Gene expression analysis of chicken p. major muscle using the NanoString nCounter technology

Tissue samples were harvested with the Keyes biopsy punch (8 mm; manufactured by HNM) from the caudal edge of the right superficial pectoral muscle perpendicular to myofibers and to the keel bone. Total RNA was isolated from p. major samples using mirVana™ miRNA Isolation Kit. Quality checks were performed by measuring the concentration and “RNA Integrity Number” of individual RNA samples using NanoDrop 1000 and Agilent Bioanalyzer 2100. The RNA samples were normalized and sent to NanoString Inc. (Seattle, WA, USA) for the quantification of gene expression levels using NanoString nCounter® technology. For this, 192 target genes, along with 12 housekeeping genes were selected based on multiple RNA-seq experiments conducted in our laboratories. This dataset include gene expression data from the p. major muscle tissue of 89 chickens, consisted of 52 Wooden Breast-unaffected, 21 partially affected and 16 markedly affected birds. Most of the samples were from a commercial crossbred population (n=67), and the rest of the samples were from purebred line B (n=8) and purebred line C (n=14).