RNA-seq of Atlantic salmon:  AGD-infected head kidney
A standard TRI  Reagent RNA extraction protocol was followed. Briefly, approximately 50 mg of  tissue was homogenized in 1 ml of TRI Reagent (Sigma, St. Louis, MO) by  shaking using 1.4 mm silica beads, then 100 l of 1-bromo-3-chloropropane  (BCP) was added for phase separation. This was followed by precipitation with  500 l of isopropanol and subsequent washes with 65-75 % ethanol. The RNA was  then resuspended in RNAse-free water and treated with Turbo DNAse (Ambion).  Samples were cleaned up using Qiagen RNeasy Mini kit columns and their  integrity was checked on Agilent 2200 Bioanalyzer (Agilent Technologies,  USA). Thereafter, the Illumina Truseq mRNA stranded RNA-Seq Library Prep Kit  protocol was followed directly. Libraries were checked for quality and  quantied using the Bioanalyzer 2100 (Agilent), before being sequenced on  three lanes of the Illumina Hiseq 4000 instrument using 75 base paired-end  sequencing at Edinburgh Genomics, UK.
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