Team:Gifu/Notebook

From 2014.igem.org

(Difference between revisions)
 
(35 intermediate revisions not shown)
Line 3: Line 3:
{{:CSS/gifu/notebook}}
{{:CSS/gifu/notebook}}
{{:CSS/gifu/tab}}
{{:CSS/gifu/tab}}
-
 
-
 
-
 
<html>
<html>
<head>
<head>
Line 16: Line 13:
</head>
</head>
<body>
<body>
-
 
<div id="tab">
<div id="tab">
-
<a class="tab-gray" href="https://2014.igem.org/Team:Gifu/Protocol">Protocols</a>
+
<a class="tab-gray" href="https://2014.igem.org/Team:Gifu/Protocol">Protocols 1</a>
 +
<a class="tab-gray" href="https://2014.igem.org/Gifu/protocols2">Protocols 2</a>
<a class="tab-white" href="https://2014.igem.org/Team:Gifu/Notebook"  >Calender</a></div>
<a class="tab-white" href="https://2014.igem.org/Team:Gifu/Notebook"  >Calender</a></div>
<div id="main">
<div id="main">
Line 24: Line 21:
<h1 id="theme" >Calender</h1>
<h1 id="theme" >Calender</h1>
<p> Click on a date to see our research activities on that day. </p>
<p> Click on a date to see our research activities on that day. </p>
-
 
