organism: Coturnix japonica
description: Protocols: F2 cross Japanese quails (Coturnix japonica) were raised in groups in floor pens of the first seventh day of life (post-hatchling). On day 8, they were transferred and kept individually in metabolic cages until sample collection at day 15. The birds were fed a commercial starter diet for the first 5 days of life and then fed with a P-restricted experimental diet from day 6 to 15 (Beck et al. 2016, Poult Sci. PMID: 26740136 and Künzel et al. 2019, Poult Sci. PMID: 31298295). Data including P utilization were recorded and determined for each individual. Discordant sib-pairs with extreme P utilization from different families were used in this study. Ileum was anatomically identified, dissected and immediately preserved in the RNAlater solution. Tissue samples were stored at -80°C until use for Intestinal tissue samples were ground into powder in liquid nitrogen, and approximately 50 mg of the sample was homogenized in 1 ml of TRIzol Reagent (Invitrogen, Karlsruhe, Germany). Total RNA was extracted according to the manufacturer's instructions. Extracted RNA was additionally treated with DNaseI using RNase-Free DNase Set (Qiagen) and purified using the RNeasy Mini Kit (Qiagen). The RNA quantity and quality was assessed using a NanoDrop ND-1000 (Peqlab) and a Bioanalyzer 2100 (Agilent Technologies), respectively. High quality RNA (RNA integrity number; RIN > 7.5) was used for mRNA-Seq library preparation using a TruSeq Stranded mRNA library preparation kit (Illumina, San Diego, CA, USA). Briefly, poly-A mRNA molecules were enriched using poly-T oligo attached magnetic beads followed by fragmentation and first strand cDNA synthesis with random primers. Each DNA library was barcoded with a different indexing truseq-adapter to enable a parallel sequencing of pooling multiple samples. The DNA libraries were quality checked using a DNA 1000 chip (Bioanalyzer) and quantified for molar concentration using the Qubit dsDNA HS assay kit (Invitrogen) prior to sequencing on the Illumina HiSeq 2500 sequencing platform.
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2020-05-15T17:06:54Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2019-12-12T15:29:14Z
attributes.tag: External Id
attributes.value: SAMEA6413167
attributes.tag: INSDC center name
attributes.value: Leibniz-Institute for Farm Animal Biology (FBN) Institute of Genome Biology/ Genomics Unit
attributes.tag: INSDC first public
attributes.value: 2020-05-15T17:06:54Z
attributes.tag: INSDC last update
attributes.value: 2019-12-12T15:29:14Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-8587:3025
attributes.tag: age
attributes.value: 15
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cohort
attributes.value: high-P utilization
attributes.tag: common name
attributes.value: Japanese quail
attributes.tag: developmental stage
attributes.value: posthatchling
attributes.tag: genotype
attributes.value: wild type genotype
attributes.tag: individual
attributes.value: 3025
attributes.tag: organism part
attributes.value: ileum
attributes.tag: sample name
attributes.value: E-MTAB-8587:3025
attributes.tag: scientific_name
attributes.value: Coturnix japonica
attributes.tag: sex
attributes.value: female