|
| Status |
Public on Nov 15, 2008 |
| Title |
Leaves-Wild type rep.2 |
| Sample type |
RNA |
| |
|
| Source name |
first two leaves of 10 day old light grown in vitro seedlings
|
| Organism |
Solanum lycopersicum |
| Characteristics |
First two leaves of tomato seedlings grown in light conditions -Wild type
|
| Treatment protocol |
No special treatments before harvesting were carried out.
|
| Growth protocol |
For fruits, tomato plants were grown in pots with growing medium containing 50% of sand and 50% of Sun Gro Redi-earth Plug and Seedling Mix (Sun Gro Horticulture). All plants grown in growth chamber of Phytotron, NCSU at day temperature 26 C, night temperature 22 C, humidity 45% and intensity of light 500 μmol.m-2.s-1. Plants were watered once at day to field capacity and fertilized on a weekly basis with fertilizer recipe as described at http://www.ncsu.edu/phytotron/manual.pdf. After 9 weeks in the growth chamber transgenic and control ripe fruits of same age were harvested.
For leaves, tomato seeds were germinated on MS medium (agar Petri plates) in light conditions. First two leaves of 10 days seedlings were harvested.
For roots, tomato seeds were germinated on MS medium (agar Petri plates) in light conditions. First two leaves of 10 days seedlings were harvested.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ripe fruits were immediately frozen in liquid nitrogen after harvesting in the greenhouses. The harvested samples were then transferred to the laboratory and grinded to a fine powder in mortars and pestles using liquid nitrogen. Total RNA was extracted using a RNeasy Plant Mini Kit (Qiagen).
Leaf tissue was immediately frozen in liquid nitrogen after harvesting in the sterile conditions. The harvested leaf samples were then transferred to the laboratory and grinded to a fine powder in mortars and pestles using liquid nitrogen. Total RNA was
Root tips were isolated from rootsand immediately frozen in liquid nitrogen after harvesting in the dark conditions. The harvested root samples were then transferred to the laboratory and grinded to a fine powder in mortars and pestles using liquid nitro
|
| Label |
biotin
|
| Label protocol |
Complimentary RNA (cRNA) was produced according to Affymetrix Eukaryotic two-cycle target labeling assay as specified in the GeneChip Expression Analysis Technical Manual (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 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 400. Hybridization reactions to Affymetrix Maize GeneChip expression arrays were done using the services of Expression Analysis Inc. (http://www.expressionanalysis.com/).
|
| Scan protocol |
Scanning of the Affymetrix Tomato GeneChip expression arrays were done using the services of Expression Analysis Inc. (http://www.expressionanalysis.com/).
|
| Description |
Gene expression data from first two leaves of tomato seedlings grown in vitro in light conditions
|
| Data processing |
Data extraction was also performed by Expression Analysis Inc. Expression values were calculated using the Affymetrix GeneChip Operating System (GCOS) and were based on the difference of the PM (Perfect Match) signal and MM (Mismatch) signal at each of the probe pairs. The fluorescent signal values from each array were normalized to achieve similar overall intensity between arrays. The fluorescent signal values of any hybridization reaction were then multiplied by a scaling factor to make their (trimmed) mean intensity equal to 500. The scaling factor is unique to each hybridization reaction and is in general below 10
|
| |
|
| Submission date |
Nov 26, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Mariya Khodakovskaya |
| E-mail(s) |
mvkhodak@ncsu.edu
|
| Phone |
919-515-2225
|
| Fax |
919-515-3436
|
| Organization name |
North Carolina State University
|
| Department |
Plant Biology
|
| Lab |
Plant Sensory Genomics Group
|
| Street address |
4218 Gardner Hall
|
| City |
Raleigh |
| State/province |
NC |
| ZIP/Postal code |
27695 |
| Country |
USA |
| |
|
| Platform ID |
GPL4741 |
| Series (1) |
| GSE9683 |
Tomato wild type, vector control and transgenic lines expressing InsP 5-ptase: mature fruits, root tips, and leaves |
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