RNA-seq of Vibrio fischeri: hmp mutant
Two-ml culture samples were treated with RNAprotect Bacteria Reagent (Qiagen) following the manufacturer s protocol, and the resultant pellets were resuspended in 2 ml of Trizol reagent (Life Technologies).   RNA was isolated using the Zymo Direct-zol RNA miniprep kit, following the manufacturer s protocol (Zymo Research, Irvine, CA).  To remove contaminating DNA, RNA samples were treated with Turbo DNA-free kit (Life Technologies), using the rigorous DNase treatment protocol.  Sequencing libraries were prepped from 3.4 mg of RNA of each sample using the ScriptSeq Complete Kit (Epicentre, Madison, WI), following the protocol from the manufacturer.  Samples were barcoded using the Epicentre ScriptSeq Index PCR primers #1-12, and combined into a single sample.