title: RNAseq of Mcc CK wt: timepoint1 replicate2
design: RNA quality was assessed on a Fragment Analyzer (Agilent Technologies) and the RNAs had an RQN between 5.8 and 10.  RNA-seq libraries were prepared from total RNA with the Illumina TruSeq Stranded mRNA reagents (Illumina), omitting the polyA selection.  The rRNA depletion was performed with QIAseq FastSelect  5S/16S/23S kit (Qiagen) from 1000 ng total RNA input.  Library preparation was then performed on a Sciclone liquid handling robot (PerkinElmer; Waltham, Massachusetts, USA) using a PerkinElmer-developed automated script.  Unique dual indexes were used for barcoding of the libraries. Libraries were quantified by a fluorimetric method (QubIT, Life Technologies) and their quality assessed on a Fragment Analyzer (Agilent Technologies).  Cluster generation was performed with 2 nM of an equimolar pool from the resulting libraries using the Illumina HiSeq 3000/4000 PE Cluster Kit reagents and sequenced on the Illumina HiSeq 4000 using HiSeq 3000/4000 SBS Kit reagents for 300 cycles (paired end 150 nt reads).  Sequencing data were demultiplexed using the bcl2fastq2 Conversion Software (version 2.20, Illumina).