-
 
<table class="newC">
<table class="newC">
   <tr>
   <tr>
Line 31: Line 26:
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td>Mon</td><td>Tue</td><td>Wed</td><td>Thr</td><td>Fri</td><td style="color:blue">Sat</td>
+
     <td>Mon</td><td>Tue</td><td>Wed</td><td>Thu</td><td>Fri</td><td style="color:blue">Sat</td>
     <td style="color:red">Sun</td>
     <td style="color:red">Sun</td>
   </tr>
   </tr>
Line 75: Line 70:
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td>Mon</td><td>Tue</td><td>Wed</td><td>Thr</td><td>Fri</td><td style="color:blue">Sat</td>
+
     <td>Mon</td><td>Tue</td><td>Wed</td><td>Thu</td><td>Fri</td><td style="color:blue">Sat</td>
     <td style="color:red">Sun</td>
     <td style="color:red">Sun</td>
   </tr>
   </tr>
Line 115: Line 110:
   </tr>
   </tr>
   <tr class="week">
   <tr class="week">
-
     <td><a href="#0929">29</a></td>
+
     <td>29</td>
     <td><a href="#0930">30</a></td>
     <td><a href="#0930">30</a></td>
     <td></td><td></td><td></td><td class="sat"></td><td class="sun"></td>
     <td></td><td></td><td></td><td class="sat"></td><td class="sun"></td>
Line 126: Line 121:
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td>Mon</td><td>Tue</td><td>Wed</td><td>Thr</td><td>Fri</td><td style="color:blue">Sat</td>
+
     <td>Mon</td><td>Tue</td><td>Wed</td><td>Thu</td><td>Fri</td><td style="color:blue">Sat</td>
     <td style="color:red">Sun</td>
     <td style="color:red">Sun</td>
   </tr>
   </tr>
Line 132: Line 127:
     <td></td><td></td>
     <td></td><td></td>
     <td>1</td>
     <td>1</td>
-
     <td>2</td>
+
     <td><a href="#1002">2</a></td>
-
     <td>3</td>
+
     <td><a href="#1003">3</a></td>
-
     <td class="sat">4</td>
+
     <td class="sat"><a href="#1004">4</a></td>
-
     <td class="sun">5</td>
+
     <td class="sun"><a href="#1005">5</a></td>
   </tr>
   </tr>
   <tr class="week">
   <tr class="week">
-
     <td>6</td>
+
     <td><a href="#1006">6</a></td>
-
     <td>7</td>
+
     <td><a href="#1007">7</a></td>
-
     <td>8</td>
+
     <td><a href="#1008">8</a></td>
-
     <td>9</td>
+
     <td><a href="#1009">9</a></td>
-
     <td>10</td>
+
     <td><a href="#1010">10</a></td>
-
     <td class="sat">11</td>
+
     <td class="sat"><a href="#1011">11</a></td>
-
     <td class="sun">12</td>
+
     <td class="sun"><a href="#1012">12</a></td>
   </tr>
   </tr>
   <tr class="week">
   <tr class="week">
-
     <td>13</td>
+
     <td><a href="#1013">13</a></td>
-
     <td>14</td>
+
     <td><a href="#1014">14</a></td>
-
     <td>15</td>
+
     <td><a href="#1015">15</a></td>
-
     <td>16</td>
+
     <td><a href="#1016">16</a></td>
-
     <td>17</td>
+
     <td><a href="#1017">17</a></td>
     <td class="sat">18</td>
     <td class="sat">18</td>
     <td class="sun">19</td>
     <td class="sun">19</td>
Line 173: Line 168:
   <dl>
   <dl>
     <dt>His</dt>
     <dt>His</dt>
-
     <dd>alphabet</dd>
+
     <dd>Histidine tag</dd>
     <dt>GFP</dt>
     <dt>GFP</dt>
     <dd>Green Fluorescence Protein</dd>
     <dd>Green Fluorescence Protein</dd>
Line 179: Line 174:
     <dd>Red Fluorescent Protein</br>This is <a href="http://parts.igem.org/Part:BBa_E1010">BBa_E1010.</a></dd>
     <dd>Red Fluorescent Protein</br>This is <a href="http://parts.igem.org/Part:BBa_E1010">BBa_E1010.</a></dd>
     <dt>5'-intron</dt>
     <dt>5'-intron</dt>
 +
    <dd>The 5’ side of the intron from td gene of T4 phage</dd>
     <dt>5'-intron M</dt>
     <dt>5'-intron M</dt>
 +
    <dd>The 5’ side of the intron from td gene of T4 phage without stop codon</dd>
     <dt>3'-intron</dt>
     <dt>3'-intron</dt>
 +
    <dd>The 3’ side of the intron from td gene of T4 phage</dd>
     <dt>Lac</dt>
     <dt>Lac</dt>
     <dd>LacI regulated promoter.</br>This is <a href="http://parts.igem.org/Part:BBa_R0010">BBa_R0010.</a></dd>
     <dd>LacI regulated promoter.</br>This is <a href="http://parts.igem.org/Part:BBa_R0010">BBa_R0010.</a></dd>
Line 201: Line 199:
     <dd>Restriction site that is cut by PstI or restriction enzyme</dd>
     <dd>Restriction site that is cut by PstI or restriction enzyme</dd>
     <dt>TTHA0715</dt>
     <dt>TTHA0715</dt>
-
     <dd>Cold shock protein with amino acid sequence cut by thrombin</dd>
+
     <dd>Cold shock protein (attached amino acid sequence cut by thrombin)</dd>
-
    <dt>TTHA0715 guanidine deposition</dt>
+
        <dt>SmtA</dt>
-
     <dd></dd>
+
     <dd>Metallothionein that can catch heavy metal ions such as Zn<sup>2+</sup>. </br>
-
    <dt>SmtA</dt>
+
        This is <a href="http://parts.igem.org/Part:BBa_K519010">BBa_K519010</a>.
-
    <dd></dd>
+
     </dd>
-
    <dt>circular RNA</dt>
+
      </dl>
-
     <dd></dd>
+
-
  </dl>
+
<br>
<br>
<h1>Prologue -before August-</h1>
<h1>Prologue -before August-</h1>
Line 221: Line 217:
   <li>pSB1K3</li>
   <li>pSB1K3</li>
  </ol>
  </ol>
-
<h3>T4 phage Multiplication with E.coli</h3>
+
<h3>T4 phage Multiplication with <i>E. coli</i></h3>
<h3>DNA Extraction from T4 phage</h3>
<h3>DNA Extraction from T4 phage</h3>
<br>
<br>
Line 228: Line 224:
<h3>Restriction Enzyme Digestion</h3>
<h3>Restriction Enzyme Digestion</h3>
-
<table>
+
  <table>
   <tr>
   <tr>
     <th>sample</th><th>restriction enzymes</th>
     <th>sample</th><th>restriction enzymes</th>
   </tr>
   </tr>
-
  <tr>
+
<tr>
     <td>His-RFP(with stop codon)</td><td>SpeI,EcoRI</td>
     <td>His-RFP(with stop codon)</td><td>SpeI,EcoRI</td>
   </tr>   
   </tr>   
Line 694: Line 690:
<p align="right"><a href="#calender">back to calender</a></p>
<p align="right"><a href="#calender">back to calender</a></p>
</noscript>
</noscript>
 +
</br>
<h2><a name="0903"></a>September 3rd</h2>
<h2><a name="0903"></a>September 3rd</h2>
Line 704: Line 701:
<p align="right"><a href="#calender">back to calender</a></p>
<p align="right"><a href="#calender">back to calender</a></p>
</noscript>
</noscript>
 +
</br>
<h2><a name="0904"></a>September 4th</h2>
<h2><a name="0904"></a>September 4th</h2>
Line 721: Line 719:
<p align="right"><a href="#calender">back to calender</a></p>
<p align="right"><a href="#calender">back to calender</a></p>
</noscript>
</noscript>
 +
</br>
<h2><a name="0905"></a>September 5th</h2>
<h2><a name="0905"></a>September 5th</h2>
Line 744: Line 743:
<p align="right"><a href="#calender">back to calender</a></p>
<p align="right"><a href="#calender">back to calender</a></p>
</noscript>
</noscript>
 +
</br>
<h2><a name="0908"></a>September 8th</h2>
<h2><a name="0908"></a>September 8th</h2>
Line 757: Line 757:
<p align="right"><a href="#calender">back to calender</a></p>
<p align="right"><a href="#calender">back to calender</a></p>
</noscript>
</noscript>
 +
</br>
<h2><a name="0909"></a>September 9th</h2>
<h2><a name="0909"></a>September 9th</h2>
Line 765: Line 766:
<p align="right"><a href="#calender">back to calender</a></p>
<p align="right"><a href="#calender">back to calender</a></p>
</noscript>
</noscript>
 +
</br>
<h2><a name="0910"></a>September 10th</h2>
<h2><a name="0910"></a>September 10th</h2>
Line 779: Line 781:
<p align="right"><a href="#calender">back to calender</a></p>
<p align="right"><a href="#calender">back to calender</a></p>
</noscript>
</noscript>
 +
</br>
<h2><a name="0911"></a>September 11th</h2>
<h2><a name="0911"></a>September 11th</h2>
Line 794: Line 797:
<p align="right"><a href="#calender">back to calender</a></p>
<p align="right"><a href="#calender">back to calender</a></p>
</noscript>
</noscript>
 +
</br>
<h2><a name="0912"></a>September 12th</h2>
<h2><a name="0912"></a>September 12th</h2>
Line 812: Line 816:
<p align="right"><a href="#calender">back to calender</a></p>
<p align="right"><a href="#calender">back to calender</a></p>
</noscript>
</noscript>
 +
</br>
<h2><a name="0913"></a>September 13th</h2>
<h2><a name="0913"></a>September 13th</h2>
Line 830: Line 835:
<p align="right"><a href="#calender">back to calender</a></p>
<p align="right"><a href="#calender">back to calender</a></p>
</noscript>
</noscript>
 +
</br>
<h2><a name="0914"></a>September 14th</h2>
<h2><a name="0914"></a>September 14th</h2>
Line 846: Line 852:
<p align="right"><a href="#calender">back to calender</a></p>
<p align="right"><a href="#calender">back to calender</a></p>
</noscript>
</noscript>
 +
</br>
<h2><a name="0915"></a>September 15th</h2>
<h2><a name="0915"></a>September 15th</h2>
Line 855: Line 862:
<p align="right"><a href="#calender">back to calender</a></p>
<p align="right"><a href="#calender">back to calender</a></p>
</noscript>
</noscript>
 +
</br>
<h2><a name="0916"></a>September 16th</h2>
<h2><a name="0916"></a>September 16th</h2>
Line 865: Line 873:
<p align="right"><a href="#calender">back to calender</a></p>
<p align="right"><a href="#calender">back to calender</a></p>
</noscript>
</noscript>
 +
</br>
-
<!--
+
<h2><a name="0917"></a>September 17th</h2>
-
<h2><a name=""></a></h2>
+
<h3>PCR</h3>
-
<h3></h3>
+
<ol class="list">
-
<h3></h3>
+
<li>EcoRI-SmtA-DT-Cm-XbaI</li>
-
<h3></h3>
+
<li>EcoRI-circularSmtA-SpeI</li>
 +
<li>EcoRI-TTHA0715-5'intron-DT-Cm-XbaI</li>
 +
</ol>
 +
<h3>Gel Extraction</h3>
 +
<h3>Ligation</h3>
 +
<ol class="list">
 +
<li>Lac-RBS + SmtA-DT-Cm</li>
 +
<li>circularSmtA + 5'intronM-DT-Cm</li>
 +
<li>Lac-3'intron-RBS + TTHA0715-5'intron-DT-Cm</li>
 +
<li>BBa_K823012(promoter) + BBa_E0240(GFP generator)</li>
 +
</ol>
<noscript>
<noscript>
<p align="right"><a href="#calender">back to calender</a></p>
<p align="right"><a href="#calender">back to calender</a></p>
</noscript>
</noscript>
-
-->
+
</br>
-
<!--
+
 
