Comparative gene expression profiling of mouse pXEN, XEN, ES, and rat XENP cells
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ABSTRACT:
PROVIDER: PRJNA415792 | ENA |
REPOSITORIES: ENA
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Project description:We derived and describe a novel mouse cell type that we name primitive XEN (pXEN) cells, and compare their gene expression profiles with other stem cell types previously derived from rodent blastocysts.
2018-05-29 | GSE106158 | GEO
Project description:Comparison of mouse ES cells and three different XEN cell cultures. Three XEN cell cultures: Two different strains (IM8A1 is PO, and XEN1-3 is ICR). And two different culture conditions (IM8A1-I versus IM8A1-II). Three biological replicates of XEN cell RNA were submitted to the Centre for Applied Genomics at the Hospital for Sick Children (Toronto, Canada) for preparation of cRNA and hybridization to the mouse U74Av2 Affymetrix gene array. QIAGEN RNeasy midi kit (QIAGEN Inc., Santa Clarita, CA) was used to extract total RNA from all samples according to manufacturer's instructions. The samples were (1) XEN1-3 cells at passage 18 (ICR strain, male) cultured on gelatin with 70% EMFI-CM, (2) IM8A1 cells at passage 27 (PO strain) cultured on gelatin with 70% EMFI-CM, (3) IM8A1 cells at passage 27 cultured on tissue culture plastic in RPMI 1640 (Gibco) supplemented with 20% FBS (CanSera, Rexdale, Canada), 1 mM sodium pyruvate, 2 mM L-glutamine, 50 mg/ml each of penicillin/streptomycin (all from Gibco), 100 uM b-mercaptoethanol (Sigma) for 4 days. RNA was also obtained from R1 ES cells grown in the absence of EMFIs in the above medium with LIF. Keywords = ES cells Keywords = XEN cells Keywords: ordered
2005-01-29 | GSE2204 | GEO
Project description:Comparison of mouse ES cells and three different XEN cell cultures. Three XEN cell cultures: Two different strains (IM8A1 is PO, and XEN1-3 is ICR). And two different culture conditions (IM8A1-I versus IM8A1-II). Three biological replicates of XEN cell RNA were submitted to the Centre for Applied Genomics at the Hospital for Sick Children (Toronto, Canada) for preparation of cRNA and hybridization to the mouse U74Av2 Affymetrix gene array. QIAGEN RNeasy midi kit (QIAGEN Inc., Santa Clarita, CA) was used to extract total RNA from all samples according to manufacturer's instructions. The samples were (1) XEN1-3 cells at passage 18 (ICR strain, male) cultured on gelatin with 70% EMFI-CM, (2) IM8A1 cells at passage 27 (PO strain) cultured on gelatin with 70% EMFI-CM, (3) IM8A1 cells at passage 27 cultured on tissue culture plastic in RPMI 1640 (Gibco) supplemented with 20% FBS (CanSera, Rexdale, Canada), 1 mM sodium pyruvate, 2 mM L-glutamine, 50 mg/ml each of penicillin/streptomycin (all from Gibco), 100 uM b-mercaptoethanol (Sigma) for 4 days. RNA was also obtained from R1 ES cells grown in the absence of EMFIs in the above medium with LIF.
2008-06-12 | E-GEOD-2204 | biostudies-arrayexpress
Project description:The conventional trophoblast stem cells represent post-implantation extraembryonic ectoderm-like state and not that of pre-implantation trophectoderm, irrespective of their origin. To capture the trophectoderm-like state we established culture conditions that facilitate the co-existence of characteristics of both the extraembryonic lineages, namely, primitive endoderm and trophectoderm. We term these cells XTE cells. We carried out RNA-seq on XTE cells from different origins, as well as XEN cells, XEN-like cells, and ES cells, to assess their transcriptional profiles and identify putative marker genes and master regulators.
2022-09-13 | E-MTAB-8788 | biostudies-arrayexpress
Project description:In this study we showed that rat XEN cells grown in the presence of a GSK3 inhibitor exhibited enhanced formation of cell contacts and decreased motility. In contrast, treatment with forskolin induced the PE formation and epithelial-mesenchymal transition (EMT) in rat XEN cells. Using microarray and real-time PCR assays, we found that VE versus PE formation of rat XEN cells was correlated with change in expression levels of VE or PE marker genes. Similar to forskolin, EMT was prompted upon treatment of rat XEN cells with recombinant parathyroid hormone related peptide (PTHRP), an activator of the cAMP pathway in vivo. Taken together, our data suggest that rat XEN cells are PrE-like cells. The activation of Wnt pathway in rat XEN cells leads to the acquisition of VE characteristics, whereas the activation of the PTHRP/cAMP pathway leads to EMT and the formation of PE.
