normalization data transformation protocol
Data were log2-transformed.
nucleic acid hybridization to array protocol
The resuspended cRNA sampels was dispensed onto BeadChips, and then incubated in the Illumina Hybridization oven to hybridize the samples onto the BeadChips.
nucleic acid labeling protocol
The Illumina TotalPrep RNA amplification Kit (Ambion Inc. USA) was used to amplify RNA for hybridization on Illumina BeadChips. To synthesize first strand cDNA by reverse transcription. we used total RNA from each sample collected above. Following the second strand cDNA synthesis and cDNA purification steps. the in vitro transcription to synthesize cRNA was prepared overnight for 12 hours.
No specific treatment. The samples concist of paired cancer and non-cancerous gastric tissue, obtained immediately following surgical resection of the tumor.
nucleic acid extraction protocol
Total RNA was isolated using RNeasy Mini (Qiagen GmBH, Germany) according to the manufacturers protocol.
2 biopsies from each of 20 patients diagnosed with gastric adenocarcinoma, including 1 from the tumor and 1 from normal mucosa. Within 5 minutes of removal of the principal surgical specimen, samples were taken from the tumor border and from healthy gastric corpal mucosa and stored on RNAlater (Applied Biosystems, United States). All samples were stored in +4C for approximately 1-2 weeks to allow complete tissue penetration of RNAlater, before samples were dried and permanently stored in -80C.