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| Status |
Public on Mar 25, 2011 |
| Title |
Expression data from Pseudomonas putida KT2440 |
| Organism |
Pseudomonas putida KT2440 |
| Experiment type |
Expression profiling by array
Expression profiling by high throughput sequencing
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| Summary |
In this study we exploited next-generation Illumina sequencing technology (Wang et al., 2009) to refine the current annotation of the KT2440 genome. Transcriptome sequencing data were queried for yet undescribed small RNAs and ORFs and employed to validate predicted operons and gene coordinates. Expression profiles were measured at 10°C and 30°C to cover the physiologic temperature profile of this mesophilic bacterium. Moreover we compared the sensitivity and specificity of transcriptome data by taking the same RNA preparations for cDNA sequencing and hybridization of Progenika and Affymetrix microarrays.
This SuperSeries is composed of the SubSeries listed below.
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| Overall design |
P. putida KT2440 (strain DSM6125) (Bagdasarian et al., 1981) was obtained from the German Resource Centre for Biological Material (DSMZ, (Braunschweig, Germany). Bacterial cultures were inoculated from a frozen stock culture of P. putida wild type, and incubated at 30°C for 8 hours at 250 rpm in LB medium. An aliquot of 0.2 mL was added to 20 mL M9 medium (Na2HPO4 33.9 g/L, KH2PO4 15.0 g/L, NaCl 2.5 g/L, NH4Cl 5.0 g/L, MgSO4 2 mM, CaCl2 0.1 mM, FeSO4 x 7 H2O 0.01 mM, pH 6.8) supplemented with 15 mM succinate as sole carbon source in a 100 mL flask and incubated overnight at 30°C. For RNA extraction, bacteria were grown in a 1.5 L batch culture (M9 + 15 mM succinate) using the BioFlo 110 Fermenter (New Brunswick Scientific Co., Edison, NJ) to ensure constant pH, aeration and agitation. When cultures reached mid-exponential phase (OD600 ~ 0.8) the temperature was decreased from 30°C to 10°C. Three samples, each for parallel RNA extraction, were subsequently taken immediately before temperature downshift (30°C) and two hours after the media had been cooled to 10°C.
The gene expression profiles of P. putida KT2440 at 30°C and 10°C were analyzed using three different transcriptome platforms: RNA-Seq (Illumina cDNA sequencing), Affymetrix microarrays and Progenika oligonucleotide microarrays.
For a detailed description of sample preparation (RNA, cDNA , labelling, hybridization etc.) refer to individual Series.
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| Contributor(s) |
Frank S |
| Citation(s) |
21355971 |
| |
| Submission date |
Sep 16, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Sarah Frank |
| E-mail(s) |
frank.sarah@mh-hannover.de
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| Organization name |
Medical School Hannover
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| Department |
Clinic for Paediatric Pneumology and Neonatology
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| Lab |
Clinical Research Group OE6711
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| Street address |
Carl-Neuberg-Str. 1
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| City |
Hannover |
| ZIP/Postal code |
30625 |
| Country |
Germany |
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| Platforms (3) |
| GPL10932 |
Affymetrix P putida KT2440 array |
| GPL10933 |
Progenika P putida KT2440 oligo array |
| GPL10934 |
Illumina Genome Analyzer II (Pseudomonas putida KT2440) |
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| Samples (9)
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| This SuperSeries is composed of the following SubSeries: |
| GSE24173 |
Expression data from Pseudomonas putida KT2440 (Affymetrix data) |
| GSE24174 |
Expression data from Pseudomonas putida KT2440 (Progenika oligo array data) |
| GSE24175 |
Expression data from Pseudomonas putida KT2440 (RNA-Seq data) |
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| Relations |
| BioProject |
PRJNA130097 |
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