|
| Status |
Public on Nov 30, 2006 |
| Title |
Cipro treated S. aureus cells 30 min replicate 5 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Total RNA from wild type bacteria at 0hr with Cipro labeled with Cyanine-3 (green).
|
| Organism |
Staphylococcus aureus |
| Characteristics |
Strain 8325
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNA extraction protocol
|
| Label |
Cy3
|
| Label protocol |
[2 ug] of total RNA were reverse transcribed to cDNA at 42°C overnight with powerscript (BD Clonetech), a 25mM 2:1 dUTP mix (Ambion) and Rnase Out (Invitrogen). RNA was degraded with NaOH and purified with MinElute PCR columns (Qiagen)."""""""""""""""""""""""""""""""
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| |
|
| Channel 2 |
| Source name |
Total RNA from cells treated with Cipro for 30 min labeled with Cyanine-5 (red).
|
| Organism |
Staphylococcus aureus |
| Characteristics |
Strain 8325
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNA extraction protocol
|
| Label |
Cy5
|
| Label protocol |
[2 ug] of total RNA were reverse transcribed to cDNA at 42°C overnight with powerscript (BD Clonetech), a 25mM 2:1 dUTP mix (Ambion) and Rnase Out (Invitrogen). RNA was degraded with NaOH and purified with MinElute PCR columns (Qiagen)."""""""""""""""""""""""""""""""
|
| |
|
| |
| Hybridization protocol |
Epoxy-coated slides were prehybridized in 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin at 42°C for 60 min. The slides then were washed at room temperature with distilled water, dipped in isopropanol, and spun dry. Equal volumes of the appropriate Cy3- and Cy5-labeled probes were combined, dried and then resuspended in a solution of 40% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate. Resuspended probes were denatured to 95ºC prior to hybridization. The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42°C. Hybridized slides were washed sequentially in solutions of 1x SSC-0.2% SDS, 0.1x SSC-0.2% SDS, and 0.1x SSC at room temperature"""""""""""""""""""""""""""""""
|
| Scan protocol |
Scanned on Axon GenePix 4000 scanner
|
| Description |
Flip dye replicate. Cipro treated S. aureus cells 30 min
|
| Data processing |
ratio statisitics normalized and inslide replicate analysis
|
| |
|
| Submission date |
Nov 02, 2006 |
| Last update date |
Aug 17, 2012 |
| Contact name |
Marcus Jones |
| E-mail(s) |
mjones@jcvi.org
|
| Organization name |
JCVI
|
| Street address |
4120 Torrey Pines Road
|
| City |
San Diego |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL4324 |
| Series (1) |
| GSE6258 |
Microarray analysis of the effect of Cipro on wt and lexA mutant S. aureus cells |
|
