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

 
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                         <li>
 
                         <li>
 
                             <a href="https://2015.igem.org/Team:William_and_Mary/Measurement">  
 
                             <a href="https://2015.igem.org/Team:William_and_Mary/Measurement">  
−
                             Measurement
+
                             Results
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:William_and_Mary/Modeling">
 +
                            Modeling
 
                             </a>
 
                             </a>
 
                         </li>
 
                         </li>
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                             <a href="https://2015.igem.org/Team:William_and_Mary/Practices">  
 
                             <a href="https://2015.igem.org/Team:William_and_Mary/Practices">  
 
                             Human Practices
 
                             Human Practices
−
                            </a>
 
−
                        </li>
 
−
                        <li>
 
−
                            <a href="http://issuu.com/wmigem/docs/wmigemsynbiodraft150806">
 
−
                            Curriculum on ISSUU.com
 
 
                             </a>
 
                             </a>
 
                         </li>
 
                         </li>
 
                         <li>
 
                         <li>
 
                             <a href="https://2015.igem.org/Team:William_and_Mary#ref">  
 
                             <a href="https://2015.igem.org/Team:William_and_Mary#ref">  
−
                             Notebook, Safety, & Attributions
+
                             References
 
                             </a>
 
                             </a>
 
                         </li>
 
                         </li>
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                             <a href="https://2015.igem.org/Team:William_and_Mary/Medal_Criteria">  
 
                             <a href="https://2015.igem.org/Team:William_and_Mary/Medal_Criteria">  
 
                             Medal Criteria
 
                             Medal Criteria
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:William_and_Mary/Team">
 +
                            Team
 
                             </a>
 
                             </a>
 
                         </li>
 
                         </li>
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                                       <div class="card animate">
 
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                                           <div class="icon">
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                                               <img alt="..." src="https://static.igem.org/mediawiki/2015/c/c7/WMGibsonIconColor.png" height= "100" width= "200"/>
+
                                               <a href = "https://2015.igem.org/Team:William_and_Mary/Protocols:Gibson"><img alt="..." src="https://static.igem.org/mediawiki/2015/c/c7/WMGibsonIconColor.png" height= "100" width= "200"/></a>
 
                                           </div>
 
                                           </div>
−
                                           <h3>Gibson Assembly</h3>
+
                                           <a href = "https://2015.igem.org/Team:William_and_Mary/Protocols:Gibson"><h3>Gibson Assembly</h3></a>
 
                                           <p>For building constructs </p>
 
                                           <p>For building constructs </p>
 
                                       </div>
 
                                       </div>
 
                                   </div>
 
                                   </div>
 +
                                 
 
                                   <div class="col-md-3">
 
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                                       <div class="card animate">
 
                                           <div class="icon">
 
                                           <div class="icon">
−
                                               <img alt="..." src="https://static.igem.org/mediawiki/2015/6/64/WMIntegrationIconColor.png" height= "100" width= "135" />
+
                                               <a href = "https://2015.igem.org/Team:William_and_Mary/Protocols:Imaging"><img alt="..." src="https://static.igem.org/mediawiki/2015/7/7c/WMMicroscopeIconColor.png" height= "100" width= "100"/></a>
 
                                           </div>
 
                                           </div>
−
                                           <h3>Integration</h3>
+
                                           <a href = "https://2015.igem.org/Team:William_and_Mary/Protocols:Imaging"><h3>Imaging</h3></a>
−
                                           <p>Integrating onto the E. coli genome</p>
+
                                           <p>Visualizing fluorescent bacteria</p>
 
                                       </div>
 
                                       </div>
 
                                   </div>
 
                                   </div>
−
                                  <div class="col-md-3">
+
<div class="col-md-3">
 
                                       <div class="card animate">
 
                                       <div class="card animate">
 
                                           <div class="icon">
 
                                           <div class="icon">
−
                                              <img alt="..." src="https://static.igem.org/mediawiki/2015/7/7c/WMMicroscopeIconColor.png" height= "100" width= "120"/>
+
                                          <a href = "https://2015.igem.org/Team:William_and_Mary/Protocols:Integration"><img alt="..." src="https://static.igem.org/mediawiki/2015/6/64/WMIntegrationIconColor.png" height= "100" width= "135" /></a>
 