2013-02-01 | GSE42438 | GEO
Project description:Rat ES cells were derived using 3I medium from E4.5 blastocysts. Rat embryonic fibroblast cells were derived form E14.5 embryos. To analyze the mechanism under the selfrenewal of rat ES cells, microarrays were used for the genome wide analysis of gene expressoin profiles in rat ES cells. Rat embryonic fibroblast cells and mouse ES cells were tested at same time as control. Our results from clustering analysis demonstrated that the gene expression profile of rat ES cells resembles mouse ES cells, but not REFs. Keyword: 3I medium; rat embryonic stem cells; mouse ES cells; rat embryonic fibroblast cells
2008-11-25 | GSE13681 | GEO
Project description:To understand the role of Sox7 in primitive endoderm differentiation, we compare the gene expression pattern of Sox7 (+/-) and Sox7 (-/-) ES cells with or without dexamethasome (Dex) treatment. Because these ES cells harbour Gata6-GR transgene, Dex treatment forces ES cells differentate into XEN-like cells. As Sox7 (-/-) ES cells can differentiate into XEN-like cell by morphology, we assessed genome wide gene expression pattern.
2015-09-14 | GSE66971 | GEO
Project description:To understand the role of Sox7 in primitive endoderm differentiation, we compare the gene expression pattern of Sox7 (+/-) and Sox7 (-/-) ES cells with or without dexamethasome (Dex) treatment. Because these ES cells harbour Gata6-GR transgene, Dex treatment forces ES cells differentate into XEN-like cells. As Sox7 (-/-) ES cells can differentiate into XEN-like cell by morphology, we assessed genome wide gene expression pattern. Sox7 (+/-) ES cells and Sox7 (-/-) ES cells are forced to differentiate into XEN-like cells by Gata6-GR transgene. To compare the gene expression, we collected RNA samples at day4 with or without dexamethasone treatment from each genotype.
2015-09-14 | E-GEOD-66971 | biostudies-arrayexpress
Project description:In this study we showed that rat XEN cells grown in the presence of a GSK3 inhibitor exhibited enhanced formation of cell contacts and decreased motility. In contrast, treatment with forskolin induced the PE formation and epithelial-mesenchymal transition (EMT) in rat XEN cells. Using microarray and real-time PCR assays, we found that VE versus PE formation of rat XEN cells was correlated with change in expression levels of VE or PE marker genes. Similar to forskolin, EMT was prompted upon treatment of rat XEN cells with recombinant parathyroid hormone related peptide (PTHRP), an activator of the cAMP pathway in vivo. Taken together, our data suggest that rat XEN cells are PrE-like cells. The activation of Wnt pathway in rat XEN cells leads to the acquisition of VE characteristics, whereas the activation of the PTHRP/cAMP pathway leads to EMT and the formation of PE. Rat XEN cells were cultured in four different conditions with 3 parallels for each condition: (1-3) without treatments control, (4-6) 2 days treated with CHIR alone, (7-9) 1 day treated with CHIR and 1 day with both CHIR and forskolin, and (10-12) 1 day treated with forskolin alone. In all samples on DAY1 cells were plated, at DAY2 cells were cultured in usual conditions (DMEM F12 medium and 10% Fetal Bovine Serum, both from Sigma) and inhibitor of GSK3 kinase 3 μM CHIR99021 (Axon Medchem) was added in samples 4-9. On DAY3 all cells were cultured in medium with 0.1% serum to exclude the influence of serum and in CONTROL (1-3) cells were cultured without experimental treatments, in CHIR (4-6) cells were further cultured with 3 μM CHIR99021, in CHIR plus FORSKOLIN cells were cultured with 3 μM CHIR99021 and 10μM Forskolin (Sigma), in FORSKOLIN cells were cultured for 1 day with 10 μM Forskolin. On DAY4 RNA was isolated.
2013-02-01 | E-GEOD-42438 | biostudies-arrayexpress
Project description:Rat ES cells were derived using 3I medium from E4.5 blastocysts. Rat embryonic fibroblast cells were derived form E14.5 embryos. To analyze the mechanism under the selfrenewal of rat ES cells, microarrays were used for the genome wide analysis of gene expressoin profiles in rat ES cells. Rat embryonic fibroblast cells and mouse ES cells were tested at same time as control. Our results from clustering analysis demonstrated that the gene expression profile of rat ES cells resembles mouse ES cells, but not REFs. Keyword: 3I medium; rat embryonic stem cells; mouse ES cells; rat embryonic fibroblast cells Rat ES cells were cultured in 3I medium; rat embryonic fibroblast cells were derived and cultured GMEM/10% FBS; mouse ES cells (C57/BL6)were cultured in GMEM/10% FBS added LIF and feeder cells were removed before RNA extraction. Three replicates each.
2010-05-15 | E-GEOD-13681 | biostudies-arrayexpress