title: Selecting superior de novo transcriptome assemblies: lessons learned by leveraging the best plant genome
design: Arabidopsis thaliana total RNA was assessed on an Agilent Bioanalyzer using the RNA 6000 Nano Kit (Agilent) with the Plant Total RNA Nano assay. Only high quality (28s/18s ratio:≥1.7; RIN ≥8; A260 /A280: ≥1.8) RNA was used to prepare Illumina Paired End mRNA libraries according to the mRNA-Seq Sample Prep Guide (Illumina, 1004898 Rev. D) following the manufacturer’s instructions. The Illumina RNA-Seq libraries were assessed on the Agilent Bioanalyzer using the DNA 1000 kit (Agilent) with the DNA 1000 assay. Sequencing of the Illumina PE mRNA-Seq libraries was done in the McCombie lab at the Cold Spring Harbor Laboratory, Cold Spring Harbor, NY USA. Each library was sequenced in one lane following a paired-end (85x85bp) sequencing cycle protocol.