|
| Status |
Public on Jul 22, 2008 |
| Title |
2 hr Hypoxia Stress Total RNA Rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
7 day old Arabidopsis Seedling 2hr Hypoxia Stress Total RNA
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
Age: 7 day old seedlings
Genotype: 35S:His6FLAG-RPL18B (Col-0)
|
| Treatment protocol |
Seven-day old seedlings were subjected to short and long hypoxia stress (HS) treatments (2h and 9h) or allowed to recover after 9h HS for 1h in air (re-oxygenation). Treatments started at the end of the light period and took place 6.5 µM m-1 s-1 light, i
|
| Growth protocol |
Seeds from single copy transgene 35S:His6FLAG-RPL18B (Col-0) (Zanetti et al., 2005) were surface sterilized with 95 % (v/v) ethanol for 5 min, followed by 10 min submergence in bleach solution (20 % (v/v) bleach and 0.1 % (v/v) Tween-20), rinsed ad vernal
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Whole seedlings were harvested into liquid nitrogen within < 3 min from release from treatment. All mRNA extraction procedures were performed at 4 oC or on ice. Approximately 5 mL of pulverized tissue was extracted in 10 mL of Polysome Extraction Buffer
|
| Label |
Biotin
|
| Label protocol |
Total and polysomal RNA samples derived from three independent biological replicate experiments were used for microarray hybridization analysis. RNA samples (3 µg) were used to synthesize double stranded cDNA, using One-Cycle cDNA synthesis Kit (Affymetri
|
| |
|
| Hybridization protocol |
Hybridizations against Arabidopsis ATH1 Genome Array (GeneChip System®, Affymetrix) chips were performed at 45 oC for 16 h, in a rotating platform, using 15 µg of Biotin-labeled cRNA.
|
| Scan protocol |
Affymetrix scan protocol
|
| Description |
Comparison of 2 and 9 hour hypoxia stress and 9 hour hypoxia stess with 1 hour recovery to non-stress seedlings
|
| Data processing |
Expression data obtained in .cel files was extracted by use of the Bioconductor package of the R statistical software. Low-level normalization followed and was carried out using Robust Multichip Average (RMA). Present, Marginal or Absent (P/M/A) calls, a
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| |
|
| Submission date |
Nov 28, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Charles Jang |
| E-mail(s) |
cjang001@student.ucr.edu
|
| Organization name |
UC Riverside
|
| Department |
Botany and Plant Sciences
|
| Lab |
Julia Bailey-Serres
|
| Street address |
2215 Batchelor Hall
|
| City |
Riverside |
| State/province |
CA |
| ZIP/Postal code |
92521 |
| Country |
USA |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE9719 |
Dynamics of mRNA abundance and translation in response to short and prolonged hypoxia and reoxygenation |
|
| Relations |
| Reanalyzed by |
GSE118579 |
| Reanalyzed by |
GSE119083 |
