Difference between revisions of "Team:William and Mary/Parts"

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{{William_and_Mary}}
 
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<html>
 
  
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<h2> Part Documentation</h2>
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<html lang="en">
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<cfheader name="X-XSS-Protection" value="1">
 +
    <head>
 +
        <meta charset="utf-8" />
 +
<link rel="icon" type="image/png" href="https://static.igem.org/mediawiki/2015/e/ea/WMFavicon.png">
  
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<p>Each team will make new parts during iGEM and will submit them to the Registry of Standard Biological Parts. The iGEM software provides an easy way to present the parts your team has created. The <code>&lt;groupparts&gt;</code> tag (see below) will generate a table with all of the parts that your team adds to your team sandbox.</p>
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        <meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1" />
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<p>Remember that the goal of proper part documentation is to describe and define a part, so that it can be used without needing to refer to the primary literature. Registry users in future years should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.</p>
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        <title>NOISE - W&M iGEM</title>
 +
        <meta content='width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=0' name='viewport' />
 +
        <link href="https://2015.igem.org/Team:William_and_Mary/bootstrap?action=raw&amp;ctype=text/css" rel="stylesheet" type="text/css"/>
 +
<link href="https://2015.igem.org/Team:Stockholm/fixbootstrap?action=raw&amp;ctype=text/css" rel="stylesheet" type="text/css"/>
 +
        <link href="https://2015.igem.org/Team:William_and_Mary/rubick?action=raw&amp;ctype=text/css" rel="stylesheet" type="text/css"/>
 +
        <link href="https://2015.igem.org/Team:William_and_Mary/demo?action=raw&amp;ctype=text/css" rel="stylesheet" type="text/css"/>
 +
        <link rel="stylesheet" type="text/css" href="https://2015.igem.org/Template:William_and_Mary/jquerybxsliderCSS?action=raw&ctype=text/css" />
  
 +
        <!--    Fonts and icons    -->
 +
        <link href="http://maxcdn.bootstrapcdn.com/font-awesome/4.2.0/css/font-awesome.min.css" rel="stylesheet" type="text/css"/>
 +
        <link href='http://fonts.googleapis.com/css?family=Droid+Serif:400,700' rel='stylesheet' type='text/css'>
 +
        <link href="https://2015.igem.org/Team:William_and_Mary/pe-icon-7-stroke?action=raw&amp;ctype=text/css" rel="stylesheet" type="text/css"/>
 +
        <link href="https://2015.igem.org/Team:William_and_Mary/Rubik-Fonts?action=raw&amp;ctype=text/css" rel="stylesheet" type="text/css"/>
 +
       
 +
<!-- the wiki settings in the section immediately below are from UC San Diego 2015 -->
 +
        <style type="text/css">
 +
/* WIKI SETTINGS*/
 +
 +
/* Hide first heading */
 +
.firstHeading {
 +
display: none;
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}
 +
 +
                /* Visited hyperlinks */
 +
                        a:visited{
 +
                                color: #b9975b;
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                        }
  
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<div class="highlightBox">
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/*-- Remove borders, float content left and remove padding/margin */
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<h4>Note</h4>
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#globalWrapper, #content{
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<p>Note that parts must be documented on the <a href="http://parts.igem.org/Main_Page"> Registry</a>. This page serves to <i>showcase</i> the parts you have made. Future teams and other users and are much more likely to find parts by looking in the Registry than by looking at your team wiki.</p>
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background-color: transparent;
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</div>
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border: none;
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float: center;
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                                width: 101%;
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margin-left: -3px;
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margin-top: -8px;
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padding: auto;
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}
  
 +
/*left align Black Menu Bar */
 +
#top_menu_inside {
 +
margin-left: 0px;
 +
}
 +
</style>
  
