|
| Status |
Public on Jan 31, 2007 |
| Title |
H37Rv-Mbovis_rep2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
M. tuberculosis culture
|
| Organism |
Mycobacterium tuberculosis |
| Characteristics |
Strain H37Rv
|
| Biomaterial provider |
Public Health Research Institute
|
| Treatment protocol |
Culture grew in Middlebrook 7H9 media supplemented with ADS, glycerol and Tween 80.
|
| Growth protocol |
Mid log phase culture was shortly centrifuged and the pellet quickly frozen with dry ice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Manganelli et al. Mol Microbiol (2001) 41(2):423-437
|
| Label |
Cy3
|
| Label protocol |
Walters et al. Mol Microbiol (2006) 60(2):312-330
|
| |
|
| Channel 2 |
| Source name |
M. bovis culture
|
| Organism |
Mycobacterium tuberculosis variant bovis |
| Characteristics |
Strain Ravenel (TMC 401)
|
| Biomaterial provider |
Public Health Research Institute
|
| Treatment protocol |
Culture grew in Middlebrook 7H9 media supplemented with ADS, pyruvate and Tween 80.
|
| Growth protocol |
Mid log phase culture was shortly centrifuged and the pellet quickly frozen with dry ice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Manganelli et al. Mol Microbiol (2001) 41(2):423-437
|
| Label |
Cy5
|
| Label protocol |
Walters et al. Mol Microbiol (2006) 60(2):312-330
|
| |
|
| |
| Hybridization protocol |
Total purified cDNA was added to the arrays in a hybridization solution containing a final concentration of 0.5 ug/ul tRNA, 2.0x SSC, 0.25% formamide and 0.1% SDS. For each array, cDNA prepared from the M. tuberculosis RNA was mixed with cDNA from M. bovis. The slides were covered by a flat 22 x 22 mm coverslip and hybridized in sealed hybridization chambers for sixteen hours at 50°C in a water bath.
|
| Scan protocol |
Prepared slides were immediately scanned using an Axon 4000A Scanner (Axon Instruments). Fluorescence intensities of Cy3 and Cy5 dies at each spot were quantified using the GenePix Pro 4.0 software.
|
| Description |
Synthesis and hybridization of labelled samples was performed as described in previously published protocols (Walters et al. Mol Microbiol (2006) 60(2):312-330)
|
| Data processing |
Intensity values obtained from spots on the chip were background subtracted and negative corrected intensities were set to +1. Corrected data were then normalized using the Lowess implementation included in GeneSpring 7.2 software (Silicon Genetics). The values are expressed as Ch2/Ch1 ratio determined from the normalized fluorescence intensity.
|
| |
|
| Submission date |
Jan 28, 2007 |
| Last update date |
Jan 30, 2007 |
| Contact name |
Germán Rehren |
| E-mail(s) |
grehren@uach.cl
|
| Organization name |
Universidad Austral de Chile
|
| Department |
Biochemistry
|
| Lab |
Prof. Zárraga
|
| Street address |
Campus Isla Teja
|
| City |
Valdivia |
| State/province |
Valdivia |
| ZIP/Postal code |
5090000 |
| Country |
Chile |
| |
|
| Platform ID |
GPL4057 |
| Series (1) |
| GSE6889 |
M. tuberculosis-M. bovis transcriptional comparison |
|
