|
| Status |
Public on Feb 15, 2011 |
| Title |
siliques WT, hypoxia, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Arabidopsis siliques after hypoxia treatment (1h)
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: Col-0
age: 11/12 days after pollination corresponding to mid phase of seed maturation
tissue: silique
treatment: hypoxia
|
| Treatment protocol |
Complete plants (45 DPG) were aerated with a gas mixture containing 10.5% oxygen (composed of a 1:1 mixture of ambient gas and N2) or ambient gas containing 21% oxygen for control samples in darkness for 1 hour. Plants were decapitated and immediately frozen in liquid nitrogen. About 70-80 siliques were dissected in liquid nitrogen for one biological replicate.
|
| Growth protocol |
Plants were grown at 22°C under 16/8-h photoperiod, a relative air humidity of 60% and an approximate light intensity of 100-150 µmol photons m-2 second-1.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from siliques using GENTRA kit (Biozym, Germany) according to the manufacturer´s instructions. RNA was further purified using RNeasy Kit (Quiagen) and subjected to DNAse digestion (Quiagen) according to the manufacturer´s instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, Affymetrix) at the RZPD Deutsches Ressourcenzentrum für Genomforschung GmbH (Berlin, Germany).
|
| |
|
| Hybridization protocol |
After fragmentation, cRNA was hybridized to GeneChip Arabidopsis ATH1 Genome Array according to Affymetrix standard protocol at RZPD. Gene Chips were washed and stained using fluidics protocol EUKGE-WS2V4_450.
|
| Scan protocol |
GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).
|
| Description |
Gene expression data after treatment
|
| Data processing |
Data were processed with the Affymetrix MicroArray Suite software package (MAS 5.0) and analyzed using Bioconductor packages in R. Data were normalized using the Robust Multi-array Average (RMA) method.
|
| |
|
| Submission date |
Aug 27, 2010 |
| Last update date |
Feb 15, 2011 |
| Contact name |
Johannes Thiel |
| E-mail(s) |
[email protected]
|
| Phone |
+49-017625559537
|
| Organization name |
IPK-Gatersleben
|
| Street address |
Corrensstrasse 3
|
| City |
Gatersleben |
| ZIP/Postal code |
06466 |
| Country |
Germany |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE23846 |
Expression data from siliques of wild type and AtHb1-overexpressing plants under moderate hypoxia and standard conditions |
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