Team:Goettingen/Project/Bioinformatical Tools

From 2012.igem.org

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== Computational Data ==
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<head>
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=== Maps ===
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        <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
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==== Tar_QC ====
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        <meta name="keywords" content="Team:Goettingen,Team:Goettingen,Team:Goettingen/Homing coli,Team:Goettingen/Human Practice/Flash coli,Team:Goettingen/Press,Team:Goettingen/Project/General information">
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For Parts K777000 - K777008 the plasmid maps were constructed in ApE. Within the maps you will find annotated features, as well. To gain more information about the parts submitted by the iGEM team Göttingen 2012 [https://2012.igem.org/Team:Goettingen/iGEM/Parts click here]. <br>
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                <link rel="shortcut icon" href="https://2012.igem.org/favicon.ico">
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Moreover, the parts were completely sequenced (except for K777000) and aligned. The original data and the reviewed data are provided in the respective Zip- files. <br>
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                <link rel="search" type="application/opensearchdescription+xml" href="https://2012.igem.org/wiki/opensearch_desc.php" title="2012.igem.org (English)">
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* [https://static.igem.org/mediawiki/2012/f/fc/Tar_receptor_under_the_control_of_constitutive_promoter.zip ApE plasmid maps]
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                <link title="Creative Commons" type="application/rdf+xml" href="https://2012.igem.org/wiki/index.php?title=Team:Goettingen&amp;action=creativecommons" rel="meta">
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*Sequencing results
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                <link rel="alternate" type="application/rss+xml" title="2012.igem.org RSS Feed" href="https://2012.igem.org/wiki/index.php?title=Special:Recentchanges&amp;feed=rss">
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**[https://static.igem.org/mediawiki/2012/2/20/K777000_in_pSB1C3.zip K777000 in pSB1C3]
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                <link rel="alternate" type="application/atom+xml" title="2012.igem.org Atom Feed" href="https://2012.igem.org/wiki/index.php?title=Special:Recentchanges&amp;feed=atom">
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**[https://static.igem.org/mediawiki/2012/e/e7/K777001_in_pSB1C3.zip K777001 in pSB1C3]
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</head>
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**[https://static.igem.org/mediawiki/2012/9/90/K777002_in_pSB1C3.zip K777002 in pSB1C3]
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<body class="mediawiki ns-0 ltr page-Team_Goettingen">
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**[https://static.igem.org/mediawiki/2012/0/0a/K777003_in_pSB1C3.zip K777003 in pSB1C3]
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**[https://static.igem.org/mediawiki/2012/a/a8/K777004_in_pSB1C3.zip K777004 in pSB1C3]
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**[https://static.igem.org/mediawiki/2012/0/07/K777005_in_pSB1C3.zip K777005 in pSB1C3]
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**[https://static.igem.org/mediawiki/2012/6/61/K777006_in_pSB1C3.zip K777006 in pSB1C3]
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**[https://static.igem.org/mediawiki/2012/3/33/K777007_in_pSB1C3.zip K777007 in pSB1C3]
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**[https://static.igem.org/mediawiki/2012/5/52/K777008_in_pSB1C3.zip K777008 in pSB1C3]
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<font face="Verdana" size="-1">Language: <img height="20", src="http://www.patrickreinke.de/igem/eng.jpg"> English</a> <br>
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==== flhDC ====
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* [https://static.igem.org/mediawiki/2012/b/b6/K777100_in_pSB1C3.zip K777100 in pSB1C3 ApE plasmid map]
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<table id="toc" class="toc"><tbody><tr><td><div id="toctitle"><h2>Contents</h2> <span class="toctoggle"><a href="javascript:toggleToc()" class="internal" id="togglelink"></a></span></div>
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==== fliC ====
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<ul>
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* [https://static.igem.org/mediawiki/2012/8/8b/K777109_in_pSB1C3.zip K777109 in pSB1C3 ApE plasmid map]
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<li class="toclevel-1"><a href="#Computational_Data"><span class="tocnumber">1</span> <span class="toctext">Computational Data</span></a></li>
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<li class="toclevel-1"><div style="text-indent:10px;"><a href="#Maps"><span class="tocnumber"></span> <span class="toctext">Maps</span></a></li>
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<li class="toclevel-1"><div style="text-indent:10px;"><a href="#Sequences"><span class="tocnumber"></span> <span class="toctext">Sequences</span></a></li>
