Gene expression data of Sox17-GFP(+) mouse definitive endoderm before and after expansion on mesenchyme.
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE25337 | GEO | 2011/01/12
SECONDARY ACCESSION(S): PRJNA134867
REPOSITORIES: GEO
Similar Datasets
Project description:Mouse embryonic stem cells containing a Sox17-GFP construct were differentiated using growth factors (Activin A and Wnt3A) to definitive endoderm. Sox17-GFP(+) cells were sorted using fluorescence activated cell sorting and either used for total RNA harvest OR continued in culture in the presence of primary pancreatic mesenchymal cell lines. At the end of 6 serial passages on mesenchyme, the Sox17-GFP(+) cells were again sorted and the RNA was harvested for arrays. Samples were prepared as described in summary, with technical duplicates for each of the following 3 categories: 1. Unpassaged (P0) endoderm, 2. Endoderm passaged 6 times (P6) on mesenchyme 1, and 3. Endoderm passaged 6 times (P6) on mesenchyme 2.
2011-01-12 | E-GEOD-25337 | biostudies-arrayexpress
Project description:Using homologous recombination in human ESC, we inserted an enhanced green fluorescent protein (eGFP) transgene into a locus encoding a postulated marker of human endoderm, SOX17 in H9 human embryonic stem cells. This allowed purification of SOX17+ hESC endodermal progeny by fluorescence activated cell sorting (FACS) to generate microarray gene expression profile.
2011-03-15 | GSE26862 | GEO
Project description:This experiment has been done to understand the dynamics of gene expression in Sox17.Epi and Endo cells using multiplex RNA-Seq technology. Sox17.Epi (Sox17^GFP+EpCAM+) and Sox17.Endo (Sox17^GFP+EpCAM-) cells were isolated by FACS from E9.5 mouse embryos. The spatial comparison between Sox17.Epi versus Sox17.Endo provides insight into which genes are differentially of specifically expressed in two populations.
2012-07-20 | E-MTAB-970 | biostudies-arrayexpress
Project description:Using homologous recombination in human ESC, we inserted an enhanced green fluorescent protein (eGFP) transgene into a locus encoding a postulated marker of human endoderm, SOX17 in H9 human embryonic stem cells. This allowed purification of SOX17+ hESC endodermal progeny by fluorescence activated cell sorting (FACS) to generate microarray gene expression profile. Using Wnt3 and Activin to differentiate hSOX17-2 to stage 1 cells, and subsequently FGF10 and cyclopamine to stage 2 cells, we isolated eGFP+ cells by FACS at each stage, performed microarray analysis.
2011-03-15 | E-GEOD-26862 | biostudies-arrayexpress
Project description:The segregation of definitive endoderm (DE) from bi-potent mesendoderm progenitors leads to the formation of two distinct germ layers. Dissecting DE commitment and onset has been challenging as it occurs within a narrow spatio-temporal window in the embryo. Here we employ a novel dual Bra/Sox17 reporter cell line to study DE onset dynamics. We find Sox17 expression initiates in a few isolated cells in vivo within a temporally restricted window. Using 2D and 3D in vitro models, we show that DE cells emerge from mesendoderm progenitors at a temporally regular, but spatially stochastic pattern, which is subsequently arranged by self-sorting of Sox17+ cells. A subpopulation of Bra-high cells commits to a Sox17+ fate independent of external Wnt signal. Self-sorting coincides with up-regulation of E-cadherin but is not necessary for DE differentiation or proliferation. Our in vivo and in vitro results highlight basic rules governing DE onset and patterning through the commonalities and differences between these systems.
2021-12-13 | GSE189224 | GEO
Project description:We investigated whether Sox17 directly or indirectly regulates extraembryonic endoderm gene expression by identifying Sox17 DNA-binding sites using chromatin-immunoprecipitation coupled with whole-genome promoter tiling array analysis (ChIP-Chip). We used the Sox17 and FLAG antibody to ask whether Sox17 was binding directly to the regulatory regions of genes in homogeneous extraembryonic endoderm (XEN) cell lines and in Sox17-inducible mouse embryonic stem (ES) cells. In XEN cells, Sox17 binding sites were located within the promoters or the introns of 2206 (3%) genes. We performed an ontology analysis for the genes with Sox17 binding sites and found that a significant number had adhesion functions in basement membrane establishment and maintenance. In addition to these ECM genes, Sox17 was also bound to promoter regions of a variety of other genes implicated in extraembryonic endoderm development including key transcription factors. Ontology analysis of all the Sox17 ChIP-chip binding targets identified in Sox17-induced ES cells, demonstrated a significant enrichment near genes involved in the cell cycle as well as genes involved in signaling pathways that function in embryonic stem cell maintenance. Sox17 was also observed to directly bind to the regulatory regions of many genes in pathways known to be functionally important for ES cell pluripotency and self-renewal. These studies suggest that one of Sox17’s functions in the differentiation of ICM and ES cells is to bind the regulatory regions of many genes that encode basement membrane components, thus leading to their activation. In addition to directly activating genes required for primitive endoderm differentiation, Sox17 may also function to activate and reinforce the transcriptional network governing differentiation.
