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Experiment Name:

Microarray analysis of gene expression under different light conditions

Accession No:

LE20

Microarray:

tomato10k

Visibility:

public

Experiment Type:

Experiment Factor(s):

developmental stage name: •leaf •pericarp
light: •0 PPF •200 PPF •1000 PPF
time: •0 weeks •1 weeks •2 weeks

Quality Control:

biological replicates

Treatment summary:

developmental stage name	light	time	# replicates
leaf	0 PPF	0 weeks	3
leaf	0 PPF	1 weeks	0
leaf	0 PPF	2 weeks	0
leaf	200 PPF	0 weeks	0
leaf	200 PPF	1 weeks	2
leaf	200 PPF	2 weeks	3
leaf	1000 PPF	0 weeks	0
leaf	1000 PPF	1 weeks	3
leaf	1000 PPF	2 weeks	3
pericarp	0 PPF	0 weeks	0
pericarp	0 PPF	1 weeks	0
pericarp	0 PPF	2 weeks	0
pericarp	200 PPF	0 weeks	0
pericarp	200 PPF	1 weeks	0
pericarp	200 PPF	2 weeks	3
pericarp	1000 PPF	0 weeks	0
pericarp	1000 PPF	1 weeks	0
pericarp	1000 PPF	2 weeks	3

Total hybridizations: 20

Description:

This experiment has been imported by PLEXdb from NCBI GEO (GSE35020)

Series_summary:
The size of tomato fruits are largely dependent on growth conditions. To obtain insights on how light intensity contributes to translocation from a leaf and a fruit, we developed a plant irradiation system based on light-emitting diodes (LEDs) to a leaf. By using this system, we investigated the changes of transcript profiles of tomato leaves and fruits grown under different light conditions.

Series_overall_design:
20 samples were analyzed (14 leaf samples and 6 pericarp samples); 2-3 biological replicates were used.

PLEXdb Curator's Note:

Key to Sample labels at GEO:
200PPF B/200PPF C = leaf/low light/1 week = 2 reps
1000PPF A/ 1000PPF B/ 1000PPF C= leaf/high light/1 week= 3 reps
0 week A /0 week B/0 week C= leaf/control/ 0 week= 3 reps
200PPF AP/200PPF BP/200PPF CP= pericarp/low light/2 weeks= 3 reps
200PPF AL/200PPF BL/200PPF CL= leaf/low light/2 weeks= 3 reps
1000PPF AP/1000PPF BP/1000PPF CP= pericarp/high light/ 2 weeks/ 3 reps
1000PPF AL/1000PPF BL/1000PPF CL=leaf/hight light/2 weeks= 3 reps

Publication:

'Exploring tomato gene functions based on coexpression modules using graph clustering and differential coexpression approaches.', Fukushima A, Nishizawa T, Hayakumo M, Hikosaka S, Saito K, Goto E, Kusano M.
Plant Physiol 2012 Apr;158(4):1487-502.
pubmed: 22307966

Created:

2012-07-10 10:22:34

Last Update:

2012-07-10 11:46:32

Released:

2012-07-10

GEO Accession

GSE35020

Submitter:

PLEXdb Curator

Experimenter:

Name:	Miyako Kusano
Institution:	RIKEN, PSC, Department of Metabolomics research group, Yokohama, Japan
Head of Laboratory:	Atsushi Fukushima
email(s):	mkusano005@psc.riken.jp,a-fukush@psc.riken.jp
Homepage:


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