alias: E-MTAB-6169:Sample 5_p
title: Illumina HiSeq 2500 paired end sequencing; Transcriptional shifts account for divergent resource allocation in feed efficient broiler chickens
design: Transcriptional shifts account for divergent resource allocation in feed efficient broiler chickens
library_construction_protocol: The study procedure was approved by the animal ethics committees of the University of Veterinary Medicine (Vienna, Austria). Chickens were humanely killed on the sample collection day. Gut tissue samples (1 cm2) were collected from the Flexura duodeni, Meckel's diverticulum and the proximal ileum. Muscle samples were collected from the bottom half of the left breast. Gut and breast muscle samples were cleaned in phosphate-buffered saline, blotted dry on paper towel, cut into small cubes (muscle samples) , snap-frozen in liquid nitrogen, and stored at -80°C until use. "residual feed intake (RFI)"  was evaluated from energy consumption like feed intake (FI) and performance measures such as body weight gain (BWG). Chickens were assigned high- or low-RFI category based on the population mean (Metzler-Zebeli et al. 2016: Comparison of growth performance and excreta composition in broiler chickens when ranked according to various feed efficiency metrics. J Anim Sci. 94: 2890-9). 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). One-day-old Cobb500FF chicks (Cobb-Vantress, Siloam Springs, AR, USA) were housed in groups of four birds for 7 days. Afterwards, they were individually penned in cages until the end of the experiment. Monitoring for health status and welfare issues were done on daily basis: chickens with signs of illness were excluded from the study. Chickens were fed corn and soybean meal based standard diets during starter (days 1 – 10), grower (days 11 – 21), and finisher periods (days 22 – 42) and had ad-libitum access to fresh water.
identifiers.namespace: Leibniz-Institute for Farm Animal Biology (FBN) Institute of Genome Biology
identifiers.id: E-MTAB-6169:Sample 5_p
attributes.tag: Experimental Factor: phenotype
attributes.value: high residual feed intake
attributes.tag: Experimental Factor: organism part
attributes.value: pectoral muscle