|
| Status |
Public on Jan 31, 2013 |
| Title |
Leaf-An1-Cold-rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Leaf-An1-Cold
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: An-1
age: 3 week-old
stress type: Cold
stress treatment: 10C for 3hrs
tissue: leaves
|
| Treatment protocol |
Combinations of high-light (800 µm photons m-2s-1), cold (10°C), heat (38°C), high salinity (100 mM NaCl), and foliar spray application of a bacterial elicitor (20 µM flagellin peptide flg22). For the Cold+HL treatment, heat from 3 sodium lamps was displaced by circulating fans and a plexiglass shield and ambient plant temperature maintained by ice trays and monitored at 10°C with an infrared thermometer (ThermaTwin TN408LC).
|
| Growth protocol |
Three week-old plants were subjected to stress treatments for three hours in triplicate, at environmentally controlled chambers (RISØ DTU National Laboratory, Roskilde, Denmark). To reduce effects of circadium rhythmicity, treatments were performed 5 hours after chamber dawn.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA samples were extracted using RiboPure kit (Ambion, Austin, TX, USA).
|
| Label |
Cy3
|
| Label protocol |
Reverse transcription of messenger RNA was performed from total RNA using a double stranded cDNA synthesis kit (Superscript, Invitrogen) and labelled with Cy3 using NimbleGen Gene Expression protocol.
|
| |
|
| Hybridization protocol |
4 ug of the labelled products were loaded onto microarrays, hybridized overnight, and washed in the NimbleGen Wash Buffer Kit following the NimbleGen protocol.
|
| Scan protocol |
Scanning was performed on a Roche 2-microns scanner and the images analyzed with the NimbleScan software.
|
| Description |
290757A05
|
| Data processing |
Data was imported into R (R Core Team, 2012) using the oligo (Carvalho and Irizarry, 2010) and pdInfoBuilder packages (Falcon, 2012) using the AgilentAT6 build. Normalization was performed using quantiles (Bolstad et al., 2003) and expression indexes calculated using RMA (Irizarry et al., 2003).
|
| |
|
| Submission date |
Oct 31, 2012 |
| Last update date |
Jan 31, 2013 |
| Contact name |
Simon Rasmussen |
| E-mail(s) |
simon@cbs.dtu.dk
|
| Phone |
+45 4525 6148
|
| Organization name |
Technical University of Denmark
|
| Department |
Department of Systems Biology
|
| Lab |
Center for Biological Sequence Analysis
|
| Street address |
Kemitorvet, Building 208
|
| City |
Kongens Lyngby |
| ZIP/Postal code |
DK-2800 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL16226 |
| Series (1) |
| GSE41935 |
Transcriptome responses to combined biotic and abiotic stresses in Arabidopsis thaliana |
|
