|
| Status |
Public on Jun 26, 2016 |
| Title |
HTCC1062_Control_Sta_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
HTCC1062_Control_Sta
|
| Organism |
Candidatus Pelagibacter ubique HTCC1062 |
| Characteristics |
strain: HTCC1062
source: Carboy 16
dmsp availability: Excess
growth phase: Stationary
ribosomal protein rna abundance: 0.26
|
| Treatment protocol |
40 ml of culture from each biological replicate were harvested via centrifugation (1 hour at 43 000 g, 10°C), then re-suspended in 1 ml of Bacteria Protect (Qiagen) for 15 min. Following RNA stabilization, cells were collected by centrifugation (30 min at 40 000 g, 10°C), the supernatant was removed, and cells were then stored frozen at -80°C prior to extraction.
|
| Growth protocol |
Artificial seawater media with 1 µM (Control) or 100 nM (Limited) DMSP, 500 µM pyruvate, 500 µM glycine betaine, 100 µM ammonium, 50 µM phosphate, 10 µM glycine, vitamins, and trace metals. Cells were grown at 16 °C with intermittent light and sparging with air.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Kit (Qiagen) and amplified using MessageAmp-II-Bacteria RNA Amplification Kit (Ambion).
|
| Label |
biotin
|
| Label protocol |
RNA was labeled with biotin labeled nucleotides during the in-vitro transcription reaction.
|
| |
|
| Hybridization protocol |
5.5 µg of labeled aRNA was hybridized to chips at 45˚C, rotating at 60 rpm for 16 hours.
|
| Scan protocol |
The samples were scanned with an Affymetrix GeneChip Scanner 3000 7G with autoloader using AGCC software.
|
| Description |
SL-27
|
| Data processing |
RMA normalization conducted with Affymetrix ExpressionConsole software package. Analysis includes only Pelagibacter ubique HTCC1062 probes.
|
| |
|
| Submission date |
Aug 24, 2011 |
| Last update date |
Jun 26, 2016 |
| Contact name |
Daniel Patrick Smith |
| Organization name |
Oregon State University
|
| Department |
Microbiology Department
|
| Lab |
Giovannoni Lab
|
| Street address |
220 Nash Hall
|
| City |
Corvallis |
| State/province |
OR |
| ZIP/Postal code |
97331-8542 |
| Country |
USA |
| |
|
| Platform ID |
GPL7330 |
| Series (1) |
| GSE31630 |
Transcriptional Response to Sulfur Limitation in Pelagibacter ubique |
|
