|
| Status |
Public on Jul 22, 2022 |
| Title |
Chassis C1 vs. MB001-rep2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Chassis C1
|
| Organism |
Corynebacterium glutamicum |
| Characteristics |
genotype: MB001(DE3) deletion mutant
condition: Chassis C1 harvested during exponential growth phase, CGXII glucose, date of experiment: 2016-06, GEO: GSE88717
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RNeasy Kit (Qiagen, Hilden, Germany) or as described by Wendisch et al. 2001.
|
| Label |
Cy5
|
| Label protocol |
Equal amounts of RNA (15-30 µg) were used for random hexamer primed synthesis of fluorescently labelled cDNA using the nucleotide analogous Cy3-dUTP or Cy5-dUTP (GE Healthcare, Eindhoven, Netherlands).
|
| |
|
| Channel 2 |
| Source name |
MB001
|
| Organism |
Corynebacterium glutamicum |
| Characteristics |
genotype: MB001
condition: MB001 harvested during exponential growth phase, CGXII glucose, date of experiment: 2016-06, GEO: GSE88717
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RNeasy Kit (Qiagen, Hilden, Germany) or as described by Wendisch et al. 2001.
|
| Label |
Cy3
|
| Label protocol |
Equal amounts of RNA (15-30 µg) were used for random hexamer primed synthesis of fluorescently labelled cDNA using the nucleotide analogous Cy3-dUTP or Cy5-dUTP (GE Healthcare, Eindhoven, Netherlands).
|
| |
|
| |
| Hybridization protocol |
Gene expression changes were compared using self-made PCR-product based DNA microarrays (Lange et al. 2003), custom-made DNA microarrays with 70-mer oligonucleotides obtained from Operon Biotechnologies (Cologne, Germany) or custom-made 4x44K 60mer DNA microarrays from Agilent Technologies (Waldbronn, Germany). Hybridization of mixtures of Cy3- and Cy5-labelled cDNA on the arrays and washing of the arrays were performed as described by Frunzke et al. 2008, Polen & Wendisch 2003, and Vogt et al. 2014.
|
| Scan protocol |
The fluorescence of DNA microarrays was determined at 532 nm (Cy2-dUTP) and 635 nm (Cy5-dUTP) at 5 or 10 µm resolution with a GenePix 4000B laser scanner and GenePix Pro Software (Molecular Devices, Sunnyvale, USA).
|
| Description |
Chassis C1 vs. MB001-rep2
Biological replicate 2 of 4
original platform:
GPL22561
|
| Data processing |
The raw results were saved as GPR-files and processed and normalized using the BioConductor R packages limma and marray (http://www.bioconductor.org). For further analysis, loess-normalized data were saved in the in-house DNA microarray database (Polen et al. 2004) including detailed information about each experiment following MIAME standards (Brazma et al. 2009). Normalized ratios of medians reflecting the relative mRNA level were filtered for a signal-to-noise ratio ((F635Median/B635Median) or (F532Median/B532Median)) higher than 3. Statistical analysis for calculation of p-values was performed with a paired Student´s t-test comparing relative RNA levels for a gene to the relative RNA levels of all other genes in the replicates.
All listed GAL files are included in a tar archive on the SERIES record. The 'ID' field of the GAL files includes the Biomax IDs. A supplementary file provides the CG IDs for the Biomax IDs.
|
| |
|
| Submission date |
Mar 22, 2021 |
| Last update date |
Jul 22, 2022 |
| 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 |
GPL29897 |
| Series (2) |
| GSE169361 |
A compendium of expression profiles for Corynebacterium glutamicum ATCC13032 [with raw data] |
| GSE171302 |
A compendium of expression profiles for Corynebacterium glutamicum ATCC13032 |
|
| Relations |
| Reanalysis of |
GSM2344667 |
