8 protocols
AccessionNameType
P-AFFY-6
feature_extraction
Title: Affymetrix CEL analysis. Description:
Affymetrix:Protocol:ExpressionStat
bioassay_data_transformation
Title: Affymetrix CHP Analysis (ExpressionStat). Description:
P-AFFY-2
labeling
RNA was isolated using the RNeasy Plant Mini Protocol (QIAGEN, Clifton Hill, Australia) and the quality of the RNA was assessed using the Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA) where spectrophotometric analysis was carried out to determine the A260 to A280 ratio and the concentration. For qRT-PCR, cDNA synthesis was carried out using the Biorad (Perth) iScript cDNA synthesis kit according to manufacturers instructions. For arrays, the cRNA was prepared from 3 ug of total RNA almost exactly as described in the Affymetrix GeneChip Expression Analysis Technical Manual.
Affymetrix:Protocol:Hybridization-FS450_0004[]
hybridization
 
pool
Equal amounts of RNA from triplicate samples were pooled.
 
nucleic_acid_extraction
Each RNA sample is obtained from seedlings of Arabidopsis. The frozen plant tissue (~100 mg) was ground in tiny mortars dipped in liquid nitrogen. The frozen powder was carefully transfered into 1.5 ml microcentrifuge tubes using small funnels and rubber spatulas also cooled with liquid nitrogen. Total RNA was extracted using RNeasy Mini kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer's instructions and purified with an RNeasy minelute cleanup (Qiagen).
 
specified_biomaterial_action
Pro35SLBD16:GR or Pro35SLBD18:GR transgenic seedlings that overexpress LBD16 or LBD18 fused to glucocorticoidsteroid hormone binding domain(GR) under CaMV35S promoter were grown for 12 days under long-day conditions (16h light/ 8h dark) on the ½ Murashige Skoog(MS) medium containing vitamins, 1.5% sucrose, 2.5 mM Mes, pH 5.7, and 0.8% agar, treated with 10 uM dexamethasone (DEX) or mock-treated for 2.5 h.
 
grow
Pro35SLBD16:GR or Pro35SLBD18:GR transgenic seedlings that overexpress LBD16 or LBD18 fused to glucocorticoidsteroid hormone binding domain(GR) under CaMV35S promoter were grown for 12 days under long-day conditions (16h light/ 8h dark) on the Murashige Skoog(MS) medium containing vitamins, 1.5% sucrose, 2.5 mM Mes, pH 5.7, and 0.8% agar, treated with 10 uM dexamethasone (DEX) or mock-treated for 2.5 h.