|
| Status |
Public on Sep 01, 2008 |
| Title |
pmr5 pmr6 double mutant without treatment, biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Arabidopsis rosette
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
Genotype: pmr5 pmr6 double mutant
Age: 3 weeks old plants
|
| Treatment protocol |
no treatment before collection
|
| Growth protocol |
The plants were grown at 22°C with 14 hrs photoperiod
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA.
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip ATH1 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Agilent GeneArray Scanner 2500.
|
| Description |
Gene expression data from 3 weeks old rosette.
|
| Data processing |
The data were analyzed with GeneChip Operating Software (GCOS1.2) using Affymetrix default analysis settings with the target intensity set to 500.
|
| |
|
| Submission date |
Dec 17, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Shauna Somerville |
| E-mail(s) |
[email protected]
|
| Organization name |
University of California at Berkeley
|
| Department |
Energy Biosciences Institute
|
| Street address |
130 Calvin Hall, Mail Code 5230
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720-5230 |
| Country |
USA |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE9957 |
Expression profiling of the plant cell wall mutants: pmr5, pmr6 and pmr5 pmr6 double mutants |
|
| Relations |
| Reanalyzed by |
GSE118579 |
| Reanalyzed by |
GSE119083 |
| Data table header descriptions |
| ID_REF |
As defined by Affymetrix, there are the probe set identifiers, each of which is unique to a specific probe set defining a specific reagion of a singal gene or set. |
| VALUE |
MAS5-calculated Signal intensity |
| ABS_CALL |
the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC) |
| DETECTION P-VALUE |
detection p-value, p-value that indicates the significance level of the detection call |
| Normalized Value |
A normalized measurement of control arrays for each probe set calculated in GeneSpring 7.2. |
