|
| Status |
Public on Apr 30, 2010 |
| Title |
Arabidopsis seedling, Col-0, rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Wild-type Col-0 3 days seedling
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
Wild-type Col-0, 3 days seedling, three independent seed lots, rep3
|
| Treatment protocol |
The mutant SPL13 (mSPL13) and non-mutated gene (SPL13) driven by the native promoter were used to transform Arabidopsis Col-0.
|
| Growth protocol |
Seeds were plated on agar medium containing MS salts and 1% w/v sucrose, incubated at 4°C for 3 days in the dark and at 22°C for 3 days under the light.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 3 days seedling using standard phenol-SDS extraction as described before (Sambrook et al., 1989), and then checked for RNA integrity with Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA, USA). Ten μg of total RNA was used to produce double-strand cDNAs which were transcribed to cRNAs.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA was synthesized from the double stranded cDNA using T7 RNA polymerase and a biotin-conjugated pseudouridine containing nucleotide mixture provided in the IVT Labeling Kit (Affymetrix, Santa Clara, CA) .
|
| |
|
| Hybridization protocol |
Twenty-five μg of cRNAs were purified and fragmented prior to hybridization in the Affymetrix GeneChip® Hybridization Oven 640, washing in the Affymetrix GeneChip® Fluidics Station 450, and then staining the arrays with biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA, USA) at the Center for Genome Research and Biocomputing Core Laboratories at Oregon State University, Corvallis OR.
|
| Scan protocol |
The arrays were scanned with an Affymetrix GeneChip® Scanner 3000 at 570 nm and signal values were obtained using statistical algorithms on Affymetrix GeneChip® Operating (GCOS) software (Affymetrix).
|
| Description |
Independent biological replicate of Col-0, SPL13, mSPL13 samples, which contain three independent seed lots each, was placed in a 9 cm plastic petri dish on agar medium containing MS salts and 1% w/v sucrose and incubated at 4°C for 3 days in the dark and at 22°C for 3 days under the light.
|
| Data processing |
Expression data generated with GCOS software (MAS5.0 method) with a scale factor of 500.
|
| |
|
| Submission date |
Feb 06, 2008 |
| Last update date |
Dec 22, 2009 |
| Contact name |
Hiro Nonogaki |
| E-mail(s) |
[email protected]
|
| Phone |
541 737 8885
|
| Fax |
541 737 3479
|
| URL |
http://hort.oregonstate.edu/isb/
|
| Organization name |
Oregon State University
|
| Department |
Horticulture
|
| Lab |
Hiro Nonogaki
|
| Street address |
4017 ALS Bldg, Dept. of Horticulture, Oregon State University
|
| City |
Corvallis |
| State/province |
OR |
| ZIP/Postal code |
97331 |
| Country |
USA |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE10414 |
microRNA156 resistant SQUAMOSA-PROMOTER-BINDING PROTEIN-LIKE13 (mSPL13) seedlings |
|
