|
| Status |
Public on Jan 31, 2009 |
| Title |
Populus x canescens root hypoxia_rep_03 |
| Sample type |
RNA |
| |
|
| Source name |
poplar root tissue flooded up to 5h
|
| Organism |
Populus tremula x Populus alba |
| Characteristics |
Experiments were performed with 3-month-old hybrid poplar plants (Populus x canescens). At the beginning of the experiment, the shoots of the trees had a size of 20 to 25 cm. To induce root hypoxia 52 trees were transferred into large plastic containers. The containers were filled with tap water until the water level exceeded the soil surface by 2-3 cm. Shoots were exposed to ambient air.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For total RNA extraction the Plant RNeasy kit (Qiagen) was used according to the manufacturer’s instructions with some minor modifications. Aliquots of 90 mg of frozen plant powder were added to 900 µl RLT buffer supplemented with 1% ß-mercaptoethanol, 1% PVPP and 2% (w/v) polyethylenglycol (PEG 10,000), and then incubated for 10 min at 58°C. The samples were further processed according to the manufacturer’s protocol. Total RNA was treated with DNase during (RNase free DNase kit, Qiagen) and after (DNA-free TM kit, Ambion) the extraction procedure.
The quality of the isolated total RNA was tested using an Agilent Bioanalyzer and spectrophotometric analysis (NanoDrop® ND-1000, NanoDrop Technologies) to determine the A260 to A280 ratio.
|
| Label |
Biotin
|
| Label protocol |
Labelling of cRNA from 3.5 µg of root total RNA was performed exactly as described in the Affymetrix GeneChip Expression Analysis Technical Manual.
|
| |
|
| Hybridization protocol |
standard Affymetrix protocol (see GeneChip Expression Analysis Technical Manual)
|
| Scan protocol |
standard Affymetrix protocol (see GeneChip Expression Analysis Technical Manual)
|
| Description |
Roots of Grey poplar 5 h hypoxia
|
| Data processing |
GCOS1,4 (Affymetrix)
|
| |
|
| Submission date |
Oct 07, 2008 |
| Last update date |
Oct 17, 2008 |
| Contact name |
Juergen Kreuzwieser |
| E-mail(s) |
juergen.kreuzwieser@ctp.uni-freiburg.de
|
| Phone |
+49 761 203 8311
|
| Fax |
+49 761 203 8302
|
| Organization name |
University of Freiburg
|
| Department |
Chair of Tree Physiology
|
| Street address |
Georges-Koehler-Allee
|
| City |
Freiburg |
| ZIP/Postal code |
79110 |
| Country |
Germany |
| |
|
| Platform ID |
GPL4359 |
| Series (1) |
| GSE13109 |
Effect of hypoxia on gene expression in Grey poplar |
|
