|
| Status |
Public on Dec 01, 2009 |
| Title |
R. amphibia, submerged, rep3 |
| Sample type |
RNA |
| |
|
| Source name |
R. amphibia, submerged, roots
|
| Organism |
Rorippa amphibia |
| Characteristics |
clonal plant origin: Clonal plants derived from a R. amphibia rhizome collected along the Yssel river near Doesburg, the Netherlands (N: 52º01'25'' E: 06º08'42'') and a R. sylvestris rhizome was collected along the river Rhine near Millingerwaard, the Netherlands (N: 51º52'02'' E: 06º08'42'')
|
| Treatment protocol |
Control plants were placed individually in opaque 16 liter plastic bucketsin the greenhouse and submerged plants were placed in the same buckets filled with rain water. Treatment started at noon and lasted 24 hours. No supplemental lighting was given, water was not stirred or replaced, plants were completely submerged during the treatment. Individuals were randomly assigned to either the control or submerged condition and to a position in the greenhouse.
|
| Growth protocol |
Rhizomes of each genotype were surface sterilized, cut into pieces and placed on agar medium in a light cabinet for 11 days for sprouts to develop. Individual meristems were excised and placed on pots filled with sand and supplemented with complete nutrient solution in a greenhouse. Plants were grown under natural daylight in the greenhouse for a further three weeks until the start of treatment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from frozen, homogenized material using the Qiagen RNeasy Plant Mini kit according to the manufacturer's instructions
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Ath1 Arabidopsis GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 7G.
|
| Description |
gene expression data from roots of 24 h submerged R. amphibia roots after applying a probe mask with genomic DNA hybridisation intensity threshold 80
|
| Data processing |
The data were analyzed with Genespring GX using the Robust Multichip Average (RMA) algorith and quantile normalization. A probe mask was applied based on the genomic DNA hybridisations and using a genomic DNA hybridisation intensity threshold of 80
|
| |
|
| Submission date |
Nov 18, 2008 |
| Last update date |
May 31, 2009 |
| Contact name |
Alex Boonman |
| Organization name |
Universiteit van Amsterdam
|
| Department |
IBED
|
| Lab |
Experimental Plant Systematics
|
| Street address |
Kruislaan 318
|
| City |
Amsterdam |
| ZIP/Postal code |
1098 SM |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE13641 |
Root transcript profiles of two Rorippa (Brassicaceae) species and their F1 hybrid after complete submergence |
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