|
| Status |
Public on Nov 18, 2008 |
| Title |
Loch Ness-0 vs RIL1050 (G/R) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
RIL1050
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
Recombinant inbred line from a cross between Eil-0 and Lc-0
|
| Growth protocol |
stratified for 48 hrs at 4°C, grown in tissue culture on basic solid medium with macro- and micronutrients (0.5 x MS) and 0.9% agar (Duchefa, Netherlands), supplemented with 2% sucrose at 21°C under continuous light of 130 μE intensity. Plant material for RNA analysis was harvested at 9 days after germination.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from plants was isolated using the Plant RNeasyTM kit (QIAGEN, Netherlands) according to the manufacturer’s instructions.
|
| Label |
Cy5
|
| Label protocol |
Total RNA from the seedling pools 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 |
Loch Ness-0
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
Arabidopsis thaliana accession Lc-0
|
| Growth protocol |
stratified for 48 hrs at 4°C, grown in tissue culture on basic solid medium with macro- and micronutrients (0.5 x MS) and 0.9% agar (Duchefa, Netherlands), supplemented with 2% sucrose at 21°C under continuous light of 130 μE intensity. Plant material for RNA analysis was harvested at 9 days after germination.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from plants was isolated using the Plant RNeasyTM kit (QIAGEN, Netherlands) according to the manufacturer’s instructions.
|
| Label |
Cy3
|
| Label protocol |
Total RNA from the seedling pools 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 |
none
|
| 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. Bioconductor open source software was used for data processing.
|
| |
|
| Submission date |
Nov 17, 2008 |
| Last update date |
Nov 17, 2008 |
| 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) |
| GSE13628 |
Comprehensive analysis of Arabidopsis expression level polymorphisms with simple inheritance |
|
