title: RNA-seq of Zea mays: biological replicate 1 of mesophyll cells collected at 22h after lights were turned on
design: Initial quality control of total RNA was performed by first doing a photometric measurement on a NanoDrop 1000 device. This was followed by RQN determination via a Fragment Analyzer System (AATI) by using the DNF-471 standard sensitivity RNA Assay. Final RNA quantification was performed by fluorometric Qubit assay (RNA HS, ThermoFisher Scientific) measurement. Library preparation of 42 samples was carried out on a PerkinElmer Sciclone NGS robotics unit by using the Illumina TruSeq stranded mRNA sample Preparation Kit (#15031047 Rev.E), following the manufacturers instructions. Input amount of total RNA was 200 ng. Final libraries were passed through an additional bead clean-up step in a 1:1 ratio (sample/beads) to get rid of primer dimer left overs. Quality control on a Fragment Analyzer System (AATI) followed to determine fragment length distribution using the DNF-474 Assay. For quantification purposes a fluorometric Qubit dsDNA HS Assay Kit was used. Libraries were diluted to 2 nM prior to equimolar pooling into 6 separate pools which were sequenced each on individual flow cell lanes. Paired-End sequencing with 2x150 bp read length was performed on an Illumina HiSeq3000 system using the HiSeq 3000/4000 PE Cluster Kit (PE-410-1001) and the HiSeq 3000/4000 SBS Kit 300 cycles (FC-410-1003).