|
| Status |
Public on Jun 22, 2015 |
| Title |
3w Control-1 |
| Sample type |
RNA |
| |
|
| Source name |
3w Control lateral root
|
| Organism |
Populus tremula x Populus alba |
| Characteristics |
tissue: control lateral root
infection: none
|
| Growth protocol |
Pre-rooted stem cuttings of P. tremula x P. alba (rooted for 4 weeks on in vitro agar half strength Murashig and skoog medium) were preparded. In parallel, Laccaria bicolor inoculum was grown on in vitro agar Pachlewski 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 10 days. Roots were destructively harvested at 3 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 quality 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 control roots. It is the first 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 |
Feb 24, 2015 |
| Last update date |
Jun 22, 2015 |
| Contact name |
Annegret Kohler |
| E-mail(s) |
annegret.kohler@inrae.fr
|
| 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 |
GPL13485 |
| Series (1) |
| GSE66237 |
Poplar-Laccaria Mycorrhizal Roots |
|
