Agilent human v2 ge 4x44k arrays

After treatment with or without 4 μg/ml doxycycline and then cotreatment with or without 5 mM sodium butyrate (NaB) for 17.5 hr, cells were washed with 1 × PBS, scraped into PBS and pelleted; the pellets were snap frozen in liquid nitrogen and sent to Genus Biosystems (Northbrook, IL) for RNA extraction and microarray analyses, utilizing the Agilent human whole genome oligo microarray. Briefly, RNA extraction and array analyses were performed by Genus as follows. RNA was extracted and purified with Ambion Ribopure isolation, with RNA quality assessed by an Agilent Bioanalyzer. Following first and second strand cDNA synthesis, cRNA target was prepared, fragmented to a uniform size, and hybridized to Agilent Human v2 GE 4x44K arrays. Slides were subsequently washed and scanned on an Agilent G2565 Microarray Analyzer and the resulting data were analyzed with Agilent Feature Extraction and GeneSpring GX v7.3.1 software. A total of six biological replicates of the experiment were performed.