                                           </div>
 
                                           </div>
−
                                           <h3>Imaging</h3>
+
                                           <a href = "https://2015.igem.org/Team:William_and_Mary/Protocols:Integration"><h3>Integration</h3></a>
−
                                           <p>Visualizing fluorescent bacteria</p>
+
                                           <p>Integrating onto the E. coli genome</p>
 
                                       </div>
 
                                       </div>
 
                                   </div>
 
                                   </div>
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                                       <div class="card animate">
 
                                       <div class="card animate">
 
                                           <div class="icon">
 
                                           <div class="icon">
−
                                               <img alt="..." src="https://static.igem.org/mediawiki/2015/1/18/WMElectroporationIconColor.png" height= "100" width= "120"/>
+
                                               <a href = "https://2015.igem.org/Team:William_and_Mary/Protocols:dCas9"><img alt="..." src="https://static.igem.org/mediawiki/2015/1/18/WMElectroporationIconColor.png" height= "100" width= "120"/><a>
 
                                           </div>
 
                                           </div>
−
                                           <h3>Promoter Repression</h3>
+
                                           <a href = "https://2015.igem.org/Team:William_and_Mary/Protocols:dCas9"><h3>Repression</h3></a>
 
                                           <p>Repressing with dCas9</p>
 
                                           <p>Repressing with dCas9</p>
 
                                       </div>
 
                                       </div>
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<!-- Section "Our Projects" example 1: 2 Columns Full Width -->
 
<!-- Section "Our Projects" example 1: 2 Columns Full Width -->
 
                       <div class="section section-we-made-1 section-with-hover" id="projects1">
 
                       <div class="section section-we-made-1 section-with-hover" id="projects1">
−
                           <div class="text-area">
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                           <div class="text-area" style="padding-top: 0px; padding-bottom: 30px;">
 
                               <div class="title">
 
                               <div class="title">
 
                                   <p class="h2WM">Monthly Timeline</p>
 
                                   <p class="h2WM">Monthly Timeline</p>
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                                       <a class="over-area color-black" href="javascript:void(0)" onclick="rubik.showModal(this)" data-target="project_1">
 
                                       <a class="over-area color-black" href="javascript:void(0)" onclick="rubik.showModal(this)" data-target="project_1">
 
                                           <div class="content">
 
                                           <div class="content">
−
                                               <h4>June</h4>
+
                                               <h3>June</h3>
 
                                               <p>Click for details.</p>
 
                                               <p>Click for details.</p>
 
                                           </div>
 
                                           </div>
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                                       <a class="over-area color-black " href="javascript:void(0)" onclick="rubik.showModal(this)" data-target="project_2">
 
                                       <a class="over-area color-black " href="javascript:void(0)" onclick="rubik.showModal(this)" data-target="project_2">
 
                                           <div class="content">
 
                                           <div class="content">
−
                                               <h4>July</h4>
+
                                               <h3>July</h3>
 
                                               <p>Click for details.</p>
 
                                               <p>Click for details.</p>
 
                                           </div>
 
                                           </div>
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                                       <a class="over-area color-black " href="javascript:void(0)" onclick="rubik.showModal(this)" data-target="project_3">
 
                                       <a class="over-area color-black " href="javascript:void(0)" onclick="rubik.showModal(this)" data-target="project_3">
 
                                           <div class="content">
 
                                           <div class="content">
−
                                               <h4>August</h4>
+
                                               <h3>August</h3>
 
                                               <p>Click for details.</p>
 
                                               <p>Click for details.</p>
 
                                           </div>
 
                                           </div>
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                                   <div class="project">
 
                                   <div class="project">
 
                                       <img alt="..." src="https://static.igem.org/mediawiki/2015/4/41/WMSeptember.jpg">
 
                                       <img alt="..." src="https://static.igem.org/mediawiki/2015/4/41/WMSeptember.jpg">
−
                                       <a class="over-area color-black " href="javascript:void(0)" onclick="rubik.showModal(this)" data-target="project_3">
+
                                       <a class="over-area color-black " href="javascript:void(0)" onclick="rubik.showModal(this)" data-target="september">
 
