|
| Status |
Public on Apr 25, 2007 |
| Title |
M. tuberculosis_capreomycin_4h_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Standard broth culture
|
| Organism |
Mycobacterium tuberculosis |
| Characteristics |
M. tuberculosis H37Rv log-phase culture
in response to capreomycin 10 ug/ml for 4 hours
|
| Biomaterial provider |
Pacific Tuberculosis and Cancer Research Organization
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cultures are mixed with an equal volume of RNALaterTM (Ambion, Austin, TX) and the bacteria harvested by centrifugation (1 min, 25000 x g, 8°C) and transferred to Fast Prep tubes (Bio 101, Vista, CA) containing Trizol (Life Technologies, Gaithersburg, MD). Mycobacteria are mechanically disrupted in a Fast Prep apparatus (Bio 101). The aqueous phase is recovered, treated with Cleanascite (CPG, Lincoln Park, NJ), and extracted with chloroform-isoamyl alcohol (24:1 v/v). Nucleic acids are ethanol precipitated. DNaseI (Ambion) treatment to digest contaminating DNA is performed in the presence of Prime RNase inhibitor (5’-3’, Boulder, CO). The RNA sample is precipitated and washed in ethanol, and redissolved to make a final concentration of 1 mg/ml.
|
| Label |
biotin
|
| Label protocol |
Standard Affymetrix Labeling Protocol
|
| |
|
| Hybridization protocol |
The assay utilized reverse transcriptase and random hexamer primers to produce DNA complementary to the RNA. The cDNA products were then fragmented by DNAase I and labeled with terminal transferase and biotinylated GeneChip DNA Labeling Reagent at the 3' terminal. The chip is stained with streptavidin-phycoerythrin after hybridization. A global normalization scheme is applied so that each array's median value is adjusted to a predefine value (500). The scale factor for achieving this transformed median value for an array is uniformly applied to all the probe set values on a specific array to result in the determined Signal value for all the probe sets on the array.
|
| Scan protocol |
The chip is scanned using GeneChip Scanner 3000.
The images are analyzed using GCOS (GeneChip Operating Software)
version 1.4.
|
| Description |
Quality control of gene expression data is based on expression
of housekeeping genes, spike controls, background values, and
noise levels (pixel-to-pixel variations).
|
| Data processing |
A global normalization scheme is applied so that each array's median value is adjusted to a predefine value (500). The scale factor for achieving this transformed median value for an array is uniformly applied to all the probe set values on a specific array to result in the determined Signal value for all the probe sets on the array.
|
| |
|
| Submission date |
Apr 23, 2007 |
| Last update date |
Apr 24, 2007 |
| Contact name |
Li Fu |
| E-mail(s) |
lifu@patcar.org
|
| Organization name |
Pacific Tuberculosis and Cancer Research Organization
|
| Street address |
8 Corporate Park, Suite 300
|
| City |
IRVINE |
| State/province |
CA |
| ZIP/Postal code |
92606 |
| Country |
USA |
| |
|
| Platform ID |
GPL4519 |
| Series (1) |
| GSE7588 |
Exploration of the Drug Action of Capreomycin on Mycobacterium tuberculosis |
|
