|
| Status |
Public on Sep 01, 2011 |
| Title |
SA_16_hr._in_vitro-3 |
| Sample type |
RNA |
| |
|
| Source name |
S. aureus recovered from Luria-Betani Broth after 16 hour incubation with shaking at 200 rpm 5:1 volume/media ratio
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: JP1
growth phase: Post exponential phase
environment: In vitro
time (hours): 16
matrix: Luria-Bertani Broth
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the Qiagen RNAeasy kit using the maufacturer's instructions.
|
| Label |
biotin-16-dUTP
|
| Label protocol |
The Ambion MessageAmp II-Bactera RNA amplification kit was used for labeling with biotin-16-dUTPaccording to the maufacturer's instruction with the exception that the biotin-16-dUTP was increased to a final concentration of 3.08 mM (41% of total UTP in the reaction).
|
| |
|
| Hybridization protocol |
Biotinylated aRNA was fragmented using Ambion RNA fragmentation reagent at 70°C for 15 minutes and 5 mg of fragmented aRNA was hybridized to Affymetrics GPL4047 microarrays at 45°C for 16 hours using Affymetrics hybridization buffers according to the manufacture's suggested procedures.
|
| Scan protocol |
Established protocol, Center for Expression Arrays, Seattle, WA, USA
|
| Description |
LOESS normalization: NO
|
| Data processing |
Probe intensities were determined using GCOS and data was background corrected, centered and nomalized using GCRMA within GeneSpring 7.3.1. Response curves exhibiting non-linearity were renormalized using LOESS in the STATA v10 Statistical package with the SA66-3_0.5_hr._in_vivo-2 data set as the reference template.
|
| |
|
| Submission date |
Jul 11, 2011 |
| Last update date |
Sep 01, 2011 |
| Contact name |
Donald O. Chaffin |
| E-mail(s) |
[email protected]
|
| Phone |
(206) 884-1974
|
| Organization name |
Seattle Children's Research Institute
|
| Street address |
1900 9th Ave.
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98101 |
| Country |
USA |
| |
|
| Platform ID |
GPL4047 |
| Series (1) |
| GSE30544 |
Changes in the Staphylococcus aureus transcriptome during early adaptation to the lung |
|
