|
| Status |
Public on Aug 05, 2010 |
| Title |
control1_Day4_repA |
| Sample type |
RNA |
| |
|
| Source name |
natural seawater bacterial community, incubated in control microcosm 1 for four days
|
| Organism |
marine metagenome |
| Characteristics |
treatment: untreated
incubation time: 4 days
fraction size: 0.22-8 µm
|
| Biomaterial provider |
Mary Ann Moran's lab, University of Georgia
|
| Growth protocol |
Microcosms were incubated at 27ºC in a temperature-controlled incubator on a 12 h light/dark cycle.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted.
|
| Label |
Alexa Fluor 647
|
| Label protocol |
Dye in each single-use vial was dissolved in 11 µl DMSO, and added to the aa-aRNA, mixed, and incubated for 1 hour in the dark at room temperature.
|
| |
|
| Hybridization protocol |
CombiMatrix CustomArray manual.
|
| Scan protocol |
Axon GenePix 4000B microarray scanner, GenePix Pro 6.0 software.
|
| Description |
Natural seawater Roseobacter community.
d4-C1a
|
| Data processing |
The background-subtracted median of pixel intensities were globally normalized among all microarrays hybridized for this experiment (20 arrays; 10 samples x 2 technical replicates) by calculating the sum of fluorescence values for all spots on each array and normalizing each array to the mean of the sums from all arrays. Bad spots were flagged according to criteria established in Burgmann et al. Environmental Microbiology 2007, 9: 2742-2755 (PMID 17922758). For the remaining probes, a combined data set was generated by averaging fluorescence values for each probe among the technical and biological replicates. The results are interpreted based on the fluorescence ratio calculated for each probe by dividing the mean fluorescence of replicated probes from experimental arrays by the mean fluorescence of replicated probes from control arrays.
|
| |
|
| Submission date |
Apr 13, 2010 |
| Last update date |
Aug 05, 2010 |
| Contact name |
Shalabh Sharma |
| E-mail(s) |
ssharmai@uga.edu
|
| Phone |
706-542-0341
|
| Organization name |
UGA
|
| Department |
Marine Science
|
| Lab |
Mary Ann Moran
|
| Street address |
Department of Marine Science
|
| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30605 |
| Country |
USA |
| |
|
| Platform ID |
GPL10323 |
| Series (1) |
| GSE21325 |
Analysis of sulfur-related transcription by Roseobacter communities using a taxon-specific functional gene microarray |
|
