(Epi)genetic regulation of zebrafish intestinal development
Ontology highlight
ABSTRACT:
ORGANISM(S): Danio rerio
PROVIDER: GSE118076 | GEO | 2018/10/24
REPOSITORIES: GEO
Similar Datasets
Project description:Expression profiles obtained from the villus and crypt layers of murine large intestine can elucidate the process of differentiation undergone by epithelial cells as they migrate from the undifferentiated bottom of the crypt to the villus tip before being shed into the intestinal lumen. This series includes profiles from wild type mice, as well as mice harboring mutations in genes (APC and p21) which play key roles in the differentiation process. We used microarrays to characterize gene expression profiles at the base of the crypt and at the villus tip of the lumenal layer of the large intestine in order to better understand the process of differentiation and eventual shedding undergone by cells of the large intestinal epithelium. Four wild type, four APC1638+/- and four p21-/- mice were sacrified and the large intestines dissected out. Cells from the villus tip and from the bottom of the crypt were isolated from the lumenal face of the each large intestine using the Weiser method of sequential elution. RNA was extracted from each eluted sample and used to hybridize to Affymetrix 3' expression arrays.
2010-10-06 | E-GEOD-19338 | biostudies-arrayexpress
Project description:Arid1a, a subunit of the SWI/SNF chromatin remodeling complex, have been reported in multiple human cancers, however, its functional role in intestinal homeostasis remains unclear. To investigate the role of Arid1a in murine intestine, we have employed whole genome microarray expression profiling of Arid1a conditional knock out mouse intestines. We found that Wnt signaling is downregulated in Arid1a conditional knock out mouse intestines compared to that of wild type mouse intestines.
2018-02-06 | GSE110181 | GEO
Project description:To identify putative KLF5 target genes that may mediate villus morphogenesis and epithelial maturation, we performed microarray analysis on intestinal samples isolated on E14.5, prior to the initiation of villus formation. Total RNA was isolated from dissected intestine segments located ~1.5 cm anterior to the cecum from E14.5 Klf5D/D and Klf5wt/wtShhEGFP/Cre+ embryos (n=3 samples/genotype, each sample a pool of two intestines). Gene expression profiles were compared using Affymetrix Mouse Gene 1.0 ST Array. Genes involved in the regulation of "epithelial cell differentiation/maturation”, “cell adhesion”, and “lipid synthesis, metabolism, and localization”. Consistent with the lack of terminally differentiated cell types in the intestines of E18.5 Klf5D/D fetuses. To identify putative KLF5 target genes that may mediate villus morphogenesis and epithelial maturation, we performed microarray analysis on intestinal samples isolated on E14.5, prior to the initiation of villus formation. Total RNA was isolated from dissected intestine segments located ~1.5 cm anterior to the cecum from E14.5 Klf5D/D and Klf5wt/wtShhEGFP/Cre+ embryos (n=3 samples/genotype, each sample a pool of two intestines). Gene expression profiles were compared using Affymetrix Mouse Gene 1.0 ST Array.
2013-01-24 | E-GEOD-39624 | biostudies-arrayexpress
Project description:To investigate how the zebrafish embryos respond to the absence of the microbiota, the intestinal tissue-associated and the kidney tissue-associated gene expressions were examined at 5 dpf and 7 dpf respectively. 32,948 cDNAs of the zebrafish genome assembly were annotated after reads mapping for further analysis. For the 5 dpf intestinal tissue samples, 948 genes (4% of the total number of genes) were differentially expressed, 371 genes were up-regulated and 577 genes were down-regulated in the GF group . For the 7 dpf kidney tissue samples, 697 genes (3% of the total number of genes) were differentially expressed, 341 genes were up-regulated and 356 genes were down-regulated in the GF group. The enrichment analysis showed that the immune and cytokine related pathways were affected by the GF treatment in the wildtype embryos (both in intestines at 5 dpf and in kidneys at 7 dpf). To investigate how the transcriptome changes in the chd8-/- zebrafish embryos, the intestinal tissue-associated and the kidney tissue-associated gene expressions were examined at 5 dpf and 7 dpf respectively.
2023-03-15 | GSE200577 | GEO
Project description:Rb and E2F are thought to play antagonistic roles in celll proliferation. However, this model is based mostly from in vitro cell culture systems. We used small intestines to test this model in vivo. We found that deletion of E2f1-3 in the small intestine of mice suppressed the ectopic expression of E2F targets and cell proliferation caused by Rb-deficiency. Surprisingly, E2f1-3 deletion failed to arrest the proliferation of intestinal cells containing an intact Rb gene, and instead led to E2F target derepression and apoptosis. Experiment Overall Design: Total RNA of crypts and villi from wild-type, Rb-/-, E2f1-/-, E2f2-/-, E2f3-/-, E2f1-/-, E2f2-/-, and E2f3-/- small intestines. Small intestines were harvested 7 days after mice were injected intraperitoneally with beta-napthoflavone.
