|
| Status |
Public on Jun 12, 2013 |
| Title |
conditional mutant strain replicate 2-2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
H37Rv mycobacterial cells_TB79
|
| Organism |
Mycobacterium tuberculosis |
| Characteristics |
strain: TB79
genotype/variation: esx-3 conditional mutant
|
| Treatment protocol |
anhydrotetracycline 100ng/ml for 48hrs
|
| Growth protocol |
The cells were grown in 35ml of Middlebrook 7H9/ADC in presence of 100ng/ml of anhydrotetracycline in rolling cultures until OD540: 0.3-0.4
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol (Manganelli et al. Mol Micro, 1999) 31:715-724
|
| Label |
cy3
|
| Label protocol |
protocol described in Casonato et al., 2012 Infect. Immun. 80(9):3132.
|
| |
|
| Channel 2 |
| Source name |
H37Rv mycobacterial cells_TB38
|
| Organism |
Mycobacterium tuberculosis |
| Characteristics |
strain: TB38
genotype/variation: parental strain
|
| Treatment protocol |
anhydrotetracycline 100ng/ml for 48hrs
|
| Growth protocol |
The cells were grown in 35ml of Middlebrook 7H9/ADC in presence of 100ng/ml of anhydrotetracycline in rolling cultures until OD540: 0.3-0.4
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol (Manganelli et al. Mol Micro, 1999) 31:715-724
|
| Label |
cy5
|
| Label protocol |
protocol described in Casonato et al., 2012 Infect. Immun. 80(9):3132.
|
| |
|
| |
| Hybridization protocol |
protocol described in Casonato et al., 2012 Infect. Immun. 80(9):3132.
|
| Scan protocol |
Microarrays were scanned using an Agilent G2565CA microarray scanner system (with Scan Control 8.1 software [Agilent Technologies]), and fluorescence intensities of the two channels at each spot were quantified using Agilent Feature Extraction 10.1 software (Agilent Technologies).
|
| Description |
TB79 rep 2-2
|
| Data processing |
Data were normalized with the Web-based tool DNMAD (diagnosis and normalization of spotted cDNA microarray data [http://dnmad.bioinfo.cnio.es/]) using the print-tip lowess method after background subtraction.
|
| |
|
| Submission date |
Jun 11, 2013 |
| Last update date |
Jun 12, 2013 |
| Contact name |
Agnese Serafini |
| E-mail(s) |
[email protected], [email protected]
|
| Organization name |
University of Padua
|
| Department |
Molecular Medicine
|
| Lab |
Microbiology
|
| Street address |
Via Gabelli 63
|
| City |
Padua |
| ZIP/Postal code |
35121 |
| Country |
Italy |
| |
|
| Platform ID |
GPL4057 |
| Series (1) |
| GSE47834 |
Mycobacterium tuberculosis ESX-3 conditional mutant expression |
|
