|
| Status |
Public on Nov 19, 2010 |
| Title |
water treated plant vs BABA treated plant replicate 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
rosette leaves from BABA treated plants
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
treatment: BABA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using lithium chloride 6M overnight at 4C
|
| Label |
Cy5
|
| Label protocol |
Total RNA from leaves was amplified using the MessageAmpTM aRNA II kit (Ambion, NY, U.S.A.). 5 microgram of amplified RNA were reverse transcribed into cyanin3 or cyanin 5 labeled cDNA, purified with QiaquickTM columns (Qiagen, Netherlands) and hybridized on custom microarrays (GEO accession number GPL6147)
|
| |
|
| Channel 2 |
| Source name |
rosette leaves from water treated plants
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
treatment: H2O
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using lithium chloride 6M overnight at 4C
|
| Label |
Cy3
|
| Label protocol |
Total RNA from leaves was amplified using the MessageAmpTM aRNA II kit (Ambion, NY, U.S.A.). 5 microgram of amplified RNA were reverse transcribed into cyanin3 or cyanin 5 labeled cDNA, purified with QiaquickTM columns (Qiagen, Netherlands) and hybridized on custom microarrays (GEO accession number GPL6147)
|
| |
|
| |
| Hybridization protocol |
Hybridisation buffer was 3xSSC and 0,4%SDS. Incubation at 64°C O/N without agitation. Washing conditions: twice for 5 minutes in 2xSSC 0.1% SDS, twice for 1 minute in 0.2xSSC, 1 minute in 0.1xSSC, 5 minutes in 0.1xSSC 0.1% TritonX100. All washes at room temperature.
|
| Scan protocol |
Agilent microarray scanner, 10 μm resolution
|
| Description |
water_BABA1
CA 790
|
| Data processing |
GenePix Pro 6.0 was used to analyse the images and generate gpr files; raw data without background substraction were print-tip loess normalized to calculate M values. LimmaGui software package (Wettenhall, J. M., and Smyth, G. K. (2004). limmaGUI: a graphical user interface for linear modeling of microarray data. Bioinformatics, 20:3705-3706) was used for data analysis.
|
| |
|
| Submission date |
May 20, 2010 |
| Last update date |
Nov 19, 2010 |
| Contact name |
Johann Weber |
| Organization name |
University of Lausanne
|
| Department |
Center for integrative Genomics
|
| Lab |
DNA array facility
|
| Street address |
Genopode Building
|
| City |
Lausanne |
| State/province |
VD |
| ZIP/Postal code |
CH 1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL6147 |
| Series (1) |
| GSE16434 |
Analysis of gene expression in Arabidopsis thaliana after priming with BABA and infection with Pseudomonas syringae pv tomato DC3000 |
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