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| - | {{Team:Aix-Marseille/header}}
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| - | <html>
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| - | <script>
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| - | // Function to handle the movement of the sidebar in the Notebook
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| - | $(document).ready(function () {
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| - | var sidebar = $('#sidebar-notebook');
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| - | var sidebarContainer = $('#sidebar-notebook-div');
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| | | | |
| - | $(window).scroll(function (event) {
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| - | var ypos = $(this).scrollTop();
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| - | var scrollTop = $(window).scrollTop(),
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| - | elementOffset = sidebar.offset().top,
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| - | distance = (elementOffset - scrollTop);
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| - |
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| - | var collision_top = sidebar.overlaps($('#stop_top'));
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| - | var collision_bot = sidebar.overlaps($('#stop_bot'));
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| - |
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| - | if (collision_top.hits.length) { /* Collision TOP */
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| - | // To fix at the top of the .row div
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| - | sidebar.css({ top: '',
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| - | bottom: '',
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| - | position: '',
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| - | width: ''
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| - | });
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| - | sidebarContainer.css({ position:'',
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| - | bottom: '',
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| - | });
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| - | if (distance < 141) {
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| - | // To fix at the top of the page while scrolling
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| - | sidebar.css({ top: '141px',
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| - | bottom: '',
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| - | position: 'fixed',
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| - | width: '262.5px'
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| - | });
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| - | sidebarContainer.css({ position: '',
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| - | bottom: '',
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| - | right: ''
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| - | }
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| - | }
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| - | else if (collision_bot.hits.length) { /* Collision BOTTOM */
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| - | // To fix at the bottom of the .row div
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| - | sidebar.css({ bottom: '',
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| - | top: '',
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| - | position: '',
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| - | width: ''
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| - | });
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| - | sidebarContainer.css({ position: 'absolute',
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| - | bottom: '0px',
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| - | right: '0px'
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| - | });
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| - | if (distance > 141) {
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| - | // To fix at the top of the page while scrolling
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| - | sidebar.css({ top: '141px',
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| - | bottom: '',
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| - | position: 'fixed',
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| - | width: '262.5px'
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| - | });
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| - | sidebarContainer.css({ position: '',
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| - | bottom: '',
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| - | right: ''
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| - | });
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| - | }
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| - | }
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| - | else {
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| - | // To fix at the top of the page while scrolling
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| - | sidebar.css({ top: '141px',
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| - | bottom: '',
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| - | position: 'fixed',
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| - | width: '262.5px'
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| - | });
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| - | sidebarContainer.css({ position: '',
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| - | bottom: '',
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| - | right: ''
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| - | });
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| - | }
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| - | });
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| - | });
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| - | </script>
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| - |
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| - |
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| - |
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| - | <!-- ======= WEEK 7 ======= -->
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| - | <div class="panel panel-info notes-panel">
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| - | <span class="note-tag" id="week7"></span>
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| - | <div class="panel-heading">
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| - | <h3 class="panel-title">Week 7 : 08/11/2014 ➡ 08/17/2014 <div class="pull-right"></div></h3>
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| - | </div>
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| - | <div class="panel-body">
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| - |
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| - | <ul class="nav nav-tabs" role="tablist">
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| - | <li class="active"><a href="#0812" role="tab" data-toggle="tab" class="date-notebook">08/12/14</a></li>
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| - | <li><a href="#0813" role="tab" data-toggle="tab" class="date-notebook">08/13/14</a></li>
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| - | <li><a href="#0814" role="tab" data-toggle="tab" class="date-notebook">08/14/14</a></li>
