|
| Status |
Public on Jun 10, 2009 |
| Title |
control, rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
3-week-old Arabidopsis leaves, control, harvested after 24 hrs
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
tissue: leaves
treatment: control
|
| Treatment protocol |
Fifty aphids were allowed to feed from 50 μL artificial diet containing sucrose and amino acids (Kim & Jander, 2007) between two layers of Parafilm (Alcan Packaging). After 24 h, artificial diet from 20 aphids and control (0 aphids) diet cups was collected and infiltrated into leaves of intact Arabidopsis plants using a 1-mL syringe without the needle. Plants for control diet and aphid saliva containing diet were grown in the same pot to allow for a paired comparison. Eighteen leaves (3 leaves from 6 plants) treated with control and aphid saliva containing diet were harvested and immediately frozen in liquid nitrogen. This experiment was repeated 3 times to function as independent biological replicates.
|
| Growth protocol |
Plants: Seeds of wild-type Arabidopsis (Arabidopsis thaliana) land race Columbia-0 (Col-0) were obtained from the Arabidopsis Biological Resource Center. Seeds were kept in 0.1% Phytagar (Invitrogen, Carlsbad, CA) for 24 h at 4°C prior to planting on Cornell mix (Landry, Chapple & Last, 1995) with Osmocoat fertilizer (Scotts). Plants were grown in Conviron growth chambers in 20x40 cm nursery flats at a photosynthetic photon flux density of 200 mmol/m2s and a 16h photoperiod. The temperature in the chambers was 23°C and the relative humidity was 50%. Unless stated differently, plants were grown for 3 weeks and used in experiments before flowering. Aphids: All experiments were conducted with a tobacco-adapted red lineage of M. persicae. Aphids were raised on cabbage (Brassica oleracea var. Wisconsin Golden Acre; Seedway) with a 16h day (150 mmol/m2s at 24°C) and an 8h night (19°C) at 50% relative humidity.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Qiagen Plant RNeasy kit (Qiagen, Valencia, CA, USA). RNA quality and quantity was assessed with an Agilent BioAnalyser 2100 (Agilent, Santa Clara, CA, USA).
|
| Label |
biotin
|
| Label protocol |
Samples were processed by the Cornell Microarray facility. Whole genome gene expression profiling was done using Affymetrix ATH1 GeneChips. Briefly, plant mRNA was converted into cRNA, labeled and hybridized to the ATH1 GeneChips.
|
| |
|
| Hybridization protocol |
Samples were processed by the Cornell Microarray facility. Whole genome gene expression profiling was done using Affymetrix ATH1 GeneChips. Briefly, plant mRNA was converted into cRNA, labeled and hybridized to the ATH1 GeneChips.
|
| Scan protocol |
Samples were processed by the Cornell Microarray facility. Whole genome gene expression profiling was done using Affymetrix ATH1 GeneChips. Briefly, plant mRNA was converted into cRNA, labeled and hybridized to the ATH1 GeneChips.
|
| Description |
Jander-2-010507.CEL
|
| Data processing |
Raw data from the microarrays was normalized at probe-level using gcRMA algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the Affymetrix GeneChip® Operating Software (GCOS) system. Significance of gene expression was determined using the LIMMA (Smyth, 2004) program and raw p values of multiple tests were corrected using False Discovery Rate (FDR).
|
| |
|
| Submission date |
Jun 08, 2009 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Georg Jander |
| E-mail(s) |
gj32@cornell.edu
|
| Phone |
+1 607 254 1365
|
| URL |
http://www.bti.cornell.edu/GeorgJander.php
|
| Organization name |
Boyce Thompson Institute for Plant Research
|
| Street address |
1 Tower Rd
|
| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE16497 |
Arabidopsis thaliana gene expression changes upon treatment with green peach aphid saliva |
|
| Relations |
| Reanalyzed by |
GSE119083 |
