Team:KIT-Kyoto/Notebook/Protocol

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<html>
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<li><a href="/Team:KIT-Kyoto/Notebook/Labnote">LabNote</a></li>   <li class="category">
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     <a href="javascript:void(0)">
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     <font color="#143">(click here!)</font>Protocol
+
     <font color="#143">Click Here To Enlarge</font> Protocol
     </a>
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     </li>
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    <ul class="slidemenu">
+
    <ul class="slidemenu">
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      <a href="">Miniprep
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       <a href="">LB medium
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       <a href="">LB agar
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       <a href="">PCR-2
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       </li>
       <li class="btn">
       <li class="btn">
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       <a href="">YPD broth/YPD medium
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       <a href="">Restriction Digest
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      <li class="btn">
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      <a href="">AGE
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       <a href="">Main Culture
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      <a href="">DNA Refinement 2
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      <a href="">Ligation
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       <a href="">Transformation (E.coli)
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       <a href="">Transformation<br> (<em>E. coli</em>)
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       <li class="btn">
       <li class="btn">
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       <a href="">Pre-culture
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       <a href="">Transformation<br> (<em>S. cerevisiae</em>)
       </a>
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       </li>
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       <li class="btn">
       <li class="btn">
-
       <a href="">Protein extraction (E.coli)
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       <a href="">Preculture
       </a>
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       <li class="btn">
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       <a href="">Colony Sweep
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       <a href="">Main Culture
       </a>
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       <li class="btn">
       <li class="btn">
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       <a href="">AGE
+
       <a href="">Protein Extraction<br> (<em>E. coli</em>)
       </a>
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       </li>
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       <li class="btn">
       <li class="btn">
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       <a href="">PCR
+
       <a href="">Protein Extraction <br>(<em>S. cerevisiae</em>)
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       </li>
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       <li class="btn">
       <li class="btn">
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       <a href="">Ligation
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       <a href="">Colony Sweep
 +
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 +
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 +
      <a href="">SDS-PAGE
       </a>
       </a>
       </li>
       </li>
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       </a>
