organism: Coturnix japonica
description: Protocols: F2 cross Japanese quails (Coturnix japonica) were raised in groups in floor pens from first to seventh day of life. 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 low-P experimental diet from day 6 to 15. Traits such as feed consumption, growth rate and P utilization were determined for each individual (Beck et al. 2016, Poult Sci. PMID: 26740136 and Künzel et al. 2019, Poult Sci. PMID: 31298295). Ileum was anatomically determined and dissected. Tissue samples were immediately preserved in the RNAlater solution and stored at -80°C until isolation of RNA. Total RNA was extracted from approximately 50 mg of tissue sample using Qiazol Lysis reagent (Qiagen) and further enriched for small RNAs using a miRNeasy Mini kit (Qiagen) according to the manufracturer's recomendations. The integrity of total RNA was assessed using an Agilent RNA 6000 Nano kit and the enrichment and concentration of microRNAs were determined using an Agilent small RNA kit and the 2100 Bioanalyzer system (Agilent Technologies). Small RNA sequencing libraries were generated from 1 µg of enriched small RNA using the SMARTer smRNA-Seq Kit for Illumina (Clontech Laboratories). Briefly, small RNA molecules were polyadenylated and reverse transcribed into first-strand cDNA using the MMLV-derived PrimeScript Reverse Transcriptase (RT). The SMART smRNA Oligo was then added to the 5´-end via the locked nucleic acid (LNA) technology. Illumina indexing adapters were incorporated during an additional PCR amplification to enable sample multiplexing. The smRNA-seq libraries were quality assessed for expected fragment length of a major peak at about 175bp using an Agilent High Sensitivity DNA kit and 2100 Bioanalyzer (Agilent Technology) and then size-selected using the BluePippin System and 3% agarose gel cassette with the internal Q2 DNA marker and size-selection parameters of 148 - 185bp (Sage Science). The molar concentration of the libraries was determined and normalized to 2nM prior to sequencing using a KAPA library quantification kit (KAPA Biosystem).
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2020-05-15T17:06:54Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2019-12-12T15:14:19Z
attributes.tag: External Id
attributes.value: SAMEA6413130
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: 2019-12-12T15:14:19Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-8586:3070
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: 3070
attributes.tag: organism part
attributes.value: ileum
attributes.tag: sample name
attributes.value: E-MTAB-8586:3070
attributes.tag: scientific_name
attributes.value: Coturnix japonica
attributes.tag: sex
attributes.value: male