Agilent feature extraction software ver 10.7.3.1

Genomic DNAs from lung AC and normal ear samples were labeled with cyanine 3-UTP or cyanine 5-dUTP, respectively, and purified using a purification column (Agilent Technologies, Santa Clara, CA). Labeled DNAs were hybridized to microarray slides (SurePrint G3 Mouse CGH, 4 3 180K; Agilent Technologies) at 678C with rotation at 20 rpm for 24 h. Then, slides were washed with Wash Buffers 1 and 2 (Agilent Technologies) and scanned using the Agilent G2505C microarray scanner. Scanned images were processed using Agilent Feature Extraction software (ver. 10.7.3.1), and the data were analyzed using Agilent Genomic Workbench software 7.0.4.0. The microarray data were deposited in the Gene Expression Omnibus database (www. ncbi.nlm.nih.gov/geo) under accession number GSE174131.

Double-stranded DNA (50 ng) was fragmented and amplified using the GenomePlex Whole Genome Amplification kit (Sigma-Aldrich, St. Louis, MO, USA). The amplified DNAs from normal liver and mammary carcinoma samples were labelled with cyanine 3-and cyanine 5-dUTP, respectively, and was purified using a purification column (Agilent Technologies, Santa Clara, CA, USA). Labelled DNA was hybridized with probes of microarrays (SurePrint G3 Rat CGH, 4×180K; Agilent Technologies) at 67°C with rotation at 20 rpm for 24 hours, and was then washed with Wash Buffers 1 and 2 (Agilent Technologies). The resolution of microarrays was ~17.5 kb (as an average) with 155,049 probes. Microarray scanning was performed using the Agilent G2505C microarray scanner. Fluorescence intensity values were obtained from the scanned images with the Agilent Feature Extraction software (ver. 10.7.3.1) and were analysed using the Agilent Genomic Workbench software 7.0.4.0.
Statistical analysis. Statistical analysis was performed using the statistical software R with the aid of a graphical user interface EZR (Jichi Medical University, Saitama, Japan) (18) (link). Comparison among three groups was performed using the Kruskal-Wallis test. Comparison between two groups was performed using the Mann-Whitney's U-test. A p-value of <0.05 was considered statistically significant.