|
| Status |
Public on Sep 18, 2012 |
| Title |
H37Rv, 4 hours, Rep B |
| Sample type |
RNA |
| |
|
| Source name |
H37Rv treated with 100 uM WR99210 for 4 hrs
|
| Organism |
Mycobacterium tuberculosis H37Rv |
| Characteristics |
treated with: 100 uM WR99210 for 4 hrs
|
| Treatment protocol |
Cultures were treated with 100 uM WR99210 for 0, 4, and 24 hours prior to RNA isolation.
|
| Growth protocol |
M. tuberculosis strain H37Rv cultures were grown in 7H9+GAT. Samples for microarray were harvested in mid-log phase (OD600 = 0.3)
|
| 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.
|
| Description |
_Molly 5_N18A10cy 5
|
| 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 |
Sep 16, 2012 |
| Last update date |
Sep 18, 2012 |
| Contact name |
Molly Nixon |
| E-mail(s) |
molly.r.nixon@gmail.com
|
| Organization name |
Seattle Biomedical Research Institute
|
| Street address |
307 Westlake Ave N Ste 500
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98112 |
| Country |
USA |
| |
|
| Platform ID |
GPL14824 |
| Series (1) |
| GSE40917 |
Expression Analysis of WR99210-treated Mycobacterium tuberculosis H37Rv |
|
