Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction

Broilers and layer hens, grown up to sexual maturation under free-feeding conditions, differed 4.0-fold in weight and 1.6-fold in ovarian-follicle counts, yet the relative accumulation of visceral fat was comparable. RNA-seq and mass-spectrometry (MS) analyses of visceral fat revealed differentially expressed genes between broilers and layers, 1,106 at the mRNA level (FDR=0.05), and 203 at the protein level (P=0.05). Total RNA was prepared using a RNA isolation kit (miRNeasy, Qiagen). Libraries of cDNA were prepared by the Uppsala sequencing platform from 1 µg RNA using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina Inc, #15031047 Rev E). The libraries were uniquely tagged and sequenced with Illumina HiSeq, producing about 64 million paired-end reads (2 x 124 bp) in two technical replicates, per library