GSM5328916: Valley Oak (SW.786) bud RNA short read sequencing (illumina); Quercus lobata; RNA-Seq
Plant tissues (100 mg each of leaves, buds and stems) were flash frozen in liquid nitrogen and ground with a mortar and pestle to a fine powder. RNA extractions were performed February 16, 2018. using a modified (see publication) version of the Conifer RNA prep protocol  from the Cronn Lab  (https://openwetware.org/wiki/Conifer_RNA_prep) and the Spectrum Plant Total RNA kit (Sigma, St. Louis, MO, USA).   RNA quality and quantity were assessed using the Agilent RNA ScreenTape System on the Agilent 2200 TapeStation system (Agilent Technologies, Santa Clara, CA, USA). Total RNA was depleted of rRNA using the Ribo-Zero rRNA Removal Kit (Plant Leaf) (Illumina,San Diego, CA, USA). Total RNA input amounts were 5 ug for the leaf, 4.2 ug for the bud, and 4.1 ug for the stem.  Libraries were constructed using the TruSeq Stranded Total RNA protocol with a positive control (Illumina, San Diego, CA, USA). Libraries were analyzed using the Agilent D1000 Screen Tape System on the Agilent 2200 TapeStation (Agilent Technologies, Santa Clara, CA, USA). Fragments were found to be too small (~275bp) so an extra size selection step was performed with AMPure XP beads at a concentration of 0.65x, to yield fragments in the 400-700 bp range.