|
| Status |
Public on Feb 04, 2009 |
| Title |
Col whole leaf, 3dpi, biological rep 3 |
| Sample type |
RNA |
| |
|
| Source name |
Col whole leaf infected with Golovinomyces orontii 3d
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
Genotype: wild type
Age: 4 weeks old at time 0 (innoculation)
tissue: whole leaf
|
| Treatment protocol |
At four weeks, a subset of boxes was infected with a moderately heavy innoculum of G.orontii using a settling tower. Moderately heavy innoculum is 2-3 fully G.O.-infected leaves with conidia 10-14 dpi. Infected plants were placed in a separate Percival growth chamber under the same conditions as the pathogen-free Percival. Infections, with the exception of the 6 hr timepoint, were performed at 2:30 pm to standardize experiments and minimize circadian effects. Samples were harvested at 0 h (just prior to infection), 6 hpi, 1 dpi, 3 dpi, 5 dpi, and 7 dpi. An uninfected 7 dpi sample was also collected. For each sample, three fully expanded mature leaves were excised per plant, with leaves from two randomly selected plants used to prepare a single RNA sample. Three independent experiments were performed with triplicate samples collected for each datapoint within each experiment. Four biological replicates were processed. One from each of the three separate experiments and an additional biological replicate from Experiment 2.
|
| Growth protocol |
Arabidopsis seeds were stratified in 0.1% agarose for 3-5 days and planted in boxes containing Metromix 200 soil. Seeds were equally distributed in each box using a template, with 9 plants per box, alternating wild type and mutant. The flats (6 boxes per flat) were covered with plastic trays for 1 week and then uncovered. Flats were watered from below and fertilized at 2-1/2 weeks. Plants were grown in Percival AR66L growth chambers at 22°C, 80% RH, 14 h photoperiod with photosynthetically active radiation=150 µE m-2 s-1.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Qiagen RNeasy Plant RNA Miniprep kit according to the manufacturer's instructions. Samples were split in two before homogenization and repooled before loading on the RNA-binding column. RNA quality was determined by the A260/A280 ratio and by its profile on an Agilent 2100 Bioanalyzer.
|
| Label |
biotin
|
| Label protocol |
Target labeling was performed according to the protocol given in the Affymetrix GeneChip Expression Analysis Technical Manual 701025 rev 1.
|
| |
|
| Hybridization protocol |
Microarray hybridizations to Affymetrix Arabidopsis ATH1 GeneChips were performed according to the protocol given in the Affymetrix GeneChip Expression Analysis Technical Manual 701025 rev 1.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneArray® 2500 Scanner at the Harvard University Bauer Center for Genomics Research.
|
| Description |
Gene expression data from wild type whole mature leaves at 3d post Golovinomyces orontii infection
|
| Data processing |
Log2 (expression values) were extracted using robust multi-array analysis (RMA) implemented in the function rma() in the Bioconductor software package affy. Background correction was performed by correcting PM (perfect match) only, to reduce noise from signal intensity. Quantile normalization was performed to make the distributions of signal intensities uniform across chips. Quality assessment was done using the weights outputted from the linear model fitting function fitPLM() in the R package AffyExtensions. One sample (Col whole leaf, 7d UI, biological rep 1; cel file MW 1.A.7) was not included in subsequent analyses as expression for this sample was not as highly correlated with its biological replicates.
|
| |
|
| Submission date |
Nov 25, 2008 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Mary C Wildermuth |
| E-mail(s) |
[email protected]
|
| Phone |
510-643-4861
|
| Organization name |
University of California Berkeley
|
| Department |
Plant and Microbial Biology
|
| Street address |
221 Koshland Hall MC3102
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE13739 |
Golovinomyces orontii time course with Col-0 and eds16-1 |
|
| Relations |
| Reanalyzed by |
GSE118579 |
| Reanalyzed by |
GSE119083 |
