Team:Goettingen/Project/Bioinformatical Tools

From 2012.igem.org

(Difference between revisions)

Latest revision as of 23:49, 26 September 2012


Home Homepage News Team Members Focus Groups Seminars Work Impressions Project Our Project Results Discussion/Outlook Lab Work Flow Notebook Overview Materials Methods Computational Data Bioinformatical Tools iGEM What is iGEM? Parts Submitted Attributions Safety > Göttingen City University of Göttingen Max-Planck-Institute S1-Demo Lab Human Practice Our Human Practice Projects Public and Media Survey Synthetic Biology Day Panel Discussion Flash Coli Sponsoring Our Sponsors Interested in...?
Deutsch / English

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.

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.

↑ Back to top!

@@ Line 1: / Line 1: @@
-{{GoettingenHeader}}
+{{GoettingenHeader|deu=Team:Goettingen/Project/Bioinformatical Tools|eng=Team:Goettingen/Project/Bioinformatical Tools}}
+{{GoettingenBlue}}
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" dir="ltr" lang="en">
+== Computational Data ==
-<head>
+=== Maps ===
-        <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+==== Tar_QC ====
-        <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">
+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>
-                <link rel="shortcut icon" href="https://2012.igem.org/favicon.ico">
+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>
-                <link rel="search" type="application/opensearchdescription+xml" href="https://2012.igem.org/wiki/opensearch_desc.php" title="2012.igem.org (English)">
+* [https://static.igem.org/mediawiki/2012/f/fc/Tar_receptor_under_the_control_of_constitutive_promoter.zip ApE plasmid maps]
-                <link title="Creative Commons" type="application/rdf+xml" href="https://2012.igem.org/wiki/index.php?title=Team:Goettingen&amp;action=creativecommons" rel="meta">
+*Sequencing results
-                <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">
+**[https://static.igem.org/mediawiki/2012/2/20/K777000_in_pSB1C3.zip K777000 in pSB1C3]
-                <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">
+**[https://static.igem.org/mediawiki/2012/e/e7/K777001_in_pSB1C3.zip K777001 in pSB1C3]
-</head>
+**[https://static.igem.org/mediawiki/2012/9/90/K777002_in_pSB1C3.zip K777002 in pSB1C3]
-<body class="mediawiki ns-0 ltr page-Team_Goettingen">
+**[https://static.igem.org/mediawiki/2012/0/0a/K777003_in_pSB1C3.zip K777003 in pSB1C3]
+**[https://static.igem.org/mediawiki/2012/a/a8/K777004_in_pSB1C3.zip K777004 in pSB1C3]
+**[https://static.igem.org/mediawiki/2012/0/07/K777005_in_pSB1C3.zip K777005 in pSB1C3]
+**[https://static.igem.org/mediawiki/2012/6/61/K777006_in_pSB1C3.zip K777006 in pSB1C3]
+**[https://static.igem.org/mediawiki/2012/3/33/K777007_in_pSB1C3.zip K777007 in pSB1C3]
+**[https://static.igem.org/mediawiki/2012/5/52/K777008_in_pSB1C3.zip K777008 in pSB1C3]
-<font face="Verdana" size="-1">Language: <img height="20", src="http://www.patrickreinke.de/igem/eng.jpg"> English</a> <br>
+==== flhDC ====
+* [https://static.igem.org/mediawiki/2012/b/b6/K777100_in_pSB1C3.zip K777100 in pSB1C3 ApE plasmid map]
-<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>
+==== fliC ====
-<ul>
+* [https://static.igem.org/mediawiki/2012/8/8b/K777109_in_pSB1C3.zip K777109 in pSB1C3 ApE plasmid map]
-<li class="toclevel-1"><a href="#Computational_Data"><span class="tocnumber">1</span> <span class="toctext">Computational Data</span></a></li>
