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Status |
Public on Jan 03, 2008 |
Title |
Halobacterium NRC-1 dark diurnal experiment 1, 36.0 hours post entrainment, Array 7343 |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
Halobacterium NRC-1 dark diurnal experiment 1, 36.0 hours post entrainment.
|
Organism |
Halobacterium salinarum NRC-1 |
Characteristics |
Halobacterium NRC-1 dark diurnal experiment 1 with cells grown at 42degrees C in aerobic conditions and entrained for 72 hours with 12:12hr light:dark cycle and sampled in darkness.0_h hours post entrainment.
|
Biomaterial provider |
Baliga Lab, Institute for Systems Biology
|
Growth protocol |
Halobacterium NRC-1 were grown in aerobic conditions (shaking at 100RPM) at 42degrees C and entrained for 72 hours with 12:12hr light:dark cycle at a light intensity of 150µE/M^2/sec. and sampled in darkness36.0 minutes post entrainment.
|
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):1025-54
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Channel 2 |
Source name |
Standard mid-log Halobacterium NRC-1 reference sample.
|
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 Group, Institute for Systems Biology
|
Growth protocol |
Standard mid-log phase (OD600 - 0.5-0.6) Halobacterium NRC-1 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 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):1025-54
|
|
|
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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):1025-54
|
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 |
Halobacterium NRC-1 dark diurnal experiment 1, 36.0 hours post entrainment versus standard reference.
|
Data processing |
AnalyzerDG software for spotfinding. see http://www.systemsbiology.org/Scientists_and_Research/Technology/Data_Management/Microarray_Pipeline for more details
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Submission date |
May 02, 2007 |
Last update date |
Jan 03, 2008 |
Contact name |
Marc Facciotti |
E-mail(s) |
mfacciotti@systemsbiology.org
|
Organization name |
Institute for Systems Biology
|
Street address |
1441 North 34th Street
|
City |
Seattle |
State/province |
WA |
ZIP/Postal code |
98103 |
Country |
USA |
|
|
Platform ID |
GPL3739 |
Series (2) |
GSE7709 |
Halobacterium NRC-1 Diurnal experiment Dark 1 |
GSE7739 |
Halobacterium NRC-1 Diurnal experiment |
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