|
| Status |
Public on Mar 19, 2014 |
| Title |
DMM.A |
| Sample type |
RNA |
| |
|
| Source name |
Antifolate treated sample
|
| Organism |
Mycobacterium tuberculosis H37Rv |
| Characteristics |
strain: H37Rv
treatment: Treated with 10 uM dimethylmethotrexate for 24 hours
|
| Treatment protocol |
To investigate the impact of antifolate treatment, cultures were supplemented with either no drug, 30 uM WR99210, 20uM DEM, or 10 uM DMM. Samples for microarray were harvested after 24 hours of exposure.
|
| Growth protocol |
M. tuberculosis strain H37Rv cultures were grown in 7H9+GAT.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted TRIzol chloroform:isopropanol phase separation using phaselock gels to separate the aqueous phase. Samples were isolated by immobilization on Qiagen RNeasy columns as per manufacturer's instructions. On- and off-column DNase treatments were performed to minimuze genomic or plasmid nucleic acid contamination of the final sample.
|
| Label |
Cy5
|
| Label protocol |
Labeling was performed using indirect labelling of amino-allyl dUTP using protocol from PFGRC (www.pfgrc.org).
|
| |
|
| Hybridization protocol |
Hybridization was performed following the standard operating protocol recommended by NimbleGen Systems Inc., Madison, WI, USA . See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed using a GenePix 4000B using a single intensity for all arrays.
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249) and quantile normalization (Bolstad et al. Bioinformatics 19(2):185).
|
| |
|
| Submission date |
Mar 18, 2014 |
| Last update date |
Mar 19, 2014 |
| Contact name |
Tige Rustad |
| E-mail(s) |
trustad@gmail.com
|
| Organization name |
Seattle BioMed
|
| Lab |
Sherman
|
| Street address |
1700 DAYTON AVE NE
|
| City |
RENTON |
| State/province |
WASHINGTON |
| ZIP/Postal code |
98056 |
| Country |
USA |
| |
|
| Platform ID |
GPL14824 |
| Series (1) |
| GSE55979 |
Folate Pathway Disruption Leads to Critical Depletion of Methionine Derivatives in Mycobacterium tuberculosis |
|
