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Browse RicePLEX Experiment Data

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Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
Ramil,Paner,Mauleon, International Rice Research Institute, Los Banos, Philippines (r.mauleon@cgiar.org)
Experiment design (17 hybridizations)
genotype
•mutant_d1 •mutant_d256 •mutant_d1137 •mutant_d2943 •mutant_g282 •mutant_g650 •mutant_g6485 •mutant_g6489 •mutant_g6603 •mutant_g6686 •mutant_g6728 •mutant_g7534 •mutant_g9799 •mutant_g6989 •mutant_f1856 •mutant_f2045 •wildtype_control

This experiment has been imported by PLEXdb from NCBI GEO (GSE15071)

Series_summary:
Rice deletion mutants have not been widely used...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
Accession No: OS26
Microarray: Rice57k
Visibility: public
Experiment Type:
Experiment Factor(s):
genotype
•mutant_d1   •mutant_d256   •mutant_d1137   •mutant_d2943   •mutant_g282   •mutant_g650   •mutant_g6485   •mutant_g6489   •mutant_g6603   •mutant_g6686   •mutant_g6728   •mutant_g7534   •mutant_g9799   •mutant_g6989   •mutant_f1856   •mutant_f2045   •wildtype_control
Quality Control: biological replicates
Treatment summary:
 genotype  # replicates
 mutant_d1  1
 mutant_d256  1
 mutant_d1137  1
 mutant_d2943  1
 mutant_g282  1
 mutant_g650  1
 mutant_g6485  1
 mutant_g6489  1
 mutant_g6603  1
 mutant_g6686  1
 mutant_g6728  1
 mutant_g7534  1
 mutant_g9799  1
 mutant_g6989  1
 mutant_f1856  1
 mutant_f2045  1
 wildtype_control  1
Total hybridizations: 17
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE15071)

Series_summary:
Rice deletion mutants have not been widely used in functional genomics, because the mutated genes are not tagged and therefore, difficult to identify. We present a microarray-based approach to identify deleted genomic regions in rice mutants selected from a large collection generated by gamma ray or fast neutron treatment. Our study focuses not only on the utility of this method for forward genetics, but also its potential as a reverse genetics tool through accumulation of hybridization data for a collection of deletion mutants harboring multiple genetic lesions. We demonstrate that hybridization of labeled genomic DNA directly onto the Affymetrix Rice GeneChip® allows rapid localization of deleted regions in rice mutants. Deletions ranged in size from one gene model to ~500 kb and were predicted on all 12 rice chromosomes. The utility of the technique as a tool in forward genetics was demonstrated in combination with an allelic series of mutants to rapidly narrow the genomic region, and eventually identify a candidate gene responsible for a lesion mimic phenotype. We demonstrate the utility of oligonucleotide arrays to discover deleted genes in rice. The density and distribution of deletions suggests the feasibility of a database saturated with deletions across the rice genome. This community resource can continue to grow with further hybridizations, allowing researchers to quickly identify mutants that harbor deletions in candidate genomic regions, for example, regions containing QTL of interest.

Note: 14 of the 16 mutants deposited are reported in the published manuscript (mutants d1137 & g6989 are not discussed).

Series_overall_design:
Genomic DNA from 16 rice deletion mutants (induced by treatment of the indica variety IR64 with DEB-treatment, Fast Neutron or gamma ray (GR) exposure) and wildtypes were hybridized to affymetrix-rice oligonucleotide array

PlexDB Curator Note: We found duplicate CEL files for the following samples:
GSM377075 a, b
GSM377082 a, b
GSM377086 1, 2
We have associated the CEL files with the -a & -1 suffix respectively at PlexDB for our analysis. This is due to the absence of any criteria to distinguish between the duplicate CEL files.
Publication: none
Created: 2009-05-22 09:44:56
Last Update: 2009-05-28 14:09:39
GEO Accession GSE15071
Submitter: PLEXdb Curator
Name: Ramil,Paner,Mauleon
Institution: International Rice Research Institute, Los Banos, Philippines
Head of Laboratory: --
email(s):
Homepage:

 
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