This .csv file contains the entire transcriptional dataset of the anaerobic to aerobic transition. The values shown are the gene-expression ratio at 2, 5, 10, 15 and 20 minutes relative to the 0 minute timepoint.
Description: This .csv file contains the entire transcriptional dataset of the anaerobic to aerobic transition. The values shown are...
SEEK ID: https://fairdomhub.org/data_files/47
- Dynamical studies for different oxygen availability in Escherichia coli
- The Escherichia coli dynamical response to oxygen: from molecular interactions to regulatory modules
- Transcriptional profiling of E. coli during anaerobic to aerobic and aerobic to anaerobic transitions
- Filtered datset - aerobic to anaerobic transition .csv
- Filtered dataset - anaerobic to aerobic .csv
- Dissolved oxygen tension aerobic to anaerobic .pdf
- Dissolved oxygen tension anaerobic to aerobic .pdf
- Entire transcriptional dataset - aerobic to anaerobic transition .csv
- Entire transcriptional dataset - anaerobic to aerobic .csv
- Evans Medium
- SUMO RNA isolation from E. coli
- SUMO Transcriptional profiling of E. coli
- SUMO chemostat conditions
- Systems analysis of transcription factor activities in environments with stable and dynamic oxygen concentrations
- Transcriptional profiling of E. coli during anaerobic to aerobic and aerobic to anaerobic transitions
- The Escherichia coli dynamical response to oxygen: from molecular interactions to regulatory modules
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Created: 16th Mar 2010 at 17:12
Last updated: 29th Aug 2012 at 14:07

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Projects: SUMO
Institutions: University of Sheffield
I am a post-doctoral research associate working in Sheffield in the SUMO consortium. My research focuses on transcriptional regulation in E. coli, with particular emaphasis on the transcriptomic analysis of steady-state chemostat cultures using both microarray and qRT-PCR approaches.
Previous experience, especially that gained during my PhD, involved work on Salmonella physiology and lag phase growth, focusing particularly on gene-expression and transcriptional regulation. Other techniques used ...
SysMO is a European transnational funding and research initiative on "Systems Biology of Microorganisms".
The goal pursued by SysMO was to record and describe the dynamic molecular processes going on in unicellular microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models.
Systems biology will raise biomedical and biotechnological research to a new quality level and contribute markedly to progress in understanding. Pooling European research ...
Projects: BaCell-SysMO, COSMIC, SUMO, KOSMOBAC, SysMO-LAB, PSYSMO, SCaRAB, MOSES, TRANSLUCENT, STREAM, SulfoSys, SysMO DB, SysMO Funders, SilicoTryp, Noisy-Strep
Web page: http://sysmo.net/
"Systems Understanding of Microbial Oxygen responses" (SUMO) investigates how Escherichia coli senses oxygen, or the associated changes in oxidation/reduction balance, via the Fnr and ArcA proteins, how these systems interact with other regulatory systems, and how the redox response of an E. coli population is generated from the responses of single cells. There are five sub-projects to determine system properties and behaviour and three sub-projects to employ different and complementary modelling ...
Programme: SysMO
Public web page: http://www.sysmo.net/index.php?index=55
Organisms: Escherichia coli, Escherichia coli K-12
Changing the oxygen availability leads to an adaptation of Escherichia coli at different biological levels. After pertubation of oxygen in chemostat experiments there are very quick responses. This investigation deals with this dynamical behaviour (transitions) of Escherichia coli within the aerobiosis scale. The change for different biological variables, in different areas of the organism like the electron transport chain, the TCA cycle or globally is investigated by wildtype and mutants experiments ...
Submitter: Matthew Rolfe
Studies: The Escherichia coli dynamical response to oxygen: from molecular intera...
Assays: Transcriptional profiling of E. coli during anaerobic to aerobic and aer...
Snapshots: No snapshots
Submitter: Matthew Rolfe
Investigation: Dynamical studies for different oxygen availabi...
Assays: Transcriptional profiling of E. coli during anaerobic to aerobic and aer...
Snapshots: No snapshots
This assay involved the determination of transcriptional profiles at 0, 2, 5, 10, 15 and 20 minutes through aerobic to anaerobic gas transitions and anaerobic to aerobic gas transitions. In each case an aerobic or anaerobic steady state was created, RNA sampled (0 min) and then the gas supply changed. RNA samples were then taken from the time at which the gas supply was changed.
For anaerobic conditions 5% CO2, 95% N2 was used.
The full transcriptional dataset is available from ArrayExpress ...
Submitter: Matthew Rolfe
Assay type: Transcriptional Profiling
Technology type: Microarray
Investigation: Dynamical studies for different oxygen availabi...
Organisms: Escherichia coli : K-12/MG1655 (wild-type / wild-type)
SOPs: Evans Medium, SUMO RNA isolation from E. coli, SUMO Transcriptional profiling of E. coli, SUMO chemostat conditions
Data files: Dissolved oxygen tension aerobic to anaerobic .pdf, Dissolved oxygen tension anaerobic to aerobic .pdf, Entire transcriptional dataset - aerobic to ana..., Entire transcriptional dataset - anaerobic to a..., Filtered dataset - anaerobic to aerobic .csv, Filtered datset - aerobic to anaerobic transiti...
Snapshots: No snapshots