Sample 14
Gallus gallus
Protocols: At the end of the trial, 18 birds [6 per feed conversion efficiency (FCE) group] were selected based on their performance during grower phase and dissected under controlled conditions. Samples were quickly removed, snap frozen in liquid nitrogen, and stored at -80°C until use. The set of tissues selected for the transcriptomic analyses comprised liver and leg muscle (M. semitendinosus) of 4 low FCE and 4 high FCE birds. Animals were selected based on their RFI-status with respect to gender and final body weight. One-day old Cobb500FF birds were housed in groups of 4-5 birds for 7 days and afterwards individually penned in cages. For each batch, 64 birds were raised until day 21, with feed intake recorded on a daily basis and weighted data recorded at days 1, 7, 14, and 21. Residual feed intake (RFI) was calculated. Based on individual feed efficiency, the top, middle, and bottom 10th percentile of chickens was identified and assigned to high, medium and low efficiency groups. Each group comprised 8 birds for which feed efficiency records were obtained during grower phase between 22 and 42 days of age. Daily feed intake was recorded and chickens were weighed at days 28, 35, and 42. Birds were checked daily for health status and welfare issues during the feeding trial. Birds had ad libitum access to fresh water. Extraction of total RNA was performed according to TRIzol Reagent protocol (Invitrogen, Darmstadt, Germany). Tissue samples were homogenized using either a syringe (duodenum, jejunum, and ileum) or a Precellys cell disruption device (breast muscle; 12sec at 5000U; Peqlab, Erlangen, Germany). Subsequently, total RNA was treated with Baseline-ZERO DNase (Biozym, Hessisch Oldendorf, Germany) and purified using the NucleoSpin RNAII kit (Macherey-Nagel, Düren, Germany) according to manufacturer's protocols. The RNA concentration was measured by NanoDrop ND-1000 (NanoDrop, Peqlab, Erlangen, Germany). The quality of RNA was assessed employing an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Samples with RNA integrity numbers (RIN) values greater than 7.8 were used for DNA libraries preparation using the TruSeq Stranded mRNA preparation kit according to the manufacturer's recommendation (Illumina, San Diego, CA, USA).