|
| Status |
Public on May 30, 2016 |
| Title |
Seeds -control rep.1 [re-analysis] |
| Sample type |
RNA |
| |
|
| Source name |
Seeds_1 day after placement on MS medium
|
| Organism |
Solanum lycopersicum |
| Characteristics |
cultivar: cv. Micro-Tom
genotype/variation: wild type
age: 1 day after placement of medium
tissue: Seeds
growth medium: regular MS agar medium
|
| Treatment protocol |
No special treatments before harvesting were carried out.
|
| Growth protocol |
Tomato seeds were collected after 1 day of placement on regular MS medium or medium supplemented with Helical MWCNT. Another part was germinated germinated on on regular MS medium or medium supplemented with Helical MWCNT 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 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 tomato seeds (1day-old) (cv. Micro-Tom)
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 |
Jul 13, 2015 |
| Last update date |
May 30, 2016 |
| 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) |
| GSE70842 |
Expression analysis of seeds and seedlings of tomato growing on regular MS medium or MS medium supplemented with Helical multi-walled carbon nanotubes (Helical MWCNTs) in concentration 25 ug/ml |
|
| Relations |
| Reanalysis of |
GSM1384360 |
