|
| Status |
Public on Nov 01, 2014 |
| Title |
rat endocarditis vegetation, diabetic sample, rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
Staphylococcus aureus
|
| Organism |
Staphylococcus aureus |
| Characteristics |
tissue: Whole cell
genotype: Wild type (strain COL)
growth phase: Diabetic vegetation
|
| Treatment protocol |
Rats were euthanized 3 days post inoculation and aortic valve vegatations were homogenzied and then suspended in RNA protect (Qiagen); Planktonic cells were pelleted and suspended in equal volume of RNA protect.
|
| Growth protocol |
S. aureus strain COL (MRSA) was grown to mid-exponential phase (Optical Density 600nm of 0.4-0.5) in BHI broth at 37C with aeration (225 rpm in a rotary shaker). Cells were then used to inoculate: 1. catherterized Sprague-Dawley rats, 2. Rats pretreated (48 hr; 60 mg/kg) with streptoxotocin to induce diabetic state, or 3. Fresh BHI medium and grown to either exponential phase or stationary phase growth.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Rat homogenate was treated with proteinase K (4 mg/ml) for 30 min to liberate bacteria and cells were then mechanically disrupted. Planktonic culture samples were mechanically disrupted. Following disruption, total bacterial RNA was isolated using RNeasy Mini kits (Qiagen).
|
| Label |
Biotin
|
| Label protocol |
10 ng were amplified using ExpressArt Nanokits (Amsbio) according to the manufacturer's recommendation for bacterial mRNA amplification except that the final transcription and labeling step was performed using Enzo BioArray Highyield RNA Transcript Labeling kits to incorporate biotinylated ribonucleotides into final RNA products.
|
| |
|
| Hybridization protocol |
1.0 ug of RNA were hybrized for 16 hr at 45C on an S. aureus Affymetrix GeneChip. GeneChips were washed and stained in an Affymetrix Fluidics Station using ProKaryotic GE-wash2 protocol.
|
| Scan protocol |
GeneChips were scanned in an Affymetrix 7G GeneArray Scanner
|
| Description |
Gene expression data from S. aureus strain COL isolated from diabetic rat endocarditis vegetation
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 using Affymetrix default analysis settings.
|
| |
|
| Submission date |
Oct 16, 2014 |
| Last update date |
Nov 01, 2014 |
| Contact name |
Paul Dunman |
| E-mail(s) |
[email protected]
|
| Phone |
585-276-5700
|
| Organization name |
University of Rochester
|
| Department |
Microbiology and Immunology
|
| Street address |
601 Elmwood Avenue
|
| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14642 |
| Country |
USA |
| |
|
| Platform ID |
GPL1339 |
| Series (1) |
| GSE62390 |
Staphylococcus aureus gene expression in a rat model of infective endocarditis |
|