                                           <div class="content">
 
                                           <div class="content">
−
                                               <h4>September</h4>
+
                                               <h3>September</h3>
 
                                               <p>Click for details.</p>
 
                                               <p>Click for details.</p>
 
                                           </div>
 
                                           </div>
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−
<footer class="footer footer-color-black" data-color="black">
+
 
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                            <div class="container">
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                                <nav class="pull-left navbar-burger">
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                                    <ul>
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                                        <li>
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                                            <a href="https://2015.igem.org/Team:William_and_Mary">
+
−
                                                Home
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                                            </a>
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                                        </li>
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                                        <li>
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                                            <a href="mailto:igem@wm.edu">
+
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                                                Contact
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                                            </a>
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                                        </li>
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                                        <li>
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                                            <a href="wmigem.weebly.com">
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                                              Blog
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                                            </a>
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                                        </li>
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                                    </ul>
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                                </nav>
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                                <div class="social-area pull-right">               
+
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                                    <a class="btn btn-social btn-facebook btn-simple">
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                                        <i class="fa fa-facebook-square"></i>
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                                    </a>
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                                    <a class="btn btn-social btn-twitter btn-simple">
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                                        <i class="fa fa-twitter"></i>
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                                    </a>
+
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                                </div>
+
−
                                <div class="copyright">
+
−
                                    © 2015 William & Mary iGEM
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                                </div>
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                            </div>
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                        </footer>
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         </div>
 
         </div>
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               <div class="container">
 
               <div class="container">
 
                 <div class="project-title">
 
                 <div class="project-title">
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                     <h5>Project Content<span>.</span></h5>
+
                     <h1>June</h1>
−
                    <h2>Example No.1</h2>
+
 
                     <div class="separator-container">
 
                     <div class="separator-container">
 
                       <div class="separator line-separator">✻</div>
 
                       <div class="separator line-separator">✻</div>
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                 </div>
 
                 <div class="row">
 
                 <div class="row">
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                   <div class="col-md-4">
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                   <div class="col-md-12">
 
                     <div class="project-text">
 
                     <div class="project-text">
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                       <p><span>Detail</span>1</p>
+
                       <h3>Week 1 (6/1-6/7)</h3>
−
                      <p><span>Detail</span>2</p>
+
<ul type="circle">
−
                      <p><span>Detail</span>3</p>
+
<li>Resuspended all parts from the kit</li>
−
                      <p><span>Detail</span>4</p>
+
<li>Designed Gibson assemblies to put various fluorescent proteins under the control of the same promoter, to get noise measurements</li>
−
                      <br>
+
<li>Began performing Gibson PCRs</li>
−
                      <p>Not him old music think his found enjoy merry. Listening acuteness dependent at or an. Apartments thoroughly unsatiable terminated sex how themselves. She are ten hours wrong walls stand early. Domestic perceive on an ladyship extended received do. Why jennings our whatever his learning gay perceive. Is against no he without subject. Bed connection unreserved preference partiality not unaffected. Years merit trees so think in hoped we as.</p>
+
</ul>
−
                      <p>Improved own provided blessing may peculiar domestic. Sight house has sex never. No visited raising gravity outward subject my cottage mr be. Hold do at tore in park feet near my case. Invitation at understood occasional sentiments insipidity inhabiting in. Off melancholy alteration principles old. Is do speedily kindness properly oh. Respect article painted cottage he is offices parlors. </p>
+
<h3>Week 2 (6/8-6/14)</h3>
 +
<ul type="circle">
 +
<li>Troubleshot Gibson PCRs</li>
 +
<li>Attempted first Gibson assembly</li>
 +
<li>Designed Gibson assemblies to put together different fluorescent proteins, each under the control of the same promoter</li>
 +
<li>Attempted to Gibson assemble YFP + CFP under control of R0010</li></ul>
 +
<h3>Week 3 (6/15-6/21)</h3>
 +
<ul type="circle">
 +
<li>Re-attempted Gibson assembly to make a double fluorescent construct with proteins under R0010</li>
 +
<li>Began assembling parts for the Interlab Study</li>
 +
<li>Received gBlocks to assemble dCas9 and some preliminary gRNAs</li>
 +
<li>Began assembling dCas9 and gRNAs</li>
 +
<li>Began learning how to use confocal microscopy</li>
 +
<li>Began assembling different promoters with our fluorescent constructs (to eventually collect noise data for each promoter)</li>
 +
<li>Designed and started the assembly process to make KanR (necessary to integrate parts onto the E. coli genome)</li></ul>
 +
<h3>Week 4 (6/22-6/28)</h3>
 +
<ul type="circle"><li>Many of our past assemblies (dCas9, double fluorescent constructs, etc) failed. We continued attempts at these assemblies.</li></ul>
 +
</p>
 +
                   
