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Status |
Public on Jul 31, 2007 |
Title |
Halobacterium_oxygen3_L2H_000min, Array 10639 |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
Halobacterium NRC1, aerobic 000 minutes after shift.
|
Organism |
Halobacterium salinarum NRC-1 |
Characteristics |
Halobacterium NRC-1 in standard growth medium at 37C; at 0% oxygen.
|
Biomaterial provider |
Baliga Lab, Institute for Systems Biology
|
Growth protocol |
Mid-log phase (OD600~0.5-0.7) Halobacterium NRC-1 was equilibrated to low (~0%) oxygen in a turbidostat for 24hr. Sample was harvested at 000 minutes after rapidly shifting to high (~100%; 5microM) oxygen for 12 hours.
|
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 547
|
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):1025-37
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Channel 2 |
Source name |
Halobacterium NRC-1, reference
|
Organism |
Halobacterium salinarum NRC-1 |
Characteristics |
Halobacterium NRC-1 standard reference grown in standard growth media to mid-log phase (OD600 0.5-0.6).
|
Biomaterial provider |
Baliga Lab, Institute for Systems Biology
|
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):1025-37
|
|
|
|
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):1025-37
|
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 |
High-oxygen 000 minutes post-shift 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 7:288
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Submission date |
Apr 19, 2007 |
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 (1) |
GSE7559 |
Halobacterium NRC-1_oxygen_response_timecourse_set3 |
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