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Sample GSM4120128 Query DataSets for GSM4120128
Status Public on Mar 24, 2020
Title Cg_GABA_urea_K2SO4_vs_glucose_urea_K2SO4_1
Sample type RNA
 
Channel 1
Source name GABA+urea+K2SO4
Organism Corynebacterium glutamicum
Characteristics agent: GABA
Treatment protocol see growth protocol
Growth protocol For precultivation of C. glutamicum, brain heart infusion (BHI) medium (Becton Dickinson and Company, New Jersey, USA) with 90 g L-1 sorbitol was used. The cells of these precultures were harvested by centrifugation (5,000×g, 4°C, 10 min), and washed twice with PBS (pH 7.0). The main cultures were inoculated to an OD600 of 1 in CGXII minimal medium with with K2SO4 (20 mM) instead of (NH4)2SO4, with urea (151mM) and glucose or GABA as carbon source (250 mM carbon each). At an OD of 5 the cells were harvested by centrifugation (4120 x g, 10 min and 4 °C). The cell pellet was subsequently frozen in liquid nitrogen and stored at -70°C. Four biological replicates were performed.
Extracted molecule total RNA
Extraction protocol The preparation of total RNA was performed as described previously with the RNeasy Kit from Qiagen (Möker, N., M. Brocker, S. Schaffer, R. Krämer, S. Morbach & M. Bott, (2004) Deletion of the genes encoding the MtrA-MtrB two-component system of Corynebacterium glutamicum has a strong influence on cell morphology, antibiotics susceptibility and expression of genes involved in osmoprotection. Mol Microbiol 54: 420-438.)
Label Cy5
Label protocol Synthesis of fluorescently labelled cDNA were carried out as described in Lange, C., D. Rittmann, V. F. Wendisch, M. Bott, and H. Sahm. 2003. Global expression profiling and physiological characterization of Corynebacterium glutamicum grown in the presence of L-valine. Appl. Environm. Microbiol. 69:2521-2532 and in Möker, N., M. Brocker, S. Schaffer, R. Krämer, S. Morbach & M. Bott. 2004. Deletion of the genes encoding the MtrA-MtrB two-component system of Corynebacterium glutamicum has a strong influence on cell morphology, antibiotics susceptibility and expression of genes involved in osmoprotection. Mol. Microbiol. 54: 420-438.
 
Channel 2
Source name glucose+urea+K2SO4
Organism Corynebacterium glutamicum
Characteristics agent: glucose
Treatment protocol see growth protocol
Growth protocol For precultivation of C. glutamicum, brain heart infusion (BHI) medium (Becton Dickinson and Company, New Jersey, USA) with 90 g L-1 sorbitol was used. The cells of these precultures were harvested by centrifugation (5,000×g, 4°C, 10 min), and washed twice with PBS (pH 7.0). The main cultures were inoculated to an OD600 of 1 in CGXII minimal medium with with K2SO4 (20 mM) instead of (NH4)2SO4, with urea (151mM) and glucose or GABA as carbon source (250 mM carbon each). At an OD of 5 the cells were harvested by centrifugation (4120 x g, 10 min and 4 °C). The cell pellet was subsequently frozen in liquid nitrogen and stored at -70°C. Four biological replicates were performed.
Extracted molecule total RNA
Extraction protocol The preparation of total RNA was performed as described previously with the RNeasy Kit from Qiagen (Möker, N., M. Brocker, S. Schaffer, R. Krämer, S. Morbach & M. Bott, (2004) Deletion of the genes encoding the MtrA-MtrB two-component system of Corynebacterium glutamicum has a strong influence on cell morphology, antibiotics susceptibility and expression of genes involved in osmoprotection. Mol Microbiol 54: 420-438.)
Label Cy3
Label protocol Synthesis of fluorescently labelled cDNA were carried out as described in Lange, C., D. Rittmann, V. F. Wendisch, M. Bott, and H. Sahm. 2003. Global expression profiling and physiological characterization of Corynebacterium glutamicum grown in the presence of L-valine. Appl. Environm. Microbiol. 69:2521-2532 and in Möker, N., M. Brocker, S. Schaffer, R. Krämer, S. Morbach & M. Bott. 2004. Deletion of the genes encoding the MtrA-MtrB two-component system of Corynebacterium glutamicum has a strong influence on cell morphology, antibiotics susceptibility and expression of genes involved in osmoprotection. Mol. Microbiol. 54: 420-438.
 
 
Hybridization protocol Purified cDNA samples to be compared were pooled and the prepared two-color samples were hybridized at 65°C while rotating for 16 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).
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 Oct 14, 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 GPL22794
Series (2)
GSE138828 Comparison of Corynebacterium glutamicum with GABA or glucose as carbon source
GSE138829 Comparison of Corynebacterium glutamicum
Relations
Reanalyzed by GSM5197060

Data table header descriptions
ID_REF
VALUE lowess normalized ratio (GABA vs. Glucose)

Data table
ID_REF VALUE
20 0.877892
21
22
23
24
25
26
27
28
29 2.991240
30
31
32 1.358400
33 0.756779
34
35
36
37 0.878241
38
39

Total number of rows: 42132

Table truncated, full table size 336 Kbytes.




Supplementary file Size Download File type/resource
GSM4120128_Cg_GABA_urea_K2SO4_vs_glucose_urea_K2SO4_1.gpr.gz 3.7 Mb (ftp)(http) GPR
Processed data included within Sample table

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