characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2015-01-19T17:03:08Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2018-03-08T21:36:49Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA2755635
characteristics.characteristic: External Id
characteristics.text: The Roslin Institute
characteristics.characteristic: INSDC center name
characteristics.text: 2015-01-19T17:03:08Z
characteristics.characteristic: INSDC first public
characteristics.text: 2018-03-08T21:36:49Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS541515
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-2909:Smith_Roslin_APL_HP_ileum_3_rep1.fastq.gz
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: mallard
characteristics.characteristic: common name
characteristics.text: Protocols: Virus Strains. A/Mallard/British Columbia/500/2005 (H5N2) was used for LPAI challenge. A/Vietnam/1203/2004 (H5N1) was used for HPAI challenge. The viruses were grown in the allantoic cavities of 10-day-old embryonated chicken eggs for 48 hours at 35 degrees C. Allantoic fluid containing virus was harvested and stored at -80 degrees C until use. Virus yield was determined as 50% egg infectious dose (EID50) per millilitre of virus stock by the method of Reed and Muench .Experimental Animals. Domestic Gray Mallards were purchased from Ideal Poultry (Cameron, TX). All experiments involving animals were approved by the Animal Care and Use Committee of St. Jude Childrenâ€™s Research Hospital and performed in compliance with relevant policies of the National Institutes of Health and the Animal Welfare Act. All animal challenge experiments were performed in an animal biosafety level 2 containment facilities for the LPAI challenges and in biosafety level 3 enhanced containment laboratories for the HPAI challenges. Ducks, except the mock infection control group, were challenged with 106 EID50 intranasally, intratracheally, and intraocularly of LPAI A/Mallard/British Columbia/500/2005 (H5N2) in phosphate buffered saline (PBS). Ducks, except the mock infection control group, were challenged with 106 EID50 intranasally, intratracheally, and intraocularly of HPAI A/Vietnam/1203/2004 (H5N1) in PBS. During LPAI and HPAI infections in ducks, mock infection control groups were also inoculated. Mock infection control birds received an equivalent volume and route of administration with PBS. Animals were monitored daily for clinical signs. : For each ileum and lung tissue, the tissue sample was homogenized in Trizol (Invitrogen Life Technologies), 0.1g tissue/1.0ml Trizol with handheld homogenizer Power Gen125 (Thermo Fisher Scientific). After homogenates were prepared, the samples were centrifuged to separate the liquid phases of Trizol homogenates. 0.5ml of the aqueous phase was passed through a QIagen RNeasy (Qiagen, Valencia, CA) spin column according to manufacturer's instructions for RNA extraction. Samples were frozen and stored at -80 degrees C until all samples were collected for analysis. Samples were prepared for mRNA sequencing using 5ug of total RNA starting material following the Illumina mRNA sequencing 8 sample preparation kit protocol.
characteristics.characteristic: description
characteristics.text: H5N1
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_102793
characteristics.characteristic: infect
characteristics.text: Anas platyrhynchos
characteristics.characteristic: organism
characteristics.text: Anas platyrhynchos
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_8839
characteristics.characteristic: organism
characteristics.text: ileum
characteristics.characteristic: organism part
characteristics.text: Anas platyrhynchos
characteristics.characteristic: scientific_name
characteristics.text: 3 day
characteristics.characteristic: time
characteristics.text: Smith_Roslin_APL_HP_ileum_3_rep1.fastq.gz
characteristics.characteristic: title