|
| Status |
Public on Jan 03, 2008 |
| Title |
Halobacterium EMS exposure experiment, Array 8164 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Halobacterium NRC1, no EMS control, 10 minutes post mock EMS dose.
|
| Organism |
Halobacterium salinarum NRC-1 |
| Characteristics |
No EMS control sample grown in standard conditions and sampled 10 minutes post mock EMS treatment
|
| Biomaterial provider |
DiRuggiero Group, University of Maryland
|
| Growth protocol |
Halobacterium NRC-1 cells grown to mid-log phase in complex media,(OD600 0.5-0.6), incubated 30 minutes in the absence of EMS, harvested by centrifugation, resuspended the same volume of complex media, allowed to recover at 37¡C for 10 minutes post 30min mock EMS treatment.
|
| 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 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):1025-37
|
| |
|
| Channel 2 |
| Source name |
Standard mid-log Halobacterium NRC-1 reference sample.
|
| Organism |
Halobacterium salinarum NRC-1 |
| Characteristics |
Halobacterium NRC-1 grown in standard growth media
|
| Biomaterial provider |
DiRuggiero Group, University of Maryland
|
| 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 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 |
No EMS control sample grown in standard conditions and sampled 10 minutes post mock EMS treatment 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
|
| |
|
| Submission date |
Apr 17, 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 (1) |
| GSE7609 |
Halobacterium NRC-1, EMS Stress Response |
|
