While there are a few microarray platforms for cotton available, we decided to use Affymetrix GeneChip Cotton Genome Array for our studies due to its technical robustness and use of multiple probes for a single gene (a total of 239,777 probe sets representing 21,854 cotton transcripts).
Given the bewildering media array vying for our attention spans 24 hours a day, it's a moment in history that has been and continues to be well storied, but at times it can be hard to detect rays of light for the underdog.
First, we employed species-specific array platforms for our expression comparison.
The array designed for our current experiments and those in previous reports were all masked for repeats.
Although this region is ∼200 kb in size, it is poorly covered with SNPs in the 650Y array used for our study (three SNPs).
Because the focus of this study was on chromosome copy number changes, rather than the duplication/deletion of single genes or genome fragments, the design for the arrays was modified for our earlier design [ 18], with oligonucleotide probes that cover all 14 chromosomes of H99 tiled at an average interval spacing of 133 bp on one strand.
Many of the detected proteins shared MF and BP GO terms identified in our arrays (for example, both enolase and nucleolin share the muscle development category), and overlapping changes were observed in binding (Figure 7A).
To correct each spot on our arrays for local background effects, within-array variation and between-array variation, we normalized the signal intensity of the two dye channels using the three-step procedure described by [22] and implemented in CARMAweb [23].
Moreover, it is noteworthy that the SK-N-AS tiling array data used for our analysis is based on hybridization of cDNA originating from polyA selected RNA to the array, which probably excludes some ncRNAs from the CRUFTS dataset.
Most importantly the opportunity for interdisciplinary work is outstanding – the law school, the business school, the school of public policy, the humanities division are located within steps of the hospital, providing a rich array of opportunities for our medical students.
