Team:Goettingen/Project/Bioinformatical Tools

From 2012.igem.org

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{{GoettingenHeader|deu=Team:Goettingen/Project/Bioinformatical Tools|eng=Team:Goettingen/Project/Bioinformatical Tools}}
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{{GoettingenBlue}}
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== 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 [https://2012.igem.org/Team:Goettingen/iGEM/Parts click here]. <br>
 +
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>
 +
* [https://static.igem.org/mediawiki/2012/f/fc/Tar_receptor_under_the_control_of_constitutive_promoter.zip ApE plasmid maps]
 +
*Sequencing results
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**[https://static.igem.org/mediawiki/2012/2/20/K777000_in_pSB1C3.zip K777000 in pSB1C3]
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**[https://static.igem.org/mediawiki/2012/e/e7/K777001_in_pSB1C3.zip K777001 in pSB1C3]
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**[https://static.igem.org/mediawiki/2012/9/90/K777002_in_pSB1C3.zip K777002 in pSB1C3]
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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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<body class="mediawiki ns-0 ltr page-Team_Goettingen">
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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]
 +
==== fliC ====
 +
* [https://static.igem.org/mediawiki/2012/8/8b/K777109_in_pSB1C3.zip K777109 in pSB1C3 ApE plasmid map]
 +
==== motA ====
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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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==== 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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                        <!-- start content -->
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==== yhjH ====
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* [https://static.igem.org/mediawiki/2012/3/3f/K777121_in_pSB1C3.zip K777121 in pSB1C3 ApE plasmid map]
 +
==== Constitutive promoter + RFP-constructs ====
 +
* [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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<style>
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=== Raw Datasets ===
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h1.firstHeading { display: none; }
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==== Characterization of constitutive promoters by qrtPCR ====
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p {text-align: justify;}
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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.
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For detailed information of generation of data and data analyzes [https://2012.igem.org/Team:Goettingen/Project/Methods#Quantitative_Real-Time_PCR click here].
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a:link { color: #004080; text-decoration: none}
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{| class="wikitable"
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a:visited { color:##003090; text-decoration: none}
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|-
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a:hover { color:#f29400; text-decoration: none}
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! scope="col"| Promoter
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a:active { color:#f29400; text-decoration: none}
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! scope="col"|
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! 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
 +
|-
 +
! rowspan="3"| J23113 <br>(Calibrator)
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! J23113
 +
| align="right"| 23.7
 +
| align="right"| 24.46
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| align="right"| 24.51
 +
|-
 +
! J23113_hkg
 +
| align="right"| 5.48
 +
| align="right"| 5.33
 +
| align="right"| 4.57
 +
|- rowspan="2"
 +
! ΔCT Calibrator <br>(CP - CP_hkg)
 +
| align="right"| 18.22
 +
| align="right"| 18.93
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| align="right"| 19.94
 +
| align="right"| 19.03
 +
| align="right"| 0.71
 +
|-
 +
! rowspan="5"| J23106
 +
! J23106
 +
| align="right"| 23.25
 +
| align="right"| 22.37
 +
| align="right"| 22.44
 +
|-
 +
! J23106_hkg
 +
| align="right"| 4.66
 +
| align="right"| 5.58
 +
| align="right"| 5.59
 +
|-
 +
! 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
 +
|-
 +
! Reinforcment
 +
| align="right"| 2.64
 +
| align="right"| 4.92
 +
| align="right"| 4.53
 +
| align="right"| 4.03
 +
| align="right"| 1.00
 +
|-
 +
! rowspan="5"| J23112
 +
! J23112
 +
| align="right"| 20.43
 +
| align="right"| 20.42
 +
| align="right"| 20.24
 +
|-
 +
! J23112_hkg
 +
| align="right"| 5.00
 +
| align="right"| 4.9
 +
| align="right"| 5.2
 +
|-
 +
! ΔCT J23112
 +
| align="right"| 15.43
 +
| align="right"| 15.52
 +
| align="right"| 15.04
 +
|-
 +
! ΔΔCT J23112
 +
| 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
 +
|-
 +
! rowspan="5"| J23114
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! J23112
 +
| align="right"| 20.35
 +
| align="right"| 20.07
 +
| align="right"| 20.88
 +
|-
 +
! J23114_hkg
 +
| align="right"| 5.77
 +
| align="right"| 6.13
 +
| align="right"| 5.75
 +
|-
 +
! ΔCT J23114
 +
| align="right"| 14.58
 +
| align="right"| 13.94
 +
| align="right"| 15.13
 +
|-
 +
! ΔΔCT J23114
 +
| align="right"| 4.45
 +
| align="right"| 5.09
 +
| align="right"| 3.90
 +
|-
 +
! Reinforcment
 +
| align="right"| 21.86
 +
| align="right"| 34.06
 +
