|
| Status |
Public on Apr 21, 2019 |
| Title |
Medic_root_myco_pot4 |
| Sample type |
RNA |
| |
|
| Source name |
whole roots
|
| Organism |
Medicago truncatula |
| Characteristics |
symbiosis: rhizobial (strain 10) and mycorrhizal (R. i. SYM5)
|
| Treatment protocol |
Both variants were treated with rhizobial solution, half of pots (myco) treated with cutted roots of leek (Allium porum) infected with Rhizophagus irregularis, the other half of pots with cutted roots of non-infected leek. Upon harvest, the shoots and roots were cleaned of soil in ice-cold water and flash-frozen in liquid nitrogen. Samples were homogenized in liquid nitrogen with a mortar and pestle.
|
| Growth protocol |
Plant were grown in 2.5L pots filled with a substrate mix consisting of autoclaved clay granules (zeolite) 1-2.5mm, autoclaved sand, and gamma irradiated local soil mixed in a ratio of 9:9:2 (v:v:v) under glasshouse conditions (25/15°C day/night, 14h photoperiod, minimum of 150 mikromol photons m-2 s-1), and inoculated either with a mycorrhizal (pot-produced with leek as a host plant) inoculum of Rhizophagus irregularis SYM5 (90 ml per pot) or mock inoculum produced under the same conditions as the mycorrhizal inoculum. All plants were additionally inoculated with a suspension of Sinorhizobium meliloti strain 10 isolated from the field soil used to prepare the planting mixture (10 billion cells per pot). The plants were grown for a total of five week, from the 3th week onwards each pot received 65 mL Long-Ashton nutrient solution with reduced (20%) of the P concentration (i.e., 0.26 mM P) weekly. Root colonization by the mycorrhizal fungus reached 44% of the root length colonized in the mycorrhizal treatment, whereas no colonization was detected in the mock-inoculated plants. This was further confirmed by qPCR with Rhizophagus-specific TaqMan probe on cDNA obtained from the RNA extracts.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Homogenized powder (3 g) + 80°C mixture of phenol (4 mL) & extraction buffer (4 mL; 1.95 g of 100mM Tris, 0.0424 g of 100mM LiCl, 0.372 g of 10mM EDTA and 1 g of 1% SDS per 100 mL of DEPC-treated water (0.1% DEPC), adjusted to pH = 6). Mixed, heated. + chlorophorm (4 mL), mixed and centrifuged; supernatant taken, mixed with additional chlorophorm (4 mL; repeated 3 times). Supernatant (2 mL) + 8M LiCl (0.68 mL) on ice overnight. Pellet resuspended in 75% EtOH (0.5 mL), centrifuged; pellet diluted in RNase-free H2O (250 uL) + 96% EtOH (500 uL) + 3M NaAcetate (25 uL) and on ice for 1 hour. Centrifuged and pellet diluted in RNase-free H2O (100 uL).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the GeneChip® 3’ IVT Express Kit Labeling Assay from 100 ng of total RNA, Array Format 49 (standard).
|
| |
|
| Hybridization protocol |
Following fragmentation, 12.5 ug of cRNA were hybridized using GeneChip® Hybridization, Wash, and Stain Kit according to manufacturers instruction.
|
| Scan protocol |
GeneChips were scanned using the Genechip scanner 7G 3000.
|
| Description |
35 dpp; 12/2014-02/2015; harvested 11-12 a.m.
|
| Data processing |
The data were normalized with the RMA algorithm, than the trimmed mean was scaled to 1000. The data processing was performed by Genevestigator curators (Nebion, Zurich, Switzerland).
|
| |
|
| Submission date |
Feb 20, 2019 |
| Last update date |
Apr 22, 2019 |
| Contact name |
Jan Konečný |
| E-mail(s) |
[email protected]
|
| Phone |
+420776154028
|
| Organization name |
Faculty of Science, Charles University
|
| Department |
Experimental Plant Biology
|
| Lab |
Plant Morphogenesis Regulatory Factors
|
| Street address |
Albertov 6
|
| City |
Prague 2 |
| ZIP/Postal code |
12843 |
| Country |
Czech Republic |
| |
|
| Platform ID |
GPL4652 |
| Series (1) |
| GSE126833 |
Rhizobial and non/mycorrhizal Medicago truncatula roots and shoots transcriptome |
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