|
| Status |
Public on Nov 28, 2015 |
| Title |
NK_Caffeat_02 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
C. glutamicum pulse
|
| Organism |
Corynebacterium glutamicum |
| Characteristics |
genotype/variation: wild type
growth phase: exponential
pulsed with: 5mM caffeic acid for 30min
|
| Treatment protocol |
CGXII medium 4 % glucose, 5 mM phenylpropanoid or 4-hydroxybenzoic acid (only for pulsing experiments), 30°C
|
| Growth protocol |
The transcriptome of C. glutamicum pulsed with 5 mM phenylpropanoid or 4-hydroxybenzoic acid was compared with the C. glutamicum ATCC13032, both grown in defined mineral medium CGXII + 4% glucose as sole carbon and energy source cultivated at 30°C. Cells were harvested at an OD600 of 5 in pre-cooled ice-filled tubes via centrifugation (4,500 x g, 10 min, and 4 °C) and subsequently frozen in liquid nitrogen as well as stored at -70°C until preparation of RNA. Transcriptome of deldetion strain C.g. deltacg0343 was compared to transcriptome of wt strain (same cultivation conditions as above).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The preparation of total RNA was performed as described elsewhere with the RNeasy Kit from Qiagen (Polen T, Schluesener D, Poetsch A, Bott M, Wendisch VF (2007) Characterization of citrate utilization in Corynebacterium glutamicum by transcriptome and proteome analysis. FEMS Microbiol Lett. 273(1):109-19).
|
| Label |
Cy5
|
| Label protocol |
Synthesis of fluorescently labelled cDNA were carried out as described in Polen T, Schluesener D, Poetsch A, Bott M, Wendisch VF (2007) Characterization of citrate utilization in Corynebacterium glutamicum by transcriptome and proteome analysis. FEMS Microbiol Lett. 273(1):109-19.
|
| |
|
| Channel 2 |
| Source name |
C. glutamicum_control
|
| Organism |
Corynebacterium glutamicum |
| Characteristics |
genotype/variation: wild type
growth phase: exponential
|
| Treatment protocol |
CGXII medium 4 % glucose, 5 mM phenylpropanoid or 4-hydroxybenzoic acid (only for pulsing experiments), 30°C
|
| Growth protocol |
The transcriptome of C. glutamicum pulsed with 5 mM phenylpropanoid or 4-hydroxybenzoic acid was compared with the C. glutamicum ATCC13032, both grown in defined mineral medium CGXII + 4% glucose as sole carbon and energy source cultivated at 30°C. Cells were harvested at an OD600 of 5 in pre-cooled ice-filled tubes via centrifugation (4,500 x g, 10 min, and 4 °C) and subsequently frozen in liquid nitrogen as well as stored at -70°C until preparation of RNA. Transcriptome of deldetion strain C.g. deltacg0343 was compared to transcriptome of wt strain (same cultivation conditions as above).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The preparation of total RNA was performed as described elsewhere with the RNeasy Kit from Qiagen (Polen T, Schluesener D, Poetsch A, Bott M, Wendisch VF (2007) Characterization of citrate utilization in Corynebacterium glutamicum by transcriptome and proteome analysis. FEMS Microbiol Lett. 273(1):109-19).
|
| Label |
Cy3
|
| Label protocol |
Synthesis of fluorescently labelled cDNA were carried out as described in Polen T, Schluesener D, Poetsch A, Bott M, Wendisch VF (2007) Characterization of citrate utilization in Corynebacterium glutamicum by transcriptome and proteome analysis. FEMS Microbiol Lett. 273(1):109-19.
|
| |
|
| |
| Hybridization protocol |
Custom-made whole-genome DNA microarrays for C. glutamicum ATCC 13032 printed with 70-mer oligonucleotides were obtained from Operon (Cologne, Germany) and are based on the genome sequence entry NC_006958. Hybridisation and stringent washing of the microarrays were performed according to the instructions of the supplier. Hybridisation was carried out for 16 - 18 h with Nexterion Oligo Hyb buffer (Shott, Jena, Germany) covered with a 25 mm x 60 mm LifterSlip (Implen, Munich, Germany) in a humid camber.
|
| Scan protocol |
After washing the microarrays were dried by centrifugation (5 min, 1600 g) and fluorescence was determined at 532 nm (Cy3-dUTP) and 635 nm (Cy5-dUTP) with 10 µm resolution using an Axon GenePix 4000B laser scanner (Axon Instruments, Sunnyvale, U.S.A).
|
| Description |
Sample 2
|
| Data processing |
Quantitative image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 7.0, Axon Instruments). For data normalization, GPR-files were processed using the BioConductor/R-packages limma and marray (www.bioconductor.org). Processed and normalized data as well as experimental details (according to MIAME) were stored in the in-house microarray database for further analysis. For determination of differentially expressed genes data were quality filtered as decribed (Polen et al., 2007) using Signal/Noise >=5 for Cy5 or Cy3 channel.
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| |
|
| Submission date |
Jun 01, 2015 |
| 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 |
GPL20268 |
| Series (2) |
| GSE69413 |
Identification of a gene cluster involved in the utilization of phenylpropanoids in Corynebacterium glutamicum [set2] |
| GSE69449 |
Identification of a gene cluster involved in the utilization of phenylpropanoids in Corynebacterium glutamicum |
|
| Relations |
| Reanalyzed by |
GSM5197218 |
