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The cDNA probes for microarray construction were obtained from two different sources.
Clones picked for microarray construction were judged to be lowly or moderately expressed.
The 1578 cDNA clones used for microarray construction were a combination of two separate libraries, namely 810 cDNA library clones and 768 cDNA-AFLP cloned fragments.
All 117 patients with EAC used for the tissue microarray construction were treated with esophagectomy at Strong Memorial Hospital/ Universityof Rochester from 1997 to 2005.
Tissue samples for tissue microarray construction were selected if primary surgery was performed by a gynaecological oncologist from the UMCG between May 1985 and June 2006 and if paraffin-embedded tumour tissue was available.
All the 110 patients with esophageal adenocarcinoma used for the tissue microarray construction were treated with esophagectomy at University of Rochester Medical Center/Strong Memorial Hospital from 1997 to 2005 without pre-operation neoadjuvant therapy.
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Oligo microarray construction was performed by Agilent Technologies Inc.
Sampling for sequencing and tissue microarray construction was limited, and intratumoral heterogeneity was not addressed.
Microarray construction was similar to that described in Whitfield et al. (2002).
The method for tissue microarray construction was described in the Appendix (online only).
Reference DNA (0.5 μg from the mix used for microarray construction) was labeled with Cy3-dUTP.
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