Transcriptome analysis of embryonic mesenchyme
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE224219 | GEO | 2023/08/07
REPOSITORIES: GEO
Similar Datasets
Project description:Axon Guidance Study in Drosophila embryos
| PRJNA98601 | ENA
Project description:A growth cone (GC) is a part of a neuron considered a hub for axon growth, motility and guidance functions. Here, we present a dataset on the protein profiling of the growth cone-enriched fractions derived from E18, P0, P3, P6 and P9 C57BL/6J mouse pups. For comparison, we analyzed non-growth cone membranes.
2019-05-03 | PXD012134 | Pride
Project description:Purpose: The aim of this study is to propose a computational model which can help in unravelling the mechanisms of initial bile duct lumen formation. Guided by the quantification of morphological features and expression of genes in developing bile ducts (cholangiocytes) from embryonic mouse liver, hypotheses for the mechanisms of biliary lumen formation were generated and tested with the model. Here, the RNA-sequencing data were collected from purified embryonic cholangiocytes at two developmental stages (E16 and E18).
2021-05-31 | GSE163062 | GEO
Project description:The surrounding microenvironment plays a crucial role in pancreas formation and differentiation. Nevertheless, its cellular composition has not been analyzed in depth and whether different cell populations exist within the mesenchyme of the developing pancreas is an open question. Similarly, the molecular mechanisms by which the mesenchyme coordinates and integrates various signaling pathways to stimulate epithelial pancreatic progenitor proliferation and differentiation remain elusive. Here, we investigate the cell composition and molecular network in the pancreatic mesenchyme, which promote pancreas differentiation. Whole transcriptome analysis and functional experiments showed that PBX in the mesenchyme promotes endocrine differentiation non-cell autonomously, acting at two different levels in the epithelial-mesenchymal crosstalk: 1) the maintenance of BM integrity and ECM and 2) regulation of soluble molecules, including guidance cues. In conclusion, this study has identified distinct pancreatic mesenchymal niches and dissected their different roles during pancreatic development. This knowledge will be useful to improve current differentiation strategies based on ECM and soluble factors to generate β-cell equivalents from pluripotent cells for future cell replacement therapies of diabetes.
2020-08-28 | GSE123759 | GEO
Project description:Examine the global gene expression changes from E16 (day 16.5) to E19 (day 18.5) in fetal SD rat skin samples E19 samples were renamed as E18 samples in the relative manuscript
2015-11-14 | GSE74976 | GEO
Project description:We profile the transcriptomes of ~30,000 mouse single cells to deconvolve the hepatic mesenchyme in healthy and fibrotic liver at high resolution. We reveal spatial zonation of hepatic stellate cells across the liver lobule, designated portal vein-associated HSC and central vein-associated HSC, and uncover an equivalent functional zonation in a mouse model of centrilobular fibrosis. Our work illustrates the power of single-cell transcriptomics to resolve key collagen-producing cells driving liver fibrosis with high precision.
