Project description: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 âSelf-Selfâ 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 âDye Swapâ 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 âRepeatâ array was hybridized on a different day using the same samples and dye assignments as the âDye Swap 2â array to ensure reproducibility of hybridization results.

2010-06-24 | E-GEOD-19452 | biostudies-arrayexpress

Analysis of the turkey skeletal muscle transcriptome through development within a genetic line (Experiment 1)

Project description:The purpose of Experiment 1 was two-fold: a) to evaluate a unique set of negative, distance, and mismatch control probes on the newly designed 6K TSKMLO microarray, and b) to identify patterns of gene expression in skeletal muscle during development. Negative and mismatch controls confirmed specific hybridization using this array, and genes identified as differentially expressed between developmental stages by microarray analysis were confirmed by qRT-PCR. Novel candidate genes and pathways were identified as playing potentially crucial roles in turkey skeletal muscle development with implications for improving turkey meat quality defects and growth-induced myopathies long-term. This experiment utilized turkeys from two genetic lines: RBC2, a randomly bred control line representative of a 1,967 commercial turkey, and F, a subline genetically selected from the RBC2 line for increased 16-week body weight. Skeletal muscle was collected at three critical developmental stages: 18-day embryo (18de; peak of hyperplasia), 1-day post-hatch (1d; shift from myoblast-mediated growth to satellite cell modulated growth by hypertrophy), and 16-week-old birds (16wk; completion of muscle formation and approximate age of commercial slaughter). Experiment 1 was designed to directly compare the three stages of skeletal muscle development: 18de vs. 1d, or 1d vs. 16wk, for each of the genetic lines. Experiment 1 contained 10 arrays per comparison, therefore, it contained 40 arrays total. Birds were randomly assigned to an array, and hybridizations were performed in random order.

2010-01-31 | E-GEOD-19531 | biostudies-arrayexpress

Project description:Response of Turkey Muscle Satellite Cells to Thermal Challenge

| PRJNA341399 | ENA