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Status |
Public on Apr 01, 2019 |
Title |
Col-5 |
Sample type |
RNA |
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|
Source name |
Arabidopsis thaliana COL control
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Organism |
Arabidopsis thaliana |
Characteristics |
ecotype: Columbia-0 (Col) genotype/variation: wild type infected with: none (control)
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Treatment protocol |
Three mature leaves of Col, WS or pme17 were infested with 60 adults of Myzus persicae during 24h, in a growth chamber at 23°C.
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Growth protocol |
Leaves of Columbia-0 (Col), Wassilewskija (WS) and pme17 (KO mutant) were used, grown at 23°C in a Percival growth room during three weeks.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extract according to Gehrig et al. 2000 and Verwoerd et al. 1989 and DNA was removed using the Ambion TURBO-DNAfree kit. RNA was quantified using Nanodrop 1000 spectrophotometer (Thermo Scientific) and RNA quality was assessed using Eukaryote total RNA Standard Sensitivity chips on the Experion system (Biorad). All extract protocols were performed at the Centre de Ressources Régionales en Biologie Moléculaire (Université de Picardie Jules Verne, Amiens).
|
Label |
Cy3
|
Label protocol |
Labeling was performed following NimbleGen One-color labeling kit instructions (Roche)
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|
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Hybridization protocol |
Hybridization was performed overnight at 42°C using a 4-position NimbleGen hybridization station
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Scan protocol |
Slides were scanned using an Axon GenePix 4400 A scanner (Molecular Devices Corporation, Sunnyvale, CA, USA) piloted by GenePix pro software (Axon). Scanned images were then imported into NimbleScan software or DEVA software (NimbleGen Systems, Inc. Madison, WI, USA) for grid alignment and expression data analyses.
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Description |
Col control biological replicate 3 technical replicate 1
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Data processing |
Raw data (.pair files) were normalized using intra-array (RMA background correction) and inter-array (quantile) normalizations using ANAIS software (Simon & Biot, 2010)
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Submission date |
Apr 28, 2016 |
Last update date |
Apr 01, 2019 |
Contact name |
Christopher Wattier |
Organization name |
Université de Picardie Jules Verne
|
Department |
Faculté des Sciences
|
Lab |
Centre de Ressources Régionales en Biologie Moléculaire
|
Street address |
33 rue Saint Leu
|
City |
Amiens |
State/province |
Somme |
ZIP/Postal code |
80000 |
Country |
France |
|
|
Platform ID |
GPL21786 |
Series (1) |
GSE80749 |
Transcript data affected by natural variation or PME17 mutation in Arabidopsis thaliana, infested or not with the aphid Myzus persicae |
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