|
| Status |
Public on May 31, 2006 |
| Title |
Halobacterium NRC-1, ura3 Knockout, sirR Knockout, Set B, 1.5mM MnSO4.H2O, Array 08901 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Halobacterium NRC-1, control
|
| 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, ura3 Knockout, sirR Knockout, Set B, 1.5mM Mn
|
| Organism |
Halobacterium salinarum NRC-1 |
| Characteristics |
Halobacterium NRC-1, ura3 Knockout, sirR Knockout grown in standard growth media, exposed to 1.5mM Mn
|
| Biomaterial provider |
Baliga Group, Institute for Systems Biology
|
| Growth protocol |
Mid-log phase (OD600-0.5 - 0.6) Halobacterium NRC-1 culture grown in standard media, innoculated with 6.0mM FeSO4 for 80 minutes when sample collected
|
| 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 the Microarray facility website at ISB for for microarray scanning details
|
| Description |
control vs. Halobacterium NRC-1, ura3 Knockout, sirR Knockout (1.5mM Mn, Set B)
|
| Data processing |
AnalyzerDG software for spotfinding. see the Microarray pipeline data management website at ISB for more details
|
| |
|
| Submission date |
May 18, 2006 |
| Last update date |
May 25, 2006 |
| Contact name |
Michael Hiroshi Johnson |
| E-mail(s) |
mjohnson@systemsbiology.org
|
| Phone |
(206) 732-1319
|
| Fax |
(206) 732-1299
|
| URL |
http://db.systemsbiology.net/users/mjohnson/
|
| Organization name |
Institute for Systems Biology
|
| Department |
Computational Biology
|
| Lab |
Hood Lab
|
| Street address |
1441 North 34th Street
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98103 |
| Country |
USA |
| |
|
| Platform ID |
GPL3739 |
| Series (2) |
| GSE4899 |
Halobacterium NRC-1, ura3 Knockout, sirR Knockout, MnSO4.H2O Stress Response |
| GSE4925 |
Halobacterium NRC-1 response to sub-lethal levels of Mn(II), Fe(II), Co(II), Ni(II), Cu(II) and Zn(II) |
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