 +
    </head>
 +
    <body class="landing-page">
 +
        <nav class="navbar navbar-default navbar-fixed-top navbar-burger" role="navigation">
 +
            <!-- if you want to keep the navbar hidden you can add this class to the navbar "navbar-burger"-->
 +
            <div class="container">
 +
                <div class="navbar-header">
 +
                    <button id="menu-toggle" type="button" class="navbar-toggle" data-toggle="collapse" data-target="#example">
 +
                    <span class="sr-only">Toggle navigation</span>
 +
                    <span class="icon-bar bar1"></span>
 +
                    <span class="icon-bar bar2"></span>
 +
                    <span class="icon-bar bar3"></span>
 +
                    </button>
 +
<a href="https://2015.igem.org/Team:William_and_Mary" class="navbar-brand">W&M iGEM 2015</a>
 +
                </div>
 +
                <div class="collapse navbar-collapse">
 +
                    <ul class="nav navbar-nav navbar-right navbar-uppercase">
 +
<p>    </p>
  
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<h4>Adding parts to the registry</h4>
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                        <li>
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<p>You can add parts to the Registry at our <a href="http://parts.igem.org/Add_a_Part_to_the_Registry">Add a Part to the Registry</a> link.</p>
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                            <a href="https://2015.igem.org/Team:William_and_Mary">  
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<p>We encourage teams to start completing documentation for their parts on the Registry as soon as you have it available. The sooner you put up your parts, the better you will remember all the details about your parts. Remember, you don't need to send us the DNA sample before you create an entry for a part on the Registry. (However, you <b>do</b> need to send us the DNA sample before the Jamboree. If you don't send us a DNA sample of a part, that part will not be eligible for awards and medal criteria.)</p>
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                            Home
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:William_and_Mary/Description">
 +
                            Project Description
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:William_and_Mary#parts">
 +
                            Parts
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:William_and_Mary/Measurement">  
 +
                            Results
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:William_and_Mary/Modeling">  
 +
                            Modeling
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:William_and_Mary/Interlab_Study">
 +
                            Interlab Study
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:William_and_Mary/Collaborations">
 +
                            Collaboration
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:William_and_Mary/Software">
 +
                          Software
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:William_and_Mary/Practices">
 +
                            Human Practices
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:William_and_Mary#ref">
 +
                            References
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:William_and_Mary/Medal_Criteria">
 +
                            Medal Criteria
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href="2015.igem.org/Team:William_and_Mary/Team">
 +
                            Team
 +
                            </a>
 +
                        </li>
 +
                    </ul>
 +
                </div>
 +
            </div>
 +
        </nav>
 +
       
 +
       
 +
        <groupparts>
 +
       
 +
       
 +
       
 +
       
 +
        <div class="wrapper">
 +
       
 +
       
 +
       
 +
            <!--    replace this line with the code generated with the rubik-builder.html              -->
  
 +
                   
 +
                        <!-- Section "Our Projects" example 2: 3 Columns Full Width -->
 +
                        <div class="section section-we-made-1 section-with-hover" id="projects1">
 +
                            <div class="text-area">
 +
                                <div class="title">
 +
                                    <p class="h2WM">All Parts (By Category)</p>
 +
<div class = "description">
 +
                                    <p>This year we submitted 25 parts to the iGEM registry. Browse them below. </div>
 +
</p>
 +
                                </div>
 +
                            </div>
 +
                            <div class="row" id="projectsLine1">
 +
                                <div class="col-md-4">
 +
                                    <div class="project">
 +
                                        <img alt="..." src="https://static.igem.org/mediawiki/2015/b/bf/Wm15integration.jpg">
 +
                                        <a class="over-area color-green" href="javascript:void(0)" onclick="rubik.showModal(this)" data-target="integrator">
 +
                                            <div class="content">
 +
                                                <h4>Integrator Cassette</h4>
 +
                                                <p>Click for details.</p>
 +
                                            </div>
 +
                                        </a>
 +
                                    </div>
 +
                                </div>
  
−
<h4>What information do I need to start putting my parts on the Registry?</h4>
 
−
<p>The information needed to initially create a part on the Registry is:</p>
 
−
<ul>
 
−
<li>Part Name</li>
 
−
<li>Part type</li>
 
−
<li>Creator</li>
 
−
<li>Sequence</li>
 
−
<li>Short Description (60 characters on what the DNA does)</li>
 
−
<li>Long Description (Longer description of what the DNA does)</li>
 
−
<li>Design considerations</li>
 
−
</ul>
 
  
−
<p>
 
−
We encourage you to put up <em>much more</em> information as you gather it over the summer. If you have images, plots, characterization data and other information, please also put it up on the part page. </p>
 
