Comment[ArrayExpressAccession]	E-GEOD-19913
MAGE-TAB Version	1.1								
Public Release Date	2013-09-23
Investigation Title	Syndecan-2 and apoptosis in osteosarcoma								
Comment[Submitted Name]	Syndecan-2 and apoptosis in osteosarcoma
Experiment Description	Syndecan-2 was found to act as a tumor suppressor in osteosarcoma and to mediate the apoptotic response to cytotoxic agents. To determine new mechanisms that control cell survival and apoptosis in osteosarcoma cells, we aim to show target genes that are involved downstream of this proteoglycan during apoptosis induction. We aim to compare the modifications induced by syndecan-2 overexpression in two different human osteosarcoma cell lines using a lentiviral vector coding the human syndecan-2. Syndecan-2 lentiviral vector (SY) and control empty lentiviral vector (VV) were transducted in two different human osteosarcoma cell lines in a dye-swap experiment.								
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl							
Person Last Name	Lebrigand	Modrowski	Barbry	Lebrigand	Mari	Fromigue			
Person First Name	Kevin	Dominique	Pascal	Kevin	Bernard	Oivia			
Person Email	mari@ipmc.cnrs.fr								
Person Affiliation	IPMC/CNRS								
Person Phone	0493957792								
Person Address	IPMC/CNRS, 660 route des lucioles, Valbonne - Sophia-Antipolis, France								
Person Roles	submitter								
Protocol Name	P-GSE19913-2	P-GSE19913-1	P-GSE19913-4	P-GSE19913-5	P-GSE19913-3	P-GSE19913-6			
Protocol Description	Interslide norm. : quantile, Intraslide norm. : printtiploess, Background norm. : Kooperberg, Software used : rscript --> VALUE data obtained from log of processed Red signal/processed Green signal. ID_REF =  VALUE = log2(635/532) per feature (processed signals used)	Interslide norm. : quantile, Intraslide norm. : printtiploess, Background norm. : Kooperberg, Software used : rscript --> VALUE data obtained from log of processed Red signal/processed Green signal. ID_REF =  VALUE = log2(532/635) per feature (processed signals used) INV_VALUE = log2(635/532) per feature (processed signals used)	Ambion protocol.	CGH-Agilent-4rpm : 750.0 ng at 62 degree_C during 17 hours	Total RNA was extracted using TRIZOL reagent (Invitrogen). Cells were lysed in TRIZOL reagent solution, chloroform was added and the homogenate was centrifugated. One volume of 70% ethanol was added to the aqueous phase and the RNA were further purified on a silica-based membrane (RNeasy kit, Qiagen).	Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.			
Protocol Type	normalization data transformation protocol	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid extraction protocol	array scanning protocol			
Experimental Factor Name	EXTRACT_CONCENTRATION	SUBJECT	CELL LINE	EXTRACT_AMOUNT	EXTRACT	TRANSDUCTION	LABEL	SAMPLE	VECTOR
Experimental Factor Type	extract_concentration	subject	cell line	extract_amount	extract	transduction	label	sample	vector
Publication Title	Calpain-6 is an endothelin-1 signaling dependent protective factor in chemoresistant osteosarcoma.								
Publication Author List	Marion A, Dieudonn� FX, Pati�o-Garcia A, Lecanda F, Marie PJ, Modrowski D								
PubMed ID	21681744								
Publication DOI	10.1002/ijc.26246								
Comment[SecondaryAccession]	GSE19913								
Comment[GEOReleaseDate]	2013-09-23								
Comment[ArrayExpressSubmissionDate]	2010-01-15								
Comment[GEOLastUpdateDate]	2013-09-24								
Comment[AEExperimentType]	transcription profiling by array								
SDRF File	E-GEOD-19913.sdrf.txt