixed tissues using laser-capture-microdissection and subjected to single-cell full-lengths transcriptome profiling using a modified version of Smart-Seq2.
2022-02-14 | E-MTAB-9367 | biostudies-arrayexpress
Project description:During mammalian embryogenesis, temporal and spatial regulation of gene expression and cell signaling influences lineage specification, the patterning of tissue progenitors and the morphogenesis of embryo. While the mouse model has been instrumental for our understanding of mammalian development, comparatively little is known about early human and non-human primate gastrulation due to the limitation of technical and ethical. Here, we present a morphological and molecular approach that reveals the systematically morphological changes and comprehensive transcriptional landscape of cell types populating the non-human primate embryos during gastrulation.
2022-09-05 | GSE182838 | GEO
Project description:To glean an appreciation of the holistic genetic activity in the gastrulating mouse embryo, we performed a genome-wide spatial transcriptome analysis (Stereo-seq), using a low-cell number sequencing protocol on laser microdissected samples of epiblast cells with retained positional address. The 3D transcriptome reveals that (i) the epiblast is partitioned into transcription domains corresponding to regions of epiblast where cells are endowed specifically with ectoderm and mesendoderm potency, (ii) novel lineage markers are identified as genes expressed in epiblast domains populated by cells displaying different lineage fates, (iii) functionally related gene regulatory circuitry and signaling pathways are acting in concert in the transcriptional domains, and (iv) the spatial information provides reference zipcodes for mapping the prospective address of cell samples from different embryos and stem cell lines. The quantified expression data can also be visualized as â3D digitized whole mount in situ hybridizationâ of all the expressed transcripts in the epiblast. (i) By using laser-microdissection, we carried out transcriptome profiling on embryo sections at a high resolution of ~20 cells per sample with the spatial information preserved. We then constructed a comprehensive spatial transcriptome map in the mid-gastrulation embryo that is visualized in a 3D embryonic model based on the sequencing data. Embryo position (A/L/P/R) and section (1-11) descriptors: A stands for laser capture microdissected samples from the anterior epiblast of the embryo; P for posterior; L for the left lateral epiblast of the embryo; R for the right lateral. The section is collected from distal to proximal, and the section 1 to 11 is the cryosection order, covering the whole embryonic part of a late mid-streak embryo. Section 1 is the most distal section and 11 is the most proximal section. (ii) Additional samples are RNA-seq data of 70 single cells from E7.0 mouse embryo. These 70 samples were randomly picked from the anterior or posterior embryonic half.
2016-03-24 | E-GEOD-65924 | biostudies-arrayexpress
Project description:Here, we constructed monkey blastoids resembling blastocysts in morphology and transcriptomics using naïve ESCs and optimized protocol. The synthetic blastoids could develop to embryonic disk stage with the structure of yolk sac, chorionic cavity, amnion cavity, primitive streak, connecting stalk along the rostral–caudal axis by in-vitro prolonged culture (IVC). Primordial germ cells, gastrulating cells, visceral endoderm/yolk-sac endoderm, three germ layers and haemato-endothelial progenitors were identified in the monkey blastoid IVC embryo by single-cell transcriptomics or immunostaining. Besides, pregnancies with early gestation sacs were achieved by transferring monkey blastoids to surrogates. Our results revealed the in-vitro gastrulation and in-vivo early pregnancy of primate synthetic embryos, providing a powerful system to dissect primate embryonic development with less ethical concerns and restrict access.
2023-04-06 | GSE218375 | GEO
Project description:Migrasomes are recently identified vesicular organelles that form on retraction fibers behind migrating cells, cellular contents are released from migrasome by a process named migracytosis. The function of migrasomes in living organisms is unknown. Here we show that migrasomes are formed during zebrafish gastrulation, signaling molecules such as chemokines are enriched in migrasomes. Migrasomes are clustered on spatially restricted area in embryo where they provide regional cues for organ morphogenesis. Our study shown migrasome is signaling organelles which integrate spatial and specific biochemical information to coordinate migrating cells in complex biological processes such as morphogenesis.