 
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                 <div class="project-title">
 
                 <div class="project-title">
−
                   <h2>Example No.2</h2>
+
                   <h1>July</h1>
 
                   <div class="separator-container">
 
                   <div class="separator-container">
 
                       <div class="separator line-separator">✻</div>
 
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                     </div>
 
                     </div>
−
                    <p>We've been working with Kingsman Studios and we are proud that they enjoy our results.</p>
+
                 
 
                 </div>
 
                 </div>
 
                 <div class="row">
 
                 <div class="row">
−
                   <div class="col-md-10 col-md-offset-1">
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                       <div class="project-text">
 
                       <div class="project-text">
−
                           <h3>Turnip greens yarrow ricebean rutabaga endive cauliflower sea lettuce<span>.</span></h3>
+
                           <h3>Week 1 (6/29-7/5)</h3>
−
                          <p>Not him old music think his found enjoy merry. Listening acuteness dependent at or an. Apartments thoroughly unsatiable terminated sex how themselves. She are ten hours wrong walls stand early. Domestic perceive on an ladyship extended received do. Why jennings our whatever his learning gay perceive. Is against no he without subject. Bed connection unreserved preference partiality not unaffected. Years merit trees so think in hoped we as.</p>
+
<ul type="circle"><li>We have assembled our gRNAs and dCas9!</li>
−
                      <p>Improved own provided blessing may peculiar domestic. Sight house has sex never. No visited raising gravity outward subject my cottage mr be. Hold do at tore in park feet near my case. Invitation at understood occasional sentiments insipidity inhabiting in. Off melancholy alteration principles old. Is do speedily kindness properly oh. Respect article painted cottage he is offices parlors<span>.</span></p>
+
<li>We ordered primers to integrate onto the E. coli genome</li>
 +
<li>Designed assembly to put a KanR operon after a fluorescent construct to integrate</li>
 +
<li>Designed a better way to assemble double fluorescent constructs</li>
 +
<li>Designed a way to make a TetR operon to integrate two different things</li>
 +
<li>Made electrocompetent cells containing our dCas9 operon</li>
 +
<li>Assembled a double fluorescent construct! CFP and YFP under R0010</li>
 +
<li>Attempted our first double electroporation-transformation to test our dCas9 and gRNAs</li></ul>
 +
<h3>Week 2 (7/6-7/12)</h3>
 +
<ul type="circle"><li>Began assembling CFP and YFP operons with each promoter that we wanted to test</li>
 +
<li>Confirmed that dCas9 and our gRNA design works</li>
 +
<li>Assembled the CFP under R0010 with KanR, so that it can be PCR’d with the integration PCRs, and integrated</li>
 +
<li>Attempted to make TetR operon</li></ul>
 +
<h3>Week 3 (7/13-7/19)</h3>
 +
<ul type="circle"><li>Attempted to test our integration protocol, by integrating KanR onto the E. coli genome</li>
 +
<li>Continued attempting to construct Interlab Parts</li>
 +
<li>Worked on our collaboration with UGA</li>
 +
<li>Designed gRNAs for other promoters to create a suite of repression parts</li>
 +
<li>Continued assembling CFP and YFP operons with promoters of interest</li>
 +
<li>Continued attempts to make TetR operon</li></ul>
 +
<h3>Week 4 (7/20-7/26)</h3>
 +
<ul type="circle"><li>Began testing integrator cassette part</li>
 +
<li>Continued working on Interlab Study</li>
 +
<li>Continued assembling CFP and YFP operons</li>
 +
<li>Continued attempts to make TetR operon</li></ul>
 +
<h3>Week 5 (7/26-8/2)</h3>
 +
<ul type="circle"><li>Ordered gBlocks for Interlab Study</li>
 +
<li>Continued working on assembling all gRNA parts</li>
 +
<li>Continued assembling CFP and YFP operons</li>
 +
<li>Imaged our single integrated fluorescent CFP (under R0010)</li>
 +
<li>Continued attempts to make TetR operon</li></ul>
 +
</p>
 
