|
Status |
Public on Jul 11, 2019 |
Title |
Dcg2460_vs_WT_IIII_csw |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
wild type ATCC 13032
|
Organism |
Corynebacterium glutamicum |
Characteristics |
growth medium: CGXII glucose genotype/variation: WT
|
Treatment protocol |
see growth protocol
|
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)
|
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)
|
|
|
Channel 2 |
Source name |
wild type ATCC 13032 [delta]cg2460
|
Organism |
Corynebacterium glutamicum |
Characteristics |
growth medium: CGXII glucose genotype/variation: [delta]cg2460
|
Treatment protocol |
see growth protocol
|
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)
|
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)
|
|
|
|
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).
|
Data processing |
For ratio calculation and ratio normalization, GPR-files were processed using the BioConductor R-packages limma and marray (http://www.bioconductor.org).
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Submission date |
Dec 17, 2018 |
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 |
GPL22792 |
Series (1) |
GSE123974 |
Comparison of Corynebacterium glutamicum Δsurf1 and wt |
|
Relations |
Reanalyzed by |
GSM5197754 |