|
Status |
Public on Mar 08, 2012 |
Title |
Aerobic_Uninduced DMSO control DosR-RNAdeg_T60_RepB |
Sample type |
RNA |
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|
Source name |
Aerobic_Uninduced DMSO control DosR-RNAdeg_T60
|
Organism |
Mycobacterium tuberculosis H37Rv |
Characteristics |
replicate: B minutes of mrna decay: 60
|
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 |
Cy5
|
Label protocol |
Labeling was performed using indirect labelling of amino-allyl dUTP using protocol from PFGRC (www.pfgrc.org).
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|
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Hybridization protocol |
Hybridization was performed following the standard operating protocol recommended by NimbleGen Systems Inc., Madison, WI, USA . See www.nimblegen.com.
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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.
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Description |
Rifampin treated M. tuberculosis
|
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.
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|
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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) |
GSE36344 |
mRNA degradation in Mycobacterium tuberculosis with DosR ectopically induced |
GSE36345 |
mRNA degradation in Mycobacterium tuberculosis |
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