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Differences in outcome between the current and the original data might be due to experimental factors such as different labeling and hybridization protocols, as well as a new reference being used for the microarray hybridizations carried out for this study.
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In either case, four independent microarray hybridizations were carried out for reproducibility.
A total of twenty-four sets (48 slides) of microarray hybridizations were carried out, including direct and dye swap comparisons.
Automated microarray hybridizations were carried out in an HS 4800 hybridization station (TECAN, Research Triangle Park, NC, USA).
The first-strand synthesis and microarray hybridizations were carried out at the Washington University Genome Sequencing Center, St Louis, MO.
Microarray hybridizations were carried out at the Genomics Unit of the National Centre for Biotechnology, CNB-CSIC, Madrid, Spain.
Microarray hybridizations were carried out overnight using a GeneTAC automated hybridization system [ 37] (Genomic Solutions, Huntingdon, UK).
Microarray hybridizations were carried out on labelled cRNAs with specificity greater than 8 using the in situ Hybridization Kit Plus (Agilent Technologies).
Microarray hybridizations were carried out on Agilent Human oligonucleotide microarrays using 2 μg Cy3-labeled 'reference' sample and 2 μg Cy5-labeled 'experimental' sample.
In each case, replicate microarray hybridizations were carried out such that a p value could be calculated for each difference in gene expression.
Microarray hybridizations were carried out in a two-color format, with 4 biological replicates per experiment including a pair of dye-flips.
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