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| - | </ul>
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| - |
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| - | <div class="tab-content">
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| - |
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| - | <div class="tab-pane fade in active" id="0812">
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| - | <ul class="list-notebook">
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| - | <li>
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| - | <p>We have control if the insert of FRT-Kan-FRT is in the gene sdaBC and CheA by PCR.</p>
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| - | <table class="table table-hover table-bordered notes-table">
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| - | <thead>
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| - | <tr>
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| - | <th>#</th>
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| - | <th>DNA Template</th>
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| - | <th>Primers Name</th>
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| - | <th>Weight of amplified DNA</th>
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| - | </tr>
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| - | </thead>
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| - | <tbody>
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| - | <tr>
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| - | <td>180</td>
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| - | <td>Genomic DNA of W3110</td>
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| - | <td>CheA_up<br>CheA_down</td>
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| - | <td>1700</td>
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| - | </tr>
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| - | <tr>
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| - | <td>181</td>
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| - | <td>CheA-</td>
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| - | <td>CheA_up<br>CheA_down</td>
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| - | <td>1500</td>
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| - | </tr>
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| - | <tr>
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| - | <td>182</td>
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| - | <td>Genomic DNA of W3110</td>
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| - | <td>sdaBC_up<br>sdaBC_down</td>
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| - | <td>3100</td>
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| - | </tr>
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| - | <tr>
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| - | <td>183</td>
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| - | <td>sdaBC- KanR</td>
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| - | <td>sdaBC_up<br>sdaBC_down</td>
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| - | <td>1500</td>
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| - | </tr>
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| - | <tr>
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| - | <td>184</td>
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| - | <td>sdaBC- KanR + pCP20</td>
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| - | <td>sdaBC_up<br>sdaBC_down</td>
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| - | <td>1500</td>
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| - | </tr>
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| - | </tbody>
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| - | </table>
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| - | <p>CheA- control is unsuccessful, we see a weight of amplification for #180 and #181 of 1700bp the gene FRT-Kan-FRT isn't insert in cheA.</p>
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| - | <p>>SdaBC- control have a problem we don't have amplification for #182 to #184.</p>
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| - | <p>Results not shown.</p>
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| - | </li>
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| - | </ul>
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| - | </div>
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| - |
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| - | <div class="tab-pane fade in" id="0813">
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| - | <ul class="list-notebook">
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| - | <li>
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| - | <p>We made a PCR with new oligo to control mutants.</p>
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| - | <table class="table table-hover table-bordered notes-table">
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| - | <thead>
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| - | <tr>
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| - | <th>#</th>
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| - | <th>DNA Template</th>
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| - | <th>Primers Name</th>
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| - | <th>Weight of amplified DNA</th>
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| - | </tr>
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| - | </thead>
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| - | <tbody>
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| - | <tr>
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| - | <td>185</td>
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| - | <td>Genomic DNA of W3110</td>
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| - | <td>CheA_check_up<br>CheA_check_down</td>
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| - | <td>1700</td>
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| - | </tr>
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| - | <tr>
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| - | <td>186</td>
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| - | <td>CheA-</td>
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| - | <td>CheA_check_up<br>CheA_check_down</td>
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| - | <td>1500</td>
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| - | </tr>
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| - | <tr>
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| - | <td>187</td>
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| - | <td>Genomic DNA of W3110</td>
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| - | <td>sdaBC_check_up<br>sdaBC_check_down</td>
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| - | <td>3100</td>
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| - | </tr>
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| - | <tr>
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| - | <td>188</td>
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| - | <td>sdaBC- KanR</td>
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| - | <td>sdaBC_check_up<br>sdaBC_check_down</td>
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| - | <td>1500</td>
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| - | </tr>
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| - | <tr>
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| - | <td>189</td>
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| - | <td>sdaBC- KanR + pCP20</td>
