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Browse MaizePLEX Experiment Data

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Evaluation of Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes
Michael Gore , Cornell University (mag87@cornell.edu, esb33@cornell.edu)
Experiment design (36 hybridizations)
protocol
•mRNA •Cot filtration (CF) •Methylation filtration (MF) •Amplified fragment restriction polymorphism (AFLP)
genotype
•B73 maize inbred •Mo17 maize inbred •CML69 maize inbred

We tested four gene enrichment and complexity reduction target preparation methods for scoring SFPs on the Affymetrix GeneChip 18k Maize Genome Arr...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Evaluation of Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes
Accession No: ZM10
Microarray: maize18k
Visibility: public
Experiment Type:
Experiment Factor(s):
protocol
•mRNA   •Cot filtration (CF)   •Methylation filtration (MF)   •Amplified fragment restriction polymorphism (AFLP)
genotype
•B73 maize inbred   •Mo17 maize inbred   •CML69 maize inbred
Quality Control: biological replicates,technical replicates
Treatment summary:
 protocol  genotype  # replicates
 mRNA  B73 maize inbred  3
 mRNA  Mo17 maize inbred  3
 mRNA  CML69 maize inbred  3
 Cot filtration (CF)  B73 maize inbred  3
 Cot filtration (CF)  Mo17 maize inbred  3
 Cot filtration (CF)  CML69 maize inbred  3
 Methylation filtration (MF)  B73 maize inbred  3
 Methylation filtration (MF)  Mo17 maize inbred  3
 Methylation filtration (MF)  CML69 maize inbred  3
 Amplified fragment restriction polymorphism (AFLP)  B73 maize inbred  3
 Amplified fragment restriction polymorphism (AFLP)  Mo17 maize inbred  3
 Amplified fragment restriction polymorphism (AFLP)  CML69 maize inbred  3
Total hybridizations: 36
Description: 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.
Publication: 'Evaluation of Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes', Michael Gore,* Peter Bradbury, Ren Hogers, Matias Kirst, Esther Verstege, Jan van Oeveren, Johan Peleman, Edward Buckler, and Michiel van Eijk
The Plant Genome [A Supplement to Crop Science].Crop Sci. 47(S2) S135S148 .July 2007 No. 2
pubmed: not in pubmed
Created: 2007-11-26 23:05:33
Last Update: 2007-11-29 16:29:49
GEO Accession GSE12770
Submitter: Michael Allen Gore
Name: Michael Gore
Institution: Cornell University
Head of Laboratory: Dr. Edward S. Buckler
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