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) Date of Experiment Term Source Name EFO Term Source Version 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 Person Roles submitter Person Roles Term Source REF Person Roles Term Accession Number Normalization Type Normalization Term Accession Number Normalization Term Source REF Replicate Type Replicate Term Accession Number Replicate Term Source REF Experimental Design Experimental Design Term Accession Number Experimental Design Term Source REF Quality Control Type Quality Control Term Accession Number Quality Control Term Source REF 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) Protocol Software Protocol Hardware Protocol Contact 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 Protocol Term Source REF Protocol Term Accession Number Experimental Factor Name CULTIVAR BIOSOURCEPROVIDER INFECTION Experimental Factor Type cultivar BioSourceProvider infection Experimental Factor Term Source REF Experimental Factor Term Accession Number Publication Title Publication Author List PubMed ID Publication DOI Publication Status Publication Status Term Source REF Publication Status Term Accession Number 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