       </a>
       </li>
       </li>
 +
      <li class="btn">
 +
      <a href="">LB Medium
 +
      </a>
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      <a href="">YPD Medium
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      </a>
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      <a href="">SD Medium
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      <a href="">KOD -Plus- Mutagenesis Kit Protocol No. 1
 +
      </a>
 +
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 +
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 +
      <a href="">KOD -Plus- Mutagenesis Kit Protocol No. 2
 +
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 +
      <a href="">KOD -Plus- Mutagenesis Kit Protocol No. 3
 +
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 +
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 +
      <a href="">KOD -Plus- Mutagenesis Kit Protocol No. 4
 +
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 +
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 +
      <li class="btn">
 +
      <a href="">KOD -Plus- Mutagenesis Kit Protocol No. 5
 +
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 +
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 +
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    <li class="btn">
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</ul>
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  <!--サイドメニュー終わり-->
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   <div id="container">
   <div id="container">
   <div class="main-contents">
   <div class="main-contents">
-
  <div class="scroll">
 
-
  </div>
 
   <h1>Protocol</h1>
   <h1>Protocol</h1>
-
   <div class="accordion">
+
<!-- Miniprep プロトコル -->
-
   <h2><a href="javascript:void(0);">LB Broth/ LB Medium</a></h2>
+
   <div class="scroll">
 +
  </div>
 +
<div class="accordion">
 +
<!--タイトル-->
 +
   <h2><a href="javascript:void(0);">Miniprep</a></h2>
 +
<!--タイトル終わり-->
   <div class="ac">
   <div class="ac">
 +
<!--本文-->
   <p class="sentence">
   <p class="sentence">
 +
<!--materials始まり-->
   <strong>Materials</strong>
   <strong>Materials</strong>
 +
<div class="m_table">
   <table class="materials">
   <table class="materials">
   <tr>
   <tr>
-
     <td>Tryptone
+
     <td>Buffer 1
     </td>
     </td>
-
     <td>final concentration: 1%(w/v)</td>
+
     <td>250μL</td>
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td>Yeast extract
+
     <td>Buffer 2
     </td>
     </td>
-
     <td>final concentration: 0.5%(w/v)</td>
+
     <td>250μL</td>
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td>Sodium chloride F.W. =58.44
+
     <td>Buffer 3</td>
-
    </td>
+
     <td>350μL</td>
-
     <td>final concentration: 1%(w/v)</td>
+
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td colspan="2">5M Sodium hydroxide solution
+
     <td>Buffer 4</td>
-
     </td>
+
     <td>500μL</td>
   </tr>
   </tr>
-
   </table>
+
   <tr>
 +
    <td>Buffer 5</td>
 +
    <td>700μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Distilled water</td>
 +
    <td>100μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Sample</td>
 +
    <td></td>
 +
  </tr>
 +
    </table>
 +
</div>
 +
<!--materials終わり-->
   <br>
   <br>
 +
<!--procedure始まり-->
   <strong>Procedure</strong>
   <strong>Procedure</strong>
   <ul class="procedure">
   <ul class="procedure">
-
     <li>Dissolve tryptone (1.0 g), yeast extract (500 mg) and sodium chloride (1.0 g) in distilled water (90 ml)
+
     <li>Suspend the sample in buffer 1 (1.5 ml sample tube)
     </li>
     </li>
-
     <li>Adjust pH to 7.0 by adding 20μL of 5M sodium chloride
+
     <li>Add buffer 2 to the sample and mix it
     </li>
     </li>
-
     <li>Dilute solution with distilled water and bring volume to 100 ml
+
     <li>Add buffer 3 to the sample and mix it
     </li>
     </li>
-
     <li>Autoclave
+