  
  
 +
                                <div class="col-md-4">
 +
                                    <div class="project">
 +
                                        <img alt="..." src="https://static.igem.org/mediawiki/2015/4/4f/Wm15antibiotic.jpg">
 +
                                        <a class="over-area color-green" href="javascript:void(0)" onclick="rubik.showModal(this)" data-target="xfp">
 +
                                            <div class="content">
 +
                                                <h4>XFPs under various promoters</h4>
 +
                                                <p>Click for details.</p>
 +
                                            </div>
 +
                                        </a>
 +
                                    </div>
 +
                                </div>
  
  
  
  
−
<h4>Inspiration</h4>
 
−
<p>We have a created  a <a href="http://parts.igem.org/Well_Documented_Parts">collection of well documented parts</a> that can help you get started.</p>
 
  
−
<p> You can also take a look at how other teams have documented their parts in their wiki:</p>
 
−
<ul>
 
−
<li><a href="https://2014.igem.org/Team:MIT/Parts"> 2014 MIT </a></li>
 
−
<li><a href="https://2014.igem.org/Team:Heidelberg/Parts"> 2014 Heidelberg</a></li>
 
−
<li><a href="https://2014.igem.org/Team:Tokyo_Tech/Parts">2014 Tokyo Tech</a></li>
 
−
</ul>
 
  
 +
                                <div class="col-md-4">
 +
                                    <div class="project">
 +
                                        <img alt="dCas9 Plates" src="https://static.igem.org/mediawiki/2015/3/36/WMdCas9Plates.png">                                   
 +
                                        <a class="over-area color-blue " href="javascript:void(0)" onclick="rubik.showModal(this)" data-target="dcas">
 +
                                            <div class="content">
 +
                                                <h4>dCas9s</h4>
 +
                                                <p>Click for details.</p>
 +
                                            </div>
 +
                                        </a>
 +
                                    </div>
 +
                                </div>
 +
                                <div class="col-md-4">
 +
                                    <div class="project">
 +
                                        <img alt="..." src="https://static.igem.org/mediawiki/2015/f/f7/WMgRNAs3.png">
 +
                                        <a class="over-area color-purple" href="javascript:void(0)" onclick="rubik.showModal(this)" data-target="grna">
 +
                                            <div class="content">
 +
                                                <h4>gRNAs</h4>
 +
                                                <p>Click for details.</p>
 +
                                            </div>
 +
                                        </a>
 +
                                    </div>
 +
                                </div>
  
  
−
<h4>Part Table </h4>
 
−
</html>
 
−
<groupparts>iGEM015 Example</groupparts>
 
−
<html>
 
  
 +
                                <div class="col-md-4">
 +
                                    <div class="project">
 +
                                        <img alt="..." src="https://static.igem.org/mediawiki/2015/c/cf/Wm15repression.jpg">
 +
                                        <a class="over-area color-black" href="javascript:void(0)" onclick="rubik.showModal(this)" data-target="antibiotic">
 +
                                            <div class="content">
 +
                                                <h4>Antibiotic Operon</h4>
 +
                                                <p>Click for details.</p>
 +
                                            </div>
 +
                                        </a>
 +
                                    </div>
 +
                                </div>
  
  
−
</div>
+
 
 +
                                <div class="col-md-4">
 +
                                    <div class="project">
 +
                                        <img alt="..." src="https://static.igem.org/mediawiki/2015/3/3c/WMG2.png">
 +
                                        <a class="over-area color-gold" href="javascript:void(0)" onclick="rubik.showModal(this)" data-target="g2">
 +
                                            <div class="content">
 +
                                                <h4>Dual Fluorescent Plasmid</h4>
 +
                                                <p>Click for details.</p>
 +
                                            </div>
 +
                                        </a>
 +
                                    </div>
 +
                                </div>
 +
                            </div>
 +
                        </div>
 +
                        <!-- End Section "Our Projects" example 2: 3 Columns Full Width -->
 +
                     
