|
| Status |
Public on Jul 31, 2019 |
| Title |
Cglu_DaceE_Dpyc_vs_Dpyc_II |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
C. glutamicum culture
|
| Organism |
Corynebacterium glutamicum ATCC 13032 |
| Characteristics |
genotype/variation: <delta>aceE <delta>pyc
media: CGXII glucose+acetate
|
| Growth protocol |
For analysis of the transcriptome, C. glutamicum ΔaceE and ΔaceE Δpyc were cultivated in triplicates as described in 2.1 in 50 ml CGXII containing 154 mM acetate and 222 mM glucose in shake flasks. After reaching exponential phase at an OD600 of around 12-15, the cell suspension was harvested by centrifugation (4256 g, 10 min, 4°C). The resulting pellet was directly frozen in liquid nitrogen and stored at -80°C. RNA preparation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The preparation of total RNA samples was performed as described previously (Baumgart M, Luder K, Grover S, Gätgens C, Besra GS, Frunzke J. 2013. IpsA, a novel LacI-type regulator, is required for inositol-derived lipid formation in Corynebacteria and Mycobacteria. BMC Biology 11).
|
| Label |
Cy5
|
| Label protocol |
Synthesis of fluorescently labelled cDNA was performed as described previously (Baumgart M, Luder K, Grover S, Gätgens C, Besra GS, Frunzke J. 2013. IpsA, a novel LacI-type regulator, is required for inositol-derived lipid formation in Corynebacteria and Mycobacteria. BMC Biology 11).
|
| |
|
| Channel 2 |
| Source name |
C. glutamicum culture
|
| Organism |
Corynebacterium glutamicum ATCC 13032 |
| Characteristics |
genotype/variation: <delta>aceE
media: CGXII glucose+acetate
|
| Growth protocol |
For analysis of the transcriptome, C. glutamicum ΔaceE and ΔaceE Δpyc were cultivated in triplicates as described in 2.1 in 50 ml CGXII containing 154 mM acetate and 222 mM glucose in shake flasks. After reaching exponential phase at an OD600 of around 12-15, the cell suspension was harvested by centrifugation (4256 g, 10 min, 4°C). The resulting pellet was directly frozen in liquid nitrogen and stored at -80°C. RNA preparation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The preparation of total RNA samples was performed as described previously (Baumgart M, Luder K, Grover S, Gätgens C, Besra GS, Frunzke J. 2013. IpsA, a novel LacI-type regulator, is required for inositol-derived lipid formation in Corynebacteria and Mycobacteria. BMC Biology 11).
|
| Label |
Cy3
|
| Label protocol |
Synthesis of fluorescently labelled cDNA was performed as described previously (Baumgart M, Luder K, Grover S, Gätgens C, Besra GS, Frunzke J. 2013. IpsA, a novel LacI-type regulator, is required for inositol-derived lipid formation in Corynebacteria and Mycobacteria. BMC Biology 11).
|
| |
|
| |
| Hybridization protocol |
Purified cDNA samples to be compared were pooled and the prepared two-color samples were hybridized at 65°C while rotating for 17 hours using Agilent’s Gene Expression Hybridization Kit, hybridization oven and hybridization chamber. After hybridization the arrays were washed using Agilent’s Wash Buffer Kit according to the manufacturer’s instructions.
|
| 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).
|
| Description |
ch1: ATCC 13032 ΔaceE Δpyc
ch2: ATCC 13032 ΔaceE
|
| 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 |
Jul 12, 2019 |
| Last update date |
Apr 14, 2021 |
| Contact name |
Tino Polen |
| E-mail(s) |
t.polen@fz-juelich.de
|
| Organization name |
Forschungszentrum Jülich GmbH
|
| Department |
IBG-1: Biotechnology
|
| Street address |
Leo Brandt Str.
|
| City |
Juelich |
| State/province |
NRW |
| ZIP/Postal code |
52425 |
| Country |
Germany |
| |
|
| Platform ID |
GPL26911 |
| Series (1) |
| GSE134218 |
Transcriptome analysis of C. glutamicum ΔaceE Δpyc versus ΔaceE |
|
| Relations |
| Reanalyzed by |
GSM5197681 |
