|
| Status |
Public on Jan 01, 2015 |
| Title |
Seeds -control rep.1 |
| Sample type |
RNA |
| |
|
| Source name |
Seeds of wild type tomato (1 day on MS medium)
|
| Organism |
Solanum lycopersicum |
| Characteristics |
cultivar: Micro-Tom
genotype/variation: wild type
growth protocol: control
tissue: seeds
|
| Treatment protocol |
No special treatments before harvesting were carried out.
|
| Growth protocol |
Tomato seeds were germinated on MS medium (Magenta boxes) in light and harvested after 1 day and 11 days of cultivation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Seeds and 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 geneChip® 3' IVT Express kit Technical Manual (http://media.affymetrix.com/support/downloads/manuals/3_ivt_express_kit_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/).
|
| Description |
Gene expression data from tomato seeds (1 day on MS medium) - Wild type (cv. Micro-Tom)- control
EA09092_278466_Tomato_NS-1
|
| 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 |
May 12, 2014 |
| Last update date |
Jul 13, 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) |
| GSE57541 |
Expression data from roots and first two leaves of tomato seedlings growing on regular MS medium or MS medium supplemented with multi-wall carbon nanohorns (25 ug/ml) |
|
| Relations |
| Reanalyzed by |
GSM1820330 |
