|
| Status |
Public on Nov 01, 2017 |
| Title |
ML-2 |
| Sample type |
RNA |
| |
|
| Source name |
Mid-Log Phase Cell Replicate 2
|
| Organism |
Nitrosopumilus maritimus SCM1 |
| Characteristics |
strain: SCM1
treatment: Mid-Log growth
|
| Treatment protocol |
The mid-log control treatment was comprised of mid-exponential phase cells after ~0.5 mM ammonia consumption. For the ammonia starvation treatment, the mid-log phase cells were harvested by filtration, resuspended in ammonia free media, and incubated for 24 hours. Ammonia-starved cells were then exposed to 1 mM NH 4 Cl and incubated for 24 hours to investigate gene expression during recovery
|
| Growth protocol |
Nitrosopumilus maritimus cells were cultured in synthetic seawater medium at 30°C in the dark.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the hot phenol extraction method and purified with DNA-free kit
|
| Label |
Cy3
|
| Label protocol |
Three biological replicate hybridizations were done for the mid-log and 24-hour ammonia-starved conditions and two replicates for recovery from ammonia starvation.
|
| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their 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.
|
| Data processing |
All microarray data were analyzed using DNAStar ArrayStar software
Data reported in Microarray Raw Data file are Fluorescent Intensities. Data reported in Log2 ratio data file are normalized expression values (averages of all probes for each individual gene) for all 1795 protein-coding genes. Data were exported from ArrayStar, log 2 transformed, and averaged among biological replicates.
|
| |
|
| Submission date |
Sep 14, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Serdar Turkarslan |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute for Systems Biology
|
| Lab |
Baliga
|
| Street address |
401 Terry Ave
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL24013 |
| Series (1) |
| GSE103848 |
Nitrosopumilus maritimus SCM1: exponential phase control vs. 24 hours starvation vs. 24 hours recovery after starvation |
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