|
| Status |
Public on May 08, 2013 |
| Title |
Hal_Supernat_005minb_vs_NRC-1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Halo grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in Dunaliella supernatant and harvested at 5 min. Replica
|
| Organism |
Halobacterium salinarum NRC-1 |
| Characteristics |
strain: NRC-1
|
| Treatment protocol |
see characteristics:source
|
| Growth protocol |
Halobacterium salinarum reference was grown in CM (Dassarma S, Fleischmann EM (1995) Archaea a Laboratory Manual: Halophiles: Cold Spring Harbor Laboratory Press) or in MM2 please check Orellana et al.2013). Dunaliella was grown in MM1 (check Orellana et al., 2011).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared the following day using the Absolutely RNA miniprep kit according to manufacturer’s instructions (Agilent Technologies, Santa Clara, CA). RNA quality was checked using an Agilent Bioanalyzer as described (Schmid et al., 2009). Freedom from DNA contamination was determined on 200 ng samples of RNA in 25 cycles of PCR.
|
| Label |
Dye 547, Dye 647
|
| Label protocol |
5 ug quality-checked total RNA was direct-labeled with Cy3 and Cy5 dyes according to manufacturer's instructions (Kreatech, Alameda, CA).
|
| |
|
| Channel 2 |
| Source name |
Standard mid-log phase (OD600 - 0.5-0.6, 37C, 225 rpm) Halobacterium salinarum reference sample.
|
| Organism |
Halobacterium salinarum NRC-1 |
| Characteristics |
strain: NRC-1
|
| Treatment protocol |
see characteristics:source
|
| Growth protocol |
Halobacterium salinarum reference was grown in CM (Dassarma S, Fleischmann EM (1995) Archaea a Laboratory Manual: Halophiles: Cold Spring Harbor Laboratory Press) or in MM2 please check Orellana et al.2013). Dunaliella was grown in MM1 (check Orellana et al., 2011).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared the following day using the Absolutely RNA miniprep kit according to manufacturer’s instructions (Agilent Technologies, Santa Clara, CA). RNA quality was checked using an Agilent Bioanalyzer as described (Schmid et al., 2009). Freedom from DNA contamination was determined on 200 ng samples of RNA in 25 cycles of PCR.
|
| Label |
Dye 647, Dye 547
|
| Label protocol |
5 ug quality-checked total RNA was direct-labeled with Cy3 and Cy5 dyes according to manufacturer's instructions (Kreatech, Alameda, CA).
|
| |
|
| |
| 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
|
| Scan protocol |
ScanArray 5000, using Packard BioChip ScanArray software. See http://www.systemsbiology.org for microarray scanning details
|
| Description |
Analysis used Halobacterium NRC-1 (grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in CM) RNA as reference samples for comparison to the experimental samples taken at 5 minutes.
|
| Data processing |
AnalyzerDG software for spotfinding. Intensities were normalized between the Alexa 546 and Alexa 647 channels by scaling all intensities in one channel such that the 75th percentile in each channel was made equal. See http://www.systemsbiology.org for more details.
|
| |
|
| Submission date |
Apr 03, 2013 |
| Last update date |
May 08, 2013 |
| Contact name |
Monica V. Orellana |
| E-mail(s) |
Monica.Orellana@systemsbiology.org
|
| Phone |
9206) 732-1302
|
| Fax |
(206) 732-1299
|
| Organization name |
Institute for Systems Biology
|
| Lab |
N. S. Baliga
|
| Street address |
401 Terry Ave North
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL13682 |
| Series (1) |
| GSE45752 |
A role for programmed cell death in the microbial loop |
|
