Dye-swap experiment: Liver gene expression in NZO/HlLt mice with CL316,243, a beta-3 adrenergic receptor agonist supplemented diet


Spotted cDNA microarrays were used to study the expression of genes in the liver related to type II diabetes. NZO/HlLt male mice represent a model of maturity-onset type II diabetes. Mice of this strain are large at weaning, and gain weight rapidly thereafter. The rapid development of post-weaning obesity leads to the development of insulin resistance, and eventually type II diabetes in males. (Leiter et al. 1998). If the diet fed to weaning mice is supplemented with 0.001% CL316,243, a beta-3 adrenergic receptor agonist, the metabolic defects are in large part normalized such that obesity is blunted and diabetes is averted.

Prototype mouse arrays were printed on CMT-GAPS coated slides. Seventy-six genes associated with growth and metabolism were spotted four times on each array and two additional genes were spotted 16 times per array, for a total of seventy-eight unique sequences. In order to screen for genes with dysregulated expression in mice whose diet is unsupplemented with CL316,243, we compared gene expression in livers of treated and control NZO/HlLt male mice. All mice were fed for 4 weeks from weaning on NIH 31 diet (4% fat). The chow of the treated mice was supplemented with 0.001% CL316,243.

Two arrays were used to compare the treated and control RNA samples. The dye-labeling was switched between the arrays. The design of this experiment is most commonly referred to as a “dye-swap”, although it has also been described as a “flip fluor” or Latin Square design (Kerr, Martin and Churchill, 2000). The README file shows the experimental layout.


Sources of Variation in Microarray Experiments (2006)
Kerr MK, Leiter EH, Picard L, Churchill GA.
In: Computational and Statistical Approaches to Genomics, 2nd Edition.
Zhang W, Shmulevich I (eds). Kluwer Academic Publishers. pp 37-48. [ Springer ] [ Amazon ]