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Expression data from various tomato plant tissues
Koh Aoki, Kazusa DNA Research Institute, Department of Biotechnology Research (kaoki@kazusa.or.jp)
Experiment design (67 hybridizations)
tissue type name
•Micro-Tom root •Micro-Tom hypocotyl •Micro-Tom cotyledon •Micro-Tom 3rd leaves 3wk •Micro-Tom all leaves 3wk •Micro-Tom all leaves 5wk •Micro-Tom flesh mature green fruit •Micro-Tom flesh yellow fruit •Micro-Tom flesh orange fruit •Micro-Tom flesh red fruit •Micro-Tom peel mature green fruit •Micro-Tom peel yellow fruit •Micro-Tom peel orange fruit •Micro-Tom peel red fruit •Aft flesh mature green fruit •Aft flesh red fruit •Aft peel of mature green fruit •Aft peel of red fruit •Line27859 flesh mature green fruit •Line27859 flesh red fruit •Line27859 peel mature green fruit •Line27859 peel red fruit •Momotaro8 flesh red fruit •Momotaro8 peel red fruit

This experiment has been imported by PLEXdb from NCBI GEO (GSE19326) Series_summary: Gene-to-gene coexpression analysis is a powerful approach...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Expression data from various tomato plant tissues
Accession No: LE7
Microarray: tomato10k
Visibility: public
Experiment Type:
Experiment Factor(s):
tissue type name
•Micro-Tom root   •Micro-Tom hypocotyl   •Micro-Tom cotyledon   •Micro-Tom 3rd leaves 3wk   •Micro-Tom all leaves 3wk   •Micro-Tom all leaves 5wk   •Micro-Tom flesh mature green fruit   •Micro-Tom flesh yellow fruit   •Micro-Tom flesh orange fruit   •Micro-Tom flesh red fruit   •Micro-Tom peel mature green fruit   •Micro-Tom peel yellow fruit   •Micro-Tom peel orange fruit   •Micro-Tom peel red fruit   •Aft flesh mature green fruit   •Aft flesh red fruit   •Aft peel of mature green fruit   •Aft peel of red fruit   •Line27859 flesh mature green fruit   •Line27859 flesh red fruit   •Line27859 peel mature green fruit   •Line27859 peel red fruit   •Momotaro8 flesh red fruit   •Momotaro8 peel red fruit
Quality Control: biological replicates
Treatment summary:
 tissue type name  # replicates
 Micro-Tom root  3
 Micro-Tom hypocotyl  2
 Micro-Tom cotyledon  2
 Micro-Tom 3rd leaves 3wk  2
 Micro-Tom all leaves 3wk  3
 Micro-Tom all leaves 5wk  3
 Micro-Tom flesh mature green fruit  3
 Micro-Tom flesh yellow fruit  2
 Micro-Tom flesh orange fruit  2
 Micro-Tom flesh red fruit  3
 Micro-Tom peel mature green fruit  3
 Micro-Tom peel yellow fruit  2
 Micro-Tom peel orange fruit  2
 Micro-Tom peel red fruit  3
 Aft flesh mature green fruit  3
 Aft flesh red fruit  3
 Aft peel of mature green fruit  3
 Aft peel of red fruit  3
 Line27859 flesh mature green fruit  3
 Line27859 flesh red fruit  3
 Line27859 peel mature green fruit  3
 Line27859 peel red fruit  3
 Momotaro8 flesh red fruit  4
 Momotaro8 peel red fruit  4
Total hybridizations: 67
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE19326)

Series_summary:
Gene-to-gene coexpression analysis is a powerful approach to infer function of uncharacterized genes. To perform non-targeted coexpression analysis of tomato genes, we collected a developmental gene expression dataset using various tissues of tomato plant. Expression data are collected from 24 different tissue types including root, hypocotyl, cotyledon, leaf at different stages, and fruit tissues at 4 different ripening stages from 4 different Solanum lycopersicum cultivars. Fruits were separated to the flesh and the peel. These two tissue types indeed showed remarkably different gene expression profiles. We also collected data from 4 different ripening stages (mature green, yellow, orange, and red) to detail the changes during ripening. By using this gene expression dataset, we calculated pair-wise Pearson’s correlation coefficients, and performed network-based coexpression analysis. The analysis generated a number of coexpression modules, some of which showed an enrichment of genes associated with specific functional categories. This result will be useful in inferring functions of uncharacterized tomato genes, and in prioritizing genes for further experimental analysis.
We used Affymetrix GeneChip Tomato genome Arrays to detail the global gene expression change using 24 different tomato tissue types (67 hybridizations).

Series_overall_design:
We collected gene expression data from 24 different tomato tissue types using 67 hybridizations. Root, hypocotyl, cotyledon, and leaf were sampled from 3-week-old or 5-week–old plant of Solanum lycopersicum cultivar Micro-Tom. Fruit tissues were sampled from S. lycopersicum cultivars Micro-Tom, Anthocyanin fruit (Aft, LA1996), Line27859, and Momotaro 8 (Takii, Japan). From Micro-Tom fruit, the peel and the flesh were separately sampled from 4 different ripening stages: mature green (MG, approximately 30 day after anthesis), yellow (Y, approximately 35 days after anthesis), orange (O, approximately 38-40 days after anthesis), and red (R, approximately 45-48 days after anthesis). From fruits of Aft and Line27859, the peel and the flesh were sampled at mature green (MG, approximately 40 days after anthesis) and red (R, approximately 50-55 days after anthesis) stages. From Momotaro 8, the peel and the flesh were sampled at red (R, 50- approximately 50-55 days after anthesis) stages. For each tissue type, 2-4 biological replicates were made in RNA preparation.
Publication: 'Coexpression analysis of tomato genes and experimental verification of coordinated expression of genes found in a functionally enriched coexpression module.', Ozaki S, Ogata Y, Suda K, Kurabayashi A, Suzuki T, Yamamoto N, Iijima Y, Tsugane T, Fujii T, Konishi C, Inai S, Bunsupa S, Yamazaki M, Shibata D, Aoki K.
DNA Res 2010;17(2):105-16.
pubmed: 20130013
Created: 2010-10-26 12:06:44
Last Update: 2010-10-26 14:04:51
Released: 2010-10-27
GEO Accession GSE19326
Submitter: PLEXdb Curator
Name: Koh Aoki
Institution: Kazusa DNA Research Institute, Department of Biotechnology Research
Head of Laboratory: Koh Aoki
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