|
| Status |
Public on Mar 26, 2011 |
| Title |
roots Rm1021 at 21d |
| Sample type |
RNA |
| |
|
| Source name |
roots harvested 21 days after Rm1021 treatment
|
| Organism |
Medicago truncatula |
| Characteristics |
cultivar: Jemalong A17
genotype: wild-type
tissue: roots
growth condition: BNM containing 2.5% (w/v) agar
treatment: Sinorhizobium meliloti Rm1021
time after treatment: 21 days
amount of total rna: 40 µg
|
| Treatment protocol |
Plants were inoculated 6 d after planting with either 1 μl of a suspension of Rm1021 (optical density at 600 nm [OD600]=0.05) or 1 μl of 0.5X BNM as a mock control.
|
| Growth protocol |
Twenty M. truncatula plants were grown per Petri plate (240835, Nunc, Rochester, NY, USA) containing buffered nodulation medium (BNM; Ehrhardt et al., 1992), pH6.5 with 1 mM α-aminoisobutyric acid (AIB). Three plates were performed at this time point and treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was used for double-stranded cDNA synthesis.
|
| Label |
biotin
|
| Label protocol |
Biotin-labeled cRNA was synthesized using the BioArray high yield RNA transcription labeling kit (Enzo diagnostics).
|
| |
|
| Hybridization protocol |
Hybridization was performed as described in the Affymetrix technical manual, at the Stanford Protein and Nucleic Acid Facility (Stanford, CA).
|
| Scan protocol |
Scanning were performed as described in the Affymetrix technical manual.
|
| Description |
A17_Rm1021_21d
Gene expression data from roots harvested 21 day after Rm 1021 treatment.
|
| Data processing |
Pixel values were extracted from scan files by using Affymetrix MAS 5.0 software, and .CEL files were analyzed by using DCHIP 1.3. Probe sets specifying bacterial genes were masked before analysis. Expression analysis was performed as described in Mitra et al., 2004 (PMID 15220482). The data from the independent biological replicates for each condition were combined.
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| |
|
| Submission date |
Mar 24, 2011 |
| Last update date |
Sep 16, 2011 |
| Contact name |
Adriana Parra Rightmyer |
| E-mail(s) |
Adriana@ArtCubeSoftware.com
|
| Organization name |
Stanford University
|
| Department |
Biology
|
| Lab |
Sharon R. Long
|
| Street address |
371 Serra Mall
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL9757 |
| Series (2) |
| GSE28173 |
Genes differentially expressed in wild-type Medicago truncatula plants during nodulation |
| GSE28174 |
Expression data from Medicago truncatula roots treated with S. meliloti wild-type or exoA mutant bacteria, or auxin transport inhibitors |
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