|
| Status |
Public on Oct 10, 2014 |
| Title |
4W ECM-2 |
| Sample type |
RNA |
| |
|
| Source name |
4W ECM
|
| Organisms |
Pseudotsuga menziesii; Laccaria bicolor S238N-H82 |
| Characteristics |
time: 4 w
tissue: mycorrhizal root tips
|
| Growth protocol |
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. One week old seedlings of Pseudotsuga menziesii 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 and 6 weeks after being put into contact with L. bicolor.
|
| 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 second of three 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.
|
| |
|
| Submission date |
Oct 09, 2014 |
| Last update date |
Oct 10, 2014 |
| Contact name |
Annegret Kohler |
| E-mail(s) |
[email protected]
|
| Phone |
+33 (0)383 394072
|
| Organization name |
INRAE
|
| Department |
UMR 1136
|
| Lab |
Interactions Arbres/Micro-organismes
|
| Street address |
Centre INRAE Grand Est Nancy
|
| City |
Champenoux |
| ZIP/Postal code |
54280 |
| Country |
France |
| |
|
| Platform ID |
GPL14641 |
| Series (1) |
| GSE62226 |
Laccaria-Douglas fir: A Timecourse of Mycorrhizal Root Tip Development |
|
