tissue: fruit pericarp and endocarp age: Approximately 50-55 days after anthesis cultivar: Line27859
Biomaterial provider
Nippon Del Monte Co. Ltd.
Growth protocol
Solanum lycopersicum Line 27859 was grown in the field under natural photo-period condition from March to July, 2006 in Gunma prefecture, Japan.
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 Line27859 red fruit flesh
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.
