Spatiotemporal and genetic cell lineage tracing of endodermal organogenesis at single-cell resolution
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1108882 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:During early mammalian development, the endoderm layer undergoes complex patterning to form the foundations of the respiratory and digestive systems. This intricate process, guided by a series of cell fate decisions, remains only partially understood. Our research introduces a pioneering genetic tracing code across 14 distinct endodermal regions by developing a group of mouse strains. By integrating high-throughput and high-precision single-cell RNA sequencing with sophisticated imaging techniques across various mouse models, we comprehensively resolve the spatiotemporal and genetic lineage differentiation processes of the endoderm at a single-cell resolution. Our findings reveal a previously unrecognized multipotentiality within early endodermal regions for differentiation into diverse organ primordia. Furthermore, this research illuminates the complex and underestimated phenomenon of multiple origins in the development of endodermal organs, prompting a reevaluation of differentiation models for these organs. This work not only advances our understanding of developmental biology, but also has significant implications for regenerative medicine and the development of organoid models, providing new insights into the intricate mechanisms that guide organogenesis.
2025-01-16 | GSE266496 | GEO
Project description:During early mammalian development, the endoderm layer undergoes complex patterning to form the foundations of the respiratory and digestive systems. This intricate process, guided by a series of cell fate decisions, remains only partially understood. Our research introduces a pioneering genetic tracing code across 14 distinct endodermal regions by developing a group of mouse strains. By integrating high-throughput and high-precision single-cell RNA sequencing with sophisticated imaging techniques across various mouse models, we comprehensively resolve the spatiotemporal and genetic lineage differentiation processes of the endoderm at a single-cell resolution. Our findings reveal a previously unrecognized multipotentiality within early endodermal regions for differentiation into diverse organ primordia. Furthermore, this research illuminates the complex and underestimated phenomenon of multiple origins in the development of endodermal organs, prompting a reevaluation of differentiation models for these organs. This work not only advances our understanding of developmental biology, but also has significant implications for regenerative medicine and the development of organoid models, providing new insights into the intricate mechanisms that guide organogenesis.
2025-01-16 | GSE266497 | GEO
Project description:During early mammalian development, the endoderm layer undergoes complex patterning to form the foundations of the respiratory and digestive systems. This intricate process, guided by a series of cell fate decisions, remains only partially understood. Our research introduces a pioneering genetic tracing code across 14 distinct endodermal regions by developing a group of mouse strains. By integrating high-throughput and high-precision single-cell RNA sequencing with sophisticated imaging techniques across various mouse models, we comprehensively resolve the spatiotemporal and genetic lineage differentiation processes of the endoderm at a single-cell resolution. Our findings reveal a previously unrecognized multipotentiality within early endodermal regions for differentiation into diverse organ primordia. Furthermore, this research illuminates the complex and underestimated phenomenon of multiple origins in the development of endodermal organs, prompting a reevaluation of differentiation models for these organs. This work not only advances our understanding of developmental biology, but also has significant implications for regenerative medicine and the development of organoid models, providing new insights into the intricate mechanisms that guide organogenesis.
2025-01-16 | GSE277789 | GEO
Project description:Spatiotemporal and genetic cell lineage tracing of endodermal organogenesis at single-cell resolution [Smart-seq3-RNA-seq]
| PRJNA1107394 | ENA
Project description:Spatiotemporal and genetic cell lineage tracing of endodermal organogenesis at single-cell resolution [10x-v3-RNA-seq]
| PRJNA1107396 | ENA
Project description:Spatiotemporal and genetic cell lineage tracing of endodermal organogenesis at single-cell resolution [Smart-seq3-RNA-seq-add]
| PRJNA1164201 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below.
2025-01-15 | GSE266977 | GEO
Project description:To study gene expression during endodermal organogenesis, we sought to identify genes expressed in restricted domains during organogenesis. For gene expression analysis, six morphologically distinct endodermal domains were dissected at E11.5: the esophageal region; the lung and distal tracheal region; the stomach region; the hepatic region; the dorsal and ventral pancreatic region; and the intestinal region. Through flow cytometric separation using EpCAM expression to distinguish endoderm from surrounding mesenchyme, pure populations of endoderm progenitors from the esophageal, lung, stomach, pancreatic, and intestinal regions were isolated. Expression of Liv2 was used to isolate a pure population of hepatic endoderm progenitors. Keywords: cell type comparison Three biological replicates each containing dissected organ domains from 10-12 pooled embryos flow cytometrically sorted to isolate endoderm were amplified using Ambion Illumina TotalPrep RNA Amplification kit and arrayed on Illumina MouseRef8 v2 chips
2010-06-24 | E-GEOD-13040 | biostudies-arrayexpress
Project description:To study gene expression during endodermal organogenesis, we sought to identify genes expressed in restricted domains during organogenesis. For gene expression analysis, six morphologically distinct endodermal domains were dissected at E11.5: the esophageal region; the lung and distal tracheal region; the stomach region; the hepatic region; the dorsal and ventral pancreatic region; and the intestinal region. Through flow cytometric separation using EpCAM expression to distinguish endoderm from surrounding mesenchyme, pure populations of endoderm progenitors from the esophageal, lung, stomach, pancreatic, and intestinal regions were isolated. Expression of Liv2 was used to isolate a pure population of hepatic endoderm progenitors. Keywords: cell type comparison
2008-12-30 | GSE13040 | GEO
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