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</td></tr></tbody></table>
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<br>
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                                <!-- Text body -->
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==== motA ====
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<tbody>
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* [https://static.igem.org/mediawiki/2012/3/37/K777113_in_pSB1C3.zip K777113 in pSB1C3 ApE plasmid map]
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<tr valign="top" align="left">
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<td style="padding: 0pt 20px 0pt 0pt;" width="910px">
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<font face="Verdana" size="-1">
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                                <!-- Ab hier kannst du editieren -->
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==== motB ====
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* [https://static.igem.org/mediawiki/2012/0/09/K777117_in_pSB1C3.zip K777117 in pSB1C3 ApE plasmid map]
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<h2><b><a name="Computational_Data"></a>Computational Data</b></h2>
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==== yhjH ====
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<p align="justify" style="line-height:1.6em">
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* [https://static.igem.org/mediawiki/2012/3/3f/K777121_in_pSB1C3.zip K777121 in pSB1C3 ApE plasmid map]
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<h3 style="margin:3px; background:#cedff2; font-size:120%; font-weight:bold; border:1px solid #a3b0bf; text-align:left; color:#000; padding:0.2em 0.4em;"<b><a name="Maps"></a>Maps</b></h3><br>
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<ol>
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<li> Tar_QC </li>
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For Parts K777000 - K777008 the plasmid maps were constructed in ApE. Within the maps you will find annotated features, as well. To gain more information about our parts, click here <a href="https://2012.igem.org/Team:Goettingen/iGEM/Parts">parts submitted </a> by the iGEM team Göttingen 2012. <br>
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-
Moreover, the parts were completely sequenced and aligned. The original data and the reviewed data are provided in the respective Zip- files. <br>
+
-
<ul>
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<li> <a href="https://static.igem.org/mediawiki/2012/f/fc/Tar_receptor_under_the_control_of_constitutive_promoter.zip">ApE plasmid maps</a></li>
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<li> Sequencing results</li>
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</ul>
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<div style="text-indent:40px;"><a href="https://static.igem.org/mediawiki/2012/2/20/K777000_in_pSB1C3.zip">K777000 in pSB1C3</a><br></div>
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<div style="text-indent:40px;"><a href="https://static.igem.org/mediawiki/2012/e/e7/K777001_in_pSB1C3.zip">K777001 in pSB1C3</a><br></div>
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<div style="text-indent:40px;"><a href="https://static.igem.org/mediawiki/2012/9/90/K777002_in_pSB1C3.zip">K777002 in pSB1C3</a><br></div>
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<div style="text-indent:40px;"><a href="https://static.igem.org/mediawiki/2012/0/0a/K777003_in_pSB1C3.zip">K777003 in pSB1C3</a><br></div>
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<div style="text-indent:40px;"><a href="https://static.igem.org/mediawiki/2012/a/a8/K777004_in_pSB1C3.zip">K777004 in pSB1C3</a><br></div>
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<div style="text-indent:40px;"><a href="https://static.igem.org/mediawiki/2012/0/07/K777005_in_pSB1C3.zip">K777005 in pSB1C3</a><br></div>
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<div style="text-indent:40px;"><a href="https://static.igem.org/mediawiki/2012/6/61/K777006_in_pSB1C3.zip">K777006 in pSB1C3</a><br></div>
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<div style="text-indent:40px;"><a href="https://static.igem.org/mediawiki/2012/3/33/K777007_in_pSB1C3.zip">K777007 in pSB1C3</a><br></div>
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<div style="text-indent:40px;"><a href="https://static.igem.org/mediawiki/2012/5/52/K777008_in_pSB1C3.zip">K777008 in pSB1C3</a><br></div>
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<br>
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<li> flhDC </li>
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<ul><li><a href="https://static.igem.org/mediawiki/2012/b/b6/K777100_in_pSB1C3.zip"> K777100 in pSB1C3 ApE plasmid map</a></li> </ul><br>
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<li> fliC </li>
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<ul><li><a href="https://static.igem.org/mediawiki/2012/8/8b/K777109_in_pSB1C3.zip"> K777109 in pSB1C3 ApE plasmid map</a></li> </ul><br>
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<li> motA </li>
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<ul><li> K777113 ApE plasmid map</li> </ul><br>
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<li> motB </li>
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<ul><li> K777117 ApE plasmid map</li> </ul><br>
