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E-GEOD-25011 - Study for evaluating the effect of cold ischemic time and RNA stabilization method on RNA integrity and gene expression measurements

Status
Released on 2 November 2011, last updated on 5 December 2011
Organism
Homo sapiens
Samples (86)
Array (1)
Protocols (7)
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.
Experiment type
transcription profiling by array 
Contacts
Christos Hatzis, Hongxia Sun, W F Symmans
Citation
Effects of Tissue Handling on RNA Integrity and Microarray Measurements From Resected Breast Cancers. Hatzis C, Sun H, Yao H, Hubbard RE, Meric-Bernstam F, Babiera GV, Wu Y, Pusztai L, Symmans WF. , PMID:22034635
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-25011.idf.txt
Sample and data relationshipE-GEOD-25011.sdrf.txt
Raw data (1)E-GEOD-25011.raw.1.zip
Processed data (1)E-GEOD-25011.processed.1.zip
Array designA-AFFY-33.adf.txt
R ExpressionSetE-GEOD-25011.eSet.r
Links