7 protocols
AccessionType
normalization data transformation protocol
Raw data were normalized by Quantile algorithm, Gene Spring Software 11.5.1 (Agilent technologies, Santa Clara, CA, US). ID_REF = VALUE = Normalized signal intensity
array scanning protocol
Slides were scanned by Agilent Microarray Scanner (Cat#G2565BA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings, Scan resolution=5 μm, PMT 100%, 10%.
hybridization protocol
Each Slide was hybridized with 1.65 μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), Stabilization and Drying Solution (Cat#5185-5979, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions.
labelling protocol
Total RNA was amplified and labeled by Low RNA Input Linear Amplification kit (Cat#5184-3523, Agilent technologies, Santa Clara, CA, US), 5-(3-aminoallyl)-UTP (Cat#AM8436, Ambion, Austin, TX,US), Cy3 NHS ester (Cat#PA13105,GE healthcare Biosciences, Pittsburgh, PA,US) followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).
nucleic acid extraction protocol
Total RNA was extracted using TRIZOL Reagent (Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (QIAGEN, GmBH, Germany).
growth protocol
Endo-dormancy plants were potted and placed in refrigeration house with temperature 0-4°C from 5 November to 30 December 2009 in Qingdao, Shandong, China.
sample treatment protocol
Mixed buds, three buds for each individual, were collected after 0d, 6d, 12d, 15d, 18d and 24d chilling requirement fulfilling during the period of bud dormancy release. Three replications (3 plants/ replication) were harvested and immediately frozen in liquid nitrogen and stored at -80°C until use.