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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).
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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.
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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.
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|
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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 |