Bulk RNA-seq of proliferating cells in the mouse stomach corpus epithelium from FUCCI mouse.
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB27097 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2610700.fastq.gz | Fastqsanger.gz | |||
| ERR2610701.fastq.gz | Fastqsanger.gz | |||
| ERR2610696.fastq.gz | Fastqsanger.gz | |||
| ERR2610697.fastq.gz | Fastqsanger.gz | |||
| ERR2610698.fastq.gz | Fastqsanger.gz |
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Project description:The purpose of this bulk RNA-seq experiment is to identify candidate genes that can mark proliferating isthmus progenitors in the mouse stomach corpus epithelium. The cycling isthmus progenitors were isolated based on mVenus expression in FUCCI mouse and used for bulk RNA-seq data generation. The corpus epithelium was stained with E-cadherin and E-cadherin+ cells were also sorted and used for the control.
2019-08-14 | E-MTAB-6850 | biostudies-arrayexpress
Project description:Objective: Tissue stem cells are central regulators of organ homeostasis. We looked for a protein that is exclusively expressed and functionally involved in stem cell activity in rapidly proliferating isthmus stem cells in the stomach corpus. Design: We uncovered the specific expression of Iqgap3 in proliferating isthmus stem cells through immunofluorescence and in situ hybridization. We performed lineage tracing and transcriptomic analysis of Iqgap3+ isthmus stem cells with the Iqgap3-2A-tdTomato mouse model. Depletion of Iqgap3 revealed its functional importance in maintenance and proliferation of stem cells. We further studied Iqgap3 expression and the associated gene expression changes during tissue repair after tamoxifen-induced damage. Immunohistochemistry revealed elevated expression of Iqgap3 in proliferating regions of gastric tumors from patient samples. Results: Iqgap3 is a highly specific marker of proliferating isthmus stem cells during homeostasis. Iqgap3+ isthmus stem cells give rise to major cell types of the corpus unit. Iqgap3 expression is essential for the maintenance of stem potential. The Ras pathway is a critical partner of Iqgap3 in promoting strong proliferation in isthmus stem cells. The robust induction of Iqgap3 expression following tissue damage indicates an active role for Iqgap3 in tissue regeneration. Conclusion: IQGAP3 is a major regulator of stomach epithelial tissue homeostasis and repair. The upregulation of IQGAP3 in gastric cancer suggests that IQGAP3 plays an important role in cancer cell proliferation.
2021-03-08 | GSE161442 | GEO
Project description:Objective: Tissue stem cells are central regulators of organ homeostasis. We looked for a protein that is exclusively expressed and functionally involved in stem cell activity in rapidly proliferating isthmus stem cells in the stomach corpus. Design: We uncovered the specific expression of Iqgap3 in proliferating isthmus stem cells through immunofluorescence and in situ hybridization. We performed lineage tracing and transcriptomic analysis of Iqgap3+ isthmus stem cells with the Iqgap3-2A-tdTomato mouse model. Depletion of Iqgap3 revealed its functional importance in maintenance and proliferation of stem cells. We further studied Iqgap3 expression and the associated gene expression changes during tissue repair after tamoxifen-induced damage. Immunohistochemistry revealed elevated expression of Iqgap3 in proliferating regions of gastric tumors from patient samples. Results: Iqgap3 is a highly specific marker of proliferating isthmus stem cells during homeostasis. Iqgap3+ isthmus stem cells give rise to major cell types of the corpus unit. Iqgap3 expression is essential for the maintenance of stem potential. The Ras pathway is a critical partner of Iqgap3 in promoting strong proliferation in isthmus stem cells. The robust induction of Iqgap3 expression following tissue damage indicates an active role for Iqgap3 in tissue regeneration. Conclusion: IQGAP3 is a major regulator of stomach epithelial tissue homeostasis and repair. The upregulation of IQGAP3 in gastric cancer suggests that IQGAP3 plays an important role in cancer cell proliferation.
2021-03-08 | GSE161443 | GEO
Project description:The purpose of this experiment is to assess temporal transcriptomic change in Troy+ chief cells upon injury in the stomach corpus in mice. Troy+-eGFP cells were sorted at each time point after stomach injury by DMP777 treatment.
