Agilent whole human genome microarray 4 44 k g4112f

Total RNA from the paracancerous tissues was isolated with TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and purified using an RNeasy kit (Qiagen, Germantown, MD, USA). RNA was then quantified using an ND‐1000UV‐VIS Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA), and RNA integrity was determined using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). All RNA samples used in this study showed optical density 260/280 ratios >1.9 and RNA integrity >6. Paracancerous tissue samples were analyzed using an Agilent Whole Human Genome Microarray 4 × 44K (G4112F). All sample labeling, hybridization, washing, and scanning steps were carried out following the manufacturer's specifications. The slides were scanned with an Agilent Microarray Scanner System (G2505B), and the fluorescence intensities were extracted and preprocessed using Agilent Feature Extraction Software version 9.1. Data extraction and annotation were carried out using GeneSpring GX version 12.6.1 (Agilent). The raw data were normalized by the median scale method using the R package “limma” ( www.r-project.org). Screening probes represented the same gene, and only the probe showing the greatest mean intensity was retained. All raw microarray data and normalized data are publicly available on the GEO website (accession no. GSE101420).