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| - | <td>sdaBC_check_up<br>sdaBC_check_down</td>
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| - | <td>1500</td>
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| - | </tr>
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| - | <tr>
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| - | <td>190</td>
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| - | <td>Genomic DNA of W3110</td>
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| - | <td>FRT_up<br>sdaBC_check_down</td>
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| - | <td>0</td>
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| - | </tr>
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| - | <tr>
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| - | <td>191</td>
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| - | <td>sdaBC- KanR</td>
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| - | <td>FRT_up<br>sdaBC_check_down</td>
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| - | <td>1600</td>
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| - | </tr>
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| - | <tr>
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| - | <td>192</td>
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| - | <td>sdaBC- KanR + pCP20</td>
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| - | <td>FRT_up<br>sdaBC_check_down</td>
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| - | <td>1600</td>
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| - | </tr>
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| - | </tbody>
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| - | </table>
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| - | <p>Second control of CheA- show us the gene FRT-Kan-FRT isn't in the gene cheA</p>
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| - | <p>SdaBC control have an other problem with amplification</p>
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| - | <p>Results not shown.</p>
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| - | </li>
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| - | </ul>
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| - | </div>
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| - |
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| - | <div class="tab-pane fade in" id="0814">
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| - | <ul class="list-notebook">
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| - | <li>
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| - | <p>We made a gradient PCR 55° to 65° with oligo sdaBC_checkdo/FRTup and W3110 sdaBC- strain and W3110 Wild type.</p>
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| - | <p>No amplification shown by the electrophoresis for all these PCR.</p>
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| - | <p>Results not shown</p>
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| - | </li>
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| - | </ul>
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| - | </div>
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| - | </div>
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| - | </div>
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| - | </div>
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| - |
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| - | <!-- ======= WEEK 8 ======= -->
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| - | <div class="panel panel-info notes-panel">
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| - | <span class="note-tag" id="week8"></span>
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| - | <div class="panel-heading">
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| - | <h3 class="panel-title">Week 8 : 08/18/2014 ➡ 08/24/2014 <div class="pull-right"></div></h3>
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| - | </div>
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| - | <div class="panel-body">
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| - |
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| - | <ul class="nav nav-tabs" role="tablist">
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| - | <li class="active"><a href="#0818" role="tab" data-toggle="tab" class="date-notebook">08/18/14</a></li>
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| - | <li><a href="#0819" role="tab" data-toggle="tab" class="date-notebook">08/19/14</a></li>
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| - | <li><a href="#0820" role="tab" data-toggle="tab" class="date-notebook">08/20/14</a></li>
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| - | <li><a href="#0821" role="tab" data-toggle="tab" class="date-notebook">08/21/14</a></li>
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| - | <li><a href="#0822" role="tab" data-toggle="tab" class="date-notebook">08/22/14</a></li>
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| - | </ul>
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| - |
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| - | <div class="tab-content">
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| - |
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| - | <div class="tab-pane fade in active" id="0818">
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| - | <ul class="list-notebook">
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| - | <li>
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| - | <p>We made Q5 PCR with oligo 1-2 and 3-4 on pKD4 template for prepare new transformation sdaBC and cheA respectively #293 and #294. After we supress the template pKD4 with </p>
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| - | </li>
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| - | <li>
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| - | <p>We purified PCR products #293 thanks to Macherey Nagel PCR Clean up Kit. </p>
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| - | <table class="table table-hover table-bordered notes-table">
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| - | <tbody>
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| - | <tr>
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| - | <td>293</td><td>22.65 ng.mL<sup>-1</sup></td>
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| - | </tr>
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| - | </tbody>
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| - | </table>
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| - | </li>
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| - | <li>
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| - | <p>We made 2 new PCR on transformed strains. With specific hybridation temperature.</p>
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| - | <table class="table table-hover table-bordered notes-table">
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| - | <thead>
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| - | <tr>
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| - | <th>#</th>
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| - | <th>DNA Template</th>
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| - | <th>Primers Name</th>
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| - | <th>Weight of amplified DNA</th>
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| - | <th>Hybridation Temperature</th>
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| - | </tr>
