Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA147207 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Transcriptional profiling of intestinal epithelial cells expressing either Negative, Sublow, Low or High levels of the Sox9-EGFP reporter transgene FACS-isolated from jejunum of non-irradiated mice or at 5 days after 14Gy abdominal irradiation. 4 distinct cell populations, FACS-isolated based on expression levels of the Sox9-EGFP reporter transgene (Sox9-EGFP Negative, Sublow, Low and High cells); 2 conditions: Non-irradiated vs Irradiated; Biological replicates: 7 independent non-irradiated mice and 3 independent irradiated (studied at day 5 post-irradiation) mice
2012-06-17 | E-GEOD-32227 | biostudies-arrayexpress
Project description:Transcriptional profiling of intestinal epithelial cells expressing either Negative, Sublow, Low or High levels of the Sox9-EGFP reporter transgene FACS-isolated from jejunum of non-irradiated mice or at 5 days after 14Gy abdominal irradiation. In both groups, mice were treated for 5 consecutive days with either IGF1 or vehicle via mini-pumps (Alzet 1007D, IGF1 at 10mg/ml) implanted subcutaneously immediately following radiation. 4 distinct cell populations FACS-isolated based on levels of expression of the Sox9-EGFP reporter transgene (Sox9-EGFP Negative, Sublow, Low and High cells). 4 conditions: Non-irradiated/vehicle vs Non-irradiated/IGF1 vs Irradiated/vehicle vs Irradiated/IGF1. Biological replicates: 7 independent non-irradiated mice treated with vehicle - 3 independent non-irradiated mice treated for 5 days with IGF1 - 3 independent irradiated mice studied at day 5 post-irradiation treated with vehicle - 3 independent irradiated mice studied at day 5 post-irradiation treated for 5 days with IGF1.
2015-04-14 | E-GEOD-42817 | biostudies-arrayexpress
Project description:We compared gene expression profile of jejunum crypt samples of Sox9 deficient mice and wild type control mice in order to identify the genes that are regulated by SOX9 in the small intestinal crypt epithelial cells.
2012-03-23 | GSE35481 | GEO
Project description:We compared gene expression profile of jejunum crypt samples of Sox9 deficient mice and wild type control mice in order to identify the genes that are regulated by SOX9 in the small intestinal crypt epithelial cells. The intestinal epithelial cells were collected from crypts of jejunum of three 3-mo-old Sox9 mutant mice and three littermate controls.
2012-03-23 | E-GEOD-35481 | biostudies-arrayexpress
Project description:Epithelial regeneration is critical for barrier maintenance and organ function after intestinal injury. Here, we found that Bach2 deficiency promotes the intestinal epithelial cell proliferation during homeostasis and facilitates the crypt regeneration after irradiation, resulting in a reduction of mortality. RNA-seq analysis of isolated crypts revealed that Bach2 deficiency altered expression of numerous genes including those regulating DSBs repair. Crypts were isolated from the small intestines of Bach2 KO and control mice (n=3, respectively) 10 days after tamoxifen administration. Total RNA was extracted for sequencing using RNA-Seq.
2021-01-12 | E-MTAB-9865 | biostudies-arrayexpress
Project description:To define the repertoire of Sox9-dependent genes that contribute to the regulation of chondrogenesis, we generated Sox9-3'enhanced green fluorescent protein (EGFP) knock-in mice (Sox9-3'EGFP) and Sox9-EGFP/EGFP null chimeras. EGFP-positive cells of Sox9-3'EGFP knock-in and Sox9-EGFP/EGFP null chimeric embryos harvested from limb buds at embryonic day 12.5 were sorted using a FACSAria flow cytometer (Becton-Dickinson). Total RNA of sorted cells was extracted using the RNeasy Mini Kit (QIAGEN) and amplified according to the instructions provided by Affymetrix. Microarray analysis using the Affymetrix Mouse Genome 430 2.0 Array was performed according to the manufacturer's instructions.
2011-02-16 | E-MTAB-537 | biostudies-arrayexpress
Project description:Transcriptional profiling of intestinal epithelial cells expressing either Negative, Sublow, Low or High levels of the Sox9-EGFP reporter transgene FACS-isolated from jejunum of non-irradiated mice or at 5 days after 14Gy abdominal irradiation.
2012-06-18 | GSE32227 | GEO
Project description:Introduction: In addition to the well-known cartilage extracellular matrix-related expression of Sox9, we demonstrated that chondrogenic differentiation of progenitor cells is driven by a sharply defined bi-phasic expression of Sox9: an immediate early and a late (extracellular matrix associated) phase expression. In this study we aimed to determine what biological processes are driven by Sox9 during this early phase of chondrogenic differentiation. Materials: Sox9 expression in ATDC5 cells was knocked-down by siRNA transfection at the day before chondrogenic differentiation or at day 6 of differentiation. Samples were harvested at 2 hours, and 7 days of differentiation. The transcriptomes (RNA-seq approach) and proteomes (Label-free proteomics approach) were compared using pathway and network analyses. Total protein translational capacity was evaluated with the SuNSET assay, active ribosomes with polysome profiling and ribosome modus with bicistronic reporter assays. Results: Early Sox9 knockdown severely inhibited chondrogenic differentiation weeks later. Sox9 expression during the immediate early phase of ATDC5 chondrogenic differentiation regulated the expression of ribosome biogenesis factors and ribosomal protein subunits. This was accompanied by decreased translational capacity following Sox9 knockdown, and this correlated to lower amounts of active mono- and polysomes. Moreover, cap- versus IRES-mediated translation was altered by Sox9 knockdown. Sox9 overexpression was able to induce reciprocal effects to the Sox9 knockdown. Conclusion: Here we identified an essential new function for Sox9 during early chondrogenic differentiation. A role for Sox9 in regulation of ribosome amount, activity and/or composition may be crucial in preparation for the demanding proliferative phase and subsequent cartilage extracellular matrix-production of chondroprogenitors in the growth plate in vivo.
2021-06-18 | PXD024715 | Pride
Project description:The currently accepted intestinal epithelial cell organization model equates crypt base columnar (CBC) cells, marked by high levels of Lgr5 expression, with the intestinal stem cell (ISC). However, recent intestinal regeneration studies have uncovered limitations of the ‘Lgr5-CBC’ model, leading to two major views: one favoring the presence of a quiescent reserve stem cell population, the other calling for differentiated cell plasticity. To test if an alternative model may help reconcile these perspectives, we studied the hierarchical organization of crypt epithelial cells in an unbiased fashion, by combining high-resolution, single-cell profiling and lineage tracing in multiple transgenic mouse models. These show that Lgr5 is not a specific ISC marker; rather, cells located in the crypt isthmus, which include Lgr5low cells, comprise the ISCs that sustain tissue homeostasis. Following irradiation or intestinal injury, surviving ISCs and progenitors, but not differentiated cells, participate in intestinal regeneration, suggesting that neither de-differentiation nor reserve stem cell populations are drivers of intestinal regeneration. Our results provide a novel viewpoint for the intestinal crypt epithelium, in which ISCs localize to the crypt isthmus, and ISC potential is restricted to stem and progenitor cells.
2024-03-24 | GSE205229 | GEO
Project description:Hippo signalling has been implicated as a key regulator of tissue regeneration. In the intestine, ex vivo organoid cultures model aspects of crypt epithelial regeneration. Therefore in order to uncover the Yap regulated transcriptional programs during crypt regeneration we performed RNA-sequencing of Yap wt and Yap deficient organoids, as well as organoids inducibly expressing Yap.
2015-10-15 | GSE66567 | GEO