Surgically isolated colorectal cancers were immediately frozen in liquid nitrogen. Tissues were lysed and total RNA was isolated using RNeasy Mini Kit (QIAGEN, Chatswort,CA) according to the manufacturer's instructions.
Label
biotin
Label protocol
Approximately 8 ug of total RNA was processed to produce biotinylated cRNA targets.
Hybridization protocol
standard Affymetrix procedures
Scan protocol
standard Affymetrix procedures
Description
Recurrence(+)
Data processing
Automated processing of image scans to absolute expression analysis was done using the Microarray Suite 5.0 software (Affymetrix, Santa Clara, CA). The software provided for each transcript "detection call," which predicted if the gene was present at levels detectable by the array. The call indicates that whether the transcript is detected (Present), undetected (Absent), or at the limit of detection (Marginal). These raw data including expression data and detection call data were loaded to GeneSpring™ software version 7.2 (Silicongenetics, Redwood, California). Gene expression data was normalized in two ways: "per chip normalization" and "per gene normalization". For "per chip normalization" all expression data on a chip is normalized to the 50th percentile of all values with detection call Present or Marginal on that chip. For "per gene normalization" the data for a given gene is normalized to the median expression level of that gene across all samples.
