Selecting superior de novo transcriptome assemblies: lessons learned by leveraging the best plant genome
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.