2022-05-05 | E-MTAB-10373 | biostudies-arrayexpress
Project description:Bulk RNA-seq of proliferating cells in the mouse stomach corpus epithelium from FUCCI mouse.
2019-08-30 | E-MTAB-6850 | ExpressionAtlas
Project description:We prepared miRNA from myofibroblats derived from normal stomach, both antrum (A) and corpus (C) separately and gastric cancers. miRCURYTM LNA Array ver5 was performed and comparisons were made by the dual (reference) method.
2016-02-01 | GSE76218 | GEO
Project description:Formation of cortical connections requires the precise coordination of several discrete stages. This is particularly significant with regard to the corpus callosum, the largest white matter structure bridging both cerebral hemispheres, whose development undergoes several dynamic stages including the crossing of axon projections, the elimination of exuberant projections, and the myelination of established tracts. To comprehensively characterize the molecular events in this dynamic process, we set to determine the distinct temporal expression of proteins regulating the formation of the corpus callosum and their respective developmental functions. Mass spectrometry-based proteomic profiling was performed on early postnatal mouse corpus callosi, for which limited evidence has been obtained previously, using stable isotope of labeled amino acids in mammals (SILAM). The analyzed corpus callosi had distinct proteomic profiles depending on age, indicating rapid progression of specific molecular events during this period. The proteomic expression profiles were then segregated into five separate protein clusters, each with distinct trajectories relevant to their intended developmental functions. Our analysis both confirms many previously-identified proteins in aspects of corpus callosum development, and identifies new candidates in understudied areas of development including callosal axon refinement. We present a valuable resource for identifying new proteins integral to corpus callosum development that will provide new insights into the development and diseases afflicting this structure.
2017-03-29 | PXD005271 | Pride
Project description:Time course bulk RNA-seq of Troy+ chief cells in the mouse stomach corpus epithelium after injury
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Project description:The alimentary tract contains a diffuse endocrine system comprising enteroendocrine cells that secrete peptides or biogenic amines to regulate digestion, insulin secretion, food intake, and energy homeostasis. Lineage analysis in the stomach revealed that a significant fraction of endocrine cells in the gastric corpus did not arise from neurogenin3-expressing cells, unlike enteroendocrine cells elsewhere in the digestive tract. We aimed to isolate enriched serotonin-secreting and enterochromaffin-like (ECL) cells from the stomach and to clarify their cellular origin. We used Neurod1 and Neurog3 lineage analysis, and examined differentiation of serotonin-producing and ECL cells in stomach tissues of Neurod1-cre;ROSAtdTom, Tph1-CFP, c-Kitwsh/wsh, and Neurog3Cre;ROSAtdTom mice, by immunohistochemistry. We used fluorescence-activated cell sorting to isolate each cell type for gene expression analysis. We performed RNA-seq analysis of ECL cells. Neither serotonin-secreting nor ECL cells of the corpus arose from cells expressing Neurod1. Serotonin-secreting cells expressed a number of mast cell genes, but not genes associated with endocrine differentiation; they did not develop in c-Kitwsh/wsh mice and were labeled with transplanted bone marrow cells. RNA-seq analysis of ECL cells revealed high expression levels of many genes common to endocrine cells including transcription factors, hormones, ion channels, and solute transporters but not markers of bone marrow cells. We used fluorescence-activated cell sorting to isolate Hdc+ cells from stomach corpus and performed RNA-seq for gene expression analysis to determine the origin of those cells.
2013-12-12 | E-GEOD-53214 | biostudies-arrayexpress
Project description:Glucocorticoids are used for the treatment of inflammatory conditions but they also cause many side-effects. We used microarrays to detail the changes in gene expression induced in the stomach upon oral glucocorticoid treatment. Female wildtype Balb/c mice were treated for three days with 50 mg/l dexamethasone (dex) via the drinking water. Control mice were left untreated. The stomach was dissected and RNA prepared from the corpus.
2014-07-18 | E-GEOD-51669 | biostudies-arrayexpress