|
| Status |
Public on Jun 07, 2012 |
| Title |
Desulfovibrio_africanus_strain_Walvis_Bay-Hg_Stationary-rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Desulfovibrio_africanus_strain_Walvis_Bay-Hg_Stationary-rep1
|
| Organism |
Desulfocurvibacter africanus subsp. africanus str. Walvis Bay |
| Characteristics |
accession: CM001160 + AFHE01000000
|
| Growth protocol |
D.africanas was grown anaerobically under N2 in MOYLS4 medium (Zane et al. 2010 AEM. 76(16):5500) modified as follows: Oak Ridge National Laboratory vitamin and mineral solutions (Phelps et al. 1989 Geomicrobiol J 7(1):79) were used in place of Thauers vitamin and trace metals, FeEDTA was removed from the medium, and 60 mM sodium lactate and 30 mM sodium sulfate added as electron donor and acceptor, respectively. 5 ug/L of Hg2+ (as NgNO3) was added at time zero of the cultuivation for Hg containing cultures. Subsamples were taking at 24 and 48 hrs from both Hg containing and Hg-free cultures conrresponding to mid-exponential and early stationary phase cultures.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trisol lysis followed by chloroform extraction and isopropyl precipitation. DNA was removed byRNeasy Kit (Qiagen). RNA quality and concentration was determined by nano drop.
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed using standard protocols from Nimblegen, with QIAquick kit (Qiagen) for purification of probes
|
| |
|
| Hybridization protocol |
Hybridization was performed following Nimblegen standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| Description |
226829A02_sc2.pair
|
| Data processing |
The raw data (.pair file) was analyzed using JMPgenomics software package. Data was standardized, normalized using Lsmeans, and log2 transformed.
|
| |
|
| Submission date |
Oct 03, 2011 |
| Last update date |
Jun 07, 2012 |
| Contact name |
James G Moberly |
| E-mail(s) |
[email protected]
|
| Organization name |
Oak Ridge National Laboratory
|
| Department |
Biosciences Division
|
| Lab |
Elias
|
| Street address |
1 Bethel Valley Rd
|
| City |
Oak Ridge |
| State/province |
TN |
| ZIP/Postal code |
37831 |
| Country |
USA |
| |
|
| Platform ID |
GPL14660 |
| Series (1) |
| GSE32580 |
Expression analysis of Desulfovibrio africanus strain Walvis Bay |
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