For colonization experiments Laccaria bicolor innoculum was grown on a substrate of peat moss:vermiculite (3:1) dampened with liquid Pachlewski medium medium (2.7 mM di-ammonium tartrate, 7.3 mM KH2PO4, 2.0 mM MgSO4·7 H2O, 13 mM maltose, 110 mM glucose, 2.9 µM thiamine-HCl, and 1 mL of a trace-element stock solution Kanieltra medium) for 3 months. Pre-rooted stem cuttings of Populus trichocarpa (rooted for 1 week in a solution of: 2.5 mM KNO3, 0.8 mM KH2PO4, 1 mM MgSO4.7 H2O, 2.3 mM Ca(NO3)2.4 H2O, 23 μM H3BO3, 4.6 μM MnCl2.4 H2O, 0.4 μM ZnSO4.7 H2O, 0.09 μM (NH4)2MoO4, 0.18 μM CuSO4.5 H2O, 20 μM FeNaEDTA, pH 5.8) were planted in a 9:1 mixture (v/v) of Terra-Green (a calcined attapulgite clay supplied by Turf-Pro, UK):L. bicolor inoculum. Each pot was given 20 mL of a dilute nutrient solution (0.8 mM KNO3, 0.8 mM Ca(NO3)2.4 H2O, 0.3 mM NaH2PO4, 0.3 mM MgSO4.7 H2O, and 20 μL trace elements solution Kanieltra per liter of solution) weekly. Roots were destructively harvested at 2, 4, 6 and 12 weeks after being put into contact with L. bicolor. Control roots without contact with the fungus were harvested at the same time points.
Extracted molecule
total RNA
Extraction protocol
RNA was extracted using the RNAeasy kit (Qiagen) as per the manufacturer’s instructions with the addition of 20 mg PEG8000/mL to the extraction RLC buffer solution and an on-column DNA digestion step with DNAse I (Qiagen). RNA qualityb was verified by Experion HighSens capillary gels (Bio-Rad). Total RNA preparations were amplified using the SMARTer PCR cDNA Synthesis Kit (Clontech) according to the manufacturer’s instructions.
Label
Cy3
Label protocol
Labelling by NimbleGen Company
Hybridization protocol
Hybridization by NimbleGen Company
Scan protocol
Scanning by NimbleGen Company
Description
This sample is from mycorrhizal root tips. It is the first of four biological replicates used in this experiment.
Data processing
Expression values reflect across-array quantile normalization and gene calls generated using the Robust Multichip Average (RMA). For information on RMA, see Biostatistics 2003 Apr; 4(2): 249-264.
