To minimize the impact of individual mouse to mouse variability on the microarray data, each biological replicate was comprised of a randomized pool of liver RNA prepared from n = 5-6 mice.
For Ning 7840, that was comprised of four microarrays evaluated at the Big Red Spots facility and two evaluated at Weill Medical College or two technical reps each of three biological reps.
The Whitehead dataset was comprised of two replicate microarrays hybridized with a spike-in mixture.
Unfortunately, while this type of system has been employed for gene microarray analysis, it is unclear whether it will be effective in the analysis of mass spectral data, which unlike microarray data, is comprised of continuous measurement operations.
The microarray data were comprised of 11 drought experiments in five different platforms, including data in 10 different growth stages (from vegetative to reproductive stage) and 13 different genotypes (indica varieties: Dagad deshi, IR20, IR64, DK 151, Bala, IR77298-14-1-2-B-10, IR77298-5-6-B-18-1R77298-5-6-B-11B-18, 1R77298-5-6-B-11, jAzucena vandeties: ZhoNakdong1, AzuceNakdong Nakdong).
Data for many probesets in a given expression microarray dataset are comprised of noise but little or no biological signal.
Samples were hybridized to Agilent 44K whole human genome microarrays, which are comprised of over 41,000 unique 60-mer oligonucleotide human sequences and transcripts.
The unexposed RNA-Seq data represent two pools of 6 and 8 individuals collected from sites on both sides of the Mississippi river, while the microarray data set is comprised of a separate set of 75 individual animals collected in the summer of 2010 from different sites along the Gulf of Mexico.
The P. metricus oligo microarrays [ 11] are comprised of 10,000 duplicate spots, representing 5000 different transcripts, corresponding to approximately 3248 different genes.
In both the study by Atias and our study, portions of each dataset are comprised of microarray samples involved in pathogen experiments.
