|
| Status |
Public on Oct 20, 2016 |
| Title |
strain Newman, anaerobic growth, DMSO treated, rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
Newman_WT_DMSO
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain background: Newman
genotype/variation: Wild type
growth condition: Anaerobic growth
sample: Whole cell
treated with: DMSO for 10min
|
| Treatment protocol |
An equal volume of ice cold acetone:ethanol (1:1) was added to inactivate bacterial ribonucleases
|
| Growth protocol |
S. aureus strain Newman or isogenic ΔsaeRS mutant cells were grown to mid-exponential phase (Optical Density 600nm of 0.5) in trypic soy broth at 37C with no aeration. Cells were then treated with 25 µM '882 or equal volume of vehicle (DMSO) for 10 min.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Culture samples were mechanically disrupted in a Bullet Blender (Next Advance; Averill Park, NY) using 0.5 mm RNase-free zirconium oxide beads. Following disruption, total bacterial RNA was precipitated using isopropyl alcohol precipitation, washed with 70% ethanol and resuspended in deionized water.
|
| Label |
Biotin
|
| Label protocol |
10 micrograms of each sample was labeled per Affymetrix (Santa Clara, CA) instructions for prokaryotic arrays (reverse transcribed, DNase I fragmentation and 3' biotinylated).
|
| |
|
| Hybridization protocol |
1.5 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 DMSO treated anaerobically grown S. aureus strain Newman biological replicate 2
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 using Affymetrix default analysis settings (Algorithm: ExpressionStat 5.0).
|
| |
|
| Submission date |
Aug 09, 2016 |
| Last update date |
Oct 20, 2016 |
| 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) |
| GSE85379 |
A small molecule inhibitor of iron-sulfur cluster assembly is toxic to Staphylococcus aureus in an Sae-dependent manner |
|
