title: RNA Seq of Allium cepa: leaf tissue infected with Alternaria porri
design: cDNA library was prepared using TruSeq  Stranded Total RNA Sample preparation kit with Ribo-Zero Plant (Illumina, San Diego, CA) according to the manufacturer's instructions. Briefly, Sera-mag Oligo (dT) magnetic beads (Illumina, San Diego, CA) were used to enrich poly (A) mRNA from 4 mg of total RNA. mRNA was fractionated to a size of ~200 bp and first strand cDNA was synthesized using random hexamer primer and SuperScript II reverse transcriptase (Invitrogen, Camarillo, CA). The second strand was synthesized and purified with AMPure magnetic XP beads (Beckman Coulter Genomics, Danvers, MA), overhangs were blunt ended using end repair mix (Illumina, CA) and adenylated with a single  A  nucleotide at the 30 ends of the cDNA fragments. Multiple indexing adapters were then ligated to the ends of the double stranded cDNA and PCR amplified to selectively augment adapter ligated DNA fragments. Sample library quality was assessed using the Agilent 2100 bioanalyzer with Agilent DNA1000 kit (Agilent Technologies, Santa Clara, CA) for the presence of a single band of z260 bp. Finally, the tagged paired-end (PE) RNA-Seq libraries were diluted and pooled in equal concentrations and sequenced on a HiSeq2500 (Illumina) platform.