2010-03-31 | GSE19026 | GEO
Project description:As Sox17 plays a critical role in the development of multiple cell types during early embryogenesis, we utilized a dual-color lineage-tracing strategy in combination with single-cell RNA sequencing (scRNAseq) to capture and analyze Sox17-expressing lineages. GFP production from Sox17GFPCre allele marks cells that currently express Sox17 or short-term progeny of Sox17 expressing progenitors. TdTomato production from R26LSL.TdTomato reporter allele in the presence of Sox17GFPCre marks long-term progeny of Sox17-expressing progenitors. In brief, GFP and Tdtomato positive cells were isolated from E9.5 embryos of specific genotypes to generate two separate scRNAseq datasets, referred to in the manuscript as the GFP and TdTomato datasets, respectively.
2023-07-20 | E-MTAB-12719 | biostudies-arrayexpress
Project description:To explore the molecular basis of functional differences observed between Nodal versus Activin-derived endoderm, we compared their respective gene expression profiles. Sox17-GFP mouse ES cells were differentiated in the presence of Nodal or Activin for 7 days, after which GFP(+) cells were purified by FACs. Undifferentiated ES cells were also included for comparison as a control. Results indicate that the two endoderm populations are nearly identical at the level of global transcription. Subtle differences suggest a difference in the degree of endoderm progression. Total RNA obtained from SOX17-GFP (+) mouse ES cells, Sox17-GFP treated with Nodal, Sox17-GFP treated with Activin. Two replicates for each sample; Sample data table contains average values of two replicates. The non_normalized.txt file contains individual signal values for each replicate.
2013-01-01 | E-GEOD-41086 | biostudies-arrayexpress
Project description:Background and aims: Cholangiocarcinoma (CCA) is a heterogeneous group of malignancies with features of biliary tract differentiation. Incidence is increasing worldwide and these cancers collectively represent the second most common primary liver tumour. CCAs are characterized by genetic and epigenetic alterations that determine their pathogenesis. Hypermethylation of the SOX17 promoter was recently reported in human CCA tumours. SOX17 seems to be a key transcription factor for biliary embryogenesis. Here, we evaluated the role of SOX17 in cholangiocyte differentiation and in cholangiocarcinogenesis. Methods: SOX17 expression and function was evaluated during the differentiation of human induced pluripotent stem cells (iPSC) into cholangiocytes, in the dedifferentiation of normal human cholangiocytes (NHC) and in cholangiocarcinogenesis. Lentiviruses overexpressing or knocking-down SOX17 (Lent-SOX17 and Lent-shRNA-SOX17, respectively) were used. Gene expression arrays were performed. Results: SOX17 expression is highly induced in the later stages of cholangiocyte differentiation from iPSC, and mediates the acquisition of the biliary markers cytokeratin (CK) 7 and 19, as well as fibronectin. In addition, SOX17 becomes progressively downregulated in NHC over serial cell passages in vitro and this event is associated with cellular senescence; however, experimental SOX17 knocking-down in differentiated NHC decreased the expression of both CK7 and 19 without affecting cellular senescence. SOX17 expression is reduced in CCA cells compared to NHC, as well as in human CCA tissue compared to human gallbladder tissue or NHC. In a murine xenograft model, overexpression of SOX17 in CCA cells decreased their tumorigenic capacity related to increased oxidative stress and apoptosis. Interestingly, overexpression of SOX17 in NHC did not affect their survival. Moreover, SOX17 overexpression inhibited the Wnt/β-catenin-dependent proliferation in CCA cells and was associated with upregulation of biliary epithelial markers and restoration of the primary cilium length. Both Wnt3a and TGFβ1 decreased SOX17 expression in NHC in a DNMT1-dependent manner. Inhibition of DNMT1 in CCA cells with siRNAs or pharmacological drugs upregulated SOX17 expression. Conclusion: SOX17 regulates the cholangiocyte phenotype and becomes epigenetically downregulated in CCA. SOX17 acts as a tumour suppressor in CCA, and restoration of its expression may have important therapeutic value.
2017-08-31 | GSE77984 | GEO
Project description:Generation of hepatocyte from embryonic stem cells (ESCs) holds great promise for hepatocyte replacement therapy to treat liver diseases. Achieving high efficiency of directed differentiation of ESCs to hepatocyte is of critical importance. Previously, Wnt3a has been reported to promote Activin A-induced human definitive endoderm (DE) differentiation, the early stage of hepatocyte differentiation. However, the underlying molecular mechanisms are not clear. Growing evidence demonstrated that microRNAs (miRNAs) are key regulators involved in various important biological processes including the regulation of stem cell differentiation. In the present study, we profiled genome wide miRNA expression during Wnt3a and Activin A induced mouse DE differentiation. We uncovered distinct miRNA expression patterns during DE differentiation with the identification of a subset of miRNAs whose expression is synergistically regulated by Wnt3a/Activin A treatment at different stages of DE differentiation. Forced expression of a pool of such synergistically regulated miRNAs alone could partially promote DE differentiation, indicating a regulatory role of them. Using TargetScan and GeneGO pathway analyses, the synergistically regulated miRNAs are predicted to regulate key pathways involved in DE differentiation; among them includes the regulation of histone acetylation. Consistently, Wnt3a and Activin A treatment increased global histone acetylation which can be partially mimicked by over expression of the pooled miRNAs. Chromatin IP (ChIP) experiments demonstrated that the promoter regions of Sox17 and Foxa2 are subjected to histone acetylation regulation. Administration of Hdac inhibitors greatly augmented DE differentiation. Our data uncovered a novel epigenetic mechanism of Wnt3a and Activin A induced DE differentiation, whereby the treatment of growth factors induced histone acetylation at least in part by the regulation of miRNA expression.
| S-EPMC3223193 | biostudies-literature