2019-11-01 | GSE137720 | GEO
Project description:During the development of the Drosophila central nervous system the process of midline crossing is orchestrated by a number of guidance receptors and ligands. Many key axon guidance molecules have been identified in both invertebrates and vertebrates, but the transcriptional regulation of growth cone guidance remains largely unknown. One open question is whether transcriptional regulation plays a role in midline crossing, or if local translation can account for the necessary fine tuning of protein levels. To investigate this issue, we conducted a genome wide analysis of transcription in Drosophila embryos using wild type and a number of well-characterized Drosophila guidance mutants and transgenics. We also analyzed a publicly available microarray time course of Drosophila embryonic development with an axon guidance focus. Using hopach, a novel clustering method which is well suited to microarray data analysis, we identified groups of genes with similar expression patterns across guidance mutants and transgenics. We then systematically characterized the resulting clusters with respect to their relevance to axon guidance using two complementary controlled vocabularies: the Gene Ontology (GO) and anatomical annotations of the Atlas of Pattern of Gene Expression (APoGE) in situ hybridization database. The analysis indicates that regulation of gene expression does play a role in the process of axon guidance in Drosophila. We also find a strong link between axon guidance and hemocyte migration, a result that agrees with mounting evidence that axon guidance molecules are co-opted in vertebrate vascularization. Cell cyclin activity in the context of axon guidance is also suggested from our array data. RNA and protein patterns of cell cyclin in axon guidance mutants and transgenics support this possible link. This study provides important insights into the regulation of axon guidance in vivo and suggests that transcription does play a role in control of axon guidance. Keywords: Mutant Analysis
2006-12-14 | GSE6515 | GEO
Project description:During the development of the Drosophila central nervous system the process of midline crossing is orchestrated by a number of guidance receptors and ligands. Many key axon guidance molecules have been identified in both invertebrates and vertebrates, but the transcriptional regulation of growth cone guidance remains largely unknown. One open question is whether transcriptional regulation plays a role in midline crossing, or if local translation can account for the necessary fine tuning of protein levels. To investigate this issue, we conducted a genome wide analysis of transcription in Drosophila embryos using wild type and a number of well-characterized Drosophila guidance mutants and transgenics. We also analyzed a publicly available microarray time course of Drosophila embryonic development with an axon guidance focus. Using hopach, a novel clustering method which is well suited to microarray data analysis, we identified groups of genes with similar expression patterns across guidance mutants and transgenics. We then systematically characterized the resulting clusters with respect to their relevance to axon guidance using two complementary controlled vocabularies: the Gene Ontology (GO) and anatomical annotations of the Atlas of Pattern of Gene Expression (APoGE) in situ hybridization database. The analysis indicates that regulation of gene expression does play a role in the process of axon guidance in Drosophila. We also find a strong link between axon guidance and hemocyte migration, a result that agrees with mounting evidence that axon guidance molecules are co-opted in vertebrate vascularization. Cell cyclin activity in the context of axon guidance is also suggested from our array data. RNA and protein patterns of cell cyclin in axon guidance mutants and transgenics support this possible link. This study provides important insights into the regulation of axon guidance in vivo and suggests that transcription does play a role in control of axon guidance. Experiment Overall Design: Several mutants and transgenics were analyzed, totalizing 17 distinct conditions. Individual descriptions are included in each microarray. For each condition there are 3 or 4 replicates. The file's name indicates the replicates, e.g., comm.a reflects the replicate a of mutant commissureless. The experiment design covers a range of mutants and transgenics of key axon guidance mutans, in different dosages. The protocol was the standard Affymetrix protocol.
2008-06-15 | E-GEOD-6515 | biostudies-arrayexpress
Project description:Samples E12/E13/E14/E16/E18: We aims to screen out different gene expression profile in Embryo kidney on different gestation stages of the Notch signaling pathway Results from the various study components can help to screening important candidate genes during embryonic kidney development. Keywords: Embryo kidney, Development, Notch signaling pathway, Oligonucleotide Array Sequence Analysis The Oligo GEArray Assay comprises various components: RNA isolation,Assesing RNA yield and quality,cRNA labeling and synthesis,Hybridization,Chemiluminescent detection and Image acquisition and data analysis. Samples E12: This study has been accomplished with Embryo kidney on gestation 12, 3 techinical replicates. Samples E13: This study has been accomplished with Embryo kidney on gestation 13, 3 techinical replicates. Samples E14: This study has been accomplished with Embryo kidney on gestation 14, 2 techinical replicates. Samples E16: This study has been accomplished with 1Embryo kidney on gestation 16, 2 techinical replicates. Samples E18: This study has been accomplished with Embryo kidney on gestation 18, 2 techinical replicates.
2011-04-20 | E-GEOD-28496 | biostudies-arrayexpress
Project description:Samples E12/E13/E14/E16/E18: We aims to screen out different gene expression profile in Embryo kidney on different gestation stages of the Notch signaling pathway Results from the various study components can help to screening important candidate genes during embryonic kidney development. Keywords: Embryo kidney, Development, Notch signaling pathway, Oligonucleotide Array Sequence Analysis
2011-04-20 | GSE28496 | GEO