|
| Status |
Public on Jun 25, 2009 |
| Title |
Halobacterium salinarum NRC-1 growth curve. Array 251596210013 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Halobacterium NRC-1 Reference sample
|
| Organism |
Halobacterium salinarum NRC-1 |
| Characteristics |
Halobacterium NRC-1 grown in standard growth media
|
| 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 mirVana miRNA isolation kit(Ambion) and analyzed by PCR to rule out DNA contamination, with Agilent Bioanalyzer to verify integrity, and in NanoDrop 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
|
| |
|
| Channel 2 |
| Source name |
Halobacterium NRC-1 growth curve
|
| Organism |
Halobacterium salinarum NRC-1 |
| Characteristics |
Halobacterium NRC-1 at OD=5.130, t=10980min , replica 1
|
| Biomaterial provider |
Baliga Group, Institute for Systems Biology
|
| Growth protocol |
Halobacterium NRC-1 grown in rich media (CM), 200mL culture in 1L flask, shaking at 125RPM) and constant light.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total DNA-free RNA prepared using the mirVana miRNA isolation kit(Ambion) and analyzed by PCR to rule out DNA contamination, with Agilent Bioanalyzer to verify integrity, and in NanoDrop 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
|
| |
|
| |
| Hybridization protocol |
see http://www.chem.agilent.com/Scripts/PDS.asp?lPage=34519 for details
|
| Scan protocol |
ScanArray 5000, using Packard BioChip ScanArray software. See http://www.systemsbiology.org/Scientists_and_Research/Technology/ISB_Facilities/Microarrayfor microarray scanning details
|
| Description |
Halobacterium NRC-1 at OD=5.130 versus standard reference.
|
| Data processing |
Agilent FeatureExtraction for spotfinding/quantitation. See http://www.systemsbiology.org/Scientists_and_Research/Technology/Data_Management/Microarray_Pipeline for more details
|
| |
|
| Submission date |
Sep 15, 2008 |
| Last update date |
Jun 25, 2009 |
| Contact name |
Tie Koide |
| E-mail(s) |
tiekoide@gmail.com
|
| Organization name |
Institute for Systems Biology
|
| Street address |
1441 N 34th street
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98103 |
| Country |
USA |
| |
|
| Platform ID |
GPL7255 |
| Series (2) |
| GSE12923 |
Halobacterium salinarum NRC-1 growth curve, tiling arrays |
| GSE13150 |
Prevalence of transcription promoters within archaeal operons and coding sequences |
|
