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Status |
Public on Aug 05, 2018 |
Title |
Wild type mechanical damage vs herbivore wounding 3 |
Sample type |
RNA |
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Channel 1 |
Source name |
WT rosette leaves mechanical damaged
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Organism |
Arabidopsis thaliana |
Characteristics |
treatment: mechanical damaged age: day 22 (growth stage 3) tissue: rosette leaves ecotype: Columbia 0 genotype: WT
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Treatment protocol |
Mechanical damage: made by pattern wheel mimicking herbivore; Herbivore wounding: Spodoptera littoralis feeding
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Growth protocol |
Arabidopsis plants (Col-0 and PDKO3) were grown as a single plant in plastic pots filled with soil. Growth chamber was set up at 23°C 16h in the light (160 μE m-2 s-1) and 8 in the dark for 22 days
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA extracted from rosette leaves using Agilent Plant RNA Isolation Mini kit including RNAse-free DNase (Qiagen) treatment
|
Label |
Cy3
|
Label protocol |
500 ng of total RNA were separately reverse-transcribed into double-strand cDNAs by the Moloney murine leukemia virus reverse transcriptase (MMLV-RT) and amplified for 2 h at 40°C using the Agilent Quick Amp Labelling Kit, two-color (Agilent Technologies). Subsequently, cDNAs were transcribed into antisense cRNA and labeled with either Cy3-CTP or Cy5-CTP fluorescent dyes for 2 h at 40°C following the manufacturer’s protocol. Cyanine-labeled cRNAs were purified using RNeasy Minikit (Qiagen). Purity and dye incorporation were assessed with the NanoDrop ND-1000 UV-VIS Spectrophotometer (Thermo Fisher Scientific) and the Agilent 2100 Bioanalyzer (Agilent Technologies).
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Channel 2 |
Source name |
WT rosette leaves herbivore wounded
|
Organism |
Arabidopsis thaliana |
Characteristics |
treatment: herbivore wounded ecotype: Columbia 0 age: day 22 (growth stage 3) tissue: rosette leaves
|
Treatment protocol |
Mechanical damage: made by pattern wheel mimicking herbivore; Herbivore wounding: Spodoptera littoralis feeding
|
Growth protocol |
Arabidopsis plants (Col-0 and PDKO3) were grown as a single plant in plastic pots filled with soil. Growth chamber was set up at 23°C 16h in the light (160 μE m-2 s-1) and 8 in the dark for 22 days
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA extracted from rosette leaves using Agilent Plant RNA Isolation Mini kit including RNAse-free DNase (Qiagen) treatment
|
Label |
Cy5
|
Label protocol |
500 ng of total RNA were separately reverse-transcribed into double-strand cDNAs by the Moloney murine leukemia virus reverse transcriptase (MMLV-RT) and amplified for 2 h at 40°C using the Agilent Quick Amp Labelling Kit, two-color (Agilent Technologies). Subsequently, cDNAs were transcribed into antisense cRNA and labeled with either Cy3-CTP or Cy5-CTP fluorescent dyes for 2 h at 40°C following the manufacturer’s protocol. Cyanine-labeled cRNAs were purified using RNeasy Minikit (Qiagen). Purity and dye incorporation were assessed with the NanoDrop ND-1000 UV-VIS Spectrophotometer (Thermo Fisher Scientific) and the Agilent 2100 Bioanalyzer (Agilent Technologies).
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Hybridization protocol |
Hybridization buffer (Agilent Gene Expression Hybridization Kit ) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential
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Scan protocol |
Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (v 9.5.1.1)
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Description |
WT mechanical damaged leaves (control) vs WT herbivore wounding leaves (treatment). Harvested 2 h after the treatments
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Data processing |
R package limma (v 3.4.4) was used for background subtraction and LOESS normalization.
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Submission date |
Aug 08, 2011 |
Last update date |
Aug 05, 2018 |
Contact name |
Cinzia Margherita Bertea |
E-mail(s) |
cinzia.bertea@unito.it
|
Phone |
+39-011-6706361
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Fax |
+39-011-6706364
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Organization name |
University of Turin
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Department |
Department of Life Sciences and Systems Biology
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Lab |
Plant Physiology Unit
|
Street address |
via Quarello 11/A
|
City |
Turin |
State/province |
To |
ZIP/Postal code |
10135 |
Country |
Italy |
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Platform ID |
GPL12621 |
Series (1) |
GSE31268 |
Arabidopsis thaliana wild type and PDKO3 mutant mechanical damage (MD) vs herbivore wounding (HW) |
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