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| Status |
Public on Mar 26, 2011 |
| Title |
skl1-1 roots NPA at 21d |
| Sample type |
RNA |
| |
|
| Source name |
skl1-1 roots harvested 21 days after NPA treatment
|
| Organism |
Medicago truncatula |
| Characteristics |
background: Jemalong A17
genotype: skl1-1
tissue: roots
growth condition: BNM containing 2.5% (w/v) agar
treatment: 200 µM NPA
time after treatment: 21 day
amount of total rna: 40 µg
|
| Treatment protocol |
Roots were flooded 6 days after planting with 20 ml of solution containing the corresponding treatment. The excess of solution was removed at the bottom of the plate. Root tips were spot-inoculated with 1 µl of a suspension of Sinorhizobium meliloti exoA (RM7031) (OD600 = 0.05) or Sinorhizobium meliloti Rm1021 (OD600 = 0.05).
Root segments (5 cm) were harvested centered on the root tip mark at the moment of treatment: ATI, bacterial or mock. Root tips (if within the 5 cm segment) and lateral roots were removed. For each preparation, total RNA was isolated from approximately 60 root segments.
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| Growth protocol |
Twenty Medicago truncatula plants were grown per Petri plate (240835, Nunc, Rochester, NY, USA) containing buffered nodulation medium (BNM; Ehrhardt et al. 1992), pH 6.5, with 1 µM 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 |
Bioarray high yield RNA transcription labeling kit (Enzo Diagnostics) following the manufacturer's instructions.
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| |
|
| Hybridization protocol |
Hybridization was performed as described in the Affymetrix technical manual, at the Stanford Protein and Nucleic Acid Facility (Stanford, CA).
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| Scan protocol |
Scanning were performed as described in the Affymetrix technical manual.
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| Description |
skl_NPA_21d
Gene expression data from roots harvested 21 day after NPA 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 16, 2011 |
| Last update date |
Mar 26, 2011 |
| Contact name |
Adriana Parra Rightmyer |
| E-mail(s) |
[email protected]
|
| 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) |
| GSE28172 |
Expression data of Medicago truncatula skl1-1 roots treated with S. meliloti wild-type or auxin transport inhibitors |
| 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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