-
<h2><a name=""></a></h2>
+
<h2><a name="0919"></a>September 19th</h2>
-
<h3></h3>
+
<h3>Colony PCR</h3>
-
<h3></h3>
+
<ol class="list">
-
<h3></h3>
+
<li>-Lac-RBS-SmtA-DT-</li>
 +
<li>-circularSmtA-5'intronM-DT-</li>
 +
<li>-Lac-3'intron-RBS-TTHA0715-5'intron-DT-</li>
 +
<li>-BBa_K823012(promoter)-BBa_E0240(GFP generator)-</li>
 +
</ol>
<noscript>
<noscript>
<p align="right"><a href="#calender">back to calender</a></p>
<p align="right"><a href="#calender">back to calender</a></p>
</noscript>
</noscript>
 +
</br>
 +
 +
<h2><a name="0920"></a>September 20th</h2>
 +
<h3>Plasmid Extraction</h3>
 +
<ol class="list">
 +
<li>-BBa_K823012(promoter)-GFP-Cm-</li>
 +
<li>-Lac-RBS-SmtA-DT-Cm-</li>
 +
<li>-Lac-3'intron-RBS-TTHA0715-5'intron-DT-Cm-</li>
 +
<li>-SmtA-5'intronM-DT-Cm-</li>
 +
</ol>
 +
<h3>PCR</h3>
 +
<ol class="list">
 +
<li>-BBa_K823012(promoter)-GFP-Cm-</li>
 +
<li>-Lac-RBS-SmtA-DT-Cm-</li>
 +
<li>-Lac-3'intron-RBS-TTHA0715-5'intron-DT-Cm-</li>
 +
<li>-SmtA-5'intronM-DT-Cm-</li>
 +
<li>EcoRI-SmtA-5'intronM-DT-Cm-XbaI</li>
 +
</ol>
 +
<h3>purification</h3>
 +
<h3>Restriction Enzyme Digestion</h3>
 +
<!--<table>
 +
  <tr>
 +
    <th>sample</th><th>restriction enzymes</th>
 +
  </tr>
 +
<tr>
-->
-->
-
<!--
+
<h3>purification</h3>
-
<h2><a name=""></a></h2>
+
<h3>Ligation</h3>
-
<h3></h3>
+
-
<h3></h3>
+
-
<h3></h3>
+
<noscript>
<noscript>
<p align="right"><a href="#calender">back to calender</a></p>
<p align="right"><a href="#calender">back to calender</a></p>
</noscript>
</noscript>
-
-->
+
</br>
-
<!--
+
 
-
<h2><a name=""></a></h2>
+
<h2><a name="0921"></a>September 21th</h2>
-
<h3></h3>
+
<h3>SDS-PAGE</h3>
-
<h3></h3>
+
-
<h3></h3>
+
<noscript>
<noscript>
<p align="right"><a href="#calender">back to calender</a></p>
<p align="right"><a href="#calender">back to calender</a></p>
</noscript>
</noscript>
-
-->
+
</br>
-
<!--
+
 
