RNA-seq of XTE cells and vesicles, XEN and XEN-like cells, and ES cells
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB36734 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3895530.fastq.gz | Fastqsanger.gz | |||
| ERR3895540.fastq.gz | Fastqsanger.gz | |||
| ERR3895531.fastq.gz | Fastqsanger.gz | |||
| ERR3895541.fastq.gz | Fastqsanger.gz | |||
| ERR3895532.fastq.gz | Fastqsanger.gz |
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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: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.
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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.
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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.
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Project description:Comparative gene expression profiling of mouse pXEN, XEN, ES, and rat XENP cells
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Project description:The transcription factor Sox17 is expressed in early primitive endoderm-fated cells of the mouse embryo and in embryo-derived extraembryonic endoderm (ExEn) stem (XEN) cells. We have shown that overexpression of Sox17 in mouse embryonic stem cells (ESCs) drives cell fate to a committed XEN-like cell state (Sox17-XEN cells). When placed back into the embryo, Sox17-XEN cells contribute exclusively to the ExEn. Transient Sox17 expression is sufficient to drive this fate change during which time cells transit through distinct intermediate states prior to the generation of functional XEN-like cells. We identified dynamic regulatory networks driving Sox17-mediated XEN conversion by analyzing a dynamic regulatory map of gene expression bifurcation points throughout conversion, created using RNA-seq time series data. We found that Sox17 orchestrates this conversion process by acting in autoregulatory and feed-forward network motifs, regulating dynamic gene regulatory networks (GRNs) directing cell fate. We have shown that Sox17-mediated XEN conversion provides a powerful tool for understanding the regulation of cell fate changes and for the elucidation of GRNs regulating lineage decisions in the mouse embryo. Total RNA was extracted during a time course of Sox17 overexpression in mouse ESCs at 7 time points as well as from wild-type ESCs and wild-type XEN cells.
2014-09-05 | E-GEOD-61102 | biostudies-arrayexpress
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.
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Project description:The transcription factor Sox17 is expressed in early primitive endoderm-fated cells of the mouse embryo and in embryo-derived extraembryonic endoderm (ExEn) stem (XEN) cells. We have shown that overexpression of Sox17 in mouse embryonic stem cells (ESCs) drives cell fate to a committed XEN-like cell state (Sox17-XEN cells). When placed back into the embryo, Sox17-XEN cells contribute exclusively to the ExEn. Transient Sox17 expression is sufficient to drive this fate change during which time cells transit through distinct intermediate states prior to the generation of functional XEN-like cells. We identified dynamic regulatory networks driving Sox17-mediated XEN conversion by analyzing a dynamic regulatory map of gene expression bifurcation points throughout conversion, created using RNA-seq time series data. We found that Sox17 orchestrates this conversion process by acting in autoregulatory and feed-forward network motifs, regulating dynamic gene regulatory networks (GRNs) directing cell fate. We have shown that Sox17-mediated XEN conversion provides a powerful tool for understanding the regulation of cell fate changes and for the elucidation of GRNs regulating lineage decisions in the mouse embryo.
2014-09-05 | GSE61102 | GEO
Project description:XEN cells are derived from the primitive endoderm of mouse blastocysts. In culture and in chimeras they exhibit properties of parietal endoderm. However, BMP signaling promotes XEN cells to form an epithelium and differentiate into visceral endoderm (VE). Of the several different subtypes of VE described, BMP induces a subtype that is most similar to the VE adjacent to the trophoblast-derived extraembryonic ectoderm. The experiment was performed to gain insight into genes regulated by BMP and activin in XEN cells, and also to more precisely define the VE subtypes formed in culture. IM8A1 XEN cells were treated for 6 days with BMP2 (20 ng/ml, R&D Systems), activin A (30 ng/ml, Peprotech), both, or neither in GMEM + 10% fetal bovine serum.
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