|
| Status |
Public on Jul 10, 2014 |
| Title |
ΔdosR/WT_Replicate3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
in vitro batch culture
|
| Organism |
Mycolicibacterium smegmatis |
| Characteristics |
genotype/variation: ΔdosR
stress: hypoxic atmosphere
|
| Treatment protocol |
M. smegmatis was grown in sealed serum vials and samples were withdrawn 10h after methylene blue decolorized.
|
| Growth protocol |
M. smegmatis was grown in Hartmans de Bont (HdB) minimal medium supplemented with 27 mM glycero in 120 ml sealed serum vials at 37°C with agitation (200 rpm).
|
| 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 |
10 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: MC2 155
genotype/variation: wild type
stress: hypoxic atmosphere
|
| Treatment protocol |
M. smegmatis was grown in sealed serum vials and samples were withdrawn 10h after methylene blue decolorized.
|
| Growth protocol |
M. smegmatis was grown in Hartmans de Bont (HdB) minimal medium supplemented with 27 mM glycero in 120 ml sealed serum vials at 37°C with agitation (200 rpm).
|
| 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 |
10 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 |
Biological Replicate 3
|
| 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 |
Mar 21, 2014 |
| Last update date |
Jul 11, 2014 |
| Contact name |
Michael Berney |
| Organization name |
Albert Einstein College of Medicine
|
| Department |
Department of Microbiology and Immunology
|
| Lab |
Jacobs lab
|
| Street address |
1301 Morris Park Avenue
|
| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
| |
|
| Platform ID |
GPL5862 |
| Series (1) |
| GSE56083 |
Determining the M. smegmatis DosR regulon |
|
