Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression data from SOX2 knock-out 2102Ep and NTera-2 human embryonal carcinoma cell lines

ABSTRACT: SOX2 is an oncogene and a core pluripotency transcription factor. SOX2 has multiple roles in various malignancies, in the maintainance of pluripotency and during various stages of embryonic development. Human embryonal carcinoma cells express SOX2 and the loss of this results in their differentiation. We silenced SOX2 in two human embryonal carcinoma cell lines and measured whole-genome mRNA expression. Many genes related to embryogenesis and tissue morphogensis were upregulated. Other upregulated genes were markers of mesodermal development and epithelial-to-mesenchymal transition. A specific and validated siRNA against SOX2 was chemically transfected in undifferentiated 2102Ep and NTera-2 embryonal carcinoma cell lines. After three days of incubation under normal growth conditions we used Affymetrix microarrays to measure whole-genome mRNA transcript expression in three biological replicates of each cell line and compared this to whole-gene expression in identical samples transfected with a non-targeting, scrambled control siRNA. SOX2 silencing was validated using qRT-PCR and Western blot prior to whole-genome expression analysis.

ORGANISM(S): Homo sapiens

SUBMITTER: Sebastian Vencken 

PROVIDER: E-GEOD-59234 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

An integrated analysis of the SOX2 microRNA response program in human pluripotent and nullipotent stem cell lines.

Vencken Sebastian F SF   Sethupathy Praveen P   Blackshields Gordon G   Spillane Cathy C   Elbaruni Salah S   Sheils Orla O   Gallagher Michael F MF   O'Leary John J JJ  

BMC genomics 20140825

<h4>Background</h4>SOX2 is a core component of the transcriptional network responsible for maintaining embryonal carcinoma cells (ECCs) in a pluripotent, undifferentiated state of self-renewal. As such, SOX2 is an oncogenic transcription factor and crucial cancer stem cell (CSC) biomarker in embryonal carcinoma and, as more recently found, in the stem-like cancer cell component of many other malignancies. SOX2 is furthermore a crucial factor in the maintenance of adult stem cell phenotypes and h  ...[more]

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