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| - | </thead>
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| - | <tbody>
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| - | <tr>
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| - | <td>300A</td>
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| - | <td>CheA-</td>
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| - | <td>CheA_check_up<br>CheA_check_down</td>
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| - | <td>1500</td>
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| - | <td>55°C</td>
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| - | </tr>
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| - | <tr>
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| - | <td>301A</td>
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| - | <td>sdaBC- KanR</td>
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| - | <td>FRT_up<br>sdaBC_check_down</td>
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| - | <td>1600</td>
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| - | <td>50°C</td>
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| - | </tr>
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| - | </tbody>
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| - | </table>
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| - | </li>
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| - | </ul>
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| - | </div>
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| - |
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| - | <div class="tab-pane fade in" id="0819">
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| - | <ul class="list-notebook">
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| - | <li>
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| - | <p>We made a PCR with new oligo to control mutants.</p>
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| - | <table class="table table-hover table-bordered notes-table">
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| - | <thead>
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| - | <tr>
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| - | <th>#</th>
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| - | <th>DNA Template</th>
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| - | <th>Primers Name</th>
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| - | <th>Weight of amplified DNA</th>
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| - | </tr>
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| - | </thead>
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| - | <tbody>
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| - | <tr>
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| - | <td>185</td>
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| - | <td>Genomic DNA of W3110</td>
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| - | <td>CheA_check_up<br>CheA_check_down</td>
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| - | <td>1700</td>
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| - | </tr>
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| - | <tr>
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| - | <td>186</td>
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| - | <td>CheA-</td>
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| - | <td>CheA_check_up<br>CheA_check_down</td>
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| - | <td>1500</td>
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| - | </tr>
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| - | <tr>
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| - | <td>187</td>
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| - | <td>Genomic DNA of W3110</td>
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| - | <td>sdaBC_check_up<br>sdaBC_check_down</td>
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| - | <td>3100</td>
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| - | </tr>
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| - | <tr>
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| - | <td>188</td>
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| - | <td>sdaBC- KanR</td>
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| - | <td>sdaBC_check_up<br>sdaBC_check_down</td>
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| - | <td>1500</td>
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| - | </tr>
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| - | <tr>
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| - | <td>189</td>
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| - | <td>sdaBC- KanR + pCP20</td>
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| - | <td>sdaBC_check_up<br>sdaBC_check_down</td>
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| - | <td>1500</td>
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| - | </tr>
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| - | <tr>
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| - | <td>190</td>
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| - | <td>Genomic DNA of W3110</td>
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| - | <td>FRT_up<br>sdaBC_check_down</td>
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| - | <td>0</td>
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| - | </tr>
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| - | <tr>
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| - | <td>191</td>
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| - | <td>sdaBC- KanR</td>
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| - | <td>FRT_up<br>sdaBC_check_down</td>
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| - | <td>1600</td>
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| - | </tr>
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| - | <tr>
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| - | <td>192</td>
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| - | <td>sdaBC- KanR + pCP20</td>
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| - | <td>FRT_up<br>sdaBC_check_down</td>
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| - | <td>1600</td>
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| - | </tr>
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| - | </tbody>
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| - | </table>
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| - | <div class="media notes-media">
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| - | <img class="https://static.igem.org/mediawiki/2014/e/ef/AMU_Team-0819-1_A.png" style="height:350px">
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| - | <img class="media-object img-rounded pull-right" src="https://static.igem.org/mediawiki/2014/c/c9/AMU_Team-0819-2_A.png" style="width:350px; margin-right:21px">
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| - | </div>
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| - | <p>After the electrophoresis, we can confirm The strain sdaBC- KanR is successful. We select 3 strains with electrophoresis control</p>
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| - | <p>C.23 and C.33 are contaminated. So we select C.43, C.53 and C.63.</p>
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| - | </li>
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| - | </ul>
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| - | </div>
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| - |
