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Sample GSM3517980 Query DataSets for GSM3517980
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).
 
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

Data table header descriptions
ID_REF
VALUE log2 Ratio ([delta]cg2460 / WT)
PRE_VALUE Ratio (Δcg2460 / WT)

Data table
ID_REF VALUE PRE_VALUE
20
22
23
25 -0.0428 0.970738
26
28 -0.0128 0.991198
29 0.2409 1.181770
31
32 0.6567 1.576430
33
34
35
36
37
39
42
44
45
46
47 -0.0952 0.936165

Total number of rows: 34251

Table truncated, full table size 367 Kbytes.




Supplementary file Size Download File type/resource
GSM3517980_CD_CGXII_wt_vs_Delta-cg2460_D.gpr.gz 3.9 Mb (ftp)(http) GPR
Processed data included within Sample table

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