|
| Status |
Public on Mar 31, 2010 |
| Title |
BatchCulture_LBTbroth_ExponentialPhase_Replicate1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
in vitro batch culture
|
| Organism |
Mycolicibacterium smegmatis |
| Characteristics |
strain: mc2155 wild type
growth stage: exponential phase (μ = 0.26 ± 0.04 h-1)
|
| Treatment protocol |
Starter cultures were grown to OD600 = 0.5 ± 0.2, samples for microarray analysis were grown in 100 ml LBT in 1 l flasks from initial OD600 = 0.005 at 37 °C on a rotary shaker till point of harvest
|
| Growth protocol |
Batch cultures were routinely grown in Luria Bertani broth supplemented with 0.05 % (w/v) Tween 80 (LBT) at 37 °C on a rotary shaker.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were harvested using ice-cold glycerol-saline, cells were disrupted by bead-beating and total RNAwas extracted with TRIzol following manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
5 µg of total RNA were reverse transcribed and labelled in a two step protocol according to SOP M007 from TIGR (Hegde, P., Qi, R., Abernathy, K. & other authors (2000). A concise guide to cDNA microarray analysis. BioTechniques 29, 548-550, 552-544, 556 passim.)
|
| |
|
| Channel 2 |
| Source name |
in vitro batch culture
|
| Organism |
Mycolicibacterium smegmatis |
| Characteristics |
strain: mc2155 ΔsigF
growth stage: exponential phase (μ = 0.26 ± 0.04 h-1)
|
| Treatment protocol |
Starter cultures were grown to OD600 = 0.5 ± 0.2, samples for microarray analysis were grown in 100 ml LBT in 1 l flasks from initial OD600 = 0.005 at 37 °C on a rotary shaker till point of harvest
|
| Growth protocol |
Batch cultures were routinely grown in Luria Bertani broth supplemented with 0.05 % (w/v) Tween 80 (LBT) at 37 °C on a rotary shaker.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were harvested using ice-cold glycerol-saline, cells were disrupted by bead-beating and total RNAwas extracted with TRIzol following manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
5 µg of total RNA were reverse transcribed and labelled in a two step protocol according to SOP M007 from TIGR (Hegde, P., Qi, R., Abernathy, K. & other authors (2000). A concise guide to cDNA microarray analysis. BioTechniques 29, 548-550, 552-544, 556 passim.)
|
| |
|
| |
| Hybridization protocol |
Hybrization was performed according to SOP M008 from TIGR (Hegde, P., Qi, R., Abernathy, K. & other authors (2000). A concise guide to cDNA microarray analysis. BioTechniques 29, 548-550, 552-544, 556 passim.)
|
| Scan protocol |
Slides were scanned using an Axon GenePix4000B microarray scanner
|
| Description |
Exponential Phase: Biological Replicate 1
|
| Data processing |
Tiff images were quantified with Spotfinder software (TIGR), data normalization using total array intensity and LOWESS algorithm with MIDAS software (TIGR)
|
| |
|
| Submission date |
Nov 23, 2009 |
| Last update date |
Mar 31, 2010 |
| Contact name |
Anja Huempel |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Otago
|
| Department |
Microbiology & Immunology
|
| Lab |
Cook
|
| Street address |
720 Cumberland St
|
| City |
Dunedin |
| ZIP/Postal code |
9016 |
| Country |
New Zealand |
| |
|
| Platform ID |
GPL5862 |
| Series (1) |
| GSE19145 |
Transciptional profile of a M. smegmatis mc2155 ΔsigF strain under standard growth conditions |
|
