|
Status |
Public on Feb 19, 2013 |
Title |
Hypoxia 12 days SG6B11 |
Sample type |
RNA |
|
|
Source name |
SG6B11
|
Organism |
Mycobacterium tuberculosis H37Rv |
Characteristics |
experiment: SG6 replicate: B time: 12 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 |
SG6B12 Hypoxia 12 days
|
Data processing |
Data was normalized using RMA normalization with the 'affy' package for R.
|
|
|
Submission date |
Feb 19, 2013 |
Last update date |
Feb 26, 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 |
|