|
| Status |
Public on Jan 05, 2015 |
| Title |
NT_2 |
| Sample type |
RNA |
| |
|
| Source name |
Control plants, bio rep 2
|
| Organism |
Solanum lycopersicum |
| Characteristics |
tissue: 3 terminal leaflets of leaf 3
genotype: def-1
cultivar: Castlemart
age: 1 month old
|
| Treatment protocol |
For herbivory response analysis 100 adult female spider mites were applied onto terminal leaflet of leaf 3 per plant and allowed to feed for 24 h. For JA response analysis plants were sprayed with 1 mM JA solution and 3 terminal leaflets of leaf 3 were collected 24 h later.
|
| Growth protocol |
Plants were grown under 200-250 µmol m-2 s-1 cool-white fluorescent light at 25 °C with a 16:8 h (light/dark) photoperiod in controlled growth chambers.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA samples were processed in triplicate from pooled samples of two plants per treatment. 3 terminal leaflets of leaf 3 were used. Total RNA was prepared using the RNeasy Plant RNA extraction kit (Qiagen, Venlo, Netherlands).
|
| Label |
biotin
|
| Label protocol |
Biotin end labeled single strand cDNA was prepared according to the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labelling Assay manual (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
5.5 ug of single stranded cDNA was hybridized for 16 h at 45 °C on GeneChip EUTOM3 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450 (Affymetrix, Santa Clara, CA).
|
| Scan protocol |
Scanning was done following Affymetrix guidelines on a GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, CA).
|
| Description |
Gene expression of def-1 control plants
|
| Data processing |
CEL files were processed in Bioconductor using RMA workflow with standard settings and GPL16358 platform CDF.
|
| |
|
| Submission date |
Sep 03, 2014 |
| Last update date |
Jan 06, 2015 |
| Contact name |
Vladimir Zhurov |
| E-mail(s) |
vzhurov2@uwo.ca
|
| Organization name |
University of Western Ontario
|
| Department |
Biology
|
| Street address |
1151 Richmond Street
|
| City |
London |
| State/province |
ON |
| ZIP/Postal code |
N6A5B7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL16358 |
| Series (2) |
| GSE61075 |
Whole genome tomato transcriptional response to jasmonic acid treatment and Tetranychus urticae herbivory [def-1] |
| GSE61076 |
Whole genome tomato transcriptional response to Tetranychus urticae herbivory |
|