| align="right"| 14.93
 +
| align="right"| 23.62
 +
| align="right"| 7.91
 +
|-
 +
! rowspan="5"| J23109
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! J23109
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| align="right"| 18.56
 +
| align="right"| 18.25
 +
| align="right"| 18.50
 +
|-
 +
! J23109_hkg
 +
| align="right"| 5.79
 +
| align="right"| 5.43
 +
| align="right"| 5.91
 +
|-
 +
! ΔCT J23109
 +
| align="right"| 12.77
 +
| align="right"| 12.82
 +
| align="right"| 12.59
 +
|-
 +
! ΔΔCT J23109
 +
| align="right"| 6.26
 +
| align="right"| 6.21
 +
| align="right"| 6.44
 +
|-
 +
! Reinforcment
 +
| align="right"| 76.64
 +
| align="right"| 74.03
 +
| align="right"| 86.82
 +
| align="right"| 79.16
 +
| align="right"| 5.52
 +
|-
 +
! rowspan="5"| J23105
 +
! J23105
 +
| align="right"| 16.05
 +
| align="right"| 16.21
 +
| align="right"| 16.13
 +
|-
 +
! J23105_hkg
 +
| align="right"| 4.98
 +
| align="right"| 5.22
 +
| align="right"| 5.18
 +
|-
 +
! ΔCT J23105
 +
| 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
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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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                        <!-- start content -->
+
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+
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+
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+
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+
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+
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<p></p><div id="header"><img src="http://www.patrickreinke.de/igem/headpicture_2.jpg" alt="Team Goettingen">
+
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<br><br></p><div class="MenuBar" id="navi">
+
-
        <ul>
+
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                <li>
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                        <!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
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                        <li><a href="https://2012.igem.org/Team:Goettingen/Team"><span><span>News</span></span></a></li>
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                </li>
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                        <!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
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                        <ul class="DropDownMenu" id="MB1-DDM5">
+
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                        <li><a href="https://2012.igem.org/Team:Goettingen/Team"><span><span>Members</span></span></a></li>
+
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                        <!--<li><a href="https://2012.igem.org/Team:Goettingen/Team#advisor"><span><span><div style="text-indent:20px;">&#8901; Advisors</div></span></span></a></li> -->
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                        <!--<li><a href="https://2012.igem.org/Team:Goettingen/Team#students"><span><span><div style="text-indent:20px;">&#8901; Students</div></span></span></a></li> -->
+
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                        <!--<li><li><a href="https://2012.igem.org/Team:Goettingen/Team#responsibitlities"><span><span><div style="text-indent:20px;">&#8901; Responsibilities</div></span></span></a></li> -->
+
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                        <li><a href="https://2012.igem.org/Team:Goettingen/Focus_Groups"><span><span>Focus Groups</span></span></a></li>
+
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                        <!--<li><li><a href="https://2012.igem.org/Team:Goettingen/groups#group1"><span><span><div style="text-indent:20px;">&#8901; #1 Selection / Swimming</div></span></span></a></li>  -->
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                        <!--<li><li><a href="https://2012.igem.org/Team:Goettingen/groups#group2"><span><span><div style="text-indent:20px;">&#8901; #2 Speed Improvement</div></span></span></a></li>  -->
+
-
                        <!--<li><li><a href="https://2012.igem.org/Team:Goettingen/groups#group3"><span><span><div style="text-indent:20px;">&#8901; #3 Chemoreceptor</div></span></span></a></li>    -->
+
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                        <!--<li><li><a href="https://2012.igem.org/Team:Goettingen/groups#library"><span><span><div style="text-indent:20px;">&#8901; Library</div></span></span></a></li>            -->
+
-
                        <li><a href="https://2012.igem.org/Team:Goettingen/Seminars"><span><span>Seminars</span></span></a></li>
+
-
                        <!--<li><li><a href="https://2012.igem.org/Team:Goettingen/seminars#announce"><span><span><div style="text-indent:20px;">&#8901; Announcements</div></span></span></a></li>    -->
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-
                        <!--<li><li><a href="https://2012.igem.org/Team:Goettingen/seminars#presentations"><span><span><div style="text-indent:20px;">&#8901; Past Presentations</div></span></span></a></li> -->
+
-
                        <li><a href="https://2012.igem.org/Team:Goettingen/Work_Impressions"><span><span>Work Impressions</span></span></a></li>
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-
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                        <!--[if lte IE 6]></td></tr></table></a><![endif]-->
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                </li>
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                <li>
