title: Whole transcriptome profiling of rat mixed tissue at mid-day ZT7 (Experiment 4)
design: The samples were prepared using the Ambion RNA-Seq Library Construction Kit to make libraries suitable for strand-specific sequencing. For each library,  10 µg of total RNA was polyA-RNA-enriched using streptavidin-coated magnetic beads; the resulting polyA RNA was fragmented using chemical fragmentation.  Adaptors, specific for 3’- and 5’-ends, were ligated to the fragmented RNA, and cDNA was synthesized from this RNA by extension of the ligated adaptors using reverse transcriptase. Size selection was performed using a 2% agarose gel. Libraries were enriched using 14 cycles of PCR and purified using Ampure XP Beads (Agencourt). Each library was run as one sample per lane on an Illumina HiSeq machine yielding strand-specific, 101-base, paired-end sequencing reads. Image analysis and base calling were done using RTA1.12.4.2 and CASAVA1.8.2.