SRX541149 GSM1385570 GSM1385570: Infected Leghorn; Gallus gallus; RNA-Seq SRP041937 SRS606026 GSM1385570 RNA-Seq TRANSCRIPTOMIC cDNA A total of eight chickens (two birds per line per treatment) were randomly selected from infected and non-infected Leghorn and Fayoumi birds, euthanized and lungs and trachea collected for RNA isolation. Total RNA was isolated using Trizol (Invitrogen, Carlsbad, CA) according to the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard Illumina protocols Illumina Genome Analyzer II http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1385570 gds 301385570 GEO Accession GSM1385570 SRX541150 GSM1385571 GSM1385571: Non-infected leghorn; Gallus gallus; RNA-Seq SRP041937 SRS606027 GSM1385571 RNA-Seq TRANSCRIPTOMIC cDNA A total of eight chickens (two birds per line per treatment) were randomly selected from infected and non-infected Leghorn and Fayoumi birds, euthanized and lungs and trachea collected for RNA isolation. Total RNA was isolated using Trizol (Invitrogen, Carlsbad, CA) according to the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard Illumina protocols Illumina Genome Analyzer II http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1385571 gds 301385571 GEO Accession GSM1385571 SRX541151 GSM1385572 GSM1385572: Infected Fayoumi; Gallus gallus; RNA-Seq SRP041937 SRS606028 GSM1385572 RNA-Seq TRANSCRIPTOMIC cDNA A total of eight chickens (two birds per line per treatment) were randomly selected from infected and non-infected Leghorn and Fayoumi birds, euthanized and lungs and trachea collected for RNA isolation. Total RNA was isolated using Trizol (Invitrogen, Carlsbad, CA) according to the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard Illumina protocols Illumina Genome Analyzer II http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1385572 gds 301385572 GEO Accession GSM1385572 SRX541152 GSM1385573 GSM1385573: Non-infected Fayoumi; Gallus gallus; RNA-Seq SRP041937 SRS606029 GSM1385573 RNA-Seq TRANSCRIPTOMIC cDNA A total of eight chickens (two birds per line per treatment) were randomly selected from infected and non-infected Leghorn and Fayoumi birds, euthanized and lungs and trachea collected for RNA isolation. Total RNA was isolated using Trizol (Invitrogen, Carlsbad, CA) according to the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard Illumina protocols Illumina Genome Analyzer II http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1385573 gds 301385573 GEO Accession GSM1385573