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<li> yhjH </li>
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<ul><li> K777121 ApE plasmid map</li> </ul><br>
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<li> Constitutive promoter + RFP-constructs </li>
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<ul><li> K777125 - K777132 ApE plasmid maps</li> </ul><br>
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</ol>
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<br>
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 +
==== Constitutive promoter + RFP-constructs ====
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* [https://static.igem.org/mediawiki/2012/0/07/K777125-K777132.zip K777125-K777132 ApE plasmid maps]
 +
=== Primers ===
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* [https://static.igem.org/mediawiki/2012/4/43/Primer_Mutagenesis.zip Mutagenesis]
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* [https://static.igem.org/mediawiki/2012/f/fc/Primer_PCR.zip PCR]
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* [https://static.igem.org/mediawiki/2012/c/cf/Primer_QC.zip QuikChange]
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* [https://static.igem.org/mediawiki/2012/4/4b/Primer_Sequencing.zip Sequencing]
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* [https://static.igem.org/mediawiki/2012/4/45/Primer_Real-Time.zip Real-time]
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<h3 style="margin:3px; background:#cedff2; font-size:120%; font-weight:bold; border:1px solid #a3b0bf; text-align:left; color:#000; padding:0.2em 0.4em;"<b><a name="Sequences"></a>Sequences</b></h3><br>
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=== Raw Datasets ===
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<ol>
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==== Characterization of constitutive promoters by qrtPCR ====
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<li> Primers</li>
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-
<ul>
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<li></li>
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</ul>
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</ol>
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 +
<li>CP (crossing point) values and relative reinforcments of promoters from the [http://partsregistry.org/Promoters/Catalog/Anderson Anderson Family]:J23100, J23104, J23105, J23106, J23109, J23112, J23113, J23114 <br>The CP values ​​of the reference housekeeping genes (hkg) are reduced by the value of 3.32 for the dilution which have been used for the reference cDNA in the experiment.
 +
For detailed information of generation of data and data analyzes [https://2012.igem.org/Team:Goettingen/Project/Methods#Quantitative_Real-Time_PCR click here].
 +
{| class="wikitable"
 +
|-
 +
! scope="col"| Promoter
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! scope="col"|
 +
! scope="col"| CP1
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! scope="col"| CP2
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! scope="col"| CP3
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! scope="col"| Average
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! scope="col"| Standard variance
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|-
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! rowspan="3"| J23113 <br>(Calibrator)
 +
! J23113
 +
| align="right"| 23.7
 +
| align="right"| 24.46
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| align="right"| 24.51
 +
|-
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! J23113_hkg
 +
| align="right"| 5.48
 +
| align="right"| 5.33
 +
| align="right"| 4.57
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|- rowspan="2"
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! ΔCT Calibrator <br>(CP - CP_hkg)
 +
| align="right"| 18.22
 +
| align="right"| 18.93
 +
| align="right"| 19.94
 +
| align="right"| 19.03
 +
| align="right"| 0.71
 +
|-
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! rowspan="5"| J23106
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! J23106
 +
| align="right"| 23.25
 +
| align="right"| 22.37
 +
| align="right"| 22.44
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|-
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! J23106_hkg
 +
| align="right"| 4.66
 +
| align="right"| 5.58
 +
| align="right"| 5.59
 +
|-
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! ΔCT J23106
 +
| align="right"| 17.63
 +
| align="right"| 16.73
 +
| align="right"| 16.85
 +
|-
 +
! ΔΔCT J23106
 +
| align="right"| 1.4
 +
| align="right"| 2.3
 +
| align="right"| 2.18
 +
|-
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! Reinforcment
 +
| align="right"| 2.64
 +
| align="right"| 4.92
 +
| align="right"| 4.53
 +
| align="right"| 4.03
 +
| align="right"| 1.00
 +
|-
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! rowspan="5"| J23112
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! J23112
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| align="right"| 20.43
 +
| align="right"| 20.42
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| align="right"| 20.24
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|-
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! J23112_hkg
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| align="right"| 5.00
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| align="right"| 4.9
 +
