Microarray Analysis of Pine Transcriptome

The 60-mer oligonucleotides custom microarray PINARRAY3 (Cañas et al., 2015 (link)) based on the P. pinaster transcriptome (Canales et al., 2015) was used. Slides were made by Agilent Technologies and hybridization was performed as described by Cañas et al. (2015) (link). Slides were scanned, and signal intensities were recorded using a GenePix 4100A microarray scanner (Molecular Devices, Sunnyvale, CA, USA). Differentially expressed genes (DEGs) were detected using the limma package for R (Smyth, 2005 ). Gene enrichment comparison was performed using the Mapman functional categories through the Mercator web tool (Lohse et al., 2014 ). The microarray data are accessible at NCBI’s Gene Expression Omnibus (Edgar et al., 2002 (link)) through the accession number GSE142093.