tissue: hypocotyl age: 3 weeks after germination cultivar: Micro-Tom
Biomaterial provider
Kazusa DNA Research Institute
Growth protocol
Seeds of cultivated tomato (S. lycopersicum cv. Micro-Tom) were sawn in the pots (500 ml) filled with mixture of vermiculite and Powersoil (1 to 1 mixing ratio, Kureha Chemical Ind., Tokyo, Japan, and Kanto Hiryou Ind., Saitama, Japan, respectively) and kept in a controlled room at 25C. After 4 days of germination, they were grown with a photoperiod of 16 hr light (7000 lux) and 8 hr dark at 25C. Hyponex (Hyponex Ltd., Osaka, Japan) at 1000-fold dilution was applied to plants once a week as a nutrient.
Extracted molecule
total RNA
Extraction protocol
Fruit peel and flesh were separated using razor blade. Total RNA was extracted from the tissues by an acid guanidinium thiocyanate-phenol-chloroform method (Chomczynski, P. and Sacchi, N. 1987, Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction, Anal Biochem, 162, 156-159). Sugars were further removed by sodium acetate-precipitation method (Tsugane, T., Watanabe, M., Yano, K., Sakurai, N., Suzuki, H. and Shibata, D. 2005, Expressed sequence tags of full-length cDNA clones from the miniature tomato (Lycopersicon esculentum) cultivar Micro-Tom, Plant Biotechnol., 22, 161-165).
Label
biotin
Label protocol
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Hybridization protocol
Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Tomato Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol
GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.
Description
Gene expression data from Micro-Tom hypocotyl
Data processing
Scanned GeneChip images were analyzed using Microarray Suite version 5.0.1 (Affymetrix) using Affymetrix default analysis settings and global scaling as normalization method.
