Mus musculus strain:C57BL/6JJcl
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB17649 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Human intestinal epithelial organoid models are rapidly emerging as novel experimental tools to investigate intestinal epithelial biology. A necessary aspect of organoid use is the passaging of cells and long term maintenance in culture. DNA methylation has been demonstrated to play a key role in regulating gene expression and cellular function. Here we explore the effect of culture duration, proinflammatory cytokine stimulation and differentiation on organoid DNA methylation. The experiment consists of RNA-seq of intestinal organoid cultures from paediatric ileum and colon.
2022-08-31 | E-MTAB-11548 | biostudies-arrayexpress
Project description:Post-transcriptional regulation of Clock instructs the emergence of robust circadian clock oscillation during mouse development
| PRJDB5724 | ENA
Project description:A Comprehensive Mouse Transcriptomic BodyMap across 17 Tissues by RNA-seq
| PRJNA375882 | ENA
Project description:C57BL/6JJcl one molecule long reading
| PRJDB4827 | ENA
Project description:Human intestinal epithelial organoid models are rapidly emerging as novel experimental tools to investigate intestinal epithelial biology. A necessary aspect of organoid use is the passaging of cells and long term maintenance in culture. DNA methylation has been demonstrated to play a key role in regulating gene expression and cellular function. Here we explore the effect of culture duration, proinflammatory cytokine stimulation and differentiation on organoid DNA methylation. The experiment consists of genome-wide DNA methylation profiling by Infinium HumanMethylationEPIC BeadChip of intestinal organoid cultures from paediatric ileum and colon. Our genome wide DNA methylation datasets represent a unique resource, which can be used by other researchers to validate their model systems.
2022-08-31 | E-MTAB-11545 | biostudies-arrayexpress
Project description:Little is known about how pro-obesity diets regulate tissue stem and progenitor cell function. Here we find that high fat diet (HFD)-induced obesity augments the numbers and function of Lgr5+ intestinal stem cells (ISCs) of the mammalian intestine. Like HFD, ex vivo treatment of intestinal organoid cultures with palmitic acid (PA), a constituent of the HFD, enhances the self-renewal potential of these organoid bodies. Mechanistically, HFD induces a robust peroxisome proliferator-activated receptor delta (PPAR-delta signature in intestinal stem and progenitor cells and pharmacologic activation of PPAR-delta recapitulates the effects that HFD has on these cells. Interestingly, HFD- and agonist-activated PPAR-delta signaling endows organoid-initiating capacity to non-stem cells and enforced PPAR-delta signaling permits these non-stem cells to form in vivo tumors upon loss of the tumor suppressor Apc. These findings highlight how diet-modulated PPAR-delta activation alters not only the function of intestinal stem and progenitor cells but also their capacity to initiate tumors. mRNA profiles of intestinal stem cells (GFP-Hi) and progenitors (GFP-Low) from WT or HFD fed mice were generated by deep sequencing using HiSeq 2000.
2016-02-16 | E-GEOD-67324 | biostudies-arrayexpress
Project description:Human intestinal epithelial organoid models are rapidly emerging as novel experimental tools to investigate intestinal epithelial biology. A necessary aspect of organoid use is the passaging of cells and long term maintenance in culture. DNA methylation has been demonstrated to play a key role in regulating gene expression and cellular function. Here we explore the effect of culture duration on organoid DNA methylation. The experiment consists of genome-wide DNA methylation profiling by Infinium HumanMethylationEPIC BeadChip of intestinal organoid cultures from paediatric ileum and colon. Our genome wide DNA methylation datasets represent a unique resource, which can be used by other researchers to validate their model systems Note: Some samples in this data set were replicated from a previously submitted to ArrayExpress under accession number E-MTAB-4957. They're clearly marked in the “Description” field in sample annotations.
2022-08-31 | E-MTAB-9748 | biostudies-arrayexpress
Project description:Acetylcholine (ACh) has been considered a neurotransmitter residing in central, parasympathetic and neuromuscular synapses of mammals. Here, experiments using crypt-villus organoids that lack nerve and immune cells in culture led us to suggest that endogenous ACh is synthesized in the intestinal epithelium to evoke growth and differentiation of the organoids through activation of muscarinic ACh receptors (mAChRs). The extracts of the cultured organoids exhibit a noticeable capacity for ACh synthesis that is sensitive to a potent inhibitor of choline acetyltransferase (ChAT). Imaging mass spectrometry reveals distribution of endogenous ACh that is localized in intestinal epithelial layer in the cultured organoids as well as in mouse small intestinal epithelium in vivo, suggesting non-neural resources of ACh. Treatment of organoids with carbachol down-regulates growth of organoids and expression of marker gene for each epithelial cell. On the other hand, antagonists for mAChRs enhances growth and differentiation of organoids, indicating involvement of mAChRs in regulating proliferation and differentiation of Lgr5-positive stem cells. Collectively, our data provide evidence that endogenous ACh released from intestinal epithelium maintains homeostasis of intestinal epithelial cell growth and differentiation via mAChRs in mice. Gene expression patters of gut, crypt, y-organoid and o-organoid, respectively
2013-08-15 | E-GEOD-49864 | biostudies-arrayexpress
Project description:Translational research is commonly performed in the C57B6/J mouse strain, chosen for its genetic homogeneity and phenotypic uniformity. Here, we evaluate the suitability of the white-footed deer mouse (Peromyscus leucopus) as a model organism for aging research, offering a comparative analysis against C57B6/J and diversity outbred (DO) Mus musculus strains. Our study includes comparisons of body composition, skeletal muscle function, and cardiovascular parameters, shedding light on potential applications and limitations of P. leucopus in aging studies. Notably, P. leucopus exhibits distinct body composition characteristics, emphasizing reduced muscle force exertion and a unique metabolism, particularly in fat mass. Cardiovascular assessments showed changes in arterial stiffness, challenging conventional assumptions and highlighting the need for a nuanced interpretation of aging-related phenotypes. Our study also highlights inherent challenges associated with maintaining and phenotyping P. leucopus cohorts. Behavioral considerations, including anxiety-induced responses during handling and phenotyping assessment, pose obstacles in acquiring meaningful data. Moreover, the unique anatomy of P. leucopus necessitates careful adaptation of protocols designed for Mus musculus. While showcasing potential benefits, further extensive analyses across broader age ranges and larger cohorts are necessary to establish the reliability of P. leucopus as a robust and translatable model for aging studies.
| S-EPMC11335981 | biostudies-literature