|
| Status |
Public on May 26, 2010 |
| Title |
Coordination of frontline defense mechanisms under severe oxidative stress. Array 10257 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Halobacterium salinarum, paraquat, recovery
|
| Organism |
Halobacterium salinarum |
| Characteristics |
od: 0.7566
time: 240 min.
strain: NRC-1
medium: CM
agent: paraquat
time course: recovery
|
| Biomaterial provider |
Baliga Group, Institute for Systems Biology
|
| Growth protocol |
Standard mid-log phase (OD600 - 0.5-0.6) Halobacterium salinarum reference sample.
|
| 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
|
| |
|
| Channel 2 |
| Source name |
Halobacterium standard reference sample
|
| Organism |
Halobacterium salinarum |
| Characteristics |
strain: NRC-1
medium: CM
|
| Biomaterial provider |
Baliga Group, Institute for Systems Biology
|
| Growth protocol |
Standard mid-log phase (OD600 - 0.5-0.6) Halobacterium salinarum reference sample.
|
| 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 546
|
| 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 |
Cells incubated under entrainment conditions
|
| Data processing |
AnalyzerDG software for spotfinding. Intensities were normalized between the Alexa 546 and Alexa 647 channels by scaling all intensities in one channel such that the 75th percentile in each channel was made equal. See http://www.systemsbiology.org/Scientists_and_Research/Technology/Data_Management/Microarray_Pipeline for more details.
|
| |
|
| Submission date |
Jul 31, 2009 |
| Last update date |
May 26, 2010 |
| Contact name |
Dan Tenenbaum |
| Organization name |
Institute for Systems Biology
|
| Street address |
1441 N. 34th St.
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98103 |
| Country |
USA |
| |
|
| Platform ID |
GPL3739 |
| Series (1) |
| GSE17515 |
Coordination of frontline defense mechanisms under severe oxidative stress. |
|
| Data table header descriptions |
| ID_REF |
|
| VALUE |
normalized log10(Alexa 647 / Alexa 546) |
| RATIO |
standard ratio (not log10) of Alexa 546 / Alexa 647 |
| X_INT |
Background subtracted, normalized intensity value of channel 1 |
| Y_INT |
Background subtracted, normalized intensity value of channel 2 |
| FLAG |
Internal Quality Control Flag(s): I - spot present in print, J - spot marginal in print, K - spot absent in print |
| INV_VALUE |
normalized log10(Alexa 546 / Alexa 647) |
