|
| Status |
Public on Mar 08, 2012 |
| Title |
HypoxicStress_RNAdeg_T1_RepA |
| Sample type |
RNA |
| |
|
| Source name |
HypoxicStress_RNAdeg_T1
|
| Organism |
Mycobacterium tuberculosis H37Rv |
| Characteristics |
replicate: A
hours of mrna decay: 1
|
| Treatment protocol |
Rifampicin was added to a final concentration of 50 ug/ul to stop transcription. Samples were taken and immediately plunged into a dry ice ethanol bath to arrest mRNA decay, pelleted at 4C, and supe discarded.
|
| Growth protocol |
M. tuberculosis H37Rv was grown to log phase (0.1-0.5 OD600) in Middlebrook 7H9 media supplemented with ADC (Difco) at 37C in a 1.3 L Bioflo 110 fermentor vessel.
|
| 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 |
Cy3
|
| 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. Resulting images were processed with the Nimblescan software to generate pair files.
|
| Description |
Rifampin treated M. tuberculosis
Bubbles in array
|
| Data processing |
Data was background subtracted using the average of 30,000 randomers, excluding the highest and lowest 5% of intensities and then normalized to tRNA Rvnt23.
|
| |
|
| Submission date |
Mar 07, 2012 |
| Last update date |
Mar 08, 2012 |
| 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 (2) |
| GSE36343 |
mRNA degradation in Mycobacterium tuberculosis during cold and hypoxic stress |
| GSE36345 |
mRNA degradation in Mycobacterium tuberculosis |
|
