characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2015-04-20T17:02:24Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2018-03-08T16:50:13Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA2205777
characteristics.characteristic: External Id
characteristics.text: University of Pennsylvania
characteristics.characteristic: INSDC center name
characteristics.text: 2015-04-20T17:02:24Z
characteristics.characteristic: INSDC first public
characteristics.text: 2018-03-08T16:50:13Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS358297
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-1930:pig 3_aortic arch
characteristics.characteristic: Submitter Id
characteristics.text: 6 month
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/UO_0000035
characteristics.characteristic: age
characteristics.text: about 250 pound
characteristics.characteristic: body weight
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: pig
characteristics.characteristic: common name
characteristics.text: Protocols: Endothelial cells were obtained from adult pigs immediately after euthanasia at a local slaughterhouse. Ascending and descending aortas were harvested, and the vessel lumen was rinsed with ice-cold PBS. Endothelial cells were freshly harvested by gentle scraping of regions (1-2 cm2) located at the inner curvature of the aortic arch (AA) and from nearby descending thoracic aorta (DT) representing athero-susceptible and athero-protective sites respectively. Genomic DNA was isolated by DNeasy Kit (Qiagen). The quality of DNA was evaluated by NanoDrop 1000 Spectrophotometer and TapeStation 2200 (Agilent Technologies). Only high quality DNA (260/280>1.8) was used in the study. The sex of each pig was determined by the presence (male) or absence (female) of sex determining region Y (SRY) gene in the Y chromosome. Genomic DNA randomly selected from two regions of 6 female and 6 male pigs were were used as biological replicates in the methylated DNA immunoprecipitation sequencing (MeDIP-seq) study. One microgram genomic DNA was sheared into ~200bp fragments using a Covaris S2 sonication system (Covaris, Woburn, MA) according to the manufacturer’s settings. MeDIP DNA Libraries were constructed using DNA Library Prep kit for Illumina (NEB) consisting of DNA end repair, 3'-dA tailing and adapter ligation. After adapter ligation, the DNA was immunoprecipitated by MagMeDIP (Diagenode) with antibody against methylated DNA according to the manufacturer's protocol. The MeDIP DNA was amplified by PCR using index primers and phusion high-fidelity DNA polymerase (NEB). The PCR cycles consisted of 98 C 30s, 15 cycles of 98 C 10s, 65 C 30s, 72 C 30s, followed by prolonged extension for 5 min at 72 C. After amplification and purification, MeDIP DNA libraries with 50-100bp insert size were selected by Sage Science’s Pippin Prep in 2% agarose gel. The libraries Library quality and quantity were evaluated using an Agilent 2100 Analyzer and DNA 1000 chips. The specificity and efficiency of MeDIP enrichment were verified by qPCR with primers targeting ACTA2 promoter (methylated in endothelial cells) and UBB promoter (unmethylated in endothelial cells). The mean ratio of methylated/unmethylated DNA was 244,700 fold, indicating highly enrichment of methylated DNA.
characteristics.characteristic: description
characteristics.text: birth
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0004950
characteristics.characteristic: initial time point
characteristics.text: Sus scrofa
characteristics.characteristic: organism
characteristics.text: Sus scrofa
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9823
characteristics.characteristic: organism
characteristics.text: aortic arch
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/UBERON_0004363
characteristics.characteristic: organism part
characteristics.text: Sus scrofa
characteristics.characteristic: scientific_name
characteristics.text: female
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/PATO_0000383
characteristics.characteristic: sex
characteristics.text: Landrace x Yorkshire
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/LBO_0001040
characteristics.characteristic: strain
characteristics.text: pig 3_aortic arch
characteristics.characteristic: title