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                        <a href="https://2012.igem.org/Team:Goettingen/Project" style="color: white;">Project<!--[if gt IE 6]><!--></a><!--<![endif]-->
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                        <!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
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                        <ul class="DropDownMenu" id="MB1-DDM2-SM3">
+
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                        <li><a href="https://2012.igem.org/Team:Goettingen/Project"><span><span>Our Project</span></span></a></li>
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-
                        <!--<li></li><li><a href="https://2012.igem.org/Team:Goettingen/Chemotaxis"><span><span><div style="text-indent:20px;">&#8901; Chemotaxis</div></span></span></a></li>  -->
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-
                        <!--<li></li><li><a href="https://2012.igem.org/Team:Goettingen/Poster"><span><span><div style="text-indent:20px;">&#8901; Poster</div></span></span></a></li>    -->
+
-
                        <li><a href="https://2012.igem.org/Team:Goettingen/Project/Materials"><span><span>Materials</span></span></a>
+
-
                        <li><a href="https://2012.igem.org/Team:Goettingen/Project/Methods"><span><span>Methods</span></span></a>
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-
                        <li><a href="https://2012.igem.org/Team:Goettingen/Project/Computational_Data"><span><span>Computational Data</span></span></a>
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                        <!--</li><li><a href="https://2012.igem.org/Team:Goettingen/Maps"><span><span><div style="text-indent:20px;">&#8901; Maps</div></span></span></a></li>
+
-
                        </li><li><a href="https://2012.igem.org/Team:Goettingen/Sequences"><span><span><div style="text-indent:20px;">&#8901; Sequences</div></span></span></a></li> -->
+
-
                        <li><a href="https://2012.igem.org/Team:Goettingen/Project/Bioinformatical_Tool"><span><span>Bioinformatical Tools</span></span></a>
+
-
                        <li><a href="https://2012.igem.org/Team:Goettingen/Project/Lab_Work_Flow"><span><span>Lab Work Flow</span></span></a>
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-
                        <!--</li><li><a href="https://2012.igem.org/Team:Goettingen/Maps"><span><span><div style="text-indent:20px;">&#8901; Golden Lab Rules</div></span></span></a></li>
+
-
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-
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-
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+
-
 
+
-
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+
-
                        <a href="https://2012.igem.org/Team:Goettingen/Notebook" style="color: white;">Notebook<!--[if gt IE 6]><!--></a><!--<![endif]-->
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-
                        <!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
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                                <ul class="DropDownMenu" id="MB1-DDM2">
+
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                                <li><a href="https://2012.igem.org/Team:Goettingen/Notebook"><span><span>Overview</span></span></a></li>
+
-
                                <li><a href="https://2012.igem.org/Team:Goettingen/Notebook/Summary"><span><span>Summary</span></span></a></li>
+
-
                                <li><a href="https://2012.igem.org/Team:Goettingen/Notebook/Discussion"><span><span>Discussion</span></span></a></li>
+
-
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                                <!--[if lte IE 6]></td></tr></table></a><![endif]-->
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                </li>
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-
                <li>
+
-
                        <a href="https://2012.igem.org/Team:Goettingen/iGEM" style="color: white;">iGEM<!--[if gt IE 6]><!--></a><!--<![endif]-->
+
-
                        <!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
+
-
                                <ul class="DropDownMenu" id="MB1-DDM6">
+
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                                <li><a href="https://2012.igem.org/Team:Goettingen/iGEM"><span><span>What is iGEM?</span></span></a></li>
+
-
                                <!--<li><a href="https://2012.igem.org/Team:Goettingen/BioBrick_System"><span><span>iGEM BioBrick System</span></span></a></li>
+
-
                                <li><a href="https://2012.igem.org/Team:Goettingen/Part_Registry"><span><span>iGEM Part Registry</span></span></a></li>  -->
+
-
                                <li><a href="https://2012.igem.org/Team:Goettingen/iGEM/Parts"><span><span>Parts Submitted</span></span></a></li>
+
-
                                <li><a href="https://2012.igem.org/Team:Goettingen/iGEM/Attributions"><span><span>Attributions</span></span></a></li>
+
-
                                <li><a href="https://2012.igem.org/Team:Goettingen/iGEM/Saftey"><span><span>Saftey</span></span></a></li>>
+
-
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-
                <li>
+
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                        <a href="https://2012.igem.org/Team:Goettingen/Goettingen" style="color: white;">Göttingen<!--[if gt IE 6]><!--></a><!--<![endif]-->
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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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