     <li>Centrifuge for 5 minutes at 13,000 rpm and apply the supernatants to the column
     </li>
     </li>
 +
    <li>Add buffer 4 and centrifuge for 1 minute at 13,000 rpm then throw away the filter paper
 +
    </li>
 +
    <li>Add buffer 5 and centrifuge for 1 minute at 13,000 rpm then throw away the filter paper
 +
    </li>
 +
    <li>Centrifuge again for 1 minute at 13,000 rpm
 +
    </li>
 +
    <li>Place the column on a new sample tube and add 100 μL distilled water
 +
    </li>
 +
    <li>Centrifuge for 1 minute at 6,000 rpm
 +
    </li>
   </ul>
   </ul>
 +
<!--procedure終わり-->
   <br>
   <br>
-
   <strong>Note</strong>
+
<!--Recipes for Buffer始まり-->
-
   <ul class="note">
+
   <strong>Recipes for Buffer</strong>
-
     <li>Add antibiotics to medium at 1/1000
+
<div class="m_table">
 +
  <table class="materials">
 +
  <tr>
 +
    <td>Buffer 1 (Suspension Buffer)
 +
    </td>
 +
    <td>50 mM Tris-HCl and 10 mM EDTA, pH 8.0 (25°C) 50 μg/ml RNase A
 +
    </td>
 +
  </tr>
 +
  <tr>
 +
    <td>Buffer 2 (Lysis Buffer)
 +
    </td>
 +
    <td>0.2 M NaOH and 1% SDS
 +
    </td>
 +
  </tr>
 +
  <tr>
 +
    <td>Buffer 3 (Neutralization and Binding Buffer)
 +
    </td>
 +
    <td>4 M guanidine hydrochloride and 0.5 M potassium acetate, pH 4.2
 +
    </td>
 +
  </tr>
 +
  <tr>
 +
    <td>Buffer 4 (Wash Buffer)
 +
    </td>
 +
    <td>5 M guanidine hydrochloride, 20 mM Tris-HCl, pH 6.6 (25°C) [final conentrations after addition of ethanol] with 38% ethanol</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Buffer 5 (Wash Buffer)
 +
    </td>
 +
    <td>20 mM NaCl, 2 mM Tris-HCl, pH 7.5 (25°C) [final conentrations after addition of ethanol] with 80% ethanol</td>
 +
  </tr> 
 +
    </table>
 +
<!--Recipes for Buffer終わり-->
 +
  <br>
 +
  </p>
 +
<!--本文終わり-->
 +
</div>
 +
  </div>
 +
  </div>
 +
<!--Miniprepプロトコル終わり-->
 +
 
 +
<!--PCR-1-->
 +
  <div class="accordion">
 +
  <div class="scroll">
 +
  </div>
 +
  <h2><a href="javascript:void(0);">PCR-1</a></h2>
 +
  <div class="ac">
 +
  <p class="sentence">
 +
  <strong>Materials</strong>
 +
<div class="m_table">
 +
  <table class="materials">
 +
  <tr>
 +
    <td>Buffer for KOD-FX-NEO</td>
 +
    <td>50μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>dNTP</td>
 +
    <td>20μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Primer mix</td>
 +
    <td>1.0μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Template DNA</td>
 +
    <td>0.5μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>KOD-FX-NEO (TOYOBO)</td>
 +
    <td>2.0μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>H2O</td>
 +
    <td>26.5μL</td>
 +
  </tr>
 +
  <tr>
 +
    <th>Total</th>
 +
    <th>100μL</th>
 +
  </tr>
 +
  </table>
 +
</div>
 +
  <br>
 +
  <strong>Procedure</strong>
 +
   <ul class="procedure">
 +
     <li>Add buffer, dNTP, primer mix, Template DNA, KOD-FX-NEO and distilled water to an Eppendorf tube and mix
     </li>
     </li>
 +
    <li>Place the PCR tubes into the PCR machine and set the program
   </ul>
   </ul>
 +
  <br>
 +
<strong>PCR Profile for KOD-FX-NEO</strong>
 +
<div class="m_table">
 +
  <table class="materials">
 +
  <tr>
 +
    <td>Predenature</td>
 +
    <td>Denature</td>
 +
    <td>Annealing</td>
 +
    <td>Extension</td>
 +
    <td>Final Extension</td>
 +
  </tr>
 +
  <tr>
 +
    <td>98.0°C KOD-FX-NEO</td>
 +
    <td>98.0°C</td>
 +
    <td>51.0°C</td>
 +
    <td>68.0°C</td>
 +
    <td>68.0°C</td>
 +
  </tr>
 +
  <tr>
 +
    <td>2 minutes</td>
 +
    <td>10 seconds</td>
 +
    <td>30 seconds</td>
 +
    <td>1 minute</td>
 +
    <td>2 minutes</td>
 +
  </tr>
 +
  <tr>
 +
    <td>1 cycle</td>
 +
    <td colspan="3" style="background-color:rgba(0,0,0,0.1);">30 cycles</td>
 +
    <td>1 cycle</td>
 +
  </tr>
 +
  </table>
 +
<!--materials始まり-->
 +
<br>
 +
  <strong>PCR Primer Design</strong>
 +
<div class="m_table">
 +
  <table class="materials">
 +
  <tr>
 +
    <th>Lot.No
 +