-
<h2><a name=""></a></h2>
+
<h2><a name="0922"></a>September 22th</h2>
-
<h3></h3>
+
<h3>SDS-PAGE</h3>
-
<h3></h3>
+
<ol class="list">
-
<h3></h3>
+
<li>long-chain RFP precipitation</li>
 +
<li>long-chain RFP supernatant</li>
 +
<li>monomeric TTHA0715 precipitation</li>
 +
<li>monomeric TTHA0715 supernatant</li>
 +
<li>long-chain TTHA0715 precipitation</li>
 +
<li>long-chain TTHA0715 supernatant</li>
 +
<li>monomeric SmtA precipitation</li>
 +
<li>monomeric SmtA supernatant</li>
 +
<li>long-chain SmtA precipitation</li>
 +
<li>long-chain SmtA supernatant</li>
 +
</ol>
 +
<h3>Miniprep</h3>
 +
<ol class="list">
 +
<li>-TTHA0715-5'intronM-DT-Cm-</li>
 +
<li>-Lac-3'intron-RBS-SmtA-5'intronM-DT-Cm-</li>
 +
<li>-BBa_K823012(promoter)-GFP-</li>
 +
</ol>
 +
<h3>PCR</h3>
<noscript>
<noscript>
<p align="right"><a href="#calender">back to calender</a></p>
<p align="right"><a href="#calender">back to calender</a></p>
</noscript>
</noscript>
-
-->
+
</br>
-
<!--
+
 
-
<h2><a name=""></a></h2>
+
<h2><a name="0923"></a>September 23th</h2>
-
<h3></h3>
+
<h3>PCR</h3>
-
<h3></h3>
+
<h3>Ligation</h3>
-
<h3></h3>
+
<h3>Transformation</h3>
<noscript>
<noscript>
<p align="right"><a href="#calender">back to calender</a></p>
<p align="right"><a href="#calender">back to calender</a></p>
</noscript>
</noscript>
-
-->
+
</br>
-
<!--
+
 
-
<h2><a name=""></a></h2>
+
<h2><a name="0924"></a>September 24th</h2>
-
<h3></h3>
+
<h3>Electrophoresis</h3>
-
<h3></h3>
+
-
<h3></h3>
+
<noscript>
<noscript>
<p align="right"><a href="#calender">back to calender</a></p>
<p align="right"><a href="#calender">back to calender</a></p>
</noscript>
</noscript>
-
-->
+
</br>
-
<!--
+
 
-
<h2><a name=""></a></h2>
+
<h2><a name="0925"></a>September 25th</h2>
-
<h3></h3>
+
<h3>Colony PCR</h3>
-
<h3></h3>
+
<h3>Liquid culture</h3>
-
<h3></h3>
+
<noscript>
<noscript>
<p align="right"><a href="#calender">back to calender</a></p>
<p align="right"><a href="#calender">back to calender</a></p>
</noscript>
</noscript>
-
-->
+
</br>
-
<!--
+
 
-
<h2><a name=""></a></h2>
+
<h2><a name="0926"></a>September 26th</h2>
-
<h3></h3>
+
<h3>Miniprep</h3>
-
<h3></h3>
+
<h3>SDS-PAGE</h3>
-
<h3></h3>
+
<noscript>
<noscript>
<p align="right"><a href="#calender">back to calender</a></p>
<p align="right"><a href="#calender">back to calender</a></p>
</noscript>
</noscript>
-
-->
+
</br>
-
<!--
+
 
-
<h2><a name=""></a></h2>
+
<h2><a name="0927"></a>September 27th</h2>
-
<h3></h3>
+
<h3>Restriction Enzyme Digestion</h3>
-
<h3></h3>
+
<h3>Ligation</h3>
-
<h3></h3>
+
<h3>Transformation</h3>
<noscript>
<noscript>
<p align="right"><a href="#calender">back to calender</a></p>
<p align="right"><a href="#calender">back to calender</a></p>
</noscript>
</noscript>
-
-->
+
</br>
-
<!--
+
 
-
<h2><a name=""></a></h2>
+
<h2><a name="0928"></a>September 28th</h2>
-
<h3></h3>
+
<h3>SDS-PAGE</h3>
-
<h3></h3>
+
<h3>Colony PCR</h3>
-
<h3></h3>
+
<noscript>
<noscript>
<p align="right"><a href="#calender">back to calender</a></p>
<p align="right"><a href="#calender">back to calender</a></p>
</noscript>
</noscript>
-
-->
+
</br>
-
<!--
+
 
-
<h2><a name=""></a></h2>
+
<h2><a name="0930"></a>September 30th</h2>
-
<h3></h3>
+
<h3>SDS-PAGE</h3>
-
<h3></h3>
+
-
<h3></h3>
+
<noscript>
<noscript>
<p align="right"><a href="#calender">back to calender</a></p>
<p align="right"><a href="#calender">back to calender</a></p>
</noscript>
</noscript>
-
-->
+
</br>
-
<!--
+
 
