|
| Status |
Public on Aug 08, 2008 |
| Title |
Sample 2 vancomycin treated 10XMIC 1 hr |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
H37Rv untreated culture
|
| Organism |
Mycobacterium tuberculosis |
| Characteristics |
Mycobacterium tuberculosis H37Rv strain untreated
|
| Biomaterial provider |
Our own laboratory
|
| Treatment protocol |
M. tuberculosis H37Rv grown in physiological conditions to exponential phase
|
| Growth protocol |
Culture grown to mid-log phase in Middlebrook 7H9 supplemented with ADC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bacteria were thawed on ice and added to prechilled 15 ml screw-capped polypropylene centrifuge tubes containing 1 ml of zirconia/silica beads (0.1 mm diameter, Biospec Products) and 1 ml of phenol-chloroform-isoamyl alcohol (25:24:1). Full details at Manganelli et al. Mol Microbiol (1999) 31:715-724
|
| Label |
Cy3
|
| Label protocol |
Combine total RNA, random primers and reaction mix (5X First-Strand buffer, 100 mM DTT, dTdNTP mix, Cy3 or Cy5). Full details at www.cag.icph.org.
|
| |
|
| Channel 2 |
| Source name |
H37Rv vancomycin treated culture
|
| Organism |
Mycobacterium tuberculosis |
| Characteristics |
Mycobacterium tuberculosis H37Rv strain vancomycin treated
|
| Biomaterial provider |
Our own laboratory
|
| Treatment protocol |
M. tuberculosis H37Rv grown in physiological conditions to exponential phase and then incubated for 1 hr with 400 ug/ml of vancomycin
|
| Growth protocol |
Culture grown to mid-log phase in Middlebrook 7H9 supplemented with ADC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
see channel 1
|
| Label |
Cy5
|
| Label protocol |
see channel 1
|
| |
|
| |
| Hybridization protocol |
Combine labeled sample with 10 mg/ml tRNA, 20X SSC, Formamide, % SDS. Full details at www.cag.icph.org
|
| Scan protocol |
After hybridization slides were immediately scanned using a 428TMArray Scanner (Affymetrix). Fluorescence intensities of Cy3 and Cy5 dyes at each spot were quantified using the ImaGene software 4.1 (BioDiscovery, Inc.)
|
| Description |
no additional information
|
| Data processing |
Data obtained from qualified spots were normalized using the print-tip LOESS with a web-based tool for Diagnosis and Normalization of spotted cDNA MicroArrayData (DNMAD) available at http://dnmad.bioinfo.cnio.es
Values are expressed as ratio Cy5/Cy3 spot's intensity determined from the normalized fluorescence intensity.
|
| |
|
| Submission date |
Aug 06, 2008 |
| Last update date |
Aug 07, 2008 |
| Contact name |
Roberta Provvedi |
| E-mail(s) |
[email protected]
|
| Phone |
+390498272364
|
| Fax |
+390498272355
|
| Organization name |
University of Padua
|
| Department |
Biologia
|
| Street address |
Via Gabelli 63
|
| City |
Padua |
| ZIP/Postal code |
35121 |
| Country |
Italy |
| |
|
| Platform ID |
GPL4057 |
| Series (1) |
| GSE12364 |
Global transcriptional response to vancomycin in Mycobacterium tuberculosis |
|