-<li class="toclevel-1"><div style="text-indent:10px;"><a href="#Maps"><span class="tocnumber"></span> <span class="toctext">Maps</span></a></li>
-<li class="toclevel-1"><div style="text-indent:10px;"><a href="#Sequences"><span class="tocnumber"></span> <span class="toctext">Sequences</span></a></li>
-</td></tr></tbody></table>
-<br>
-                                 <!-- Text body -->
+==== motA ====
-<tbody>
+* [https://static.igem.org/mediawiki/2012/3/37/K777113_in_pSB1C3.zip K777113 in pSB1C3 ApE plasmid map]
-<tr valign="top" align="left">
-<td style="padding: 0pt 20px 0pt 0pt;" width="910px">
-<font face="Verdana" size="-1">
-                                 <!-- Ab hier kannst du editieren -->
+==== motB ====
+* [https://static.igem.org/mediawiki/2012/0/09/K777117_in_pSB1C3.zip K777117 in pSB1C3 ApE plasmid map]
-<h2><b><a name="Computational_Data"></a>Computational Data</b></h2>
+==== yhjH ====
-<p align="justify" style="line-height:1.6em">
+* [https://static.igem.org/mediawiki/2012/3/3f/K777121_in_pSB1C3.zip K777121 in pSB1C3 ApE plasmid map]
-<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>
-<ol>
-<li> Tar_QC </li>
-<ul>
-<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>
-<li> Sequencing results</li>
-</ul>
-<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 style="text-indent:40px;"><a href="https://static.igem.org/mediawiki/2012/e/e7/K777001_in_pSB1C3.zip">K777001 in pSB1C3</a><br>
-<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 style="text-indent:40px;"><a href="https://static.igem.org/mediawiki/2012/0/0a/K777003_in_pSB1C3.zip">K777003 in pSB1C3</a><br>
-<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 style="text-indent:40px;"><a href="https://static.igem.org/mediawiki/2012/0/07/K777005_in_pSB1C3.zip">K777005 in pSB1C3</a><br>
-<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 style="text-indent:40px;"><a href="https://static.igem.org/mediawiki/2012/3/33/K777007_in_pSB1C3.zip">K777007 in pSB1C3</a><br>
-<div style="text-indent:40px;"><a href="https://static.igem.org/mediawiki/2012/5/52/K777008_in_pSB1C3.zip">K777008 in pSB1C3</a><br>
-</ol>
-<br>
+==== Constitutive promoter + RFP-constructs ====
+* [https://static.igem.org/mediawiki/2012/0/07/K777125-K777132.zip K777125-K777132 ApE plasmid maps]
+=== Primers ===
+* [https://static.igem.org/mediawiki/2012/4/43/Primer_Mutagenesis.zip Mutagenesis]
+* [https://static.igem.org/mediawiki/2012/f/fc/Primer_PCR.zip PCR]
+* [https://static.igem.org/mediawiki/2012/c/cf/Primer_QC.zip QuikChange]
+* [https://static.igem.org/mediawiki/2012/4/4b/Primer_Sequencing.zip Sequencing]
+* [https://static.igem.org/mediawiki/2012/4/45/Primer_Real-Time.zip Real-time]
-<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>
+=== Raw Datasets ===
-<ol>
+==== Characterization of constitutive promoters by qrtPCR ====
-<li> Biobrick Sequences</li>
-<ul>
-<li></li>
-</ul>
-</ol>
+<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
+! scope="col"|
+! scope="col"| CP1
+! scope="col"| CP2
+! scope="col"| CP3
+! scope="col"| Average
+! scope="col"| Standard variance
+|-
+! rowspan="3"| J23113 <br>(Calibrator)
+! J23113
+| align="right"| 23.7
+| align="right"| 24.46
+| 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
+| 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
+! 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
+! J23109
+| 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
+|}
+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>
-<br>
-<br>
-<body id="top">
-<a href="#top">&uarr; Return to top</a>
-<br>
-<br>
-</body>
-</html>
 {{GoettingenFooter}}