| align="right"| 5.2
 +
|-
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! ΔCT J23112
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| align="right"| 15.43
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| align="right"| 15.52
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| align="right"| 15.04
 +
|-
 +
! ΔΔCT J23112
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| align="right"| 3.6
 +
| align="right"| 3.51
 +
| align="right"| 3.99
 +
|-
 +
! Reinforcment
 +
| align="right"| 12.13
 +
| align="right"| 11.39
 +
| align="right"| 15.89
 +
| align="right"| 13.14
 +
| align="right"| 1.97
 +
|-
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! rowspan="5"| J23114
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! J23112
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| align="right"| 20.35
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| align="right"| 20.07
 +
| align="right"| 20.88
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|-
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! J23114_hkg
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| align="right"| 5.77
 +
| align="right"| 6.13
 +
| align="right"| 5.75
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|-
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! ΔCT J23114
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| align="right"| 14.58
 +
| align="right"| 13.94
 +
| align="right"| 15.13
 +
|-
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! ΔΔCT J23114
 +
| align="right"| 4.45
 +
| align="right"| 5.09
 +
| align="right"| 3.90
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|-
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! Reinforcment
 +
| align="right"| 21.86
 +
| align="right"| 34.06
 +
| align="right"| 14.93
 +
| align="right"| 23.62
 +
| align="right"| 7.91
 +
|-
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! rowspan="5"| J23109
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! J23109
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| align="right"| 18.56
 +
| align="right"| 18.25
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| align="right"| 18.50
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|-
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! J23109_hkg
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| align="right"| 5.79
 +
| align="right"| 5.43
 +
| align="right"| 5.91
 +
|-
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! ΔCT J23109
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| align="right"| 12.77
 +
| align="right"| 12.82
 +
| align="right"| 12.59
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|-
 +
! ΔΔCT J23109
 +
| align="right"| 6.26
 +
| align="right"| 6.21
 +
| align="right"| 6.44
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|-
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! Reinforcment
 +
| align="right"| 76.64
 +
| align="right"| 74.03
 +
| align="right"| 86.82
 +
| align="right"| 79.16
 +
| align="right"| 5.52
 +
|-
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! rowspan="5"| J23105
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! J23105
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| align="right"| 16.05
 +
| align="right"| 16.21
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| align="right"| 16.13
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|-
 +
! J23105_hkg
 +
| align="right"| 4.98
 +
| align="right"| 5.22
 +
| align="right"| 5.18
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|-
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! ΔCT J23105
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| align="right"| 11.07
 +
| align="right"| 10.99
 +
| align="right"| 10.95
 +
|-
 +
! ΔΔCT J23105
 +
| align="right"| 7.96
 +
| align="right"| 8.04
 +
| align="right"| 8.08
 +
|-
 +
! Reinforcment
 +
| align="right"| 249.00
 +
| align="right"| 263.20
 +
| align="right"| 270.60
 +
| align="right"| 260.93
 +
| align="right"| 8.96
 +
|-
 +
! rowspan="5"| J23104
 +
! J23104
 +
| align="right"| 15.76
 +
| align="right"| 16.50
 +
| align="right"| 15.85
 +
|-
 +
! J23104_hkg
 +
| align="right"| 4.66
 +
| align="right"| 5.58
 +
| align="right"| 5.03
 +
|-
 +
! ΔCT J23104
 +
| align="right"| 11.10
 +
| align="right"| 10.92
 +
| align="right"| 10.82
 +
|-
 +
! ΔΔCT J23104
 +
| align="right"| 7.93
 +
| align="right"| 8.11
 +
| align="right"| 8.21
 +
|-
 +
! Reinforcment
 +
| align="right"| 243.88
 +
| align="right"| 276.28
 +
| align="right"| 296.11
 +
| align="right"| 272.09
 +
| align="right"| 21.53
 +
|-
 +
! rowspan="5"| J23100
 +
! J23100
 +
| align="right"| 14.02
 +
| align="right"| 13.53
 +
| align="right"| 14.21
 +
|-
 +
! J23100_hkg
 +
| align="right"| 4.06
 +
| align="right"| 4.23
 +
| align="right"| 5.12
 +
|-
 +
! ΔCT J23100
 +
| align="right"| 9.96
 +
| align="right"| 9.30
 +
| align="right"| 9.09
 +
|-
 +
! ΔΔCT J23100
 +
| align="right"| 9.07
 +
| align="right"| 9.73
 +
| align="right"| 9.94
 +
|-
 +
! Reinforcment
 +
| align="right"| 537.45
 +
| align="right"| 849.22
 +
| align="right"| 982.29
 +
| align="right"| 789.65
 +
| align="right"| 186.42
 +
 +
|}
 +
 +
Here you can find the according [https://static.igem.org/mediawiki/2012/4/4e/Qrt-PCR_18.0912_uploaded_igem_goettingen_2012.xls excel sheet] and a more detailed description of the [https://2012.igem.org/Team:Goettingen/Notebook/Results#.233_-_Chemoreceptor_Library results].<br>
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{{GoettingenFooter}}
{{GoettingenFooter}}

