|
| Status |
Public on Aug 18, 2006 |
| Title |
Gamma Radiation Response, Array 06993 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Halobacterium NRC-1, reference
|
| Organism |
Halobacterium salinarum NRC-1 |
| Characteristics |
Halobacterium NRC-1 grown in standard growth media
|
| Biomaterial provider |
Baliga Group, Institute for Systems Biology
|
| Growth protocol |
Mid-log phase (OD600-0.5 - 0.6) Halobacterium NRC-1
|
| 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, Control 30 min
|
| Organism |
Halobacterium salinarum NRC-1 |
| Characteristics |
Halobacterium NRC-1 control culture in standard growth media at 42 C.
|
| Biomaterial provider |
Baliga Group, Institute for Systems Biology
|
| Growth protocol |
Mid-log phase (OD600-0.4 - 0.7) Halobacterium NRC-1 control culture
|
| 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[optional]
|
| |
|
| |
| 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[optional]
|
| 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 |
Gamma Control 30 min vs. reference
|
| Data processing |
AnalyzerDG software for spotfinding. see http://www.systemsbiology.org/Scientists_and_Research/Technology/Data_Management/Microarray_Pipeline for more details
|
| |
|
| Submission date |
Aug 10, 2006 |
| Last update date |
Aug 17, 2006 |
| Contact name |
Nitin Baliga |
| E-mail(s) |
nbaliga@systemsbiology.org
|
| Organization name |
Institute for Systems Biology
|
| Street address |
1441 North 34th St.
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98103 |
| Country |
USA |
| |
|
| Platform ID |
GPL3739 |
| Series (1) |
| GSE5557 |
An integrated systems approach for understanding cellular responses to gamma radiation. |
|
