organism: Sus scrofa
description: Protocols: Longissimus muscle between 13th and 14th thoracic vertebrae was dissected immediately after slaughter. Tissue samples were flash frozen in liquid nitrogen and kept at -80 °C until DNA extraction. All experimental procedures including animal care and tissue sample collection were followed the guidelines for safeguarding and good scientific practice in accordance with the German Law of Animal Protection, officially authorized by the Animal Care Committee and authorities [Niedersächsischen Landesamt für Verbraucherschutz und Lebensmittelsicherheit (LAVES) 33.42502/01-47.05]. Genomic DNA was extracted from samples using a DNeasy kit (Qiagen) according to the manufacturer's recommendation including proteinase K digestion and RNase A treatment to obtain high purity DNA. 2 µg of DNA with a 1% spike-in control (unmethylated cl857 Sam7 Lambda DNA, Promega) was digested for 7 hours with 100U MspI (New England Biolabs) and then overnight with 50U TaqαI. The double-enzyme digested DNA fragments were end-repaired, A-tailed and ligated to TruSeq DNA adapters using a TruSeq Nano DNA library prep kit (Illumina). The adapter-ligated DNA fragments were size-selected to obtain inserts between 40 – 240bp. The DNA library was subjected to a bisulfite conversion using an EZ DNA Methylation Kit (Zymo Research). Library amplification was performed using a PfuTurbo Cx Hotstart DNA Polymerase kit (Stratagene). The quality of libraries was assessed on 2100 Bioanalyzer using a DNA chip (Agilent Technologies).
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2020-01-03T15:59:14Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2018-10-25T11:57:41Z
attributes.tag: External Id
attributes.value: SAMEA5044520
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: 2020-01-03T15:59:14Z
attributes.tag: INSDC last update
attributes.value: 2018-10-25T11:57:41Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-7338:Duroc_43
attributes.tag: age
attributes.value: 180
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: common name
attributes.value: pig
attributes.tag: developmental stage
attributes.value: adult
attributes.tag: genotype
attributes.value: wild type genotype
attributes.tag: organism part
attributes.value: longissimus thoracic muscle
attributes.tag: phenotype
attributes.value: wild type phenotype
attributes.tag: sample name
attributes.value: E-MTAB-7338:Duroc_43
attributes.tag: scientific_name
attributes.value: Sus scrofa
attributes.tag: sex
attributes.value: female
attributes.tag: breed
attributes.value: Duroc