|
| Status |
Public on Nov 30, 2012 |
| Title |
923 3 |
| Sample type |
RNA |
| |
|
| Source name |
MRSA USA300
|
| Organism |
Staphylococcus aureus subsp. aureus USA300 |
| Characteristics |
genotype/variation: wildtype
agent: none
|
| Treatment protocol |
Overnight cultures were diluted 1:100 in Tryptic Soy Broth, incubated in a 37°C with shaking for 1 hr (OD600 ~0.2) and treated with water or Oxacillin (1 _g/ml) for 1 hr.
|
| Growth protocol |
Overnight cultures were diluted 1:100 in Tryptic Soy Broth, incubated in a 37°C with shaking for 1 hr (OD600 ~0.2) and treated with water or Oxacillin (1 _g/ml) for 1 hr.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The pellets were suspended in TE buffer containing lysostaphin (200 _g/ml), incubated at room temperature for 10 min, and then extracted using the Qiagen RNeasy kit with DNase treatment. The RNA purity & concentration were determined using a NanoDrop 1000
|
| Label |
biotin
|
| Label protocol |
Ten microg of total RNA was processed for biotin labeled target preparation for hybridization to Affymetrix Staphylococcus aureus expression arrays according to Genechip Expression analysis technical manual (Affymetrix, Inc).
|
| |
|
| Hybridization protocol |
Four µg of fragmented and biotin-labeled targets were hybridized to the array for 16 h at 45°C and 60 rpm in an Affymetrix Hybridization Oven 640. Arrays were washed and stained with Streptavidin Phycoerythrin. The fluorescent signals were amplified usin
|
| Scan protocol |
The signals were detected in a GeneChip Scanner 3000 7G.
|
| Description |
USA300 wildtype untretaed
|
| Data processing |
The expression data were extracted using the Gene Chip Operating Software (MicroArray Suite 5.0 software, Affymetrix). The cel files were imported into GeneSpring version 11.5 (Agilent) to identify differentially expressed genes.
|
| |
|
| Submission date |
Jul 25, 2012 |
| Last update date |
Nov 30, 2012 |
| Contact name |
Susan Boyle-Vavra |
| E-mail(s) |
[email protected]
|
| Phone |
773 702-6401
|
| Organization name |
University of Chicago
|
| Street address |
900 E 57th Street
|
| City |
CHICAGO |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL1339 |
| Series (1) |
| GSE39627 |
Comparison of the oxacillin stress response in vraS and vraT mutants |
|
