|
| Status |
Public on Mar 03, 2014 |
| Title |
MTB at T30, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Mycobacterium tuberculosis treated with bedaquiline and harvested after 30 min
|
| Organism |
Mycobacterium tuberculosis H37Rv |
| Characteristics |
agent: 1 µM Bedaquiline
timepoint: 30'
|
| Treatment protocol |
Mycobacterium tuberculosis was treated with 1 µM Bedaquiline
|
| Growth protocol |
Mycobacterium tuberculosis was Grown in Middlebrook 7H9 broth
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bacteria were pelletted, resuspended in RLT-buffer with ß-mercaptoethanol and mechanically disrupted with Mixer Mill MM 310. Only the supernatant was used for RNA extraction using RNeasy Protect Bacteria Mini kit (Qiagen). RNA was eluted in RNAse free water.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mycobacterium tuberculosis ‘TB-All-Antisense’ Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip scanner 3000
|
| Description |
Gene expression data from Mycobacterium tuberculosis treated with bedaquiline and harvested after 30 min
|
| Data processing |
The data were analyzed with R (version 2.15.1) and BioConductor (package affy version 1.34.0). Preprocessing was done using the function expresso (settings: bg.correct = FALSE, normalize.method = vsn, pmcorrect.method = pmonly, summary.method = medianpolish) plus the CDF tballantisensecdf as provided by Affymetrix.
|
| |
|
| Submission date |
Jan 25, 2013 |
| Last update date |
Mar 03, 2014 |
| Contact name |
Steven Osselaer |
| E-mail(s) |
[email protected]
|
| Organization name |
Janssen Pharmaceutica NV
|
| Street address |
Turnhoutseweg 30
|
| City |
Beerse |
| ZIP/Postal code |
2340 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL4519 |
| Series (1) |
| GSE43749 |
Global Gene expression data from Mycobacterium tuberculosis treated with new TB drug named Bedaquiline |
|
