|
| Status |
Public on Jul 31, 2007 |
| Title |
Halobacterium Oxygen1 L 407 min 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Halobacterium NRC-1, 407 minutes, 45 minutes after shift from high back to low oxygen
|
| Organism |
Halobacterium salinarum NRC-1 |
| Characteristics |
Halobacterium NRC-1 in standard growth medium at 37C
cells at 3.0% oxygen in turbidostat
|
| Treatment protocol |
10mL of cells were harvested from turbidostat, pelleted at 13,000rpm for 0.5 min, and snap-frozen in a dry-ice ethanol bath. Samples were stored at -80C until RNA extraction
|
| Growth protocol |
Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0.5%) oxygen in a turbidostat for 12hr. Culture was rapidly shifted to from low to high (~90-100%, 5uM) oxygen, equilibrated at high oxygen for 6 hours, then harvested 45 minutes after shifting back to low oxygen (407 total minutes elapsed in time course).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total DNA-free RNA prepared using the Absolutely RNA miniprep kit (Stratagene) and analyzed by PCR to rule out DNA contamination, with Agilent Bioanalyzer to verify integrity, and in the spectrophotometer for quantification.
|
| Label |
Alexa 532
|
| Label protocol |
see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35
|
| |
|
| Channel 2 |
| Source name |
Halobacterium NRC-1, reference
|
| Organism |
Halobacterium salinarum NRC-1 |
| Characteristics |
Halobacterium NRC-1 in standard growth medium at 37C
|
| Growth protocol |
Mid-log phase (OD600-0.5 - 0.6) Halobacterium NRC-1 grown at 225 rpm
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total DNA-free RNA prepared using the Absolutely RNA miniprep kit (Stratagene) and analyzed by PCR to rule out DNA contamination, with Agilent Bioanalyzer to verify integrity, and in the spectrophotometer for quantification.
|
| Label |
Alexa 647
|
| Label protocol |
see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35
|
| |
|
| |
| Hybridization protocol |
see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35
|
| Scan protocol |
ScanArray 5000, using Packard BioChip ScanArray software. See http://www.systemsbiology.org/Scientists_and_Research/Technology/ISB_Facilities/Microarray for microarray scanning details
|
| Description |
low oxygen, 407 minutes vs. reference
|
| Data processing |
AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:286
|
| |
|
| Submission date |
Sep 27, 2006 |
| Last update date |
Jul 31, 2007 |
| Contact name |
Amy K Schmid |
| E-mail(s) |
aschmid@systemsbiology.org
|
| Fax |
206-1299
|
| Organization name |
Institute for Systemsbiology
|
| Lab |
Nitin Baliga Halobacterium Lab
|
| Street address |
1441 N 34th St
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98103 |
| Country |
USA |
| |
|
| Platform ID |
GPL3739 |
| Series (2) |
| GSE5924 |
RNA expression data from Halobacterium NRC-1 in response to oxic/anoxic transitions, initial experiment |
| GSE5929 |
Halobacterium NRC-1 in response to oxic/anoxic transitions (initial and verification experiments) |
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