Gata6 induced XEN-like cells w/o Sox7
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE66971 | GEO | 2015/09/14
SECONDARY ACCESSION(S): PRJNA278525
REPOSITORIES: GEO
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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: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
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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:Stem cells self-renew or differentiate under the governance of a stem cell-specific transcriptional program with each transcription factor orchestrating the activities of a particular set of genes. Here we demonstrate that a single transcription factor is able to regulate distinct core circuitries in two different blastocyst-derived stem cell lines, embryonic stem (ES) and extra-embryonic endoderm (XEN) cells. The transcription factor, Sall4, is required for early embryonic development and for ES cell pluripotency. Sall4 is also expressed in XEN cells and depletion of Sall4 disrupts self-renewal and induces differentiation. Genome-wide analysis reveals Sall4 is regulating different gene sets in ES and XEN cells, and depletion of Sall4 targets in the respective cell types induces differentiation. With Oct4, Sox2 and Nanog, Sall4 forms a crucial interconnected auto-regulatory network in ES cells. In XEN cells, Sall4 regulates key XEN lineageassociated genes, Gata4, Gata6, Sox7 and Sox17. Our findings demonstrate how Sall4 functions as an essential stemness factor for two different stem cell lines. Keywords: ES/XEN comparison, ES Sall4 KD/control KD comparison, and XEN Sall4 KD/control KD comparison
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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:We investigated SOX7 binding events on the chromatin under basal conditions in human umbilical vein endothelial cells, upon overexpression of human SOX7-mCherry and immunoprecipitating mCherry. Cells overexpressing only the mCherry tag were used as negative control condition, and peaks called here were substracted from the SOX7-mCherry peaks.
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Project description:Specification of the mesodermal lineages requires a complex set of morphogenetic events orchestrated by interconnected signaling pathways and gene regulatory networks. The transcription factor Sox7 has critical functions in differentiation of multiple mesodermal lineages, including cardiac, endothelial, and hematopoietic. Using a doxycycline-inducible mouse embryonic stem cell (mESC) line, we have previously shown that expression of Sox7 in cardiovascular progenitor cells promotes expansion of endothelial progenitor cells. Here, we show that the ability of Sox7 to promote endothelial cell fate occurs at the expense of the cardiac lineage. Using ChIP-Seq coupled with ATAC-Seq we identify downstream target genes of Sox7 in cardiovascular progenitor cells and, by integrating these data with transcriptomic analyses, we define Sox7-dependent gene programs specific to cardiac and endothelial progenitor cells. Further, we demonstrate a protein-protein interaction between SOX7 and GATA4 and provide evidence that Sox7 interferes with the transcriptional activity of Gata4 on cardiac genes. In addition, we show Sox7 modulates WNT and BMP signaling during cardiovascular differentiation. Our data represent the first genome-wide analysis of Sox7 function and reveal a critical role for Sox7 in regulating signaling pathways that affect cardiovascular progenitor cell differentiation.
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Project description:As a transcription factor, SOX7 suppresses cancer development. However, only a few genes were demonstrated as SOX7-activated targets in cancer-irrelevant contexts. We used microarray chips to determine SOX7 target genes in breast cancer cells and discovered multiple signaling pathways altered by ectopic SOX7. We also investigated several genes for their roles in SOX7-mediated tumor suppression. Our study innovatively revealed SOX7 target gene profile in a cancer-relevant context and identified several SOX7-repressed target genes.
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Project description:Vascular development involves complex changes in gene expression necessary to dictate the behaviour of differentiating endothelial cells within the emerging vascular network. However, the transcriptional programs regulating vascular development are poorly understood. Here we use a DamID approach to profile for the first time the global DNA binding pattern of SOX7, FLI1 and ERG in endothelial precursor cells. We uncover that SOX7, FLI1 and ERG bind together at endothelial specific regulatory regions to drive a transcriptional program important for vascular development.
2017-11-25 | GSE63645 | GEO
Project description:Transcription factor-mediated reprogramming is a powerful method to study cell fate changes. In this work, we demonstrate that the transcription factor Gata6 can initiate reprograming of multiple cell types to induced extraembryonic endoderm (iXEN) cells. Intriguingly, Gata6 is sufficient to drive iXEN cells from mouse pluripotent cells and differentiated neural cells. Furthermore, GATA6 induction in human ES (hES) cells also downregulates pluripotency gene expression and upregulates extraembryonic endoderm genes, revealing a conserved function in mediating this cell fate switch. Profiling transcriptional changes following Gata6 induction in mES cells reveals step-wise pluripotency factor disengagement, with initial repression of Nanog and Esrrb, then Sox2 and finally Oct4, alongside step-wise activation of extraembryonic endoderm genes. Chromatin immunoprecipitation and subsequent high-throughput sequencing analysis shows Gata6 enrichment near both pluripotency and endoderm genes, suggesting that Gata6 functions as both a direct repressor and activator. Together this demonstrates that Gata6 is a versatile and potent reprogramming factor that can act alone to drive a cell fate switch from diverse cell types. (1) Microarray analysis of Gata6 overexpressing cells from 12 to 144 hours of doxycycline treatment in mouse embryonic stem (mES) cells compared to uninduced mES cells, embryo-derived XEN cells and Sox7 overexpressing mES cells after 144 hours of doxycycline treatment. (2) ChIP-seq analysis of Gata6 binding 36 hours following doxycycline treatment. (3) ChIP-seq analysis of Gata6 binding in embryo-derived XEN cells. (4) RNA-seq analysis of GATA6 overexpressing cells following 144 hours of induction in hES cells.
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