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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression profiles of SOX17 overexpression in the KYSE170 luciferase cell

ABSTRACT: SOX17 is a transcriptional factor containing DNA-binding domain HMG box, we hypothesized that there are more genes other than in Wnt singnaling pathway to be transcriptionally regulated by SOX17 in esophageal squamous cell carcinoma. We performed the GeneChips expression array analyses to reveal more transcriptional target for SOX17. In this study, the esophageal cancer cell line, KYSE170-luc, were transfection with empty vector and expression plasmids of SOX17 for 12 hours. Total RNA were prepared for microarray assays.

ORGANISM(S): Homo sapiens

SUBMITTER: Yi-Ching Wang

PROVIDER: E-GEOD-35975 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Low SOX17 expression is a prognostic factor and drives transcriptional dysregulation and esophageal cancer progression.

Kuo I-Ying IY Wu Ching-Chi CC Chang Jia-Ming JM Huang Yu-Lin YL Lin Chien-Hsun CH Yan Jing-Jou JJ Sheu Bor-Shyang BS Lu Pei-Jung PJ Chang Wei-Lun WL Lai Wu-Wei WW Wang Yi-Ching YC

International journal of cancer 20140110 3

The transcriptional network of the SRY (sex determining region Y)-box 17 (SOX17) and the prognostic impact of SOX17 protein expression in human cancers remain largely unclear. In this study, we evaluated the prognostic effect of low SOX17 protein expression and its dysregulation of transcriptional network in esophageal squamous cell carcinoma (ESCC). Low SOX17 protein expression was found in 47.4% (73 of 154) of ESCC patients with predicted poor prognosis. Re-expression of SOX17 in ESCC cells ca ...[more]

PMID: 24407731

Similar Datasets

Gene expression profiles of SOX17 overexpression in the KYSE170 luciferase cell

Project description:SOX17 is a transcriptional factor containing DNA-binding domain HMG box, we hypothesized that there are more genes other than in Wnt singnaling pathway to be transcriptionally regulated by SOX17 in esophageal squamous cell carcinoma. We performed the GeneChips expression array analyses to reveal more transcriptional target for SOX17.

2014-02-12 | GSE35975 | GEO

Transcription factor SOX17 overexpression in hematopoietic stem cells

Project description:This SuperSeries is composed of the following subset Series: GSE30444: Retroviral Sox17 over-expression adult hematopoietic stem/progenitor cells microarray GSE30445: Sox17-transgenic hematopoietic stem cell microarray Refer to individual Series

2011-07-14 | E-GEOD-30446 | biostudies-arrayexpress

Gene Expression Analysis of Sox17-induced Mouse Embryonic Stem Cells

Project description:To determine the effect of Sox17 overexpression in mouse embryonic stem (ES) cells, we performed gain-of-function analysis by generating ES cell lines carrying a doxycycline inducible FLAG-tagged Sox17 transgene. We treated Sox17-inducible ES cells with doxycycline, collected RNA and performed genome-wide transcriptional analysis. We found that genes invovled in adhesion function and basement membrane establishment were transcriptionally upregulated in ES cells upon induction of Sox17. We also observed downregulation in the transcription of genes involved in pathways known to be functionally important for ES cell pluripotency and self-renewal. However, Sox17 expression was not sufficient to rapidly down-regulate Sox2, Nanog, and Oct4. Two independent doxycycline inducible Sox17-overexpressing mouse embryonic stem cells were derived. The genes expression changes in the Sox17-induced cells were compared to untreated (no doxycycline) controls and to control cells treated with or without doxycycline. The total RNA from these samples were amplified using Ambion Illumina TotalPrep RNA Amplification kit and arrayed on Illumina MouseRef8 v2 chips.

2010-03-31 | E-GEOD-19028 | biostudies-arrayexpress

Sox17-transgenic hematopoietic stem cell microarray

Project description:The transcription factor SOX17 is expressed by fetal, but not adult hematoipoietic stem cells (HSCs), and is required for the maintenance of fetal and neonatal, but not adult, HSCs. In the current study we show that ectopic expression of Sox17 in adult HSCs and transiently reconstituting multipotent progenitors was sufficient to confer increased self-renewal potential and the expression of fetal HSC genes including fetal HSC surface markers. To assess the acute effects of ectopic Sox17 expression on global gene expression in adult HSCs, we performed microarray analysis to compare the gene expression profile of adult Sox17-trangenic and control HSCs after short induction of Sox17-transgene expression. Total RNA were isolated from 5 independent, freshly isolated aliquots of 10,000 HSCs isolated from 8-week old Sox17-transgenic ((tetO)7CMVSox17-IRES-NucEGFP;B6.Cg-Gt(ROSA)26Sortm1(rtTA*M2)Jae/J double transgenic) or littermate control mice that were treated with doxycycline for 5 days to induce transgene expression. Purified RNA was reverse transcribed and amplified using the WT-Ovation™ Pico RNA Amplification system (NuGEN Technologies) following the manufacturer’s instructions. Sense strand cDNA was generated using WT-Ovation™ Exon Module (NuGEN), then fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN). 2.5µg of labeled cDNA were hybridized to Affymetrix Mouse Gene ST 1.0 microarrays.

