|
| Status |
Public on Aug 09, 2010 |
| Title |
wrky72-2-MOCK-REP2 |
| Sample type |
RNA |
| |
|
| Source name |
Aerial tissues of 2 week old soil grown Arabidopsis seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype/variation: wrky72-2 mutant
t-dna insertion line: SALK-055293
infection: mock treated
|
| Treatment protocol |
Aerial tissues of 2 week old soil grown Arabidopsis seedlings were sprayed with 3X10^4 spores/ml of HpaNoco2 or mock solution and harvested at 96 h after the treatment. Mock treatments were sprayed with water only. Three independent biological replicates were performed for each treatment.
|
| Growth protocol |
Arabidopsis thaliana plants (accessions Col-0 and homozygous T-DNA insertion lines SALK_145765 and SALK-055293) were grown on soil in a semi-sterile growth chamber under fluorescent lights (14 hours light, 10 hours dark, 21 centi grades, 100 Einstein/m2/s).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For harvesting, the aerial plant parts were shock-frozen in liquid nitrogen. Total RNA was isolated from seedlings using TRIZOL (Invitrogen) follwing the manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Arabidopsis Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 with 7G.
|
| Description |
Gene expression data in mock treated wrky72 mutant
|
| Data processing |
Microarray analysis was performed in the R statistical programming environment using Bioconductor packages (http:/www.bioconductor.org). Values were normalized using the robust multichip averaging (RMA) algorithm in Bioconductor. Statistical analysis was performed with the LIMMA package. The p values were adjusted using the Benjamini and Hochberg method for False Discovery Rate (FDR) of 0.05. Significant up- and down-regulated genes were selected based on an adjusted p-value ≤ 0.01 compared to mock treatments.
|
| |
|
| Submission date |
Sep 29, 2009 |
| Last update date |
Sep 03, 2021 |
| Contact name |
Kishor Kumar Bhattarai |
| E-mail(s) |
bkk33@cornell.edu
|
| Phone |
607-254-6424
|
| Organization name |
University of California
|
| Department |
Plant Pathology
|
| Lab |
Kaloshian
|
| Street address |
9000 University Avenue
|
| City |
Riverside |
| State/province |
CA |
| ZIP/Postal code |
92521 |
| Country |
USA |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE18329 |
Transcriptome changes triggered by Hyaloperonospora parasitica arabidopsis Noco2 in WT and wrky72 mutants at 96 hpt |
|
| Relations |
| Reanalyzed by |
GSE118579 |