Latest revision as of 23:49, 26 September 2012

Deutsch  / English 

Contents

Computational Data

Maps

Tar_QC

For Parts K777000 - K777008 the plasmid maps were constructed in ApE. Within the maps you will find annotated features, as well. To gain more information about the parts submitted by the iGEM team Göttingen 2012 click here.
Moreover, the parts were completely sequenced (except for K777000) and aligned. The original data and the reviewed data are provided in the respective Zip- files.

flhDC

fliC

motA

motB

yhjH

Constitutive promoter + RFP-constructs

Primers

Raw Datasets

Characterization of constitutive promoters by qrtPCR

  • CP (crossing point) values and relative reinforcments of promoters from the [http://partsregistry.org/Promoters/Catalog/Anderson Anderson Family]:J23100, J23104, J23105, J23106, J23109, J23112, J23113, J23114
    The CP values ​​of the reference housekeeping genes (hkg) are reduced by the value of 3.32 for the dilution which have been used for the reference cDNA in the experiment. For detailed information of generation of data and data analyzes click here.
    Promoter CP1 CP2 CP3 Average Standard variance
    J23113
    (Calibrator)     		J23113 23.7 24.46 24.51
    J23113_hkg 5.48 5.33 4.57
    ΔCT Calibrator
    (CP - CP_hkg)     		18.22 18.93 19.94 19.03 0.71
    J23106 J23106 23.25 22.37 22.44
    J23106_hkg 4.66 5.58 5.59
    ΔCT J23106 17.63 16.73 16.85
    ΔΔCT J23106 1.4 2.3 2.18
    Reinforcment 2.64 4.92 4.53 4.03 1.00
    J23112 J23112 20.43 20.42 20.24
    J23112_hkg 5.00 4.9 5.2
    ΔCT J23112 15.43 15.52 15.04
    ΔΔCT J23112 3.6 3.51 3.99
    Reinforcment 12.13 11.39 15.89 13.14 1.97
    J23114 J23112 20.35 20.07 20.88
    J23114_hkg 5.77 6.13 5.75
    ΔCT J23114 14.58 13.94 15.13
    ΔΔCT J23114 4.45 5.09 3.90
    Reinforcment 21.86 34.06 14.93 23.62 7.91
    J23109 J23109 18.56 18.25 18.50
    J23109_hkg 5.79 5.43 5.91
    ΔCT J23109 12.77 12.82 12.59
    ΔΔCT J23109 6.26 6.21 6.44
    Reinforcment 76.64 74.03 86.82 79.16 5.52
    J23105 J23105 16.05 16.21 16.13
    J23105_hkg 4.98 5.22 5.18
    ΔCT J23105 11.07 10.99 10.95
    ΔΔCT J23105 7.96 8.04 8.08
    Reinforcment 249.00 263.20 270.60 260.93 8.96
    J23104 J23104 15.76 16.50 15.85
    J23104_hkg 4.66 5.58 5.03
    ΔCT J23104 11.10 10.92 10.82
    ΔΔCT J23104 7.93 8.11 8.21
    Reinforcment 243.88 276.28 296.11 272.09 21.53
    J23100 J23100 14.02 13.53 14.21
    J23100_hkg 4.06 4.23 5.12
    ΔCT J23100 9.96 9.30 9.09
    ΔΔCT J23100 9.07 9.73 9.94
    Reinforcment 537.45 849.22 982.29 789.65 186.42

    Here you can find the according excel sheet and a more detailed description of the results.


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