2011-07-14 | E-GEOD-30445 | biostudies-arrayexpress

Gene expression data of Sox17-GFP(+) mouse definitive endoderm before and after expansion on mesenchyme.

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

Retroviral Sox17 over-expression adult hematopoietic stem/progenitor cells microarray

Project description:The transcription factor SOX17 is expressed by fetal, but not adult hematoipoietic stem cells (HSCs), and is required for the maintenance of fetal and neonatal, but not adult, HSCs. In the current study we show that ectopic expression of Sox17 in adult HSCs and transiently reconstituting multipotent progenitors was sufficient to confer increased self-renewal potential and the expression of fetal HSC genes including fetal HSC surface markers. To assess the mechanisms by which ectopic Sox17 expression in adult hematopoietic progenitors increased self-renewal potential and conferred fetal HSC properties, we compared the gene expression profiles of E16.5 fetal liver HSCs, young adult bone marrow HSCs, young adult bone marrow CD48+LSK cells, and Sox17-expressing CD48+LSK cells isolated from mice that had been transplanted with MSCV-Sox17-infected bone marrow cells 12 weeks earlier. Total RNA (~5ng) was isolated from 3 independent, freshly isolated aliquots of 10,000 E16.5 fetal liver HSCs, 10,000 fetal liver CD48+LSK cells, 10,000 adult bone marrow HSCs, 10,000 adult bone marrow CD48+LSK cells, 10,000 Sox17-expressing CD48+LSK cells isolated from primary recipients 12 weeks after transplantation of MSCV-Sox17-infected bone marrow cells. Purified RNA was reverse transcribed and amplified using the WT-Ovation™ Pico RNA Amplification system (NuGEN Technologies) following the manufacturer’s instructions. Sense strand cDNA was generated using WT-Ovation™ Exon Module (NuGEN), then fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN). 2.5µg of labeled cDNA were hybridized to Affymetrix Mouse Gene ST 1.0 microarrays.

2011-07-14 | E-GEOD-30444 | biostudies-arrayexpress

Transcriptional regulation of Sox17 in HUVEC

Project description:We identified Sox17 as a novel angiogenic transcription factor in the context of tumor. Our data revealed that Sox17 promotes tumor angiogenesis and tumor vessel abnormality. We found that Sox17 is specifically expressed in tumor endothelial cells within tumors. Our study elucidates a novel transcriptional regulation for tumor angiogenesis Control HUVECs vs. Sox17 knockdown HUVECs. Biological replicates: 3 control replicates, 3 transfected replicates.

2012-12-17 | E-GEOD-37395 | biostudies-arrayexpress

Expression data from livers in wildtype and Sox17+/-mice at 17dpc

Project description:The onset of the liver inflamentation in the Sox17+/- embryos. The expression of Cxcl10, Cxcl2, Cxcl1 and stress-induced heat shock protein Hspa1a and Hspa1b were elevated in Sox17+/- livers at 17dpc, as compared with the wildtype livers. Total RNAs from liver tissues of wildtype and Sox17+/- mice at 17dpc were subjected to microarray analyses. Two biological replicates of each genotype were analyzed.

2013-01-09 | E-GEOD-33106 | biostudies-arrayexpress

Temporal RNA-seq expression profiling of Sox17-medaited XEN conversion of ESCs

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

Transcription profiling by array of human embryonic stem cells over-expression SOX7 and SOX17

Project description:This study aimed to understand the transcriptional networks regulating endoderm specification from HESC and therefore explored the phenotype of CA1 and CA2 HESC constitutively over-expressing SOX7 or SOX17. Cell lines were created using an inducible construct whereby clonal populations containing transgene integration are selected by Neomycin resistance without expressing of the gene of interest (NoCre controls). Transgene expression is induced via Cre-mediated recombination and selected for puromycin resistance (SOX O/E). The phenotype of the resulting cells suggests that SOX7 expressing HESC represent stable extraembryonic endoderm progenitors, while SOX17 expressing HESC represent early definitive endoderm progenitors. Both in vitro and in vivo SOX7 expressing HESC are restricted to the extraembryonic endoderm lineage, while SOX17 expressing HESC demonstrate mesendodermal specificity. In vitro, SOX17 expressing HESC efficiently produce mature definitive endoderm derivatives. The molecular phenotype of the resulting SOX7 and SOX17 expressing HESC was characterized by microarray analysis Experiment Overall Design: Total RNA was extracted from confluent monolayer cultures of SOX7 over-expressing HESC, SOX17 over-expressing HESC, and their respective control parental HESC lines (designated NoCre Sox7 and NoCre Sox17).

2008-10-20 | E-GEOD-10809 | biostudies-arrayexpress

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