Tiling Array analysis of glucose strarved B. subtilis cells
B. subtilis was grown in M9 media with glucose as carbon source and the samples were harvested during exponential phase (OD600nm- 0.4), early stationary phase(OD600nm- 1.3), late stationary phase(OD600nm- 1.0). All the samples were analysed for transcriptome as biological triplicates.
SEEK ID: https://fairdomhub.org/assays/53
Experimental assay
Projects: BaCell-SysMO
Investigation: Redefining the Complete Transcriptome of Bacillus subtilis using Tiling Array Technology.
Study: Transcriptome analysis of glucose starvation in B. subtilis
Assay position:
Assay type: Transcriptomics
Technology type: Microarray
Organisms: Bacillus subtilis : 168 Trp+ (wild-type / tryptophan prototroph)
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Created: 18th May 2010 at 13:47
Last updated: 8th Nov 2017 at 14:21
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Projects: BaCell-SysMO
Institutions: University of Greifswald
I am PhD student at Prof.Uwe Voelker lab in Department of Functional Genomics. My area of research is microbial functional genomics in particular analysing the whole transcriptome(by microarray and other molecular biolology methods) of B.subtilis under various stress conditions. I use QconCAT strategy for absolute quantification of carbon metabolic enzymes via MRM(multiple reaction monitoring) by LC-MS/MS. I also perofrm experiments for understanding of dynamics of SigmaB network for modelling.
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/
BaCell-SysMO 2 Modelling carbon core metabolism in Bacillus subtilis – Exploring the contribution of protein complexes in core carbon and nitrogen metabolism.
Bacillus subtilis is a prime model organism for systems biology approaches because it is one of the most advanced models for functional genomics. Furthermore, comprehensive information on cell and molecular biology, physiology and genetics is available and the European Bacillus community (BACELL) has a well-established reputation for applying ...
Programme: SysMO
Public web page: http://www.sysmo.net/index.php?index=53
Bacillus subtilis was subjected to various stress conditions like high temperature(57°C), low temperature(16°C), high osmalarity(1.2M NaCl). The above mentioned stress conditions are again split into two different types as 'continuous stress condition' and 'sudden shock'. All the conditions were then done in biological triplicates. Transcriptome for these samples was then analysed with Nimblegen Tiling array.
Submitter: Praveen kumar Sappa
Studies: Transcriptome analysis of glucose starvation in B. subtilis, Transcriptome of continuously stressed B. subtilis, Transcriptome of shocked B. subtilis cells
Assays: Tiling Array analysis of glucose strarved B. subtilis cells, Tiling Array analysis of shocked B. subtilis cells, Tiling array analysis of continuous growth stress conditions in SMM
Submitter: Praveen kumar Sappa
Investigation: Redefining the Complete Transcriptome of Bacill...
Assays: Tiling Array analysis of glucose strarved B. subtilis cells
Submitter: Praveen kumar Sappa
Provider Name: Not specified
Provider's strain ID: 168 Trp+
Organism: Bacillus subtilis
Genotypes: wild-type
Phenotypes: tryptophan prototroph
Comment: Trp+ derivative of B. subtilis 168 wild type.
Recent studies revealed the unsuspected complexity of the bacterial transcriptome but its systematic analysis across many diverse conditions remains a challenge. Here we report the condition-dependent transcriptome of the prototype strain B. subtilis 168 across 104 conditions reflecting the bacterium's life-styles. This data set composed of 269 tiling array hybridizations allowed to observe ~85% of the annotated CDSs expressed in the higher 30% in at least one hybridization and thus provide an ...
Creators: Leif Steil, Ulrike Mäder, Colin Harwood, Rick Lewis, Ruben Mars, Priyanka Nannapaneni, Praveen kumar Sappa, Joerg Stuelke, Jan Maarten van Dijl, Michael Hecker, Uwe Voelker
Submitter: Leif Steil
Relationship type: Not specified
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Isolation of total RNA from Bacillus Subtilis using phenol-chloroform extraction method by maintaining cryogenec conditions initailly to prevent RNA degradation. Quality of the obtained RNA is then tested with Agilent Bioanalyser before proceeding for gene expression analysis.
Creator: Praveen kumar Sappa
Submitter: Praveen kumar Sappa
SOP for shake flask cultivation of B.Subtilis in Bacell-Sysmo
Creator: Praveen kumar Sappa
Submitter: Praveen kumar Sappa
Abstract (Expand)
Authors: Pierre Nicolas, , Etienne Dervyn, Tatiana Rochat, Aurélie Leduc, Nathalie Pigeonneau, Elena Bidnenko, Elodie Marchadier, Mark Hoebeke, Stéphane Aymerich, Dörte Becher, Paola Bisicchia, Eric Botella, Olivier Delumeau, Geoff Doherty, Emma L Denham, Mark J Fogg, Vincent Fromion, Anne Goelzer, Annette Hansen, Elisabeth Härtig, , Georg Homuth, Hanne Jarmer, Matthieu Jules, Edda Klipp, Ludovic Le Chat, François Lecointe, , Wolfram Liebermeister, Anika March, , , David Noone, Susanne Pohl, Bernd Rinn, Frank Rügheimer, , Franck Samson, Marc Schaffer, Benno Schwikowski, , , Thomas Wiegert, Kevin M Devine, Anthony J Wilkinson, , , , Philippe Bessières, Philippe Noirot
Date Published: 3rd Mar 2012
Publication Type: Not specified