2019-06-03 | PXD013835 | Pride
Project description:Emerging spatial profiling technology has enabled high-plex molecular profiling in biological tissues, preserving the spatial and morphological context of gene or protein expression. Here we describe expanded chemistry for the Digital Spatial Profiling platform to quantify whole transcriptomes in human and mouse tissues using a wide range of spatial profiling strategies and sample types. We designed multiplexed in situ hybridization probe pools targeting the protein-coding genes in the human and mouse transcriptomes, hereafter referred to as the human or mouse Whole Transcriptome Atlas (WTA). We validated the human and mouse WTA assays using cell lines to demonstrate concordance with orthogonal gene expression profiling methods in profiled region sizes ranging from ∼10-500 cells. By benchmarking against bulk RNAseq and single-molecule fluorescence in situ hybridization, we demonstrate robust transcript detection possible down to ∼100 transcripts per region. To assess the performance of WTA across tissue and sample types, we applied WTA to biological questions in cancer, molecular pathology, and developmental biology. We show that spatial profiling with WTA can detect expected spatial gene expression differences between tumor and tumor microenvironment, identify spatial disease-specific heterogeneity in gene expression in histological structures of the human kidney, and comprehensively map transcriptional programs in anatomical substructures of nine organs in the developing mouse embryo. Digital Spatial Profiling technology with the WTA assays provides a flexible method for spatial whole transcriptome profiling applicable to diverse tissue types and biological contexts.
2022-03-01 | GSE186594 | GEO
Project description:A single embryo, single cell time-resolved model for mouse gastrulation
| PRJNA715656 | 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:Our understanding of human early development is severely hampered by limited access to embryonic tissues. Due to their close evolutionary relationship with humans, non-human primates (NHPs) are often used as surrogates to understand human development but currently suffer from a lack of in vivo datasets, especially from gastrulation to early organogenesis during which the major embryonic cell types are dynamically specified. To fill this gap, we have collected six Carnegie stage (CS) 8-CS11 cynomolgus monkey embryos and performed in-depth transcriptome analyses of 56,636 single cells. Our analyses reveal transcriptomic features of major peri-gastrulation cell types, which help shed light on morphogenetic events including primitive streak (PS) development, somitogenesis, gut tube formation, neural tube patterning, and neural crest regionalization in primates. In addition, comparative analyses with mouse embryos and human embryoids uncover conserved and divergent features of peri-gastrulation development across species, e.g. species-specific dependency on Hippo signaling during presomitic mesoderm differentiation, and provide an initial assessment of relevant stem cell models of human early organogenesis. This comprehensive single-cell transcriptome atlas not only fills the knowledge gap in the NHP research field but also serves as an invaluable resource for understanding human embryogenesis and developmental disorders.
2022-10-26 | GSE193007 | GEO
Project description:Knowledge detailing human pre-gastrulation embryonic development including spatial self-organization and cell type ontogeny remains limited by available twodimensional technological platforms that do not recapitulate the in vivo condition. Here, we report a three-dimensional (3D) blastocyst-culture system, which enables human blastocyst development through primitive streak anlage (PSA) formation. These 3D-embryos mimic in vivo developmental landmarks and 3D-architectures, including embryonic disc, amnion, basement membrane, primary and primate unique secondary yolk sac, anterior-posterior polarity formation and PSA. Using single cell transcriptome profiling, we delineate ontology and regulatory networks underlying epiblast, hypoblast and trophoblast segregation. Compared to epiblast, the grown amniotic epithelium shows unique and characteristic phenotypes. After implantation, specific pathways and transcription factors trigger differentiation of cytotrophoblasts, extravillous cytotrophoblasts and syncytiotrophoblasts. Epiblast undergoes pluripotency transition upon implantation and maintains its transcriptome until PSA generation as coordinated by different pluripotent factors. Using our 3D-culture approach, our findings elucidate the molecular and morphogenetic developmental landscape during early human embryogenesis.
2019-11-26 | GSE136447 | GEO