|
| Status |
Public on Dec 02, 2011 |
| Title |
Col-0 treated with 9-KOT vs Col-0 treated with water, after both treated with PstDC3000 48h Rep 4 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
9-KOT/Pst DC3000/48h
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
|
| Treatment protocol |
The plants were treated and with 150uM 9-KOT or water; the plants were treated and with 150uM 9-KOT or water and after both with PstDC3000 (106ufc/ml)
|
| Growth protocol |
Seeds were sown on soil, vernalized for three days at 4°, and grown in chamber at 22° and 70% relative humidity under a 14 hours light, 10 hours dark photoperiod at 250 uE m-2 sec-1 fluorescent illumination. Plants were treated and examined between 3 and 4 weeks after seed germination.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The frozen plant tissue (~100 mg) was ground in tiny mortars dipped in liquid nitrogen. The frozen powder was carefully transfered into 1.5 ml microcentrifuge tubes using small funnels and rubber spatulas also cooled with liquid nitrogen. Total RNA was extracted using TRIzol reagent (Invitrogen, 15596-026) according to manufacturer's instructions and purified with an RNeasy mini kit (Qiagen, 74104).1 ug of total RNA was amplified via the aRNA MessageAmp II kit (Ambion, 1751)
|
| Label |
Hyper5
|
| Label protocol |
5 ug of aminoallyl-labeled aRNA were resuspended in 0.1 M Na2CO3 (pH 9.0) and labeled with Hyper5 and Cy3 Mono NHS Ester (CyTMDye Post-labeling Reactive Dye Pack, Amersham). Samples were purified following the manufacturer's instructions for Megaclear TM (Ambion) and Hyper5 and Cy3 incorporation was measured using 1 ul of the probe in the Nanodrop
|
| |
|
| Channel 2 |
| Source name |
water/Pst DC3000/48h
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
|
| Treatment protocol |
The plants were treated and with 150uM 9-KOT or water; the plants were treated and with 150uM 9-KOT or water and after both with PstDC3000 (106ufc/ml)
|
| Growth protocol |
Seeds were sown on soil, vernalized for three days at 4°, and grown in chamber at 22° and 70% relative humidity under a 14 hours light, 10 hours dark photoperiod at 250 uE m-2 sec-1 fluorescent illumination. Plants were treated and examined between 3 and 4 weeks after seed germination.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The frozen plant tissue (~100 mg) was ground in tiny mortars dipped in liquid nitrogen. The frozen powder was carefully transfered into 1.5 ml microcentrifuge tubes using small funnels and rubber spatulas also cooled with liquid nitrogen. Total RNA was extracted using TRIzol reagent (Invitrogen, 15596-026) according to manufacturer's instructions and purified with an RNeasy mini kit (Qiagen, 74104).1 ug of total RNA was amplified via the aRNA MessageAmp II kit (Ambion, 1751)
|
| Label |
Cy3
|
| Label protocol |
5 ug of aminoallyl-labeled aRNA were resuspended in 0.1 M Na2CO3 (pH 9.0) and labeled with Hyper5 and Cy3 Mono NHS Ester (CyTMDye Post-labeling Reactive Dye Pack, Amersham). Samples were purified following the manufacturer's instructions for Megaclear TM (Ambion) and Hyper5 and Cy3 incorporation was measured using 1 ul of the probe in the Nanodrop
|
| |
|
| |
| Hybridization protocol |
The hybridization experiment was performed according to the manufacture's protocol (Agilent technologies, Agilent 60-mer oligo microarray processing protocol: Two color microarray based gene expression analysis, G4140-90050 ver 5.7)
|
| Scan protocol |
Images from Cy3 and Hyper5 channels were equilibrated and captured with a GenePix 4000B (Axon) and spots were converted into numerical data using GenPix software (Axon).
|
| Description |
Biological replicate 4 of 4. Gene expression of Col-0 treated with 9-KOT vs Col-0 treated with water, after both treated with Pst DC3000, 48h
|
| Data processing |
Raw intensities were background-substracted by NORMEXP method with a offset of 50. Signals (in log2 scale) were then normalized by LOWESS algorithm (intra-arrays normalization) followed by adjustment of their quantiles (inter-arrays normalization).
|
| |
|
| Submission date |
Dec 01, 2011 |
| Last update date |
Dec 02, 2011 |
| Contact name |
Jorge Vicente |
| E-mail(s) |
jvicente@cnb.csic.es
|
| Organization name |
CSIC
|
| Street address |
Darwin
|
| City |
Madrid |
| ZIP/Postal code |
28049 |
| Country |
Spain |
| |
|
| Platform ID |
GPL9020 |
| Series (1) |
| GSE34081 |
Role of 9-Lipoxygenase and α-Dioxygenase oxylipin pathways as modulators of local and systemic defense |
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