NASCArrays Information at The BAR

Welcome to NASCArrays information at the BAR. This page hosts meta-information from the NASCArrays service (2002-2013). This information was parsed from text files available on the NASCArrays site. NASCArrays data is on iPlant server. To download experiment data from iPlant, please click on the experiment number. To download the CEL files, please click on the ftp link.

Title:Gene expression changes in Arabidopsis thaliana treated with Myzus persicae saliva
Description:Reference:De Vos and Jander, 2009 - Plant, Cell, and EnvironmentAim:Identification of genes responding to aphid saliva.Background:During feeding on phloem sap aphids repeatedly salivate into the sieve element. It is thought that compounds in aphid saliva play a role in sustainable feeding. These compounds may include proteins and small molecules, which can function as virulence factors.Growth conditionsPlants: Seeds of wild-type Arabidopsis thaliana (Col-0) were obtained from the were kept in 0.1% Phytagar (Invitrogen, Carlsbad, CA) for 24 h at 4°C prior to planting on Cornell mix with Osmocoat fertilizer. Plants were grown in Conviron growth chambers in 20- x 40-cm nursery flats at a photosynthetic photon flux density of 200 mmol m-2 s-1 and a 16-h photoperiod. The temperature in the chambers was 23°C and the relative humidity was 50%. 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) with a 16-h day (150 mmol m-2 s-1 at 24°C) and an 8-h night (19°C) at 50% relative humidity.Experimental set-up/treatment:Fifty aphids were allowed to feed from 50 µL artificial diet, containing sucrose and amino acids (Kim and Jander, 2007) between two layers of Parafilm. 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.RNA extraction + processing:RNA was extracted using the Qiagen Plant RNeasy kit. RNA quality and quantity was assessed with an Agilent BioAnalyser 2100. Samples were processed by the Cornell Microarray facility. Whole genome gene expression profiling was done using Affymetrix ATH1 GeneChips.Data analysis: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 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).
ftp Link:ftp Link

Slide Information:
Slide IDSlide NameGenetic BackgroundTissueStock CodeCel File
DeVos_1-1_Control_Rep1_ATH17779179 CS60000DeVos_1-1_Control_Rep1_ATH1.CEL
DeVos_1-2_Treatment_Rep1_ATH17779180 CS60000DeVos_1-2_Treatment_Rep1_ATH1.CEL
DeVos_1-3_Control_Rep2_ATH17779181 CS60000DeVos_1-3_Control_Rep2_ATH1.CEL
DeVos_1-4_Treatment_Rep2_ATH17779182 CS60000DeVos_1-4_Treatment_Rep2_ATH1.CEL
DeVos_1-5_Control_Rep3_ATH17779183 CS60000DeVos_1-5_Control_Rep3_ATH1.CEL
DeVos_1-6_Treatment_Rep3_ATH17779184 CS60000DeVos_1-6_Treatment_Rep3_ATH1.CEL