After flowering in Summer 2010, we removed leaves and trusses from each plant except for the second truss, a leaf below the second truss and the meristem. LED irrigation was directly applied to the leaf using the plant irradiation system. Plant material was harvested after 0, 1 and 2 weeks.
Growth protocol
Seeds from tomatoes (Solanum lycopersicum, cv. Reiyo) were sown in pots (volume: 2 l) with rockwool (Nittobo, Japan) and grown in a hydroponics system with a nutrient solution containing N, P, and K at 122, 21, and 156.6 mg/l, respectively (one-fourth concentration of Otsuka Hydroponic Composition, Otsuka Chemical, Japan), in a growth chamber at 25 °C/20 °C (light/dark) and 900 ppm CO2 concentration with a light/dark cycle of 16 h/8 h at Chiba University, Matsudo, Japan. Photosynthetic photon flux (PPF) level in the growth chamber was adjusted to 450-500 pmol m-2 s-1 when we measured at the meristem of each tomato plant (light source: Ceramic metal halide lamps).
Extracted molecule
total RNA
Extraction protocol
Total RNA isolation was performed using RNeasy Plant Mini Kit (QIAGEN, Valencia, CA, USA) according to the manufacturer's instruction.
Label
biotin
Label protocol
Biotinylated cRNA was labeled using a biotinylated nucleotide analog/ribonucleotide mix using GeneChip IVT Labeling Kit (Affymetrix, Inc., Santa Clara, CA, USA).
Hybridization protocol
Following fragmentation, 5 ug of cRNA were hybridized for 16 hr on GeneChip Tomato Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol
GeneChips were scanned using the GeneChip scanner 3000 integrated with Affymetrix® Microarray Suite software.
Description
SK058
Data processing
The microarray data normalization and background correction was performed using robust multi-array average (RMA) with Bioconductor package 'simpleaffy'.
