title: BGISEQ-500 sequencing; RNA-seq of etiolated 9 day old maize seedling second leaves after exposure to either blue, red or no light conditions for three hours
design: RNA-seq of etiolated 9 day old maize seedling second leaves after exposure to either blue, red or no light conditions for three hours
library_construction_protocol: Etiolated seedling second leaves were identified 9 days after planting. Leaf sections were cut 5cm from the tip following 3 hours of exposure to either 100micromols of red or blue light applied using a licor-6800 fluorometer head (flow rate 500 µmol s⁻¹, 400 µmol mol⁻¹ CO2, leaf temperature 28°C and 60% humidity, fluorescence measured every 15 minutes) or no light. Cut leaves were immediately frozen in liquid nitrogen and stored at -80oC. B73 maize seeds were planted in vermiculite and grown in 28oC growth cabinets in the dark for 9 days Leaf samples were ground using a tissuelyser and RNA was extracted using Trizol reagent protocol. DNA was removed using a TurboDNAse treatment. Samples were then frozen at -80oC again. Samples were sent to BGI, Hong Kong, for library preparation. Libraries were constructed following a custom protocol from samples that passed quality controls (mass > 2µg, concentration>80ng/microl, OD260/280 ~= 2.00, OD260/230 ~= 2.20, RIN>6.5, 28S/18S<1.0, baseline smooth).