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| - | <div class="tab-pane fade in" id="0820">
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| - | <ul class="list-notebook">
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| - | <li>
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| - | <p>We prepare seven starter of W3110 sdaBC- KanR strain with Kan50.</p>
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| - | </li>
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| - | </ul>
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| - | </div>
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| - |
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| - | <div class="tab-pane fade in" id="0821">
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| - | <ul class="list-notebook">
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| - | <li>
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| - | <p>We realize day 7 of Lambda Red protocol on W3110 sdaBC- pCP20 strain.</p>
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| - | </li>
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| - | </ul>
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| - | </div>
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| - |
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| - | <div class="tab-pane fade in" id="0822">
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| - | <ul class="list-notebook">
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| - | <li>
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| - | <p>We realize day 8 of Lambda Red protocol on W3110 sdaBC- strain.</p>
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| - | </li>
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| - | </ul>
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| - | </div>
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| - | </div>
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| - | </div>
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| - | </div>
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| - |
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| - | <!-- ======= WEEK 9 ======= -->
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| - | <div class="panel panel-info notes-panel last-note">
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| - | <span class="note-tag" id="week9"></span>
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| - | <div class="panel-heading">
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| - | <h3 class="panel-title">Week 9 : 08/25/2014 ➡ 08/31/2014 <div class="pull-right"></div></h3>
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| - | </div>
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| - | <div class="panel-body">
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| - |
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| - | <ul class="nav nav-tabs" role="tablist">
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| - | <li class="active"><a href="#0825" role="tab" data-toggle="tab" class="date-notebook">08/25/14</a></li>
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| - | <li><a href="#0826" role="tab" data-toggle="tab" class="date-notebook">08/26/14</a></li>
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| - | <li><a href="#0827" role="tab" data-toggle="tab" class="date-notebook">08/27/14</a></li>
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| - | <li><a href="#0828" role="tab" data-toggle="tab" class="date-notebook">08/28/14</a></li>
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| - | </ul>
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| - |
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| - | <div class="tab-content">
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| - |
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| - | <div class="tab-pane fade in active" id="0825">
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| - | <ul class="list-notebook">
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| - | <li>
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| - | <p>We realize day 9 of Lambda Red protocol on W3110 sdaBC- strain, and day 2 of Lambda Red protocol on W3110 sdaBC- strain with #294 PCR product</p>
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| - | </li>
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| - | </ul>
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| - | </div>
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| - |
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| - | <div class="tab-pane fade in" id="0826">
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| - | <ul class="list-notebook">
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| - | <li>
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| - | <p>We realize day 3 of Lambda Red protocol on W3110 sdaBC- strain CheA- KanR.</p>
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| - | </li>
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| - | <li>
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| - | <p>Check the construction 200(2) (RBS B0034 + RFP E1010) by digestion.</p>
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| - | <p>7µL E1010 (control) (500ng)<br>36µL H2O<br>5µ NEB Buffer 2.1<br>1µL XbaI<br>1µL EcoRI</p>
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| - | <br>
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| - | <p>2µL 200(2) (500ng)<br>36µL H2O<br>5µ NEB Buffer 2.1<br>1µL XbaI<br>1µL EcoRI</p>
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| - | <p>Incubation 53' at 37°C. Then, inactivation of enzymes 25' at 80°C.</p>
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| - | <div class="media notes-media">
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| - | <img class="https://static.igem.org/mediawiki/2014/e/e7/AMU_Team-0826.png" style="width:350px">
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| - | <div class="media-body">
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| - | <p>It is difficult to see if 200(2) possesses the RBS. The plasmid 200(2) is sent to sequencing and it's OK.</p>
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| - | </div>
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| - | </div>
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| - | </li>
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| - | </ul>
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| - | </div>
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| - | <div class="tab-pane fade in" id="0827">
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| - | <ul class="list-notebook">
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| - | <li>
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| - | <p>We realize day 4 of Lambda Red protocol on W3110 sdaBC- strain CheA- KanR. strain.</p>
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| - | </li>
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| - | </ul>
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| - | </div>
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| - | <div class="tab-pane fade in" id="0828">
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| - | <ul class="list-notebook">
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| - | <li>
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| - | <p>We realize day 5 of Lambda Red protocol on W3110 sdaBC- CheA- KanR strain. </p>
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| - | </li>
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| - | </ul>
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