For each probe set we conducted a two-way ANOVA with diet and batch as factors, and compared pairs of diets using the Tukey HSD post hoc test (we utilized the "TukeyHSD" function in the R "stats" package).
To accomplish the incongruence test we utilized the unlink command in MrBayes, which allows the user to let parameters as well as topologies to be unlinked between partitions.
To test this we utilized the in vitro AI-2 synthesis reaction described above with the wildtype LuxS enzyme and the cell-free supernatant as the source of substrate.
To test VARiD, we utilized the dataset of Harismendy et al. (2009), who sequenced several regions of the human genome, spanning a total of 260 kb, from four individuals (NA17156, NA17275, NA17460 and NA17773), both with the AB SOLiD platform and the 454/Roche Pyrosequencer.
To test this hypothesis, we utilized the clinically relevant male-specific antigen HY and studied the fate of adoptively transferred, HY-CD8+ T cells (HY-CD8) against a HY-expressing epithelial tumor (MB49) and pre-B cell leukemia (HY-E2APBX ALL) in BMT recipients.
To test this question, we utilized the estrogen receptor-negative/progesterone receptor-negative MDA-MB-231 cell line.
To test this hypothesis, we utilized the data from the Cancer Genome Atlas Research Network, 2011 (TCGA, [2011]), where the processed LOH data for high-grade serous ovarian tumors is readily available.
