As a result, amplified arrays are propagated as circular YAC/BACs in yeast cells and can be transferred into E. coli cells if needed.
A "virtual correlation coefficient" for a given amplification protocol was obtained by comparing the virtual amplified array (averaged expression level for each clone from multiple amplified samples) to the virtual gold standard unamplified array for BC91.
Most amplified array sets were the stamen development (GSE4733) and the Type III effectors on plant defense response (NASCarrays-59).
Arrays derived from total RNA had higher Pearson's correlations than did arrays derived from amplified RNA when considering the entire unprocessed dataset, however, when considering a gene set of high signal intensity, the amplified arrays had superior correlation coefficients than did the total RNA arrays.
This suggests the following further breakdown: Z = Zc + Zs, where Zc is a common expression component, with variance about 0.6, and Zs is a specific expression component, with variance about 0.04 for the amplified arrays and 0.14 for the unamplified arrays.
In addition, the amplified arrays of Y′-associated telomeric repeats would increase the amount of G-rich telomeric repeat DNA present at each chromosome, which provides a reservoir of G-rich telomeric repeat DNA for recombination onto the extreme terminus of chromosomes.
For the amplified arrays, 28 pairs of arrays can be formed, and the average correlation coefficient was 0.90 (ranging from 0.82 to 0.96).
To measure the level of variability within an amplified group, the 0.5 μg arrays within a treatment group were compared (Table 4, 0.5 vs. 0.5).
Nygaard et al. recently published that 0.2 μg of total RNA amplified 2 rounds yields an average correlation between amplified and non-amplified arrays ranging from 0.71 to 0.84 [ 18].
Conversely we found 17 windows with too-high coverage, 13 of which are true positive hits located in the GTP cyclohydrolase I locus (Additional file 5), an amplified region already highlighted by CGH array technology [ 11].
The average correlation between amplified and non-amplified arrays was 0.79 (ranging from 0.71 to 0.84).
