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Understanding the complexity of fruit ripening by transcriptome analysis of rin mutant fruit
Arun K. Sharma, Delhi university, Department of Plant Molecular Biology, Delhi, India (arun@genomeindia.org)
Experiment design (18 hybridizations)
genotype
•wild type •rin mutant
developmental stage name
•immature green fruit •breaker fruit •red-ripe fruit

This experiment has been imported by PLEXdb from NCBI GEO (GSE20720)

Series_summary:
[original title] Understanding the complexity of...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Understanding the complexity of fruit ripening by transcriptome analysis of rin mutant fruit
Accession No: LE19
Microarray: tomato10k
Visibility: public
Experiment Type:
Experiment Factor(s):
genotype
•wild type   •rin mutant
developmental stage name
•immature green fruit   •breaker fruit   •red-ripe fruit
Quality Control: biological replicates
Treatment summary:
 genotype  developmental stage name  # replicates
 wild type  immature green fruit  3
 wild type  breaker fruit  3
 wild type  red-ripe fruit  3
 rin mutant  immature green fruit  3
 rin mutant  breaker fruit  3
 rin mutant  red-ripe fruit  3
Total hybridizations: 18
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE20720)

Series_summary:
[original title] Understanding the complexity of fruit ripening by transcriptome analysis of rin mutant fruit and in silico analysis of promoters of differentially regulated genes
A tomato MADS-box transcription factor, LeMADS-RIN, controls fruit ripening and mutation in this gene results in non-ripening phenotype of fruit. This mutation down-regulates certain ripening related ethylene responses, however, other ethylene responses are normal. A complete understanding of this mutation and its effect on fruit transcriptome during ripening is not clear. In this study, microarray analysis has been used to investigate the influence of rin mutation on fruit transcriptome at different stages of ripening. A total of 2,398 genes were found to be differentially expressed in wild type fruit pericarp, which on cluster analysis indicated a major shift in their expression profiles in rin mutant fruit. A total of 1,802 genes were found to be differentially expressed between wild type and rin mutant fruits and 17% of these genes encoded regulatory elements, suggesting that mutation in LeMADS-RIN results in disturbance in the regulatory transcriptional networks during ripening. Since LeMADS-RIN has been reported to bind to the CArG box of LeACS2 promoter, in-silico analysis of 51 putative promoter sequences of the genes, that showed ripening associated up-regulation in wild type but showed impairment in up-regulation in rin mutant fruit during ripening, were searched for presence of CArG box along with ethylene and auxin responsive elements. The study revealed that only 24 putative promoter sequences harbor LeMADS-RIN specific CArG box suggesting an alternative mode of regulation by LeMADS-RIN for CArG box deficient genes.

Series_overall_design:
Three chronological stages of tomato (Solanum lycopersicon) fruit ripening were compared between wild type and rin mutant


PLEXdb Curator's Note:
The samples from the wildtype may serve as an atlas data set.

Keys to sample names extracted from GEO:
age: 35 days after planting (DAP) = developmental stage: immature green fruit, IMG
age: 40 days after planting (DAP) = developmental stage: breaker fruit, B
age: 45 days after planting (DAP) = developmental stage: red-ripe fruit, RR
Publication: 'Transcriptome analysis of rin mutant fruit and in silico analysis of promoters of differentially regulated genes provides insight into LeMADS-RIN-regulated ethylene-dependent as well as ethylene-independent aspects of ripening in tomato.', Kumar R, Sharma MK, Kapoor S, Tyagi AK, Sharma AK.
Mol Genet Genomics 2012 Mar;287(3):189-203.
pubmed: 22212279
Created: 2012-04-20 09:42:29
Last Update: 2012-04-24 10:54:33
Released: 2012-04-26
GEO Accession GSE20720
Submitter: PLEXdb Curator
Name: Arun K. Sharma
Institution: Delhi university, Department of Plant Molecular Biology, Delhi, India
Head of Laboratory: Arun K. Sharma
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