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Expression survey of Rpp1 soybean line PI200492 resistant to P. pachyrhizi
katherine,,schneider, USDA, Ft. Detrick, MD (katherine.schneider@ars.usda.gov)
Experiment design (27 hybridizations)
pathogen isolates
•HW94-1(resistant) •TW72-1(susceptible) •mock
time
•0 hai •6 hai •12 hai •24 hai •48 hai

This experiment has been imported by PLEXdb from NCBI GEO (GSE8432)

Series_summary:
Affymetrix soybean genome arrays were used to id...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Expression survey of Rpp1 soybean line PI200492 resistant to P. pachyrhizi
Accession No: GM15
Microarray: Soybean
Visibility: public
Experiment Type:
Experiment Factor(s):
pathogen isolates
•HW94-1(resistant)   •TW72-1(susceptible)   •mock
time
•0 hai  •6 hai  •12 hai  •24 hai  •48 hai
Quality Control: biological replicates
Treatment summary:
 pathogen isolates  time  # replicates
 HW94-1(resistant)  0 hai  0
 HW94-1(resistant)  6 hai  3
 HW94-1(resistant)  12 hai  3
 HW94-1(resistant)  24 hai  3
 HW94-1(resistant)  48 hai  3
 TW72-1(susceptible)  0 hai  0
 TW72-1(susceptible)  6 hai  3
 TW72-1(susceptible)  12 hai  3
 TW72-1(susceptible)  24 hai  3
 TW72-1(susceptible)  48 hai  3
 mock  0 hai  3
 mock  6 hai  0
 mock  12 hai  0
 mock  24 hai  0
 mock  48 hai  0
Total hybridizations: 27
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE8432)

Series_summary:
Affymetrix soybean genome arrays were used to identify genes differentially expressed in the immune resistance response at 6, 12, 24, and 48 hours after inoculation with Phakopsora pachyrhizi isolates TW72-1 or HW94-1 soybean + HW94-1 = resistant; soybean + TW72-1 = susceptible


Keywords: time course

Series_overall_design:
For each of 4 time points (6, 12, 24 and 48 hours post inoculation) a soybean PI200492 plant was inoculated with 2 treatments: HW94-1, or TW72-1. A mock inoculation was performed and sampled at time 0. There were three biological replicates of the entire experiment, for a total of 27 samples. During data analysis two samples failed the quality control metrics and were removed from the analysis, leaving 25 samples in the final data set.

PLEXdb Curator's Note:
The original contributors have indicated that two samples failed the quality control metrics and were removed from their own analysis, leaving 25 samples in the final data set.
Publication: 'A microarray analysis for differential gene expression in the soybean genome using Bioconductor and R', Gregory Alvord W, Roayaei JA, QuiƱones OA, Schneider KT
Brief Bioinform 2007 Nov;8(6):415-31
pubmed: 17906332
Created: 2009-06-04 11:49:54
Last Update: 2009-06-04 12:34:15
GEO Accession GSE8432
Submitter: PLEXdb Curator
Name: katherine,,schneider
Institution: USDA, Ft. Detrick, MD
Head of Laboratory: --
email(s):
Homepage:

 
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