-
<h2><a name=""></a></h2>
+
<h2><a name="1002"></a>October 2nd</h2>
-
<h3></h3>
+
<h3>RNA extraction</h3>
-
<h3></h3>
+
<h3>PCR</h3>
-
<h3></h3>
+
<noscript>
<noscript>
<p align="right"><a href="#calender">back to calender</a></p>
<p align="right"><a href="#calender">back to calender</a></p>
</noscript>
</noscript>
-
-->
+
</br>
 +
<h2><a name="1003"></a>October 3rd</h2>
 +
<h3>PCR</h3>
 +
<noscript>
 +
<p align="right"><a href="#calender">back to calender</a></p>
 +
</noscript>
 +
</br>
 +
 +
<h2><a name="1004"></a>October 4th</h2>
 +
<h3>PCR</h3>
 +
<noscript>
 +
<p align="right"><a href="#calender">back to calender</a></p>
 +
</noscript>
 +
</br>
 +
 +
<h2><a name="1005"></a>October 5th</h2>
 +
<h3>PCR</h3>
 +
<noscript>
 +
<p align="right"><a href="#calender">back to calender</a></p>
 +
</noscript>
 +
</br>
 +
 +
<h2><a name="1006"></a>October 6th</h2>
 +
<h3>PCR</h3>
 +
<noscript>
 +
<p align="right"><a href="#calender">back to calender</a></p>
 +
</noscript>
 +
</br>
 +
 +
<h2><a name="1007"></a>October 7th</h2>
 +
<h3>PCR</h3>
 +
<noscript>
 +
<p align="right"><a href="#calender">back to calender</a></p>
 +
</noscript>
 +
</br>
 +
 +
<h2><a name="1008"></a>October 8th</h2>
 +
<h3>PCR</h3>
 +
<noscript>
 +
<p align="right"><a href="#calender">back to calender</a></p>
 +
</noscript>
 +
</br>
 +
 +
<h2><a name="1009"></a>October 9th</h2>
 +
<h3>PCR</h3>
 +
<noscript>
 +
<p align="right"><a href="#calender">back to calender</a></p>
 +
</noscript>
 +
</br>
 +
 +
<h2><a name="1010"></a>October 10th</h2>
 +
<h3>PCR</h3>
 +
<noscript>
 +
<p align="right"><a href="#calender">back to calender</a></p>
 +
</noscript>
 +
</br>
 +
<h2><a name="1011"></a>October 11th</h2>
 +
<h3>PCR</h3>
 +
<noscript>
 +
<p align="right"><a href="#calender">back to calender</a></p>
 +
</noscript>
 +
</br>
 +
 +
<h2><a name="1012"></a>October 12th</h2>
 +
<h3>PCR</h3>
 +
<noscript>
 +
<p align="right"><a href="#calender">back to calender</a></p>
 +
</noscript>
 +
</br>
 +
 +
<h2><a name="1013"></a>October 13th</h2>
 +
<h3>PCR</h3>
 +
<noscript>
 +
<p align="right"><a href="#calender">back to calender</a></p>
 +
</noscript>
 +
</br>
 +
 +
<h2><a name="1014"></a>October 14th</h2>
 +
<h3>PCR</h3>
 +
<noscript>
 +
<p align="right"><a href="#calender">back to calender</a></p>
 +
</noscript>
 +
</br>
 +
 +
<h2><a name="1015"></a>October 15th</h2>
 +
<h3>PCR</h3>
 +
<noscript>
 +
<p align="right"><a href="#calender">back to calender</a></p>
 +
</noscript>
 +
</br>
 +
 +
<h2><a name="1016"></a>October 16th</h2>
 +
<h3>PCR</h3>
 +
<noscript>
 +
<p align="right"><a href="#calender">back to calender</a></p>
 +
</noscript>
 +
</br>
 +
 +
<h2><a name="1017"></a>October 17th</h2>
 +
<h3>PCR</h3>
 +
<noscript>
 +
<p align="right"><a href="#calender">back to calender</a></p>
 +
</noscript>
 +
</br>
</div>
</div>
</div>
</div>
 +
<br>
</body>
</body>
</html>
</html>

Latest revision as of 03:58, 18 October 2014

head home team project note result more

factory1

Calender

Click on a date to see our research activities on that day.

August
MonTueWedThuFriSat Sun
123
45678910
11 12 13 14 15 16 17
18 19 20 21 22 23 24
25 26 27 28 29 30 31
September
MonTueWedThuFriSat Sun
1 2 3 4 5 6 7
8 9 10 11 12 13 14
15 16 17 18 19 20 21
22 23 24 25 26 27 28
29 30
October
MonTueWedThuFriSat Sun
1 2 3 4 5
6 7 8 9 10 11 12
13 14 15 16 17 18 19
20212223242526
2728293031

Glossary

His
Histidine tag
GFP
Green Fluorescence Protein
RFP
Red Fluorescent Protein
This is BBa_E1010.
5'-intron
The 5’ side of the intron from td gene of T4 phage
5'-intron M
The 5’ side of the intron from td gene of T4 phage without stop codon
3'-intron
The 3’ side of the intron from td gene of T4 phage
Lac
LacI regulated promoter.
This is BBa_R0010.
Amp
Ampicillin resistance gene
Cm
Chloramphenicol resistance gene.
This is pSB1C3.
RBS
Ribosome Binding Sites.
This is BBa_B0034.
DT
Double Terminator consisting of BBa_B0010 and BBa_B0012.
This is BBa_B0015.
EcoRI
Restriction site that is cut by EcoRI or restriction enzyme
XbaI
Restriction site that is cut by XbaI or restriction enzyme
SpeI
Restriction site that is cut by SpeI or restriction enzyme
PstI
Restriction site that is cut by PstI or restriction enzyme
TTHA0715
Cold shock protein (attached amino acid sequence cut by thrombin)
SmtA
Metallothionein that can catch heavy metal ions such as Zn2+.
This is BBa_K519010.

Prologue -before August-

Parts amplification with PCR

  1. Lac
  2. RBS
  3. RFP
  4. DT
  5. Cm (pSB1C3)
  6. pSB1A3
  7. pSB1K3

T4 phage Multiplication with E. coli

DNA Extraction from T4 phage


August

August 11th

Restriction Enzyme Digestion

samplerestriction enzymes
His-RFP(with stop codon)SpeI,EcoRI
5'-intron MSpeI,EcoRI
Lac-3'intron-RBSSpeI,EcoRI
His-RFP(without stop codon)XbaI,EcoRI
RBS-AmpSpeI,EcoRI

Ligation

  1. EcoRI-His-RFP(with stop codon)-SpeI + XbaI-DT-Cm-EcoRI
  2. EcoRI-5'intron M-SpeI + XbaI-DT-Cm-EcoRI
  3. EcoRI-Lac-3'intron-RBS-SpeI + XbaI-His-RFP(without stop codon)-5'intron-DT-Cm-EcoRI
  4. EcoRI-His-RFP(without stop codon)-SpeI + SpeI-Amp-EcoRI

