Labeled cDNA was produced with the kit Array 900 HS from Genisphere and Superscript II from Invitrogen.
Methylation measurements were done using the Illumina Infinium HumanMethylation450 BeadChip Kit array (referred to as 450 K array in the following).
miRNA was polyadenylated and labelled with Cy3 using the mirVana miRNA labelling kit and arrays were hybridised and washed as described by Ambion.
Protein expression profiles were assayed using the specific human pluripotent Stem Cell array kit 'Proteome Profiler Array' (R&D Systems Europe, Abingdon, UK; ARY010) following the manufacturer's instructions.
About 10 µg of total RNA from each biological replicate were used for a reverse transcription reaction with the Genisphere® Labelling and Detection Kit, 3DNA Array 900 Cy3/Cy5.
Total RNA (10 μg) from each sample was split into two aliquots and each was reverse-transcribed into cDNA using Cy3 or Alexa Fluro 647-specific primers provided with the Genesphere kit 3DNA array 50 kit.
Total RNA from leaves and flowers (25 μg) was used for cDNA synthesis and labeling with either Cy3 or Cy5 dye, using the 3DNA Expression Array Detection kit for microarrays (Array 50, version 2, Genisphere, Hatfield, PA, USA).
These experiments were made using the Genisphere 3DNA Array Detection Array 350™ Kit (Cy3/Alexa647) and Genisphere 3DNA Array Detection Array 50™ Kit (Cy3/Cy5) for the embryos and juveniles respectively and followed the protocols of the vendor.
Infected mouse spleens were screened using the R&D Systems Proteome Profiler™ Mouse Cytokine Array Panel A Array Kit as per the manufacturer's instructions.
The proteome profiler Human Cytokine Array Panel A Array Kit (R&D Systems) was used according to the manufacturer's instructions.
