Team:Groningen/Notebook/Wetwork 12July2012

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Slide images were analyzed using ArrayPro 4.5 (Media Cybernetics Inc., Silver Spring, MD). The obtained data was processed and normalized (Lowess normalization) using the MolGen software MicroPrep (Garcia de la Nava et. al, 2003). A statistical analysis was done using the webservice CyberT (Baldi et. al, 2001) A gene was considered differentially expressed when the Bayes p value was lower than 0.001 and the difference in expression (the fold) was >2 or <-2.  
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The genes obtained using the CyberT analysis were ordered by locus tag and fold. This list was processed further using different analysis tools. With use of the in-house software Genome2d (Baerends et. al, 2004), operons with expression difference were identified and figures showing these operons were made.
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''Baerends R, Smits W, De Jong A, Hamoen L, Kok J, Kuipers O (2004). "Genome2D: a visualization tool for the rapid analysis of bacterial transcriptome data." Genome Biol, 5(5):R37.''
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''Baldi , Lond, A. D. (2001): "A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes", Bioinformatics 17(6):509-519.''
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''Garcia de la Nava J; van Hijum S; Trelles O (2003). "Title: PreP: gene expression data pre-processing." Bioinformatics 19 (17):2328-2329.''
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Arjan/Renske<br>
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Slide images were analyzed using ArrayPro 4.5 (Media Cybernetics Inc., Silver Spring, MD). The obtained data was processed and normalized (Lowess normalization) using the MolGen software MicroPrep (Garcia de la Nava et. al, 2003). A statistical analysis was done using the webservice CyberT (Baldi et. al, 2001) A gene was considered differentially expressed when the Bayes p value was lower than 0.001 and the difference in expression (the fold) was >2 or <-2.
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Nisa
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The genes obtained using the CyberT analysis were ordered by locus tag and fold. This list was processed further using different analysis tools. With use of the in-house software Genome2d (Baerends et. al, 2004), operons with expression difference were identified and figures showing these operons were made.<br>
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Double restriction of the biobricks isolated on 11-07-2012 with EcoRI and SpeI.
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<i>Baerends R, Smits W, De Jong A, Hamoen L, Kok J, Kuipers O (2004). "Genome2D: a visualization tool for the rapid analysis of bacterial transcriptome data." Genome Biol, 5(5):R37.<br>
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GFP primers recieved
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<br>
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Baldi , Lond, A. D. (2001): "A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes", Bioinformatics 17(6):509-519.<br>
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<br>
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Garcia de la Nava J; van Hijum S; Trelles O (2003). "Title: PreP: gene expression data pre-processing." Bioinformatics 19 (17):2328-2329.</i><br>
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Nisa/Emeraldo<br>
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Double restriction of the biobricks isolated on 11-07-2012 with EcoRI and SpeI.<br>
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<br>
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GFP primers recieved<br>
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<br>
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E.coli Dh5a transformed with 30 ng/ul PDRIII GFP optimized (MolGen). The PDRIII has Apicillin resistance and spectinomycin resistance. For E.coli Amp + Spec, but for Bacillus subtilis only Spectinomycin because Ampicillin resistance is cleaved by double cross over (genomic integration plasmid).<br>
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<A HREF="https://2012.igem.org/Team:Groningen/Notebook"><FONT COLOR=#ff6700>Back to notebook</FONT></A>
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E.coli Dh5a transformed with 30 ng/ul PDRIII GFP optimized (MolGen). The PDRIII has Apicillin resistance and spectinomycin resistance. For E.coli Amp + Spec, but for Bacillus subtilis only Spectinomycin because Ampicillin resistance is cleaved by double cross over (genomic integration plasmid).
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Latest revision as of 21:04, 25 September 2012







Arjan/Renske

Slide images were analyzed using ArrayPro 4.5 (Media Cybernetics Inc., Silver Spring, MD). The obtained data was processed and normalized (Lowess normalization) using the MolGen software MicroPrep (Garcia de la Nava et. al, 2003). A statistical analysis was done using the webservice CyberT (Baldi et. al, 2001) A gene was considered differentially expressed when the Bayes p value was lower than 0.001 and the difference in expression (the fold) was >2 or <-2. The genes obtained using the CyberT analysis were ordered by locus tag and fold. This list was processed further using different analysis tools. With use of the in-house software Genome2d (Baerends et. al, 2004), operons with expression difference were identified and figures showing these operons were made.


Baerends R, Smits W, De Jong A, Hamoen L, Kok J, Kuipers O (2004). "Genome2D: a visualization tool for the rapid analysis of bacterial transcriptome data." Genome Biol, 5(5):R37.

Baldi , Lond, A. D. (2001): "A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes", Bioinformatics 17(6):509-519.

Garcia de la Nava J; van Hijum S; Trelles O (2003). "Title: PreP: gene expression data pre-processing." Bioinformatics 19 (17):2328-2329.


Nisa/Emeraldo

Double restriction of the biobricks isolated on 11-07-2012 with EcoRI and SpeI.

GFP primers recieved

E.coli Dh5a transformed with 30 ng/ul PDRIII GFP optimized (MolGen). The PDRIII has Apicillin resistance and spectinomycin resistance. For E.coli Amp + Spec, but for Bacillus subtilis only Spectinomycin because Ampicillin resistance is cleaved by double cross over (genomic integration plasmid).


Back to notebook



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