Fig. 1

Microarray hybridization design and data analysis pipeline. Genomic DNA and total RNA profiles of MOSE cells were obtained with cDNA microarrays. Double arrows in opposite directions indicate that a common reference design plus repeated dye-swap design was used for the two series. Reference DNA was genomic DNA isolated from peripheral whole blood of adult C57BL6 male mice. Reference RNA was from a whole newborn male C57BL/6 mouse (Wnbm) as in previous studies [21, 22]. Test RNA and DNA samples were co-purified from the same cultures samples, labeled and hybridized on NIA-15 K cDNA microarrays as described [22]. Raw RNA and DNA datasets were separately normalized by print-tip loess with DNMAD. Limma (linear analysis of microarray data) analysis was performed in Pomelo2. DNA data was visualized in chromosomal format and smoothed with the WebaCGH tool [60]. Differential expression and copy number were subjected to functional genomics analyses (see details in Results section)