                       </div>
 
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−
                  <h5 >Project Content</h5>
+
                     <h1>August</h1>
−
                     <h2>Example No.3</h2>
+
 
                     <div class="separator-container">
 
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+
                       <div class="project-text">
−
                           <p>Pencil’s certified Bluetooth Smart wireless delivers a fast, stable connection with industry-leading power conservation</p>
+
                           <h3>Week 1 (8/3-8/9)</h3>
−
                          <p>Each Pencil is milled from a single, solid piece of material. Graphite brushed aluminum model shown.</p>
+
<ul type="circle"><li>Continued assembling CFP and YFP operons</li>
 +
<li>Began assembling CFP operons with KanR (to integrate)</li>
 +
<li>Continued attempts to make TetR operon</li></ul><br>
 +
<h2>8/10-8/23: School mandates that we leave</h2>
 +
<ul type="circle"><li>During this time, we learned that TetR had been mislabelled, and the part we were actually looking to assemble to confer tetracycline resistance was “TetA”</li>
 +
<li>We designed PCRs to assemble TetA</li></ul><br>
 +
<h3>Week 4 (8/24-8/30)</h3>
 +
<ul type="circle"><li>Continued working on Interlab Study</li>
 +
<li>Began assembling YFP operons with TetA (to integrate)</li>
 +
<li>Began attempts to integrate YFP operons with TetA for which there was a corresponding CFP operon with KanR</li>
 +
</ul>
 
                       </div>
 
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+
                          
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                          <img alt="..." src="assets/img/rubik_background3.png"/>
+
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+
 
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+
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                       <div class="project-text">
 
                       <div class="project-text">
−
                          <p>Pencil’s certified Bluetooth Smart wireless delivers a fast, stable connection with industry-leading power conservation</p>
+
                       
−
                          <p>Each Pencil is milled from a single, solid piece of material. Graphite brushed aluminum model shown.</p>
+
 
                         </div>
 
                         </div>
 
                     </div>
 
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 +
          <div>
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            <div class="project-details">
 +
              <span class="icon-close"><i class="pe-7s-close-circle"></i></span>
 +
              <div class="container">
 +
                <div class="project-title">
 +
                  <h1>September</h1>
 +
                  <div class="separator-container">
 +
                      <div class="separator line-separator">✻</div>
 +
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 +
                 
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                <div class="row">
 +
                  <div class="col-md-12">
 +
                    <div class="article">
 +
                      <div class="project-text">
 +
                          <h3>Week 1 (8/31-9/6)</h3>
 +
<ul type="circle">
 +
<li>Integrated CFP operons with KanR</li>
 +
<li>Integrated YFP operons with TetA into E. coli containing integrated CFPs</li></ul>
 +
<h3>Week 2 (9/7-9/13)</h3>
 +
<ul type="circle">
 +
<li>Continued attempts to integrate YFPs into E. coli containing integrated CFPs</li>
 +
<li>Imaged successful double integrations for R0010, R0011, R0051</li>
 +
<li>Analyzed data from double integrations</li></ul>
 +
                      </div>
 +
                    </div>
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                  </div>
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                                        <li>
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                                            <a href="https://2015.igem.org/Team:William_and_Mary">
 +
                                                Home
 +
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                                            <a href="mailto:igem@wm.edu">
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                                                Contact
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                                    <a href="https://www.facebook.com/wmigem2015">
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                                    © 2015 William & Mary iGEM
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Latest revision as of 04:37, 21 November 2015

NOISE - W&M iGEM

Our Notebook

On this page you can view the work we did each month, from June through September. You can also find our protocols.

...