    </th>
 +
    <th>Oligo</th>
 +
    <th>Base Number</th>
 +
    <th>Sequence</th>
 +
  </tr>
 +
  <tr>
 +
    <td>T14F190235
 +
    </td>
 +
    <td>pGEX6P-2F1</td>
 +
    <td>30</td>
 +
    <td>CACACAGGAACTAGTATTCATGTCCCCTAT</td>
 +
  </tr>
 +
  <tr>
 +
    <td>T14F190236
 +
    </td>
 +
    <td>pGEX6P-2F2</td>
 +
    <td>30</td>
 +
    <td>GGATCTGGAAGTTCTGTTCCACTAGTCCCT</td>
 +
  </tr>
 +
  <tr>
 +
    <td>T14F190237
 +
    </td>
 +
    <td>pGEX6P-2R</td>
 +
    <td>29</td>
 +
    <td>TCATCACCGAAACGCTCGAGGCAGATCGT</td>
 +
  </tr>
 +
    </table>
 +
</div>
 +
<!--PCR Primer Design終わり-->
 +
  <br>
 +
 +
</div>
   <br>
   <br>
   </p>
   </p>
   </div>
   </div>
   </div>
   </div>
 +
<!--PCR-1終わり-->
 +
 +
<!--PCR-2-->
 +
  <div class="accordion">
   <div class="scroll">
   <div class="scroll">
   </div>
   </div>
-
  <div class="accordion">
+
   <h2><a href="javascript:void(0);">PCR-2</a></h2>
-
   <h2><a href="javascript:void(0);">LB Agar</a></h2>
+
   <div class="ac">
   <div class="ac">
   <p class="sentence">
   <p class="sentence">
   <strong>Materials</strong>
   <strong>Materials</strong>
 +
 +
<div class="m_table">
   <table class="materials">
   <table class="materials">
   <tr>
   <tr>
-
     <td>Agar powder
+
     <td>Taq Buffer</td>
-
    </td>
+
     <td>50μL</td>
-
     <td>final concentration: 1.5 %(w/v)</td>
+
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td colspan="2">LB medium
+
     <td>dNTP</td>
-
     </td>
+
    <td>20μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Primer mix</td>
 +
    <td>1.0μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Template DNA</td>
 +
    <td>0.5μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Taq polymerase</td>
 +
    <td>2.0μL</td>
 +
  </tr>
 +
  <tr>  
 +
     <td>H2O</td>
 +
    <td>26.5μL</td>
 +
  </tr>
 +
  <tr>
 +
    <th>Total</th>
 +
    <th>100μL</th>  
   </tr>
   </tr>
   </table>
   </table>
 +
</div>
   <br>
   <br>
-
  </dp>
 
   <strong>Procedure</strong>
   <strong>Procedure</strong>
   <ul class="procedure">
   <ul class="procedure">
-
     <li>Add agar powder (6.0 g) to LB medium (400 ml)
+
     <li>Add buffer, dNTP, primer mix, Template DNA, Taq polymerase and distilled water to an Eppendorf tube and mix
-
    </li>
+
-
    <li>Dissolve it by autoclaving
+
-
    </li>
+
-
    <li>Stir up with magnetic stirrer
+
-
    </li>
+
-
    <li>Cool it down to the room temperature in order to make it to gel form
+
     </li>
     </li>
 +
    <li>Place the PCR tubes into the PCR machine and set the program
   </ul>
   </ul>
   <br>
   <br>
-
   </p>
+
<strong>PCR Profile for KOD-FX-NEO</strong>
 +
<div class="m_table">
 +
  <table class="materials">
 +
  <tr>
 +
    <th>Predenature</th>
 +
    <th>Denature</th>
 +
    <th>Annealing</th>
 +
    <th>Extension</th>
 +
    <th>Final Extension</th>
 +
  </tr>
 +
  <tr>
 +
    <td>98.0°C Taq polymerase</td>
 +
    <td>95.0°C</td>
 +
    <td>53.0°C</td>
 +
    <td>72.0°C</td>
 +
    <td>72.0°C</td>
 +
  </tr>
 +
  <tr>
 +
    <td>30 seconds</td>
 +
    <td>30 seconds</td>
 +
    <td>45 seconds</td>
 +
    <td>2 minutes</td>
 +
    <td>1 minute</td>
 +
  </tr>
 +
  <tr>
 +
    <td>1 cycle</td>
 +
    <td colspan="3" style="background-color:rgba(0,0,0,0.2);">30 cycles</td>
 +
    <td>1 cycle</td>
 +
  </tr>
 +
   </table>
</div>
</div>
 +
  <br>
 +
<!--materials始まり-->
 +
<br>
 +
  <strong>PCR Primer Design</strong>
 +
<div class="m_table">
 +
  <table class="materials">
 +
  <tr>
 +
    <th>Lot.No
 +
    </th>
 +
    <th>Oligo</th>
 +
    <th>Base Number</th>
 +
    <th>Sequence</th>
 +
  </tr>
 +
  <tr>
 +
    <td>T14H280166
 +
    </td>
 +
    <td>Terpinene3-suffix-Spe1</td>
 +
    <td>30</td>
 +
    <td>CAGTCAGTCACGAACTAGTTTAAGGATGGG</td>
 +
  </tr>
 +
  <tr>
 +
    <td>T14H280167
 +
    </td>
 +
    <td>Terpinene3-prefix-Xba1</td>
 +
    <td>30</td>
 +
    <td>CCGGGTTCTAGATGGCTGCATCCACTACTT</td>
 +
