|
| Status |
Public on May 25, 2021 |
| Title |
Cglutamicum_ pAN6-cg1978_vs_pAN6_C_csw |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
ATCC13032 pAN6 CGXII glucose
|
| Organism |
Corynebacterium glutamicum ATCC 13032 |
| Characteristics |
overexpression: pAN6 empty vector
|
| Treatment protocol |
see growth protocol
|
| Growth protocol |
For transcriptome analysis, C. glutamicum ATCC13032 pAN6-cg1978 and ATCC13032 pAN6 cells were grown in 5 ml BHI (Brain Heart Infusion, Difco) with 25 µg/ml Kanamycin for about 8 hours at 30°C. A second precultivation was performed in CGXII minimal medium containing 2% (w/v) glucose as carbon source with 25 µg/ml Kanamycin. The main cultures were inoculated to an OD600 of 1 in CGXII minimal medium with 2% (w/v) glucose, 25 µg/ml Kanamycin and 50 µM IPTG. At OD600 of 6, the cells were centrifuged and harvested on ice and the cell pellet was subsequently frozen in liquid nitrogen and stored at -80°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA sample preparation, labelling, hybridization and comparative transcriptome analysis was performed as described previously (Vogt et al., 2014).
|
| Label |
Cy5
|
| Label protocol |
RNA sample preparation, labelling, hybridization and comparative transcriptome analysis was performed as described previously (Vogt et al., 2014).
|
| |
|
| Channel 2 |
| Source name |
ATCC13032 pAN6-cg1978 CGXII glucose
|
| Organism |
Corynebacterium glutamicum ATCC 13032 |
| Characteristics |
overexpression: pAN6-cg1978
|
| Treatment protocol |
see growth protocol
|
| Growth protocol |
For transcriptome analysis, C. glutamicum ATCC13032 pAN6-cg1978 and ATCC13032 pAN6 cells were grown in 5 ml BHI (Brain Heart Infusion, Difco) with 25 µg/ml Kanamycin for about 8 hours at 30°C. A second precultivation was performed in CGXII minimal medium containing 2% (w/v) glucose as carbon source with 25 µg/ml Kanamycin. The main cultures were inoculated to an OD600 of 1 in CGXII minimal medium with 2% (w/v) glucose, 25 µg/ml Kanamycin and 50 µM IPTG. At OD600 of 6, the cells were centrifuged and harvested on ice and the cell pellet was subsequently frozen in liquid nitrogen and stored at -80°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA sample preparation, labelling, hybridization and comparative transcriptome analysis was performed as described previously (Vogt et al., 2014).
|
| Label |
Cy3
|
| Label protocol |
RNA sample preparation, labelling, hybridization and comparative transcriptome analysis was performed as described previously (Vogt et al., 2014).
|
| |
|
| |
| Hybridization protocol |
RNA sample preparation, labelling, hybridization and comparative transcriptome analysis was performed as described previously (Vogt et al., 2014).
|
| Scan protocol |
Fluorescence of hybridized DNA microarrays was determined at 532 nm (Cy3) and 635 nm (Cy5) at 5 μm resolution with a GenePix 4000B laser scanner and GenePix Pro 6.0 software (Molecular Devices, Sunnyvale, CA, USA). Fluorescence images were saved to raw data files in TIFF format (GenePix Pro 6.0). Quantitative TIFF image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 6.0).
|
| Data processing |
For ratio calculation and ratio normalization, GPR-files were processed using the BioConductor R-packages limma and marray (http://www.bioconductor.org).
|
| |
|
| Submission date |
May 26, 2020 |
| Last update date |
May 25, 2021 |
| Contact name |
Max Hünnefeld |
| E-mail(s) |
m.huennefeld@fz-juelich.de
|
| Phone |
(+49) 2461 61-3953
|
| Organization name |
Forschungszentrum Jülich
|
| Department |
Institute for Bio- and Geosciences 1: Biotechnology
|
| Lab |
Bacterial Networks and Interactions
|
| Street address |
Wilhelm-Johnen-Straße
|
| City |
Jülich |
| ZIP/Postal code |
52428 |
| Country |
Germany |
| |
|
| Platform ID |
GPL26911 |
| Series (1) |
| GSE151224 |
Comparison of Corynebacterium glutamicum ATCC 13032 + pAN6-cg1978 with ATCC 13032 + pAN6 |
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