Expression profile of Chicken Early Embryonic Endodermal Tissues
Ontology highlight
ABSTRACT:
ORGANISM(S): Gallus gallus
PROVIDER: GSE22222 | GEO | 2013/06/08
SECONDARY ACCESSION(S): PRJNA128779
REPOSITORIES: GEO
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Project description:In vertebrates the endoderm which gives rise to the epithelial lining of the digestive tract becomes regionalized along its antero-posterior axis after gastrulation. The molecular basis of the initial step of this regionalization has largely remained unclear. Using chick model, we generated high-quality transcriptomic datasets of different stages/regions of the endoderm and analyzed their molecular heterogeneity. Total RNA from HH stage 4-5 entire definitive endoderm, HH stages 10-11 foregut endoderm and HH stages 8-10 mid/hindgut endoderm were purified. 5 M-NM-<g of RNA from each sample were used to screen Affymetrix Chicken Genome Array without an amplification step.
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Project description:A major role of yolk sac endoderm is the uptake of lipids and other constituents from the yolk and transfer of these components into the embryonic circulation. The molecular basis of the initial step of this regionalization has largely remained unclear. Using chick as a model system, we generated high-quality transcriptomic datasets of different stages of the yolksac endoderm and analyzed their molecular heterogeneity.
2012-07-09 | GSE27958 | GEO
Project description:A major role of yolk sac endoderm is the uptake of lipids and other constituents from the yolk and transfer of these components into the embryonic circulation. The molecular basis of the initial step of this regionalization has largely remained unclear. Using chick as a model system, we generated high-quality transcriptomic datasets of different stages of the yolksac endoderm and analyzed their molecular heterogeneity. Two independent samples of total RNA were isolated from yolk sac endodermal tissues on embryonic day 1, 2, 3, and 4. 5 M-NM-<g of RNA from each sample (total of 8 samples) were used to screen Affymetrix Chicken Genome Array without an amplification step.
2012-07-08 | E-GEOD-27958 | biostudies-arrayexpress
Project description:Hox cluster genes play crucial roles in the establishment of the body plan along the antero-posterior axis during animal development. Hox genes are expressed in the chordate endodermal tissues, and unraveling functions there is necessary for elucidating the mechanisms of endoderm specification. In the invertebrate chordate Ciona intestinalis, the endodermal tissues are in the premature state at the larval stage, and they form the differentiated digestive tract during metamorphosis. In this study, we showed that a Hox gene Ci-Hox10 is required for the formation of the intestine during metamorphosis. To know the downstream genes that are controlled by Hox10, microarray analysis of Hox10 knock-down embryos was performed.
2013-10-01 | GSE45475 | GEO
Project description:Hox cluster genes play crucial roles in the establishment of the body plan along the antero-posterior axis during animal development. Hox genes are expressed in the chordate endodermal tissues, and unraveling functions there is necessary for elucidating the mechanisms of endoderm specification. In the invertebrate chordate Ciona intestinalis, the endodermal tissues are in the premature state at the larval stage, and they form the differentiated digestive tract during metamorphosis. In this study, we showed that a Hox gene Ci-Hox10 is required for the formation of the intestine during metamorphosis. To know the downstream genes that are controlled by Hox10, microarray analysis of Hox10 knock-down embryos was performed. Gene expressions in the tail region of Hox10 knockdown embryos that were injected with Hox10 morpholino (MO) and control embryos of Ciona intestinalis were examined by comparative analysis with two color detection. Dye-swap analysis was carried out.
2013-10-01 | E-GEOD-45475 | biostudies-arrayexpress
Project description:The endoderm is classically defined as the innermost layer of three Metazoan germ layers. During organogenesis, the endoderm gives rise to the digestive and respiratory tracts as well as associated organs such as the liver, pancreas, and lung. At present, however, how the endoderm forms the variety of cell types of digestive and respiratory tracts as well as the budding organs is not well understood. In order to investigate the molecular basis and mechanism of organogenesis and to identify the endodermal organ-related marker genes, we carried out microarray analysis using Xenopus cDNA chips. To achieve this goal, we isolated the Xenopus gut endoderm from three different stages of Xenopus organogenesis, and separated each stage of gut endoderm into anterior and posterior region. Competitive hybridization of cDNA between the anterior and posterior endoderm regions, to screen genes that specifically expressed in the major anterior organs, revealed 891 candidates. We then selected 104 clones for in situ hybridization analysis. Here, we report the identification and expression patterns of the 104 Xenopus endodermal genes, which would serve as useful markers for studying endodermal organ development. Keywords: Xenopus, endoderm, microarray, organogenesis
2007-03-31 | GSE7129 | GEO
Project description:Abstract from Vermillion et al: During vertebrate development, progenitor cells give rise to tissues and organs through a complex choreography that commences at gastrulation. A hallmark event of gastrulation is the formation of the primitive streak, a linear assembly of cells along the anterior-posterior (AP) axis of the developing organism. To examine the primitive streak at a single-cell resolution, we measured the transcriptomes of individual chick cells from the streak or the surrounding tissue (the rest of the area pellucida) in Hamburger-Hamilton stage 4 embryos. The single-cell transcriptomes were then ordered by the statistical method Wave-Crest to deduce both the relative position along the AP axis and the prospective lineage of single cells. The ordered transcriptomes reveal intricate patterns of gene expression along the primitive streak.
2018-04-18 | GSE89910 | GEO
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:To comprehensively delineate the ontogeny of an organ system, we generated 112,217 single- cell transcriptomes representing all endoderm populations within the mouse embryo until midgestation. We employed graph-based approaches to model differentiating cells for spatio- temporal characterization of developmental trajectories. Our analysis reveals the detailed architecture of the emergence of the first (primitive or extra-embryonic) endodermal population and pluripotent epiblast. We uncover an unappreciated relationship between descendants of these lineages, before the onset of gastrulation, suggesting that mixing of extra-embryonic and embryonic endoderm cells occurs more than once during mammalian development. We map the trajectories of endoderm cells as they acquire embryonic versus extra-embryonic fates, and their spatial convergence within the gut endoderm; revealing them to be globally similar but retaining aspects of their lineage history. We observe the regionalized localization of cells along the forming gut tube, reflecting their extra-embryonic or embryonic origin, and their coordinate patterning into organ-specific territories along the anterior-posterior axis.
2019-04-10 | GSE123124 | GEO
Project description:To comprehensively delineate the ontogeny of an organ system, we generated 112,217 single- cell transcriptomes representing all endoderm populations within the mouse embryo until midgestation. We employed graph-based approaches to model differentiating cells for spatio- temporal characterization of developmental trajectories. Our analysis reveals the detailed architecture of the emergence of the first (primitive or extra-embryonic) endodermal population and pluripotent epiblast. We uncover an unappreciated relationship between descendants of these lineages, before the onset of gastrulation, suggesting that mixing of extra-embryonic and embryonic endoderm cells occurs more than once during mammalian development. We map the trajectories of endoderm cells as they acquire embryonic versus extra-embryonic fates, and their spatial convergence within the gut endoderm; revealing them to be globally similar but retaining aspects of their lineage history. We observe the regionalized localization of cells along the forming gut tube, reflecting their extra-embryonic or embryonic origin, and their coordinate patterning into organ-specific territories along the anterior-posterior axis.
2019-04-10 | GSE123046 | GEO