|
| Status |
Public on Apr 25, 2019 |
| Title |
WT Eth I vs WT Gly II [Msmeg] |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
WT Eth I
|
| Organism |
Mycolicibacterium smegmatis |
| Characteristics |
genotype/variation: wildtype
treatment: Ethanol
replicate: biol. replicate 1
|
| Treatment protocol |
Carbon utilization assays were performed using minimal medium and cholesterol (0.01%), ethanol (0.01%–1%) and glycerol.
|
| Growth protocol |
M. smegmatis mc2155 was propagated in Middlebrook 7H9 broth supplemented with albumin-dextrose-catalase enrichment (Becton Dickinson, MD, USA) , 0.2% glycerol, and 0.05% Tyloxapol at 37°C with agitation (100 rpm) or on Middlebrook 7H11 agar containing 10% v/v oleic acid-albumin-dextrose-catalase enrichment (Becton Dickinson).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with TRIzol reagent according to the manufacturer’s instructions. Cell lysis was achieved through three cycles of bead beating in a Mini-Beadbeater (Biospec) at 5,000 rpm for 30 s.
|
| Label |
Cy3
|
| Label protocol |
RNA labeling was performed with the Quick-Amp Labeling Kit (Agilent Technologies) according supplier's instructions.
|
| |
|
| Channel 2 |
| Source name |
WT Gly II
|
| Organism |
Mycolicibacterium smegmatis |
| Characteristics |
genotype/variation: wildtype
treatment: Glycerol
replicate: biol. replicate 2
|
| Treatment protocol |
Carbon utilization assays were performed using minimal medium and cholesterol (0.01%), ethanol (0.01%–1%) and glycerol.
|
| Growth protocol |
M. smegmatis mc2155 was propagated in Middlebrook 7H9 broth supplemented with albumin-dextrose-catalase enrichment (Becton Dickinson, MD, USA) , 0.2% glycerol, and 0.05% Tyloxapol at 37°C with agitation (100 rpm) or on Middlebrook 7H11 agar containing 10% v/v oleic acid-albumin-dextrose-catalase enrichment (Becton Dickinson).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with TRIzol reagent according to the manufacturer’s instructions. Cell lysis was achieved through three cycles of bead beating in a Mini-Beadbeater (Biospec) at 5,000 rpm for 30 s.
|
| Label |
Cy5
|
| Label protocol |
RNA labeling was performed with the Quick-Amp Labeling Kit (Agilent Technologies) according supplier's instructions.
|
| |
|
| |
| Hybridization protocol |
Commercial-custom M.smegmatis 4x44k microarrays were done according to the supplier’s protocol (Agilent Technologies).
|
| Scan protocol |
Scanning of microarrays was performed with 5 µm resolution and extended range (XDR) using a DNA microarray laser scanner (Agilent Technologies)
|
| Description |
polarity(-)
|
| Data processing |
Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.11.5.1.1, Agilent). The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware). Intra-array data were normalized with the GE2_1105_Oct12 extraction protocol and interarray normalization was done by the mean of trimmed positive non-flagged/non-control reporters.
|
| |
|
| Submission date |
Oct 17, 2018 |
| Last update date |
Apr 25, 2019 |
| Contact name |
Hans-Joachim Mollenkopf |
| E-mail(s) |
mollenkopf@mpiib-berlin.mpg.de
|
| Phone |
+49 30 28460 482
|
| Organization name |
Max-Planck-Institute for Infection Biology
|
| Lab |
Microarray/Genomics Core Facility
|
| Street address |
Charitéplatz 1
|
| City |
Berlin |
| ZIP/Postal code |
10117 |
| Country |
Germany |
| |
|
| Platform ID |
GPL25686 |
| Series (1) |
| GSE121398 |
Mycofactocin is associated with ethanol metabolism in Mycobacteria |
|
