|
| Status |
Public on Jul 20, 2015 |
| Title |
LND_C |
| Sample type |
RNA |
| |
|
| Source name |
Ancestral mites treatment, bio rep 3
|
| Organism |
Solanum lycopersicum |
| Characteristics |
cultivar: Moneymaker
tissue: 3 terminal leaflets of leaves 3 and 4
age: 1 month old
batch: 2
treatment: RB mites
|
| Treatment protocol |
100 adult female spider mites were applied onto terminal leaflets of leaves 3 and 4 per plant and allowed to feed for 24 hours (200 mites total).
|
| Growth protocol |
Plants were grown under 200-250 µmol m-2 s-1 cool-white fluorescent light at 26 °C at 60% relative humidity with a 16:8 h (light/dark) photoperiod in controlled growth chambers.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA samples were processed from pooled samples of two plants per treatment. 3 terminal leaflets of leaves 3 and 4 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).
|
| Data processing |
CEL files were processed in Bioconductor using RMA workflow with standard settings and GPL16358 platform CDF followed by batch effect removal using ComBat-n.
|
| |
|
| Submission date |
Jun 29, 2015 |
| Last update date |
Jul 20, 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 (1) |
| GSE70375 |
Whole genome tomato transcriptional response to tomato-adapted and non-adapted Tetranychus urticae herbivory |
|