Transformation

  1. -His-RFP(with stop codon)-DT-Cm-
  2. -5'intron M-DT-Cm-
  3. -Lac-3'intron-RBS-His-RFP(without stop codon)-5'intron-DT-Cm-
  4. -His-RFP(without stop codon)-Amp-

Densitometry

sampleconcentration(ng/µL)
His-RFP(with stop codon) EcoRI-SpeI162.6
5'intron M EcoRI-SpeI45.4
Lac-3'intron-RBS EcoRI-SpeI120.9
His-RFP(without stop codon) EcoRI-SpeI160.0
His-RFP(without stop codon)-5'intron-DT-Cm XbaI-EcoRI 174.0
Amp EcoRI-SpeI101.8

August 12th

Colony PCR

  1. His-RFP(with stop codon)-DT-Cm
  2. 5'intron M-DT-Cm
  3. Lac-3'intron-RBS-His-RFP(without stop codon)-5'intron-DT-Cm:[1]turning red
  4. Lac-3'intron-RBS-His-RFP(without stop codon)-5'intron-DT-Cm:[2]turning pink
  5. Lac-3'intron-RBS-His-RFP(without stop codon)-5'intron-DT-Cm:[3]turning white
  6. His-RFP(without stop codon)-Amp

Electrophoresis

  1. His-RFP(with stop codon)-DT
  2. His-RFP
  3. 5'intron M-DT
  4. 5'intron M
  5. Lac-3'intron-RBS-His-RFP(without stop codon)-5'intron-DT:[1]
  6. Lac-3'intron-RBS-His-RFP(without stop codon)-5'intron-DT:[2]
  7. Lac-3'intron-RBS-His-RFP(without stop codon)-5'intron-DT:[3]
  8. His-RFP(without stop codon)-5'intron-DT
  9. His-RFP(without stop codon)

Liquid Culture

  1. His-RFP(with stop codon)-DT
  2. 5'intron M-DT
  3. Lac-3'intron-RBS-His-RFP(without stop codon)-5'intron-DT:[1]
  4. Lac-3'intron-RBS-His-RFP(without stop codon)-5'intron-DT:[3]
  5. His-RFP(without stop codon)

August 13th

Miniprep

PCR

By use of KAPA HiFi DNA Polymerase

  1. His-RFP(with stop codon)-DT-Cm
  2. 5'intron M-DT-Cm

By use of Taq DNA Polymerase

  1. Lac-3'intron-RBS-His-RFP(without stop codon)-5'intron-DT-Cm:[1]turning red
  2. Lac-3'intron-RBS-His-RFP(without stop codon)-5'intron-DT-Cm:[3]turning white

Electrophoresis

  1. His-RFP(with stop codon)-DT-Cm
  2. 5'intron M-DT-Cm
  3. DNA Ladder Markers DNA Ladder One(Broad Range)
  4. Lac-3'intron-RBS-His-RFP(without stop codon)-5'intron-DT-Cm:[1]turning red
  5. Lac-3'intron-RBS-His-RFP(without stop codon)-5'intron-DT-Cm:[3]turning white

Restriction Enzyme Digestion

samplerestriction enzymes
His-RFP(with stop codon)-DT-CmEcoRI,XbaI
5'intron M-DT-CmEcoRI,XbaI

Densitometry

sampleconcentration(ng/µL)
EcoRI-Lac-RBS-SpeI65.0
XbaI-His-RFP(with stop codon)-DT-Cm-EcoRI188.8
EcoRI-His-RFP(with stop codon)-SpeI160.0
EcoRI-His-RFP(without stop codon)-SpeI160.0
XbaI-5'intron M-DT-Cm-EcoRI167.8

Ligation

  1. EcoRI-Lac-RBS-SpeI + XbaI-His-RFP(with stop codon)-DT-Cm-EcoRI
  2. EcoRI-His-RFP(with stop codon)-SpeI + XbaI-5'intron M-DT-Cm-EcoRI
  3. EcoRI-His-RFP(without stop codon)-SpeI + XbaI-5'intron M-DT-Cm-EcoRI

Transformation

  1. -Lac-RBS-His-RFP(with stop codon)-DT-Cm-
  2. -His-RFP(with stop codon)-5'intron M-DT-Cm-
  3. -His-RFP(without stop codon)-5'intron M-DT-Cm-

August 16th

Liquid Culture


August 18th

Plasmid Extraction

  1. -Lac-RBS-His-RFP(with stop codon)-DT-Cm-
  2. -His-RFP(with stop codon)-5'intron M-DT-Cm-
  3. -His-RFP(without stop codon)-5'intron M-DT-Cm-

Plasmid Purification

  1. -5'intron M-His-RFP(with stop codon)-
  2. -5'intron M-His-RFP(without stop codon)-

Miniprep

Colony PCR

Restriction Enzyme Digestion

samplerestriction enzymes
-His-RFP(with stop codon)-5'intron M-DT-Cm-EcoRI,XbaI
-His-RFP(without stop codon)-5'intron M-DT-Cm-EcoRI,XbaI

Densitometry

sampleconcentration(ng/µL)
EcoRI-Lac-3'intron-RBS-SpeI120.0
XbaI-His-RFP(with stop codon)-5'intron M-DT-Cm-EcoRI187.8
XbaI-His-RFP(without stop codon)-5'intron M-DT-Cm-EcoRI158.9

