Investigation Title	Transcription profiling of human radioresistant and radiosensitive tumors and cell lines	
Comment[Submitted Name]	Radioresistant and radiosensitive tumors and cell lines	
Experimental Design	unknown_experiment_design_type	transcription profiling by array	
Experimental Design Term Source REF		EFO	
Comment[AEMIAMESCORE]	4	
Comment[ArrayExpressReleaseDate]	2008-06-16	
Comment[SecondaryAccession]	GSE9716	
Comment[ArrayExpressAccession]	E-GEOD-9716	
Comment[MAGETAB TimeStamp_Version]	2010-08-09 16:11:16 Last Changed Rev: 13058	
Experimental Factor Name	
Experimental Factor Type	
Experimental Factor Term Source REF	
Person Last Name	Khodarev	
Person First Name	Nikolai	
Person Mid Initials	N.	
Person Email	nikolai@rover.uchicago.edu	
Person Phone	
Person Fax	
Person Address	Radiation and Cellular Oncology, The University of Chicago, 5841 South Maryland Avenue, Chicago, 60637, USA	
Person Affiliation	The University of Chicago	
Person Roles	submitter	
Person Roles Term Source REF	The MGED Ontology	
Quality Control Type	
Quality Control Term Source REF	
Replicate Type	
Replicate Term Source REF	
Normalization Type	
Normalization Term Source REF	
Date of Experiment	
Public Release Date	2008-06-16	
PubMed ID	14755057	
Publication DOI	14755057	
Publication Author List	Nikolai N Khodarev, Michael Beckett, Edwardine Labay, Thomas Darga, Bernard Roizman, Ralph R Weichselbaum	
Publication Title	STAT1 is overexpressed in tumors selected for radioresistance and confers protection from radiation in transduced sensitive cells.	
Publication Status	journal_article	
Publication Status Term Source REF	The MGED Ontology	
Experiment Description	This SuperSeries is composed of the following subset Series:; GSE9712: Detection of genes differentially expressed in radioresistant tumors; GSE9713: Detection of genes differentially expressed in radioresistant and radiosensitive tumors before and after irradiation; GSE9714: Interferon response of radioresistant and radiosensitive human head&neck tumor cell lines Experiment Overall Design: Refer to individual Series	
Protocol Name	P-G9716-1	P-G9716-6	P-G9716-5	P-G9716-2	P-G9716-7	P-G9716-4	P-G9716-3	Affymetrix:Protocol:Hybridization-Unknown	Affymetrix:Protocol:Hybridization-EukGE-WS2v4	P-AFFY-6	
Protocol Type	grow	grow	grow	specified_biomaterial_action	specified_biomaterial_action	nucleic_acid_extraction	labeling	hybridization	hybridization	feature_extraction	
Protocol Description	SCC-61 and nu61 xenografts were generated and allowed to grow to a volume of 150-200 mm3. At that time,tumors were either irradiated at 3Gy or left un-treated and 5 hours later they were collected for RNA purification	nu61 and SCC61 cell lines were maintained in DMEM/F12 (GIBCO, Carlsbad, CA), supplemented with 20% FBS, 1% hydrocortisone and !% penicillin/streptomicin at 37C, 100% humidity and 5% CO2.IFNs alpha, beta and gamma were from R&D Systems, Minneapolis, MN)	SCC-61 and nu61 xenografts were generated and allowed to grow to a volume of 150-200 mm3. At that time,tumors were either irradiated at 3Gy or left un-treated and 5 or 24 hours later they were collected for RNA purification	Tumors were excised, frozen in liquid nitrogen and stored at -80C	cell lines were grown to confluence: cells were transferred in 6-well plates with density 10^6/well and left overnight. Next morning, mixture of IFNa, IFNb and IFNg were added in concentrations of 100, 100 and 5 ng/ml respectively and cells were incubated 5 hours. After this, medium was decanted and cells were processed for RNA extraction.	Trizol extraction of total RNA was performed according to the manufacturer's instructions.	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).	Title: Affymetrix Generic Hybridization. Description: 	Title: Fluidics Station Protocol. Description: 	Title: Affymetrix CEL analysis. Description: 	
Protocol Parameters	
Protocol Hardware	
Protocol Software								MicroArraySuite 5.0	MicroArraySuite 5.0	MicroArraySuite 5.0	
Protocol Contact	
Protocol Term Source REF								mo	
SDRF File	E-GEOD-9716.sdrf.txt	
Term Source Name	mo		The MGED Ontology	ArrayExpress	EFO	The MGED Ontology	mo	
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php		http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/arrayexpress	http://www.ebi.ac.uk/efo/	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://mged.sourceforge.net/ontologies/MGEDontology.php	
Term Source Version