TSKMLO microarray validation experiment

A 6K oligonucleotide microarray (TSKMLO) was designed as a community resource for researchers interested in domestic turkey muscle biology as it pertains to growth and development and their association with downstream meat quality. A series of quality control experiments performed to assess the functionality of the newly constructed array, which included a set of validation hybridizations performed in order to initially assess the functionality and repeatability of the newly designed TSKMLO array. Strong correlations between these test comparisons confirmed that the array was able to hybridize fluorescently-labeled aRNA samples from turkey skeletal muscle at different developmental stages, that there was little dye bias, and that results were repeatable. Three experiments were designed. 1) A “Self-Self” array was hybridized using the same RNA sample (a randomly chosen RBC2, 18de) divided into two aliquots: one labeled with Cy3 and the other with Cy5 to ensure equal hybridization of each fluorescent dye-labeled sample. 2) Two “Dye Swap” arrays were hybridized using randomly chosen F, 18de and F, 1d samples. The fluorescent dye assignments were reversed in the two arrays. The objectives of this experiment were to observe expected differential expression between embryonic (hyperplasia) and neonatal (hypertrophy) muscle samples as well as to ensure similar hybridization regardless of dye assignment. 3) A “Repeat” array was hybridized on a different day using the same samples and dye assignments as the “Dye Swap 2” array to ensure reproducibility of hybridization results.