 +
       
 +
       
 +
        <!--  Here are the examples of the content for each project that is viewed inside of the page. You can create how many projects you want if you set the specific #id     
 +
        -->
 +
       
 +
        <div class="project-content" id="integrator">
 +
          <div>
 +
            <div class="project-details">
 +
              <span class="icon-close"><i class="pe-7s-close-circle"></i></span>
 +
              <div class="container">
 +
                <div class="project-title">
 +
                  <p class "h2WM">Integrator Cassette</p>
 +
                    <p class="large"><a href = "https://2015.igem.org/Team:William_and_Mary/Composite_Part"> The Composite Part</a></p>
 +
                </div>
 +
                <div class="row">
 +
                  <div class="col-md-6">
 +
                    <div class="project-text">
 +
                      <p><span><a href = "http://parts.igem.org/Part:BBa_K1795023">BBa_K1795023</a></span></p>
 +
                      <br>
 +
                      <p>For our method of <a href = "https://2015.igem.org/Team:William_and_Mary/Protocols:Integration">genome integration</a> the input is linear DNA, generated by PCR, containing what you would like to integrate onto the genome and an antibiotic resistance cassette to allow for selection. The galK Integrator allows digestion with the standard BioBrick enzymes and 3A assembly of your part of interest to create the integration construct (see right).
 +
 
 +
This product can then be amplified using primers (<a href = "https://2015.igem.org/Team:William_and_Mary/Protocols:Integration">details found here</a>) and then used in the integration protocol. We have successfully used the integrator to incorporate stretches of DNA up to 2.1kb into the galK locus, not including the resistance cassette (1179 bp).</p>
 +
                    </div>
 +
                  </div>
 +
                  <div class="col-md-6">
 +
                    <div>
 +
                        <div>
 +
                            <div class="project-image">
 +
                              <img alt="..." src="https://static.igem.org/mediawiki/2015/b/ba/WMIntegratorDiagram.png"/>
 +
                            </div>
 +
                        </div>
 +
                    </div>
 +
                  </div>
 +
                </div>
 +
              </div>
 +
            </div>
 +
          </div>
 +
        </div>
 +
 
 +
              <div class="project-content" id="antibiotic">
 +
          <div>
 +
            <div class="project-details">
 +
              <span class="icon-close"><i class="pe-7s-close-circle"></i></span>
 +
              <div class="container">
 +
                <div class="project-title">
 +
                    <p class "h2WM">Antibiotic Operon</p>
 +
                </div>
 +
                <div class="row">
 +
                  <div class="col-md-4">
 +
                    <div class="project-text">
 +
                      <p><span><a href = "http://parts.igem.org/Part:BBa_K1795024">BBa_K1795024</a></span></p>
 +
                      <br>
 +
                      <p>Provides Kanamycin Resistance to the cell under the Promoter R0010.</p>
 +
                    </div>
 +
                  </div>
 +
                  <div class="col-md-8">
 +
                    <div class="row">
 +
                        <div class="col-md-6">
 +
                            <div class="project-image">
 +
                              <img alt="..." src="https://static.igem.org/mediawiki/2015/4/4a/WMFKanRMap.png"/>
 +
                            </div>
 +
                        </div>
 +
                    </div>
 +
                  </div>
 +
                </div>
 +
              </div>
 +
            </div>
 +
          </div>
 +
        </div>
 +
 
 +
 
 +
              <div class="project-content" id="dcas">
 +
          <div>
 +
            <div class="project-details">
 +
              <span class="icon-close"><i class="pe-7s-close-circle"></i></span>
 +
              <div class="container">
 +
                <div class="project-title">
 +
                    <p class "h2WM">dCas9s</p>
 +
<p class="large"><a href = "https://2015.igem.org/Team:William_and_Mary/Basic_Part"> The Basic Part</a></p>
 +
                </div>
 +
 