2010-01-19 | E-GEOD-16454 | biostudies-arrayexpress
Project description:We sequenced the transcriptome of the proliferative progenitor cells of the intestine to determine how the microbiome was affecting growth in wild-type intestines and those with Notch-deficient tumors
2019-10-09 | GSE138555 | GEO
Project description:This experiment was investigating how gut commensal bacteria and intestinal inflammation affect miRNA expression. We analyzed miRNA expression of spleen and intestine from specific pathogen free (SPF) B6 mice, germ-free (GF) B6 mice, and IL-10 knockout mice which have severe colitis by microarray. Thus we have total 6 samples: GF spleen; GF intestines; SPF spleen; SPF intestine; IL-10 KO spleen and IL-10 KO intestine. We directly isolated RNA from whole spleens or intestines without any treatments, and then did microarray analysis.
2011-11-23 | E-MEXP-3406 | biostudies-arrayexpress
Project description:To identify putative KLF5 target genes that may mediate villus morphogenesis and epithelial maturation, we performed microarray analysis on intestinal samples isolated on E14.5, prior to the initiation of villus formation. Total RNA was isolated from dissected intestine segments located ~1.5 cm anterior to the cecum from E14.5 Klf5D/D and Klf5wt/wtShhEGFP/Cre+ embryos (n=3 samples/genotype, each sample a pool of two intestines). Gene expression profiles were compared using Affymetrix Mouse Gene 1.0 ST Array. Genes involved in the regulation of "epithelial cell differentiation/maturation”, “cell adhesion”, and “lipid synthesis, metabolism, and localization”. Consistent with the lack of terminally differentiated cell types in the intestines of E18.5 Klf5D/D fetuses.
2013-01-24 | GSE39624 | GEO
Project description:Background: A recently developed animal model of the genetic disease is the cystic fibrosis (CF) rat, which similar to other animal models of CF exhibits a lethal intestinal phenotype. To begin characterizing the CF rat intestinal phenotype, we investigated global gene expression in the CF rat small intestine. Methods: Total RNA was extracted from full thickness of the entire small intestines of wild type (WT) and CF rats just before weaning. Results: There were 890 genes with significantly different expression levels (1.2-fold cutoff) comparing CF to wild type (WT), including 485 genes increased and 405 decreased in the CF intestine. The major pathways associated with these changes were inflammation, lipid metabolism, cytochrome P450-mediated degradative pathways, and cell growth/death. Comparison of the rat RNA-Seq dataset to earlier microarray analysis using a CFTR knockout mouse showed significant overlap with the CF rat small intestine. Conclusions: The small intestine of the new CF rat model exhibits numerous alterations in gene expression similar to other animal models of CF which indicate this will be an additional new model to study the gut effects CF.
2016-09-23 | GSE81114 | GEO
Project description:The nematode intestine is the primary site for nutrient uptake and storage as well as the synthesis of important molecules; parts of its functions rely on a type of lysosome-related organelle known as gut granules. However, aspects of the intestine are not well understood, including the exporting of its molecules and that of the gut granules, in which only a few of the organelle’s protein content is identified. Here, we report a mass-spectrometry-based proteomic analysis of the intestine of the Caenorhabditis elegans and of these lysosome-related organelles. We identified around 5000 proteins each in the intestine and the gonad and showed that most of these proteins can be identified using samples extracted from a single worm, suggesting the feasibility of individual-level proteomic-based genetics analysis. Comparing the proteome to that of the transcriptome, we identify proteins that may be synthesized in the intestine and transferred to the gonad. To identify gut granule proteins, we compared the intestinal proteome of individual intestines that largely lack gut granules to that of the wild-type. The identified gut granule proteome includes proteins previously known to be exclusively localized to the granules, and we validated two more with immunohistochemistry analysis, including a worm ortholog of the mammalian ABCC6/MRP6, suggesting that our strategy was effective in identifying the gut granule proteome. Our results demonstrate the practicability of single tissue mass-spectrometry-based proteomic analyses in small organisms such as nematodes, as well as its utility for making discoveries in a previously prohibitive area.
2024-05-23 | PXD047792 | Pride