Ligation&Transformation

  1. EcoRI-Lac-3'intron-RBS-SpeI + XbaI-His-RFP(with stop codon)-5'intron M-DT-Cm-EcoRI
  2. EcoRI-Lac-3'intron-RBS-SpeI + XbaI-His-RFP(without stop codon)-5'intron M-DT-Cm-EcoRI

Polyethylene glycol Precipitation


August 19th

Colony PCR

  1. -Lac-3'intron-RBS-His-RFP(with stop codon)-5'intron M-DT-Cm-
  2. -Lac-3'intron-RBS-His-RFP(without stop codon)-5'intron M-DT-Cm-

Electrophoresis

  1. -Lac-3'intron-RBS-His-RFP(with stop codon)-5'intron M-DT-Cm-
  2. -Lac-3'intron-RBS-His-RFP(without stop codon)-5'intron M-DT-Cm-
  3. marker
  4. -His-RFP(with stop codon)-5'intron M-DT-Cm-
  5. -His-RFP(without stop codon)-5'intron M-DT-Cm-

Shaking Culture


August 20th

Colony PCR

  1. -Lac-3'intron-RBS-His-RFP(without stop codon)-5'intron M-DT-Cm-

by use of another colony differs from 8/19

Electrophoresis

  1. -Lac-3'intron-RBS-His-RFP(without stop codon)-5'intron M-DT-Cm-
  2. marker
  3. -His-RFP(without stop codon)-5'intron M-DT-Cm-

August 21th

Reagent Preparation

Protein Extraction

SDS-PAGE


August 22th

Prorein Purification by use of Ni-NTA

SDS-PAGE


August 23th

Prorein Purification by use of Ni-NTA

SDS-PAGE


August 24th

Extraction of plasmid device

  1. -Lac-RBS-His-RFP(with stop codon)-DT-Cm-
  2. -Lac-RBS-3'intron-His-RFP(without stop codon)-5'intron-DT-Cm-
  3. -Lac-RBS-3'intron-His-RFP(with stop codon)-5'intron M-DT-Cm-
  4. -Lac-RBS-3'intron-His-RFP(without stop codon)-5'intron M-DT-Cm-

PCR&Electrophoresis

  1. EcoRI-His-RFP(with stop codon)-PstI
  2. EcoRI-His-RFP(without stop codon)-PstI
  3. EcoRI-5'intron M-PstI
  4. EcoRI-Lac-3'intron-RBS-PstI

August 25th

Extraction of plasmid device

SDS-PAGE

  1. Lac-3'intron-RBS-His-RFP-5'intron M-DT-Cm

August 26th

PCR

Restriction Enzyme Digestion

samplerestriction enzymes
His-RFP(with stop codon)EcoRI,PstI
His-RFP(without stop codon)EcoRI,PstI
5'intron MEcoRI,PstI
Lac-3'intron-RBSEcoRI,PstI
TTHA0175EcoRI,SpeI

Densitometry

sampleconcentration(ng/µL)
His-RFP(with stop codon)180.7
His-RFP(without stop codon)164.6
5'intron M37.7
Lac-3'intron-RBS107.5
TTHA0175112.7

Ligation&Transformation

  1. EcoRI-His-RFP(with stop codon)-PstI + EcoRI-Cm-PstI
  2. EcoRI-His-RFP(without stop codon)-PstI + EcoRI-Cm-PstI
  3. EcoRI-5'intron M-PstI + EcoRI-Cm-PstI
  4. EcoRI-Lac-3'intron-RBS-PstI + EcoRI-Cm-PstI
  5. EcoRI-TTHA0175-SpeI + EcoRI-5'intron M-DT-Cm-XbaI

August 27th

Colony PCR

  1. -His-RFP(with stop codon)-Cm-
  2. -TTHA0175-Amp-
  3. -TTHA0175-5'intron M-DT-Cm-

Shaking Culture

  1. -His-RFP(with stop codon)-Cm-
  2. -TTHA0175-Amp-
  3. -TTHA0175-5'intron M-DT-Cm-

Enrichment Culture


August 28th

Plasmid Purification

  1. -His-RFP(with stop codon)-5'intron M-Cm-
  2. -TTHA0175-5'intron M-DT-Cm-

PCR

  1. -His-RFP(with stop codon)-Cm-
  2. -Lac-3'intron-RBS-Cm-
  3. -His-RFP(without stop codon)-Cm-
  4. -5'intron M-Cm-

August 29th

Densitometry

sampleconcentration(ng/µL)
EcoRI-TTHA0175-5'intron M-DT-Cm-XbaI118.8

Ligation

  1. EcoRI-TTHA0175-5'intron M-DT-Cm-XbaI + EcoRI-Lac-3'intron-RBS-SpeI

SDS-PAGE

Electrophoresis

  1. EcoRI-TTHA0175-5'intron M-DT-Cm-XbaI

August 30th

Colony PCR

  1. -Lac-3'intron-RBS-TTHA0715-5'intron M-DT-Cm-
  2. Plate4 3G

August 31th

Colony PCR

Because result of Colony PCR on 8/30 is not good, We chose 5 colonies and put them on PCR.


