Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA117023 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:After gut tube patterning in early embryos, the cellular and molecular changes of developing stomach and intestine remain largely unknown. Here, combining single-cell RNA-sequencing and spatial RNA-sequencing, we constructed a spatiotemporal transcriptomic landscape of the mouse stomach and intestine during embryonic day E9.5-E15.5. We observed regionalization and heterogeneity of both the epithelium and mesenchyme in the gastrointestinal (GI) tract at E9.5 and dynamic cell evolution afterwards. The spatiotemporal distributions of cell clusters and the epithelium-mesenchyme interactions indicate a coordinated development of the epithelium and mesenchyme. The cell evolution and signaling events regulate the stomach regionalization and intestine segmentation. Using the gut tube-derived organoids, we found that the cell fate of the foregut and hindgut could be switched by the regional niche factors. Together, this work demonstrates the important function of the epithelium-mesenchyme interactions in early GI tract development, laying a foundation for further dissection of the mechanisms governing this process.
2022-07-12 | GSE186525 | GEO
Project description:In the adult mouse, distinct morphological and transcriptional differences separate stomach from intestinal epithelium. Remarkably, the epithelial boundary between these two organs is literally one cell thick. This discrete junction is established suddenly and precisely at embryonic day (E) 16.5, by sharpening a previously diffuse intermediate zone. In the present study, we define the dynamic transcriptome of stomach, pylorus and intestinal tissues between E14.5 and E16.5. We show that establishment of this boundary is concomitant with the induction of over a thousand genes in intestinal epithelium, and these gene products provide intestinal character. Hence, we call this process intestinalization. We identify specific transcription factors (Hnf4g, Creb3l3 and Tcfec) and examine signaling pathways (Hedgehog and Wnt) that may play a role in this process. Finally, we define a unique expression domain at the pylorus itself and detect novel pylorus-specific patterns for the transcription factor Gata3 and the secreted protein nephrocan. Experiment Overall Design: Stomach, pylorus and duodenum tissue from E14.5 and E16.5 mouse embryos were collected for RNA extraction and hybridization on Affymetrix microarrays. We sought to study the gene expression profiles and identify genes and pathways enriched in these three tissues at two important developmental times.
2009-10-09 | E-GEOD-15872 | biostudies-arrayexpress
Project description:In adult stomach, Lgr5 is a marker of epithelial glandular stem cells that grow in the three dimensional ex vivo culture system as organoids. However, little is known about the markers that characterize fetal progenitors before cytodifferentiation and their potential involvement in regenerative processes in adults. Using the ex vivo culture system, we isolated epithelial progenitors from the fetal stomach. These cells generated stable undifferentiated immortal spheroids showing lower growth factor requirements as compared to the adult-type gastric Lgr5-expressing organoids. Although very similar in their gene expression profiles, cultured fetal gastric and intestinal spheroids differentially expressed Sox2/Cdx2 genes involved in regional pre-patterning. Accordingly, gastric but not intestinal spheroids, spontaneously converted into the cell lineages of the adult glandular stomach ex vivo. In vivo, the Trop2 marker enriched in the fetal gastric spheroids was transiently expressed in the gastric epithelium before cytodifferentiation while it remained barely detectable under glandular homeostasis in adults. However, upon specific ablation of the Lgr5 stem cell pool, highly proliferative Trop2-expressing cells rapidly emerged in the adult epithelium, qualifying Trop2 as a marker of Lgr5-independent gastric stem cells. Together, these data indicate that the Trop2 receptor identifies gastric fetal progenitors and adult stem/progenitor cells involved in regeneration of glandular stomach.
2016-05-11 | GSE65395 | GEO
Project description:The development of digestion tract is critical for proper digestion of food and absorbance of nutrient for an individual. It includes the spatial segregation into esophagus, stomach, small and large intestine. The temporal-spatial gene expression profiles of human digestion tract in vivo have never been analyzed at single-cell resolution.Here we analyzed esophagus, stomach, small intestine (SI) and large intestine (LI) from multiple human embryos between 6 and 25 weeks of gestation by single cell RNA-seq analyses.We firstly identified 51 clusters of different types of cells using t- Distributed Stochastic Neighbor Embedding (t-SNE) analysis.Moreover,cell type of each organ were identified according to the known marker genes and new cell types were further analyzed.The dynamic change of each cell type were tracked during the human embryonic digestive tract development.We found HOX family geens paly different roles in the regulation of digestion tract developemnt. In addition, Hedgehog,TGFβ and BMP signaling pathway are essential for SI and LI development in human fetal. The function of nutrient digestion and absorption was increased as the SI development in human fetal.Finally, we demonstrated that the immune system was established at late stage of human fetal and verified the immune-like cells,such as T cell, B cells and macrophage. In summary, by using single cell RNA seq technique, we identified the waves of signaling pathways and critical cell types for the human digestion tract development.
2018-04-05 | GSE95630 | GEO
Project description:In the adult mouse, distinct morphological and transcriptional differences separate stomach from intestinal epithelium. Remarkably, the epithelial boundary between these two organs is literally one cell thick. This discrete junction is established suddenly and precisely at embryonic day (E) 16.5, by sharpening a previously diffuse intermediate zone. In the present study, we define the dynamic transcriptome of stomach, pylorus and intestinal tissues between E14.5 and E16.5. We show that establishment of this boundary is concomitant with the induction of over a thousand genes in intestinal epithelium, and these gene products provide intestinal character. Hence, we call this process intestinalization. We identify specific transcription factors (Hnf4g, Creb3l3 and Tcfec) and examine signaling pathways (Hedgehog and Wnt) that may play a role in this process. Finally, we define a unique expression domain at the pylorus itself and detect novel pylorus-specific patterns for the transcription factor Gata3 and the secreted protein nephrocan.
