High resolution microarray scanner model g2505c

An Agilent Technologies, High-Resolution Microarray Scanner (Model G2505C, Agilent Technologies, Santa Clara, CA, USA) was used to scan microarray images at 2 μm resolution. Data were extracted using Agilent Feature Extraction software, version 9.5.1 (Agilent Technologies). Internal control spots were analyzed to confirm that signal data was within the linear range of detection. GeneSpring version GX 11.0.2 (Agilent Technologies) was used to normalize data using quantile normalization followed by baseline transformation to the median of all samples. Statistical analysis was performed using GeneSpring where two-way ANOVA (p ≤ 0.05) with Benjamini-Hochberg multiple-testing correction and 1.5 fold-change cutoff was used to identify differentially expressed transcripts. Principal components analysis and hierarchical clustering analysis for transcripts with significant differential expression were conducted using GeneSpring and Multi-Experiment Viewer software version 4.9 [23 (link)], respectively.

An Agilent Technologies, High‐Resolution Microarray Scanner (Model G2505C, Agilent Technologies) was used to scan microarray images at 2‐μm resolution. Data were extracted from microarray images using agilent feature extraction software, version 9.5.1 (Agilent Technologies). Microarray data were normalized to the 75th percentile within each array followed by median scaling among all exposures using genespring Software version GX12.5 (Agilent Technologies). Methods for the statistical analysis of microarray data are provided in Section 2.8.