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Sample GSM480217 Query DataSets for GSM480217
Status Public on Feb 01, 2010
Title Line27859 flesh of red fruit, biological rep 3
Sample type RNA
 
Source name Line27859 flesh of red fruit (approximately 50-55 days after anthesis)
Organism Solanum lycopersicum
Characteristics 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.
 
Submission date Dec 04, 2009
Last update date Dec 04, 2009
Contact name Koh Aoki
E-mail(s) kaoki@kazusa.or.jp
Phone +81-438-52-3947
Fax +81-438-52-3948
Organization name Kazusa DNA Research Institute
Department Department of Biotechnology Research
Lab Lab of Bioengineering
Street address 2-6-7 Kazusa-Kamatari
City Kisarazu
State/province Chiba
ZIP/Postal code 292-0818
Country Japan
 
Platform ID GPL4741
Series (1)
GSE19326 Expression data from various tomato plant tissues

Data table header descriptions
ID_REF
VALUE MAS 5.0 Signal Intensity
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 274.271 P 6.02111e-05
AFFX-BioB-M_at 344.061 P 4.42873e-05
AFFX-BioB-3_at 245.688 P 4.42873e-05
AFFX-BioC-5_at 697.644 P 4.42873e-05
AFFX-BioC-3_at 571.096 P 4.42873e-05
AFFX-BioDn-5_at 1427.84 P 4.42873e-05
AFFX-BioDn-3_at 2341.43 P 4.42873e-05
AFFX-CreX-5_at 7297.31 P 4.42873e-05
AFFX-CreX-3_at 7191.14 P 4.42873e-05
AFFX-DapX-5_at 188.998 P 7.00668e-05
AFFX-DapX-M_at 479.197 P 5.16732e-05
AFFX-DapX-3_at 634.167 P 4.42873e-05
AFFX-LysX-5_at 23.2487 P 0.000445901
AFFX-LysX-M_at 36.5393 P 0.000509415
AFFX-LysX-3_at 101.435 P 8.14279e-05
AFFX-PheX-5_at 56.9803 P 0.000126798
AFFX-PheX-M_at 67.3318 P 6.02111e-05
AFFX-PheX-3_at 67.8537 P 7.00668e-05
AFFX-ThrX-5_at 71.243 P 0.000126798
AFFX-ThrX-M_at 123.593 P 4.42873e-05

Total number of rows: 10209

Table truncated, full table size 398 Kbytes.




Supplementary file Size Download File type/resource
GSM480217.CEL.gz 1.4 Mb (ftp)(http) CEL
GSM480217.CHP.gz 2.6 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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