2009-10-01 | GSE15872 | GEO
Project description:The process that partitions the nascent vertebrate central nervous system into forebrain, midbrain, hindbrain, and spinal cord after neural induction is of fundamental interest in developmental biology, and is known to be dependent on Wnt/beta-catenin signaling at multiple steps. Neural induction specifies neural ectoderm with forebrain character that is subsequently posteriorized by graded Wnt signaling: embryological and mutant analyses have shown that progressively higher levels of Wnt signaling induce progressively more posterior fates. However, the mechanistic link between Wnt signaling and the molecular subdivision of the neural ectoderm into distinct domains in the anteroposterior (AP) axis is still not clear. To better understand how Wnt mediates neural AP patterning, we performed a temporal dissection of neural patterning in response to manipulations of Wnt signaling in zebrafish. We show that Wnt-mediated neural patterning in zebrafish can be divided into three phases: (I) a primary AP patterning phase, which occurs during gastrulation, (II) a mes/r1 (mesencephalon-rhombomere 1) specification and refinement phase, which occurs immediately after gastrulation, and (III) a midbrain-hindbrain boundary (MHB) morphogenesis phase, which occurs during segmentation stages. A major outcome of these Wnt signaling phases is the specification of the major compartment divisions of the developing brain: first the MHB, then the diencephalic-mesencephalic boundary (DMB). The specification of these lineage divisions depends upon the dynamic changes of gene transcription in response to Wnt signaling, which we show primarily involves transcriptional repression or indirect activation. We show that otx2b is directly repressed by Wnt signaling during primary AP patterning, but becomes resistant to Wnt-mediated repression during late gastrulation. Also during late gastrulation, Wnt signaling becomes both necessary and sufficient for expression of wnt8b, en2a, and her5 in mes/r1. We suggest that the change in otx2b response to Wnt regulation enables a transition to the mes/r1 phase of Wnt-mediated patterning, as it ensures that Wnts expressed in the midbrain and MHB do not suppress midbrain identity, and consequently reinforce formation of the DMB. These findings integrate important temporal elements into our spatial understanding of Wnt-mediated neural patterning and may serve as an important basis of a better understanding of neural patterning defects that have implications in human health.
2020-02-29 | GSE146124 | GEO
Project description:Gene expression was studied using PancChip5.0 in 15 tissues. Most tissues were from the adult mouse, except for fetal pancreas (e18.5) and placenta. Adult tissues studied were: adrenal gland, pancreas, brain, heart, kidney, liver, lung, ovary, parotid gland, pituitary gland, small intestine, stomach and testis. All were studied in duplicate except for the pituitary, the liver, and the stomach. All samples were pooled samples. Tissues were taken from 3 males and 3 females, with the exception of the gonadal tissues, and the fetal tissues were sex was not determined.
2014-12-04 | E-MTAB-3151 | biostudies-arrayexpress
Project description:The early-life organ development and maturation process shapes the fundamental blueprint for later-life phenotype. However, the proteome atlas of self-multi-organs from infancy to adulthood is currently not available. Herein, we present a comprehensive proteomic analysis of ten mice organs (brain, heart, lung, liver, kidney, spleen, stomach, intestine, muscle and skin) acquired from the same individuals at three essential developmental stages (1-week, 4-week and 8-week after birth) by data-independent acquisition mass spectrometry.
2024-05-02 | PXD041400 | Pride
Project description:The squamous–columnar junction (SCJ) is a boundary consisting of precisely positioned transitional epithelium between the squamous and columnar epithelium. Transitional epithelium is a hotspot for precancerous lesions, and is therefore clinically important; however, the origins and physiological properties of transitional epithelium have not been fully elucidated. Here, by using mouse genetics, lineage tracing, and organoid culture, we examine the development of the SCJ in the mouse stomach, and thus define the unique features of transitional epithelium. We find that two transcription factors, encoded by Sox2 and Gata4, specify primitive transitional epithelium into squamous and columnar epithelium. The proximal–distal segregation of Sox2 and Gata4 expression establishes the boundary of the unspecified transitional epithelium between committed squamous and columnar epithelium. Mechanistically, Gata4-mediated expression of the morphogen Fgf10 in the distal stomach and Sox2-mediated Fgfr2 expression in the proximal stomach induce the intermediate regional activation of MAPK/ERK, which prevents the differentiation of transitional epithelial cells at the SCJ boundary. Our results have implications for tissue regeneration and tumorigenesis, which are related to the SCJ.
2020-12-17 | GSE143217 | GEO
Project description:The intestine is composed of an epithelial layer, containing rapidly proliferating cells that mature into two distinct anatomic regions, the small and the large intestine. Although previous studies have identified stem cells as the cell-of-origin for the whole intestine, no studies have compared stem cells derived from the small and large intestine. Here, we report intrinsic differences between these two populations of cells. Primary epithelial cells isolated from human fetal small and large intestine and expanded with Wnt agonist, R-spondin 2, displayed differential expression of stem cell markers and separate hierarchical clustering of gene expression involved in differentiation, proliferation and disease pathways. Using a three-dimensional in vitro differentiation assay, single cells derived from small and large intestine formed distinct organoid architecture with cellular hierarchy similar to that found in primary tissue. Our characterization of human fetal intestinal stem cells defies the classical definition proposed by most where small and large intestine are repopulated by an identical epithelial stem cell and raises the question of the importance of intrinsic and extrinsic cues in the development of intestinal diseases. 12 samples were analyzed. They consisted of human fetal small and large intestine (SI; n=6 and LI; n=6) stem cells, expanded with Wnt agonist and R-spondin 2. Differential expression of genes in epithelial cells from both the large and small intestine were observed.
2015-01-15 | E-GEOD-56525 | biostudies-arrayexpress