|
| Status |
Public on Jul 04, 2014 |
| Title |
TFOE_1539_3840 |
| Sample type |
RNA |
| |
|
| Source name |
TFOE_1539_3840
|
| Organism |
Mycobacterium tuberculosis H37Rv |
| Characteristics |
experiment: Rv3840
stress: Rv3840 overexpression
time (hours): 18
concentration (ng): 100
|
| Treatment protocol |
Transcription factor overexpression experiments done at 100 ng/ml of anhydrotetracycline after 18 hours of induction.
|
| 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 |
H37RvC:pEXCF-3840
|
| Data processing |
Data was normalized using RMA normalization with the 'affy' package for R.
|
| |
|
| Submission date |
Jul 03, 2014 |
| Last update date |
Jul 04, 2014 |
| Contact name |
Tige Rustad |
| E-mail(s) |
trustad@gmail.com
|
| Organization name |
Seattle BioMed
|
| Lab |
Sherman
|
| Street address |
1700 DAYTON AVE NE
|
| City |
RENTON |
| State/province |
WASHINGTON |
| ZIP/Postal code |
98056 |
| Country |
USA |
| |
|
| Platform ID |
GPL14824 |
| Series (1) |
| GSE59086 |
Mapping and manipulating the M. tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network |
|
