Comment[ArrayExpressAccession]	E-GEOD-25011
Public Release Date	2011-11-02							
Investigation Title	Study for evaluating the effect of cold ischemic time and RNA stabilization method on RNA integrity and gene expression measurements							
Comment[Submitted Name]	Study for evaluating the effect of cold ischemic time and RNA stabilization method on RNA integrity and gene expression measurements
Experiment Description	Time series of eleven breast cancer samples subjected to different cold ischemic stress of up to 3 hr post tumor excision. A different 2x2 factorial within this study evaluated the effect of stabilization method (RNAlater vs snap freezing) and stablization delay (0 and 40 min) at room temperature. Tissue samples were collected at surgery, cut into 1-2 mm pieces and divided into 8 portions.  Portions were put in RNAlater or fresh frozen at baseline, 20, 40, 60, 120, and 180 minutes thereafter, or snap frozen in dry ice in a pre-chilled sample vial at baseline and 40 minutes thereafter.							
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Term Source Name	EFO
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Term Source File	http://www.ebi.ac.uk/efo/efo.owl							
Person Last Name	Hatzis	Symmans	Sun	Hatzis				
Person First Name	Christos	W	Hongxia	Christos				
Person Mid Initials		F						
Person Email	christos@nuverabio.com							
Person Affiliation	Nuvera Biosciences							
Person Phone	781-938-3830							
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Person Address	Nuvera Biosciences, 400 West Cummings Park, Suite 5350, Woburn, MA, USA							
Person Roles	submitter							
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Protocol Name	P-GSE25011-1	P-GSE25011-6	P-GSE25011-5	P-GSE25011-2	P-GSE25011-3	P-GSE25011-4	P-GSE25011-7	
Protocol Description	ID_REF = <br>VALUE = MAS5.0 signal intensity for each array was log2 transformed and scaled to a reference distribution of 1322 breast cancer specific genes.	GeneChips were scanned using the diagnostic-grade Affymetrix scanner 3000DX	Following fragmentation, 10 ug of cRNA were hybridized overnight at 46C on Affymetrix U133A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.	Fresh tissue surgical excision specimens from breast cancer collected at time of surgery.  The tissue was then cut into pieces of 1-2 mm in a petri dish using a sterile blade, mixed, and divided into 8 equal portions.  A portion was placed into 1.5 ml RNAlater RNA stabilization reagent (Ambion, Inc., Austin TX) at baseline and 20, 40, 60, 120, and 180 minutes thereafter, or snap frozen in dry ice in a pre-chilled sample vial at baseline and 40 minutes thereafter. The time that each tissue portion was placed into contact with RNAlater solution or in the pre-chilled vial was recorded. Samples were stored at -70°C until RNA extraction.	Total RNA was extracted from tissue using Qiagen Rneasy columns	A single-round T7 amplification was used to generate biotin-labeled cRNA for hybridization.  At least 1 ug of RNA is required for cRNA synthesis.	Probe intensities were quantified with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.  CEL files were normalized using global scaling with a trimmed mean target intensity of each array arbitrarily set to 600 using the MAS5 algorithm from the simpleaffy package (http://bioconductor.org/packages/2.4/bioc/html/simpleaffy.html).	
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Protocol Type	bioassay_data_transformation	image_aquisition	hybridization	specified_biomaterial_action	nucleic_acid_extraction	labeling	feature_extraction	
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Experimental Factor Name	EXTRA_COLD_ISCHEMIC_TIME_MIN	PATIENT ID	RNA_CONCENTRATION_NGPUL	TRUE_COLD_ISCHEMIC_TIME_MIN	RNA_INTEGRITY_NUMBER (AS REPORTED BY THE AGILLENT BIOANALYZER)	PASSEDQC	STABILIZATION	RNA_260_280
Experimental Factor Type	extra_cold_ischemic_time_min	patient id	rna_concentration_ngpul	true_cold_ischemic_time_min	rna_integrity_number (as reported by the agillent bioanalyzer)	passedqc	stabilization	rna_260_280
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Publication Title	Effects of Tissue Handling on RNA Integrity and Microarray Measurements From Resected Breast Cancers.							
Publication Author List	Hatzis C, Sun H, Yao H, Hubbard RE, Meric-Bernstam F, Babiera GV, Wu Y, Pusztai L, Symmans WF							
PubMed ID	22034635							
Publication DOI	10.1093/jnci/djr438							
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Comment[SecondaryAccession]	GSE25011							
Comment[GEOLastUpdateDate]	2011-11-02
Comment[AEExperimentType]	transcription profiling by array							
Comment[GEOReleaseDate]	2011-11-02
Comment[ArrayExpressSubmissionDate]	2010-10-28
SDRF File	E-GEOD-25011.sdrf.txt