 +
                <div class="row">
 +
                  <div class="col-md-6">
 +
                    <div class="project-text">
 +
                      <p><span><a href = "http://parts.igem.org/Part:BBa_K1795000">BBa_K1795000</a></span></p>
 +
                      <p><span><a href = "http://parts.igem.org/Part:BBa_K1795001">BBa_K1795001</a></span></p>
 +
                      <br>
 +
                      <p>Part BBa_K1795000 is a dCas9 protein-coding region that has been optimized for expression in <i>E. coli</i>. Additionally, we created a functional dCas9 operon (<a href="http://parts.igem.org/Part:BBa_K1795001">BBa_K1795001</a>) that, when transformed into <i>E. coli</i> is constitutively expressed.  For further details, please see our <a href="https://2015.igem.org/Team:William_and_Mary/Basic_Part">Basic Part</a> page.</p>
 +
                    </div>
 +
                  </div>
 +
                  <div class="col-md-6">
 +
                    <div class="row">
 +
                            <div class="project-image">
 +
                              <img alt="..." src="https://static.igem.org/mediawiki/2015/1/10/WMFdCas9Map.png"/>
 +
                            </div>
 +
                        </div>
 +
                    </div>
 +
                  </div>
 +
                </div>
 +
              </div>
 +
            </div>
 +
          </div>
 +
        </div>
 +
 
 +
 
 +
              <div class="project-content" id="grna">
 +
          <div>
 +
            <div class="project-details">
 +
              <span class="icon-close"><i class="pe-7s-close-circle"></i></span>
 +
              <div class="container">
 +
                <div class="project-title">
 +
                    <p class "h2WM">gRNAs</p>
 +
<p class="large"><a href = "https://2015.igem.org/Team:William_and_Mary/Part_Collections">The Part Collection</a></p>
 +
                </div>
 +
                <div class="row">
 +
                  <div class="col-md-6">
 +
                    <div class="project-text">
 +
                      <p><span><a href ="http://parts.igem.org/Part:BBa_K1795002">Part:BBa_K17950002</a></span> R0010 gRNA</p>
 +
                      <p><span><a href ="http://parts.igem.org/Part:BBa_K1795003">Part:BBa_K17950003</a></span>R0051 gRNA</p>
 +
                      <p><span><a href ="http://parts.igem.org/Part:BBa_K1795004">Part:BBa_K17950004</a></span>R0062 gRNA</p>
 +
                      <p><span><a href ="http://parts.igem.org/Part:BBa_K1795005">Part:BBa_K17950005</a></span>R0011 gRNA</p>
 +
<p><span><a href ="http://parts.igem.org/Part:BBa_K1795006">Part:BBa_K17950006</a></span>J23100 gRNA</p>
 +
<p><span><a href ="http://parts.igem.org/Part:BBa_K1795007">Part:BBa_K17950007</a></span>J23101 gRNA</p>
 +
<p><span><a href ="http://parts.igem.org/Part:BBa_K1795008">Part:BBa_K17950008</a></span>J23106 gRNA</p>
 +
<p><span><a href ="http://parts.igem.org/Part:BBa_K1795009">Part:BBa_K17950009</a></span>J23117 gRNA</p>
 +
<p><span><a href ="http://parts.igem.org/Part:BBa_K1795010">Part:BBa_K17950010</a></span>J23119 gRNA</p>
 +
<p><span><a href ="http://parts.igem.org/Part:BBa_K1795011">Part:BBa_K17950011</a></span>I13453 gRNA</p>
 +
<p><span><a href ="http://parts.igem.org/Part:BBa_K1795012">Part:BBa_K17950012</a></span>I0500 gRNA</p>
 +
<p><span><a href ="http://parts.igem.org/Part:BBa_K1795013">Part:BBa_K17950013</a></span>Scrambled gRNA</p>
 +
                      <br>
 +
                     
 +
                    </div>
 +
                  </div>
 +
                  <div class="col-md-6">
 +
                    <div class="row">
 +
                            <div class="project-image">
 +
                              <img alt="..." src="https://static.igem.org/mediawiki/2015/6/6a/WMgRNAMap.png"/>
 +
                        </div>
 +
                       
