genotype: Wild-type phenotype: normal accession: CS[ ] tissue: whole seedling
Growth protocol
Each biological replicate included 48, 10 day-old Arabidopsis thaliana seedlings pooled for each treatment. Col-0 seedlings were pre-treated for 2 hours with either 60% DMSO, 250mM 3AB (dissolved in 60% DMSO), or 250mM 3MB (dissolved in 60% DMSO). Col-0 seedlings were then treated for one hour with either ddH2O or 1uM flg22, or 1uM elf18, and parg1 seedlings were treated for one hour with either ddH2O or 1uM elf18.
Extracted molecule
total RNA
Extraction protocol
Total RNA was extracted using Rneasy Mini Kit (Qiagen), and DNA was removed by DNase digestion with the RNase-free DNase Set (Qiagen) RNA quality and concentration was determined using an Agilent 2100 bioanalyzer at the Gene Expression Center at University of Wisconsin-Madison Biotechnology Center, Madison, WI, USA).
Label
Cy3
Label protocol
Labeling was performed by the Gene Expression Center, Madison, WI USA, following Nimblegen's standard operating protocol. See www.nimblegen.com.
Hybridization protocol
Hybridization was performed by the Gene Expression Center, Madison, WI USA, following Nimblegen's standard operating protocol. See www.nimblegen.com.
Scan protocol
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
Description
This sample is of wild-type Arabidopsis thaliana, treated with the MAMP flg22. It is the first of three biological replicates.
Data processing
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
