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Transcriptomic raw data were obtained by scanning of the microarray slides using Illumina GenomeStudio V2010.3.
Labeled DNAs were hybridized onto the microarray slides using a Tecan HS 4800™ Pro hybridization station (Tecan Deutschland GmbH, Crailsheim, Germany).
The fluorescence signals were measured from the microarray slides using a ScanArray Express® instrument (Perkin-Elmer Life Sciences, Boston, MA).
The 6144 amplicons of the rice library were spotted on amino-silane-coated microarray slides using a microarrayer.
We acquired fluorescent images of microarray slides using a ScanArray confocal laser microarray scanner (Packard BioChip Technologies, Billerica, MA, USA).
Immunohistochemical staining for EGFR was performed on the tissue microarray slides using the EGFR PharmDx kit (DAKO Cytomation) according to the manufacturer's instructions.
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The microarray slides used were custom-designed 8×15k or 8×60k arrays synthesized by Agilent Technologies, each containing 11,956 Virochip 70-mer oligonucleotide probes in common.
There were three technical replicates for each of the three biological samples, resulting in a total of nine DNA microarray slides used in this study.
JD is responsible for the production of the pan- Neisseria microarray slides used in this study and provided support in the preparation of the manuscript.
The cDNA microarray slides used were produced at the Swegene DNA Microarray Resource Center, Department of Oncology, Lund University and contained 27649 spots with sequence-verified IMAGE clones from the Research Genetics IMAGE clone library.
Secondly, the microarray slides used in this study cannot detect the expression of unique WCH16-specific genes that are absent in TIGR4 and R6 genomes represented on the slides.
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