title: Illumina HiSeq 2500 sequencing; Resistant and susceptible chicken lines show distinctive responses to Newcastle disease virus infection in the lung transcriptome
design: Resistant and susceptible chicken lines show distinctive responses to Newcastle disease virus infection in the lung transcriptome
library_construction_protocol: 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: Experimental Factor: infect
attributes.value: PBS control
attributes.tag: Experimental Factor: breed
attributes.value: Fayoumi
attributes.tag: Experimental Factor: sampling time point
attributes.value: 6