|
| Status |
Public on Dec 01, 2010 |
| Title |
Roots -control rep.2 |
| Sample type |
RNA |
| |
|
| Source name |
10 day old roots of wild type tomato
|
| Organism |
Solanum lycopersicum |
| Characteristics |
sample type: Roots of 10 days-old tomato - Wild type (cv. Micro-Tom) - control
cultivar: Micro-Tom
tissue: Roots
protocol: control
|
| Treatment protocol |
No special tretments before harvesting were carried out.
|
| Growth protocol |
Tomato seeds were germinated on MS medium (Magenta boxes) in light and harvested after 10 days of cultivation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Roots and first two leaves were isolated and immediately frozen in liquid nitrogen. The harvested root and leaf 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).
|
| 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, 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 roots of 10 days seedlings of tomato (cv. Micro-Tom)
|
| 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 |
Jul 07, 2010 |
| Last update date |
Dec 01, 2010 |
| Contact name |
Mariya Khodakovskaya |
| E-mail(s) |
mvkhodakovsk@ualr.edu
|
| Phone |
501-371-7506
|
| Fax |
501-569-8020
|
| Organization name |
University of Arkansas at Little Rock
|
| Department |
Applied Science
|
| Street address |
2801 S. University Avenue
|
| City |
Little Rock |
| State/province |
AR |
| ZIP/Postal code |
72204 |
| Country |
USA |
| |
|
| Platform ID |
GPL4741 |
| Series (1) |
| GSE22803 |
Expression data from roots and first two leaves of tomato seedlings growing on regular MS medium or MS medium supplemented with multi-wall carbon nanotubes (0, 50, 100, 200 ug/ml) or activated carbon (50 mg/ml) |
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