Important Protocols

Easy access to our most complex protocols.

...

Gibson Assembly

For building constructs

...

Imaging

Visualizing fluorescent bacteria

...

Integration

Integrating onto the E. coli genome

...

Repression

Repressing with dCas9

June

✻

Week 1 (6/1-6/7)

  • Resuspended all parts from the kit
  • Designed Gibson assemblies to put various fluorescent proteins under the control of the same promoter, to get noise measurements
  • Began performing Gibson PCRs

Week 2 (6/8-6/14)

  • Troubleshot Gibson PCRs
  • Attempted first Gibson assembly
  • Designed Gibson assemblies to put together different fluorescent proteins, each under the control of the same promoter
  • Attempted to Gibson assemble YFP + CFP under control of R0010

Week 3 (6/15-6/21)

  • Re-attempted Gibson assembly to make a double fluorescent construct with proteins under R0010
  • Began assembling parts for the Interlab Study
  • Received gBlocks to assemble dCas9 and some preliminary gRNAs
  • Began assembling dCas9 and gRNAs
  • Began learning how to use confocal microscopy
  • Began assembling different promoters with our fluorescent constructs (to eventually collect noise data for each promoter)
  • Designed and started the assembly process to make KanR (necessary to integrate parts onto the E. coli genome)

Week 4 (6/22-6/28)

  • Many of our past assemblies (dCas9, double fluorescent constructs, etc) failed. We continued attempts at these assemblies.

July

✻

Week 1 (6/29-7/5)

  • We have assembled our gRNAs and dCas9!
  • We ordered primers to integrate onto the E. coli genome
  • Designed assembly to put a KanR operon after a fluorescent construct to integrate
  • Designed a better way to assemble double fluorescent constructs
  • Designed a way to make a TetR operon to integrate two different things
  • Made electrocompetent cells containing our dCas9 operon
  • Assembled a double fluorescent construct! CFP and YFP under R0010
  • Attempted our first double electroporation-transformation to test our dCas9 and gRNAs

Week 2 (7/6-7/12)

  • Began assembling CFP and YFP operons with each promoter that we wanted to test
  • Confirmed that dCas9 and our gRNA design works
  • Assembled the CFP under R0010 with KanR, so that it can be PCR’d with the integration PCRs, and integrated
  • Attempted to make TetR operon

Week 3 (7/13-7/19)

  • Attempted to test our integration protocol, by integrating KanR onto the E. coli genome
  • Continued attempting to construct Interlab Parts
  • Worked on our collaboration with UGA
  • Designed gRNAs for other promoters to create a suite of repression parts
  • Continued assembling CFP and YFP operons with promoters of interest
  • Continued attempts to make TetR operon

Week 4 (7/20-7/26)

  • Began testing integrator cassette part
  • Continued working on Interlab Study
  • Continued assembling CFP and YFP operons
  • Continued attempts to make TetR operon

Week 5 (7/26-8/2)

  • Ordered gBlocks for Interlab Study
  • Continued working on assembling all gRNA parts
  • Continued assembling CFP and YFP operons
  • Imaged our single integrated fluorescent CFP (under R0010)
  • Continued attempts to make TetR operon

August

✻

Week 1 (8/3-8/9)

  • Continued assembling CFP and YFP operons
  • Began assembling CFP operons with KanR (to integrate)
  • Continued attempts to make TetR operon

8/10-8/23: School mandates that we leave

  • During this time, we learned that TetR had been mislabelled, and the part we were actually looking to assemble to confer tetracycline resistance was “TetA”
  • We designed PCRs to assemble TetA

Week 4 (8/24-8/30)

  • Continued working on Interlab Study
  • Began assembling YFP operons with TetA (to integrate)
  • Began attempts to integrate YFP operons with TetA for which there was a corresponding CFP operon with KanR

September

✻

Week 1 (8/31-9/6)

  • Integrated CFP operons with KanR
  • Integrated YFP operons with TetA into E. coli containing integrated CFPs

Week 2 (9/7-9/13)

  • Continued attempts to integrate YFPs into E. coli containing integrated CFPs
  • Imaged successful double integrations for R0010, R0011, R0051
  • Analyzed data from double integrations