RNA-seq transcriptome sequencing was performed on leaves and roots. Samples were ground to a fine powder in liquid nitrogen and total RNA was isolated (TRI Reagent® (MRC, Cincinnati, OH))25 (link). Then, it was treated with DNase and RNA quality was confirmed with Experion™ Automated Electrophoresis System, Nanodrop™ and gel electrophoresis. Total RNA was used for mRNA preparation, fragmentation and cDNA synthesis.
The preparation of mRNA libraries was done using the TrueSeq Stranded mRNA Sample Preparation kit (Illumina Inc., San Diego, CA). The library quality validation (concentration and length of DNA fragments) was performed by Fragment Analyzer using the standard and high sensitivity DNA kits (Agilent Technologies, Santa Clara, CA) and by qPCR (LightCycler 480; Roche Diagnostics, Meylan, France). MGX-Montpellier GenomiX platform made RNA-seq library preparation and sequencing using a HiSeq. 2500 instrument (Illumina Inc.). Six libraries were sequenced per lane (around 30 millions reads per replicate), with 100 nucleotides sequence length per read.
The preparation of mRNA libraries was done using the TrueSeq Stranded mRNA Sample Preparation kit (Illumina Inc., San Diego, CA). The library quality validation (concentration and length of DNA fragments) was performed by Fragment Analyzer using the standard and high sensitivity DNA kits (Agilent Technologies, Santa Clara, CA) and by qPCR (LightCycler 480; Roche Diagnostics, Meylan, France). MGX-Montpellier GenomiX platform made RNA-seq library preparation and sequencing using a HiSeq. 2500 instrument (Illumina Inc.). Six libraries were sequenced per lane (around 30 millions reads per replicate), with 100 nucleotides sequence length per read.