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Series GSE59234 Query DataSets for GSE59234
Status Public on Aug 15, 2014
Title Gene expression data from SOX2 knock-out 2102Ep and NTera-2 human embryonal carcinoma cell lines
Organism Homo sapiens
Experiment type Expression profiling by array
Summary 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.
 
Overall design 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.
 
Contributor(s) Vencken SF, Sethupathy P, Blackshields G, Spillane C, ElBaruni S, Sheils O, Gallagher MF, O’Leary JJ
Citation(s) 25156079
Submission date Jul 09, 2014
Last update date Jul 26, 2018
Contact name Sebastian Vencken
E-mail(s) venckens@tcd.ie
Organization name University College Dublin
Department Clinical Research Centre
Street address Catherine McAuley Centre, Nelson Street
City Dublin
ZIP/Postal code Dublin 7
Country Ireland
 
Platforms (1)
GPL6244 [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]
Samples (12)
GSM1431066 2102Ep cells negative control, biological replicate 1
GSM1431067 2102Ep cells negative control, biological replicate 2
GSM1431068 2102Ep cells negative control, biological replicate 3
This SubSeries is part of SuperSeries:
GSE59381 Differential gene and microRNA expression in two SOX2-silenced human embryonal carcinoma cell lines
Relations
BioProject PRJNA254789

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE59234_RAW.tar 52.7 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file
Processed data included within Sample table

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