02_RNAex_libraries.md

Note: 
- This is a somewhat polished protocol as found in a publication. 
- This is not an example for a typical lab protocol or method. 

RNA Extraction, Preparation, and Sequencing of Illumina Libraries

The topmost mature unshaded leaves (of approximately 3–4.5 cm length) of T. triangulare were harvested in the middle of the light or the middle of the dark period and immediately frozen in liquid nitrogen. RNA was isolated from ground tissue using the GeneMatrix Universal RNA Purification Kit (EURx Ltd.). Residues of DNA were removed with DNase (New England Biolabs). RNA integrity, sequencing library, and fragment size were analyzed on a 2100 Bioanalyzer (Agilent). Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina) and quantified with a Qubit 2.0 (Invitrogen). Samples were multiplexed with 12 libraries per lane and sequenced in single-end mode (Rapid Run, 150 bp read length) on an Illumina HiSeq 2000 platform.