 +
                    </div>
 +
<p>To complete our creation of a codon-optimized dCas9 parts, we created functional gRNAs that target the most commonly used promoters in iGEM. These parts (BBa_K1795002- BBa_K1795012), when transformed into <i>E. coli</i>, constitutively express gRNA that, in complex with our dCas9 variant, will repress transcription of the targeted promoter.  We have also contributed a Scrambled gRNA (<a href ="http://parts.igem.org/Part:BBa_K17950013">Part:BBa_K17950013</a>) that does not target any region in the <i>E. coli</i> genome and can be used as a negative control. For further details about our gRNAs, please see our <a href = "https://2015.igem.org/Team:William_and_Mary/Part_Collection">Part Collection</a> page.
 +
</p>
 +
                  </div>
 +
                </div>
 +
              </div>
 +
            </div>
 +
          </div>
 +
        </div>
 +
       
 +
 
 +
              <div class="project-content" id="xfp">
 +
          <div>
 +
            <div class="project-details">
 +
              <span class="icon-close"><i class="pe-7s-close-circle"></i></span>
 +
              <div class="container">
 +
                <div class="project-title">
 +
                    <p class "h2WM">CFPs/YFPs Under Various Promoters</p>
 +
                </div>
 +
                <div class="row">
 +
                  <div class="col-md-6">
 +
                    <div class="project-text">
 +
                      <p><span><a href ="http://parts.igem.org/Part:BBa_K1795014">Part:BBa_K1795014</a></span>YFP-LVA under R0040</p>
 +
                      <p><span><a href ="http://parts.igem.org/Part:BBa_K1795015">Part:BBa_K1795015</a></span>CFP-LVA under R0011</p>
 +
                      <p><span><a href ="http://parts.igem.org/Part:BBa_K1795016">Part:BBa_K1795016</a></span>YFP-LVA under R0011</p>
 +
                      <p><span><a href ="http://parts.igem.org/Part:BBa_K1795017">Part:BBa_K1795017</a></span>YFP-LVA under R0062</p>
 +
<p><span><a href ="http://parts.igem.org/Part:BBa_K1795018">Part:BBa_K1795018</a></span>CFP-LVA under I13453</p>
 +
<p><span><a href ="http://parts.igem.org/Part:BBa_K1795019">Part:BBa_K1795019</a></span>YFP-LVA under I13453</p>
 +
<p><span><a href ="http://parts.igem.org/Part:BBa_K1795020">Part:BBa_K1795020</a></span>CFP-LVA under R0051</p>
 +
<p><span><a href ="http://parts.igem.org/Part:BBa_K1795021">Part:BBa_K1795021</a></span>CFP-LVA under I0500</p>
 +
                      <br>
 +
                     
 +
                    </div>
 +
                  </div>
 +
                  <div class="col-md-6">
 +
                    <div class="row">
 +
                            <div class="project-image">
 +
                              <img alt="..." src="https://static.igem.org/mediawiki/2015/c/cd/WMCFPMapExample.png"/>
 +
                            </div>
 +
                    </div>
 +
<p>In order to test multiple promoters for their intrinsic noise, we needed to construct composite parts that had the structure seen to the right.
 +
 
 +
In each construct the <a href="http://parts.igem.org/Part:BBa_B0034">RBS</a> and <a href="http://parts.igem.org/Part:BBa_B0015">DT</a> were kept constant throughout, but the promoter used to drive transcription was changed. Each construct was made in a CFP and YFP variant. Both the <a href="http://parts.igem.org/Part:BBa_E0022">CFP</a> and <a href="http://parts.igem.org/Part:BBa_E0032">YFP</a> used in this project have an LVA tag, decreasing the half-life of the protein. All of these parts have been sequenced confirmed and functionally validated.</p>
 +
                  </div>
 +
                </div>
 +
              </div>
 +
            </div>
 +
          </div>
 +
        </div>
 +
 
