Comment[ArrayExpressAccession] E-GEOD-27612
Public Release Date 2011-07-31
Investigation Title Differential gene expression in resistant and susceptible peanut cultivars during Aspergillus infection
Comment[Submitted Name] Differential gene expression in resistant and susceptible peanut cultivars during Aspergillus infection
Experiment Description To identify peanut Aspergillus-interactive and Aspergillus-resistance genes, we carried out a large scale peanut Expressed Sequence Tag (EST) project followed by a peanut microarray study. For expression profiling, resistant and susceptible peanut cultivars were infected with a mixture of Aspergillus flavus and parasiticus spores. Microarray analysis identified 65 and 1 genes in resistant (C20) and susceptible (TF) cultivars, respectively, that were up-regulated in response to Aspergillus infection. In addition we identified 40 putative Aspergillus-resistance genes that were constitutively up-expressed in the resistant cultivar in comparison to the susceptible cultivar. Some of these genes were homologous to peanut, corn, and soybean genes previously shown to confer resistance to fungal infection. These results provide a comprehensive genome-scale platform for future studies focused on developing Aspergillus-resistant peanut cultivars through conventional breeding, marker-assisted breeding, or biotechnological methods by gene manipulation. Four samples were analyzed with four hybs. Two samples were obtained from resistant (C20) and and susceptible (TF) cultivars. Two factors were varied in the experimental design: (i) peanut cultivars (resistant (GT-C20) and susceptible (TF)) and (ii) Aspergillus exposure. A combination of these factors produced four hybridizations as follows: (1) C20Y vs. TFY (GT-C20 infected vs. TF infected) (2) C20Y vs. C20N (GT-C20 infected vs. not infected) (3) TFY vs. TFN (TF infected vs. not infected) (4) C20N vs. TFN (GT-C20 not infected vs. TF not infected)
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Term Source Name EFO
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Term Source File http://www.ebi.ac.uk/efo/efo.owl
Person Last Name Fedorova Guo Fedorova Chen Wan Nierman Bhatnagar Yu
Person First Name Natalie Baozhu Natalie Xiaoping Chun-Hua William Deepak Jiujiang
Person Mid Initials D C
Person Email natalief@jcvi.org
Person Affiliation JCVI
Person Phone 301-795-7756
Person Fax 301-838-0208
Person Address Infectious Disease, JCVI, 9704 Medical Center Dr, Rockville, MD, USA
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Protocol Name P-GSE27612-3 P-GSE27612-4 P-GSE27612-2 P-GSE27612-1 P-GSE27612-9 P-GSE27612-6 P-GSE27612-11 P-GSE27612-10 P-GSE27612-12 P-GSE27612-13 P-GSE27612-5 P-GSE27612-7 P-GSE27612-8
Protocol Description ID_REF =
VALUE = Lowess normalized log2 of channel 2 (C20N) over channel 1 (C20Y) ID_REF =
VALUE = Lowess normalized log2 of channel 2 (TFN) over channel 1 (C20N) ID_REF =
VALUE = Lowess normalized log2 of channel 2 (TFY) over channel 1 (TFN) ID_REF =
VALUE = Lowess normalized log2 of channel 2 (TFY) over channel 1 (C20Y) Hybridization was performed according to the JCVI’s protocols (http://www.pga.tigr.org/sop/M005_1a.pdf) Peanut immature kernel seeds harvested 90 days after planting LOWESS normalized, flip-dye analyzed, inslide replicate averaged log2 ratio (experimental/control) After washing, slides were scanned with a GenePix 4000b scanner using GenePix Pro 3.0 software. PMT gains were changed in order to generate images with red:green ratios of as close to 1:1 as possible. Images were saved as .TIF files and TIGR Spotfinder (Saeed et al, 2003) was used to quantitate fluorescent intensities. Poor quality spots were identified manually and flagged. After Spotfinder analysis, resulst were exported as TIGR software compatible MEV files following local background subtraction. not inoculated with Aspergillus flavus and A. paraciticus not inoculated with Aspergillus flavus and A. paraciticus inoculated with Aspergillus flavus and A. paraciticus spores 60 days after planting and harvested 30 days after inoculation Frozen kernels were ground in liquid nitrogen, and total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA). The amount and quality of the total RNA was measured with a NanoDrop Spectrophotometer (NanoDrop Technologies, Wilmington, DE). Labeling was performed according to the JCVI’s protocols (http://www.pga.tigr.org/sop/M005_1a.pdf)
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Protocol Type bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation hybridization grow feature_extraction image_aquisition specified_biomaterial_action specified_biomaterial_action specified_biomaterial_action nucleic_acid_extraction labeling
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Experimental Factor Name CULTIVAR BIOSOURCEPROVIDER INFECTION
Experimental Factor Type cultivar BioSourceProvider infection
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Comment[SecondaryAccession] GSE27612
Comment[GEOLastUpdateDate] 2011-07-31
Comment[AEExperimentType] transcription profiling by array
Comment[GEOReleaseDate] 2011-07-30
Comment[ArrayExpressSubmissionDate] 2011-03-01
SDRF File E-GEOD-27612.sdrf.txt