Microarray manufacture, DNA fragmentation and labeling, sample hybridization and imaging, and fluorescence intensity measurement were performed by Roche NimbleGen, Inc. as previously described [ 1].
We wish to thank the SFGF for microarray manufacture, SMD for database support, and members of the Pollack lab for helpful discussion.
Microarray manufacture was synthesized in situ by photolithography on glass slides using a random positional pattern by NimbleGen (http://www.nimblegen.com/).
In the multifaceted experiments, all six consortium centers used two common platforms: an oligo microarray manufactured at one of the centers and the commercial Agilent mouse microarray platform, developed by TRC investigators working collaboratively with Agilent and the NCT microarray resource contractor, Paradigm Genetics.
Complementary RNA was synthesized in vitro from double stranded cDNA, biotin-labeled and hybridized to a Syngenta custom-designed maize GeneChip microarray, manufactured by Affymetrix.
NS conceived of the pan- Neisseria microarray and its use in this kind of study, was the primary designer of the probes for the microarray, manufactured the pan- Neisseria microarray-v2 slides used in this study, supervised this work, and provided support in the preparation of the manuscript.
Capture probes complementary to each of the barcode sequences were immobilized on each electrode of a low-cost electrode microarray manufactured on standard printed circuit board (PCB) substrates.
Expression profiling was conducted using the Rice 3′-Tiling microarray manufactured by NimbleGen (http://www.nimblegen.com), which contains 27,448 genes deposited at the International Rice Genome Sequencing Project Rice Annotation Project 1 database (http://rapdb.dna.affrc.go.jp).jp
Cy3-labelled cRNA (600 ng/sample) was hybridised to our custom Cavia porcellus oligonucleotide microarray (manufactured by Agilent) in randomised sample order, which generated 61,657 measures per sample (18,073 annotated genes).
The cDNA microarrays were manufactured and hybridized as previously described [ 38, 40] (also see [ 41]).
