KRK carried out the tissue collection, performed RNA extractions, array hybridizations, and real-time PCR.
JSM participated in the design of the study and sample collection, carried out all RNA extractions, array and qPCR analyses, and drafted the manuscript.
A detailed well testing program was undertaken to assist in the design of the injection and extraction well array, and to assess the possibility of off-site heat and contaminant migration.
Scanning, data extraction, and array calibrations were performed by NimbleGen Systems , Inc
These samples were treated as biological replicates for mRNA extraction and array analysis.
Thirteen (13) of 21 diploid tumors had sufficient numbers of nuclei for DNA extraction and array CGH.
Furthermore, we also tried to directly detect fungi by trapping airborne spores in a buffer, followed by centrifugation, DNA extraction, and array hybridization.
These results illustrate the efficacy of our protocols in restricting biological and technical variation between replicates that may be introduced by experimental procedures such as tissue isolation, RNA extraction, and array hybridization.
Within-mouse variance captures variation due to heterogeneity of gene expression within tissues, RNA-extraction, and array processing.
In our current analysis, more detailed ANOVA models were used to describe and subsequently remove non-biological sources of variability specific to each platform, such as batch effects due to RNA extraction and array- and dye-specific bias.