 +
 
 +
              <div class="project-content" id="g2">
 +
          <div>
 +
            <div class="project-details">
 +
              <span class="icon-close"><i class="pe-7s-close-circle"></i></span>
 +
              <div class="container">
 +
                <div class="project-title">
 +
                    <p class "h2WM">Dual Fluorescent Plasmid</p>
 +
                </div>
 +
                <div class="row">
 +
                  <div class="col-md-4">
 +
                    <div class="project-text">
 +
                      <p><span><a href = "http://parts.igem.org/Part:BBa_K1795022">Part:BBa_K1795022</a></span></p>
 +
                      <br>
 +
                      <p>This plasmid consists of both a CFP-LVA driven by R0010 and YFP-LVA driven by R0010. This allows future teams to use this part to investigate transcriptional noise either on a low copy number plasmid or by integrating this part using our <a href= "http://parts.igem.org/Part:BBa_K1795023">galK integrator</a>. </p>
 +
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                              <img alt="..." src="https://static.igem.org/mediawiki/2015/2/2f/WMG2PlasmidMap.png"/>
 +
                        </div>
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Latest revision as of 04:45, 21 November 2015

NOISE - W&M iGEM

Integrator Cassette

The Composite Part

BBa_K1795023


For our method of genome integration the input is linear DNA, generated by PCR, containing what you would like to integrate onto the genome and an antibiotic resistance cassette to allow for selection. The galK Integrator allows digestion with the standard BioBrick enzymes and 3A assembly of your part of interest to create the integration construct (see right). This product can then be amplified using primers (details found here) and then used in the integration protocol. We have successfully used the integrator to incorporate stretches of DNA up to 2.1kb into the galK locus, not including the resistance cassette (1179 bp).

...

Antibiotic Operon

BBa_K1795024


Provides Kanamycin Resistance to the cell under the Promoter R0010.

...

dCas9s

The Basic Part

BBa_K1795000

BBa_K1795001


Part BBa_K1795000 is a dCas9 protein-coding region that has been optimized for expression in E. coli. Additionally, we created a functional dCas9 operon (BBa_K1795001) that, when transformed into E. coli is constitutively expressed. For further details, please see our Basic Part page.

...

gRNAs

The Part Collection

Part:BBa_K17950002 R0010 gRNA

Part:BBa_K17950003R0051 gRNA

Part:BBa_K17950004R0062 gRNA

Part:BBa_K17950005R0011 gRNA

Part:BBa_K17950006J23100 gRNA

Part:BBa_K17950007J23101 gRNA

Part:BBa_K17950008J23106 gRNA

Part:BBa_K17950009J23117 gRNA

Part:BBa_K17950010J23119 gRNA

Part:BBa_K17950011I13453 gRNA

Part:BBa_K17950012I0500 gRNA

Part:BBa_K17950013Scrambled gRNA


...

To complete our creation of a codon-optimized dCas9 parts, we created functional gRNAs that target the most commonly used promoters in iGEM. These parts (BBa_K1795002- BBa_K1795012), when transformed into E. coli, constitutively express gRNA that, in complex with our dCas9 variant, will repress transcription of the targeted promoter. We have also contributed a Scrambled gRNA (Part:BBa_K17950013) that does not target any region in the E. coli genome and can be used as a negative control. For further details about our gRNAs, please see our Part Collection page.

CFPs/YFPs Under Various Promoters

Part:BBa_K1795014YFP-LVA under R0040

Part:BBa_K1795015CFP-LVA under R0011

Part:BBa_K1795016YFP-LVA under R0011

Part:BBa_K1795017YFP-LVA under R0062

Part:BBa_K1795018CFP-LVA under I13453

Part:BBa_K1795019YFP-LVA under I13453

Part:BBa_K1795020CFP-LVA under R0051

Part:BBa_K1795021CFP-LVA under I0500


...

In order to test multiple promoters for their intrinsic noise, we needed to construct composite parts that had the structure seen to the right. In each construct the RBS and DT were kept constant throughout, but the promoter used to drive transcription was changed. Each construct was made in a CFP and YFP variant. Both the CFP and YFP used in this project have an LVA tag, decreasing the half-life of the protein. All of these parts have been sequenced confirmed and functionally validated.

Dual Fluorescent Plasmid

Part:BBa_K1795022


This plasmid consists of both a CFP-LVA driven by R0010 and YFP-LVA driven by R0010. This allows future teams to use this part to investigate transcriptional noise either on a low copy number plasmid or by integrating this part using our galK integrator.

...