|
| Status |
Public on Sep 17, 2014 |
| Title |
crpvsYPIII_FLUX_GEO_sample01 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Yersinia pseudotuberculosis wild type exponential phase culture grown in Yersinia minimal medium at 25°C
|
| Organism |
Yersinia pseudotuberculosis |
| Characteristics |
strain: YPIII pIB1 wild type
|
| Growth protocol |
Y. pseudotuberculosis YPIII or the isogenic crp mutant strain were cultivated at 25°C under aeration on a rotary shaker. First pre-cultures were grown in a 1:1 mixture of HAM’s F-12 Nutrient Mixture (Invitrogen, Carlsbad, US) and liquid DMEM medium (Biochrom, Berlin, DE). Second pre-cultures and main cultures were grown in a Yersinia minimal medium (YMM), which was developed in the present work. It contained per liter: 8 g glucose, 6.62 g KH2PO4, 13.26 g K2HPO4, 0.31 g NaCl, 5 g (NH4)2SO4, 0.20 g MgSO4∙7H2O, 30 mg 3,4-dihydroxybenzoic acid, 0.5 mg FeSO4∙7H2O, 0.5 mg ZnSO4∙7H2O, 2 mg FeCl3∙6H2O, 2 mg MnSO4∙H2O, 0.8 mg ZnSO4∙7H2O, 0.2 mg CuCl2∙2H2O, 0.2 mg Na2B4O7∙10H2O and 0.1 mg (NH4)6Mo7O24∙4H2O. The analysis comprised three biological replicates for each strain. In addition, samples, taken at three different time points of the exponential growth phase, were used to validate constant expression during the cultivation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using the SV Total RNA Isolation System (Promega)
|
| Label |
Cy5
|
| Label protocol |
RNA samples were labelled either with Cy3 (mutant) or Cy5 (wild type) using the ULS fluorescent labelling kit (Kreatech, Germany)
|
| |
|
| Channel 2 |
| Source name |
Yersinia pseudotuberculosis crp mutant exponential phase culture grown in Yersinia minimal medium at 25°C
|
| Organism |
Yersinia pseudotuberculosis |
| Characteristics |
strain: YPIII pIB1 crp mutant; YP89
|
| Growth protocol |
Y. pseudotuberculosis YPIII or the isogenic crp mutant strain were cultivated at 25°C under aeration on a rotary shaker. First pre-cultures were grown in a 1:1 mixture of HAM’s F-12 Nutrient Mixture (Invitrogen, Carlsbad, US) and liquid DMEM medium (Biochrom, Berlin, DE). Second pre-cultures and main cultures were grown in a Yersinia minimal medium (YMM), which was developed in the present work. It contained per liter: 8 g glucose, 6.62 g KH2PO4, 13.26 g K2HPO4, 0.31 g NaCl, 5 g (NH4)2SO4, 0.20 g MgSO4∙7H2O, 30 mg 3,4-dihydroxybenzoic acid, 0.5 mg FeSO4∙7H2O, 0.5 mg ZnSO4∙7H2O, 2 mg FeCl3∙6H2O, 2 mg MnSO4∙H2O, 0.8 mg ZnSO4∙7H2O, 0.2 mg CuCl2∙2H2O, 0.2 mg Na2B4O7∙10H2O and 0.1 mg (NH4)6Mo7O24∙4H2O. The analysis comprised three biological replicates for each strain. In addition, samples, taken at three different time points of the exponential growth phase, were used to validate constant expression during the cultivation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using the SV Total RNA Isolation System (Promega)
|
| Label |
Cy3
|
| Label protocol |
RNA samples were labelled either with Cy3 (mutant) or Cy5 (wild type) using the ULS fluorescent labelling kit (Kreatech, Germany)
|
| |
|
| |
| Hybridization protocol |
300ng of each Cy3- and Cy5-labelled RNA and hybridized to the microarray at 65°C for 17 hours using the Agilent Hybridization Chamber according to the Agilent instructions
|
| Scan protocol |
The array were scanned at a resolution of 5μm using the Axon GenePix Personal 4100A microarray scanner (Axon instruments) and features were extracted using GenePix Pro 6
|
| Description |
Biological replicate 1 of 3.
|
| Data processing |
For feature extraction the software Feature Extraction 10.7.3.1 (Agilent Technologies, USA) was used, data processing was carried out using the Bioconducter – Linear Models for Microarray analysis (LIMMA) package of the R language (http://www.r-project.org).
|
| |
|
| Submission date |
Jan 30, 2014 |
| Last update date |
Sep 17, 2014 |
| Contact name |
Ann Kathrin Heroven |
| E-mail(s) |
Annkathrin.Heroven@helmholtz-hzi.de
|
| Phone |
+49-(0)53161815705
|
| Organization name |
Helmholtz Centre for Infection Research
|
| Department |
Molecular Infection Biology
|
| Street address |
Inhoffenstr. 7
|
| City |
Braunschweig |
| State/province |
Niedersachsen |
| ZIP/Postal code |
38124 |
| Country |
Germany |
| |
|
| Platform ID |
GPL15095 |
| Series (2) |
| GSE54544 |
The pyruvate-tricarboxylic acid cycle node: a focal point of virulence control in the enteric pathogen Yersinia pseudotuberculosis [crp mutant] |
| GSE54547 |
The pyruvate-tricarboxylic acid cycle node: a focal point of virulence control in the enteric pathogen Yersinia pseudotuberculosis |
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