|
| Status |
Public on Feb 19, 2013 |
| Title |
Hypoxia 2 days SG2_D2 |
| Sample type |
RNA |
| |
|
| Source name |
SG2_D2
|
| Organism |
Mycobacterium tuberculosis H37Rv |
| Characteristics |
experiment: SG2
replicate: D
time: 2 days
treatment: Hypoxia
|
| Treatment protocol |
TFOE experiments done at indicated concentration of anhydrotetracycline. Hypoxic experiments conducted as described previously (Rustad et al., 2008)
|
| Growth protocol |
H37Rv was grown to log phase (0.1-0.5 OD600) in Middlebrook 7H9 media supplemented with ADC (Difco) at 37C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).
|
| 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 12 arrays on each slide.
|
| Description |
SG2_D2
Hypoxia
2
days
|
| Data processing |
Data was normalized using RMA normalization with the 'affy' package for R.
|
| |
|
| Submission date |
Feb 19, 2013 |
| Last update date |
Feb 19, 2013 |
| Contact name |
Tige Rustad |
| E-mail(s) |
tige.rustad@sbri.org
|
| Phone |
206-256-7207
|
| Organization name |
Seattle Biomedical Research Institute
|
| Department |
Pathobiology
|
| Lab |
Sherman
|
| Street address |
307 Westlake Avenue N, Suite 500
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL14824 |
| Series (1) |
| GSE43466 |
Reconstruction of the Mycobacterium tuberculosis Regulatory Network and Deconstruction of the Hypoxic Response |
|
