|
| Status |
Public on Feb 01, 2012 |
| Title |
Wild type_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Bacterial cells, pelleted
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: RN4220
|
| Treatment protocol |
2.5 ml of bacterial culture was added to 2.5 ml of a 1:1 ethanol:acetone mixture and snap frozen. Samples were stored at -80°C prior to RNA extraction
|
| Growth protocol |
Strains were grown in TSB medium at 37°C with shaking
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total bacterial RNA was isolated utilizing the Qiagen RNeasy mini kit and contaminating DNA was removed by treatment with Ambion DNA-free
|
| Label |
biotin
|
| Label protocol |
Fifty nangorams of total RNA was amplified with the Sigma Whole Transcriptome Amplifcation kit (WTA1) according to the manufacturer's protocol. The resulting amplified DNA was fragmented with Dnase I and biotin-labeled with terminal deoxynucleotidyl Transferase, supplied by Affymetrix.
|
| |
|
| Hybridization protocol |
Ten micrograms of amplified, labeled DNA was hybridized to Affymetrix S. Aureus Genome Arrays for 16 hours at 45° C according to the manufacturer's protocol. The arrays were washed and stained using the ProkGE-WS2v3_450 fluidics script on the Affymetrix FS450 fluidics station.
|
| Scan protocol |
The arrays were scanned with an Affymetrix GCS 3000 7G Scanner.
|
| Description |
RN4220_2
|
| Data processing |
The .cel files were analyzed using the MAS5 algorithm in the Affymetrix Expression Console software. The trimmed mean target intensity of each array was set to 500.
|
| |
|
| Submission date |
Jan 25, 2012 |
| Last update date |
Feb 01, 2012 |
| Contact name |
Ronan Kevin Carroll |
| E-mail(s) |
[email protected]
|
| Phone |
813-974-5259
|
| Fax |
813-974-1614
|
| Organization name |
University of South Florida
|
| Department |
CMMB
|
| Street address |
4202 E Fowler Ave
|
| City |
Tampa |
| ZIP/Postal code |
33620 |
| Country |
USA |
| |
|
| Platform ID |
GPL1339 |
| Series (1) |
|