September 1st

Shaking Culture

  1. -Lac-3'intron-RBS-TTHA0715-5'intron M-DT-Cm-

Cell body Crush&SDS-PAGE(gel 10%)


September 3rd

Culture

  1. -Lac-3'intron-RBS-RFP(without stop codon)-5'intron M-DT-Cm- 20 mL
  2. -Lac-3'intron-RBS-RFP(with stop codon)-5'intron M-DT-Cm- 5 mL

September 4th

Make circular RNA

  1. TTHA0715
  2. RFP(without stop codon)
  3. RFP(with stop codon)

Cell body Crush

  1. TTHA0715
  2. RFP(without stop codon)
  3. RFP(with stop codon)

September 5th

SDS-PAGE

  1. GFP
  2. TTHA0715 supernatant1(no wash)
  3. TTHA0715 supernatant2(first wash)
  4. TTHA0715 supernatant3(second wash)
  5. TTHA0715 deposition
  6. TTHA0715 deposition two fold dilution
  7. marker
  8. RFP(without stop codon) supernatant1
  9. RFP(without stop codon) deposition
  10. RFP(with stop codon) supernatant1
  11. RFP(with stop codon) deposition
  12. RFP(without stop codon) supernatant2
  13. RFP(without stop codon) supernatant3
  14. RFP(with stop codon) supernatant2
  15. RFP(with stop codon) supernatant3

September 8th

SDS-PAGE

  1. marker
  2. supernatant
  3. refined RFP


September 9th

HisTag refining


September 10th

SDS-PAGE with 10% gel

  1. TTHA0715 deposition
  2. TTHA0715 supernatant
  3. marker
  4. RFP and fungus bodies
  5. dialyzed RFP
  6. guanidine deposition

September 11th

SDS-PAGE

  1. culture supernatant on September 1st
  2. TTHA0715 supernatant on September 1st
  3. TTHA0715 deposition on September 1st
  4. marker
  5. TTHA0715 supernatant on September 4th
  6. TTHA0715 deposition on September 4th
  7. TTHA0715 guanidine deposition

September 12th

Ligation

  1. promoter + RBS-GFP-DT-Cm
  2. TTHA0715 + 5'intron-DT-Cm
  3. Lac + RBS-GFP-DT-Cm

Transformation

  1. -promoter-RBS-GFP-DT-Cm-
  2. -Lac-3'intron-RBS-TTHA0715-5'intron-DT-Cm-
  3. -BBa_K519010-pSB1C3-
  4. -Lac-RBS-GFP-DT-Cm-

September 13th

RNA Extraction

  1. circular RNA (RFP without stop codon)

Densitometry

  1. circular RNA (RFP without stop codon)

DNase treatment

RNase treatment

reverse transcription PCR

cDNA synthesis

PCR for confirming existence of circular RNA


September 14th

Miniprep

  1. -BBa_K519010-pSB1C3-
  2. -TTHA-5'intron-DT-Cm-

PCR

  1. -BBa_K519010-pSB1C3-
  2. -TTHA-5'intron-DT-Cm-

Ethanol Precipitation


September 15th

Ethanol Precipitation

Densitometry

reverse transcription PCR

PCR


September 16th

RNase treatment

reverse transcription PCR

cDNA synthesis

PCR for confirming existence of circular RNA


September 17th

PCR

  1. EcoRI-SmtA-DT-Cm-XbaI
  2. EcoRI-circularSmtA-SpeI
  3. EcoRI-TTHA0715-5'intron-DT-Cm-XbaI

Gel Extraction

Ligation

  1. Lac-RBS + SmtA-DT-Cm
  2. circularSmtA + 5'intronM-DT-Cm
  3. Lac-3'intron-RBS + TTHA0715-5'intron-DT-Cm
  4. BBa_K823012(promoter) + BBa_E0240(GFP generator)

September 19th

Colony PCR

  1. -Lac-RBS-SmtA-DT-
  2. -circularSmtA-5'intronM-DT-
  3. -Lac-3'intron-RBS-TTHA0715-5'intron-DT-
  4. -BBa_K823012(promoter)-BBa_E0240(GFP generator)-

September 20th

Plasmid Extraction

  1. -BBa_K823012(promoter)-GFP-Cm-
  2. -Lac-RBS-SmtA-DT-Cm-
  3. -Lac-3'intron-RBS-TTHA0715-5'intron-DT-Cm-
  4. -SmtA-5'intronM-DT-Cm-

PCR

  1. -BBa_K823012(promoter)-GFP-Cm-
  2. -Lac-RBS-SmtA-DT-Cm-
  3. -Lac-3'intron-RBS-TTHA0715-5'intron-DT-Cm-
  4. -SmtA-5'intronM-DT-Cm-
  5. EcoRI-SmtA-5'intronM-DT-Cm-XbaI

purification

Restriction Enzyme Digestion

purification

Ligation


September 21th

SDS-PAGE


September 22th

SDS-PAGE

  1. long-chain RFP precipitation
  2. long-chain RFP supernatant
  3. monomeric TTHA0715 precipitation
  4. monomeric TTHA0715 supernatant
  5. long-chain TTHA0715 precipitation
  6. long-chain TTHA0715 supernatant
  7. monomeric SmtA precipitation
  8. monomeric SmtA supernatant
  9. long-chain SmtA precipitation
  10. long-chain SmtA supernatant

Miniprep

  1. -TTHA0715-5'intronM-DT-Cm-
  2. -Lac-3'intron-RBS-SmtA-5'intronM-DT-Cm-
  3. -BBa_K823012(promoter)-GFP-

PCR


September 23th

PCR

Ligation

Transformation


September 24th

Electrophoresis


September 25th

Colony PCR

Liquid culture


September 26th

Miniprep

SDS-PAGE


September 27th

Restriction Enzyme Digestion

Ligation

Transformation


September 28th

SDS-PAGE

Colony PCR


September 30th

SDS-PAGE


October 2nd

RNA extraction

PCR


October 3rd

PCR


October 4th

PCR


October 5th

PCR


October 6th

PCR


October 7th

PCR


October 8th

PCR


October 9th

PCR


October 10th

PCR


October 11th

PCR


October 12th

PCR


October 13th

PCR


October 14th

PCR


October 15th

PCR


October 16th

PCR


October 17th

PCR



Retrieved from "http://2014.igem.org/Team:Gifu/Notebook"