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Series GSE12770 Query DataSets for GSE12770
Status Public on Sep 16, 2008
Title Evaluation of Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes
Organism Zea mays
Experiment type Other
Summary We tested four gene enrichment and complexity reduction target preparation methods for scoring SFPs on the Affymetrix GeneChip 18k Maize Genome Array (Maize GeneChip). Methylation filtration (MF), Cot filtration (CF), mRNA-derived cRNA, and amplified fragment length polymorphism (AFLP) methods were applied to three diverse maize inbred lines (B73, Mo17, and CML69) with three replications per line (36 Maize GeneChips). Due to large amounts of repetitive, mobile DNA, the maize genome requires a target preparation method that offers both a high level of gene enrichment and accurate scoring of SFPs. The objectives of this research are (i) to determine which target preparation method (CF, MF, mRNA, or AFLP) optimally enriches for gene sequences complementary to probe sequences on the Affymetrix GeneChip Maize Genome Array and (ii) to estimate SFP detection power for each target method. The AFLP technology is covered by patents, and patent applications owned by Keygene N.V. AFLP is a registered trademark of Keygene N.V. GeneChip. This work was supported in part by U.S. National Science Foundation grant DBI-0321467 and USDA-ARS. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Michael Gore. The equivalent experiment is ZM10 at PLEXdb.]
 
Overall design protocol: mRNA - genotype: B73 maize inbred(3-replications)
protocol: mRNA - genotype: Mo17 maize inbred(3-replications)
protocol: mRNA - genotype: CML69 maize inbred(3-replications)
protocol: Cot filtration (CF) - genotype: B73 maize inbred(3-replications)
protocol: Cot filtration (CF) - genotype: Mo17 maize inbred(3-replications)
protocol: Cot filtration (CF) - genotype: CML69 maize inbred(3-replications)
protocol: Methylation filtration (MF) - genotype: B73 maize inbred(3-replications)
protocol: Methylation filtration (MF) - genotype: Mo17 maize inbred(3-replications)
protocol: Methylation filtration (MF) - genotype: CML69 maize inbred(3-replications)
protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: B73 maize inbred(3-replications)
protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: Mo17 maize inbred(3-replications)
protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: CML69 maize inbred(3-replications)
Web link http://www.plexdb.org/modules/PD_browse/experiment_browser.php?experiment=ZM10
 
Contributor(s) Gore M
Citation Evaluation of Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes. Michael Gore, Peter Bradbury, René Hogers, Matias Kirst, Esther Verstege, Jan van Oeveren, Johan Peleman, Edward Buckler, and Michiel van Eijk. Crop Sci. 47(S2) S135-S148. 14 July 2007. The Plant Genome [A Supplement to Crop Science] July 2007 No. 2
Submission date Sep 13, 2008
Last update date Mar 20, 2012
Contact name PLEXdb Curator, Sudhansu Dash
Organization name Iowa State University
Department Virtual Reality Application Center
Lab PLEXdb
Street address 1023 Crop Genomes Informatics Lab (Iowa State University)
City Ames
State/province IA
ZIP/Postal code 50011
Country USA
 
Platforms (1)
GPL4032 [Maize] Affymetrix Maize Genome Array
Samples (36)
GSM320438 protocol: mRNA - genotype: B73 maize inbred - rep1
GSM320439 protocol: mRNA - genotype: B73 maize inbred - rep2
GSM320440 protocol: mRNA - genotype: B73 maize inbred - rep3
Relations
BioProject PRJNA112763

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE12770_RAW.tar 75.8 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table
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