maize plants inoculated with H. seropedicae ZAE94 and grown in 3 mM of nitrate
Total RNA was isolated from root plants using Trizol (Invitrogen, CA, USA) as described by Thiebaut et al. (2014). RNA concentration was measured with a Nano-Drop 2000c spectrophotometer (Thermo Scientific, USA), and integrity was evaluated with an Agilent-2100 Bioanalyzer (Agilent Technologies; RNA 6000 NanoChips). Plant samples with a 10 ug total RNA were sent to Fasteris Life Sciences SA (Plan-les-Ouates, Switzerland) for RNA-seq library constructions and subsequent sequencing by Illumina technology. To prepare the eight libraries two protocols were combined. Total RNA samples were depleted using the module for rRNA depletion from the Illumina TruSeq Stranded total RNA Library Prep kit Plant. Depleted RNA was then used as input for library preparation with the Ovation Complete Prokaryotic RNA-Seq DR Multiplex System 1-8 from Nugen. Briefly, cDNA sequencing library was prepared from the rRNA-depleted using the mRNA-Seq HiSeq SBS Kit V4 (Illumina, San Diego, CA). Sequencing of paired-end RNA-seq libraries was performed using an Illumina HiSeq 2500 instrument at Fasteris Life Sciences SA (Plan-les-Ouates, Switzerland), following the manufacturers protocol.