title: Sample 20
organism: Gallus gallus
description: Protocols: Chickens were housed in 4 separate rooms (2 challenged rooms, 2 non-challenged rooms) and the two breeds were intermixed in each room in a biosafety level 2 facility. To obtain tissue samples at 2, 6, and 10 days post inoculation, approximately one-third of the birds were euthanized with sodium pentobarbital solution at each of the three time points. The lung was harvested and placed into RNAlater® solution (ThermoFisher Scientific, Waltham, Massachusetts) for short-term storage. Within a week, the lung tissue was removed from RNA-later and moved to -80°C freezer for long-term storage. Challenged chickens were inoculated with a high titered lentogenic Newcastle Disease Virus (NDV) strain via the eyes and nostrils at three weeks of age. Non-challenged chickens were given PBS via the same route. RNA was isolated from the lung tissue using the RNAqueous® kit (ThermoFisher Scientific, Waltham, Massachusetts) and samples were then DNase treated using the DNA-free™ kit (ThermoFisher Scientific, Waltham, Massachusetts). The quality of all samples was validated (RNA quality number>8.0) using the Fragment Analyzer™ (Advanced Analytical Technologies, Ankeny, Iowa). A 500 ng input for each sample was utilized to construct the cDNA library using TruSeq® RNA Sample Preparation v2 Guide (Illumina, San Diego, California) using the high throughput protocol. Following cDNA library validation using the Fragment Analyzer™ (Advanced Analytical Technologies, Ankeny, Iowa).
attributes.tag: ENA first public
attributes.value: 2017-07-28
attributes.tag: ENA last update
attributes.value: 2017-07-12
attributes.tag: External Id
attributes.value: SAMEA104161567
attributes.tag: INSDC center alias
attributes.value: Iowa State University
attributes.tag: INSDC center name
attributes.value: Iowa State University
attributes.tag: INSDC first public
attributes.value: 2017-07-28T17:03:31Z
attributes.tag: INSDC last update
attributes.value: 2017-07-12T11:06:08Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-5859:Sample 20
attributes.tag: age
attributes.value: 31
attributes.tag: breed
attributes.value: Leghorn
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: common name
attributes.value: chicken
attributes.tag: disease
attributes.value: Newcastle disease
attributes.tag: individual
attributes.value: LG1525
attributes.tag: organism part
attributes.value: lung
attributes.tag: phenotype
attributes.value: susceptible
attributes.tag: sample name
attributes.value: E-MTAB-5859:Sample 20
attributes.tag: sex
attributes.value: male