|
| Status |
Public on Jun 15, 2015 |
| Title |
Seedlings control rep.2 |
| Sample type |
RNA |
| |
|
| Source name |
17 day old Seedlings of wild type tomato
|
| Organism |
Solanum lycopersicum |
| Characteristics |
age: 17 day-old seedlings
genotype/variation: Wild type (cv. Micro-Tom)
treatment: exposed to continous light for 7 days
|
| Treatment protocol |
No special treatments before harvesting were carried out.
|
| Growth protocol |
Tomato seedlings were germinated on MS medium (Magenta boxes) in growth chambers at 12 h day-light and 12 h dark. After 10 days seedlings were transferred to continous light (50 umol m-2 s-1) for 7 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After light incubation seedlings were isolated and immediately frozen in liquid nitrogen. The harvested seeds and seedlings 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).
|
| Label |
biotin
|
| Label protocol |
Complimentary RNA (cRNA) was produced according to Affymetrix 3' IVT Expression Kit as specified in the GeneChip Expression Analysis Technical Manual (http://media.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf )
|
| |
|
| 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 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/).
|
| 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 |
Jun 16, 2014 |
| Last update date |
Jun 15, 2015 |
| Contact name |
Mariya Khodakovskaya |
| E-mail(s) |
m_khod@yahoo.com
|
| Organization name |
University of Arkansas at Little Rock
|
| Department |
Biology
|
| Street address |
2801 S. University Avenue
|
| City |
Little Rock |
| State/province |
AR |
| ZIP/Postal code |
72204 |
| Country |
USA |
| |
|
| Platform ID |
GPL4741 |
| Series (1) |
| GSE58521 |
Expression data from seedligs of wild type tomato seedlings (control) and InsP 5-ptase tansgenic line (L7) exposed to light stress |
|