  </tr>
 +
  <tr>
 +
    <td>T14H180317
 +
    </td>
 +
    <td>Terpinene3-mutagenesis-FP</td>
 +
    <td>28</td>
 +
    <td>TTGGAGTTCTTGCAGGATTCTCCCGATA</td>
 +
  </tr>
 +
  <tr>
 +
　　<td>T14H180318</td>
 +
    <td>Terpinene3-mutagenesis-RP</td>
 +
    <td>26</td>
 +
    <td>GGCCTCCTTTGTTATTGGATTTGCTG</td>
 +
    </table>
</div>
</div>
 +
<!--PCR Primer Design終わり-->
 +
  <br>
 +
  </p>
 +
  </div>
 +
  </div>
 +
<!--PCR-2終わり-->
 +
 +
<!-- Restriction Digest プロトコル -->
 +
  <div class="scroll">
 +
  </div>
 +
<div class="accordion">
 +
<!--タイトル-->
 +
  <h2><a href="javascript:void(0);">Restriction Digest</a></h2>
 +
<!--タイトル終わり-->
 +
  <div class="ac">
 +
<!--本文-->
 +
  <p class="sentence">
 +
<!--materials始まり-->
 +
  <strong>Materials</strong>
 +
<div class="m_table">
 +
  <table class="materials">
 +
  <tr>
 +
    <td>DNA sample
 +
    </td>
 +
    <td>6μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Buffer
 +
    </td>
 +
    <td>1μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Restriction Enzyme</td>
 +
    <td>0.5μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Distilled water
 +
    </td>
 +
    <td>2.5μL</td>
 +
  </tr>
 +
  </table>
 +
</div>
 +
<!--materials終わり-->
 +
  <br>
 +
<!--procedure始まり-->
 +
  <strong>Procedure</strong>
 +
  <ul class="procedure">
 +
    <li>Add all materials to a tube and mix them gently    </li>
 +
    <li>Incubate at 37˚C for the enzyme reaction for 15 minutes    </li>
 +
  </ul>
 +
<!--procedure終わり-->
 +
  <br>
 +
  <br>
 +
  </p>
 +
<!--本文終わり-->
 +
  </div>
 +
  </div>
 +
<!--Restriction Digestプロトコル終わり-->
 +
 +
<!--AGE-->
   <div class="accordion">
   <div class="accordion">
   <div class="scroll">
   <div class="scroll">
   </div>
   </div>
-
   <h2><a href="javascript:void(0);">YPD Broth/YPD Medium</a></h2>
+
   <h2><a href="javascript:void(0);">AGE</a></h2>
   <div class="ac">
   <div class="ac">
   <p class="sentence">
   <p class="sentence">
Line 220: Line 567:
   <table class="materials">
   <table class="materials">
   <tr>
   <tr>
-
     <td>Peptone 
+
     <td>Sample
     </td>
     </td>
-
     <td>final concentration: 2%(w/v)</td>
+
     <td>5μL</td>
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td>Yeast extract
+
     <td colspan="2">Agarose gel
     </td>
     </td>
-
    <td>final concentration: 1%(w/v)</td>
 
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td>Glucose
+
     <td>2X Loading Buffer Triple Dye (NIPPON GENE)
     </td>
     </td>
-
     <td>final concentration: 2%(w/v)</td>
+
     <td>5μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>1X TAE Buffer
 +
    </td>
 +
    <td></td>
   </tr>
   </tr>
   </table>
   </table>
Line 238: Line 589:
   <strong>Procedure</strong>
   <strong>Procedure</strong>
   <ul class="procedure">
   <ul class="procedure">
-
     <li>Dissolve peptone (2.0 g), yeast extract (1.0 g) and glucose (2.0 g) to distilled water (90 ml)
+
     <li>Set an agarose gel on an electrophoresis chamber
     </li>
     </li>
-
     <li>Dilute solution with distilled water and bring up volume to 100 ml
+
     <li>Add 1X TAE buffer to the electrophoresis chamber
 +
    <br>
 +
    <strong>Note</strong>: Do not generate bubbles under the gel
     </li>
     </li>
-
     <li>Sterilize by autoclave
+
     <li>Add 2X loading buffer to electrophoresis samples
     </li>
     </li>
-
  </ul>
+
    <li>Apply samples on agarose gel wells
-
  <br>
+
    </li>
-
  <strong>Note</strong>
+
    <li>Set an appropriate voltage (100 V) and run the electrophoresis
-
  <ul class="note">
+
    </li>
-
     <li>To make agar plate, add agar powder (final concentration: 1.5%) at procedure 1.
+
    <li>Stop the electrophoresis when the BPB reaches 2/3 of the gel
 +
     </li>
 +
    <li>Soak the gel in EtBr (ethidium bromide) solution and dye it for 20 minutes
 +
    </li>
 +
    <li>Place plastic cooking wrap on the trans-illuminator and irradiate UV to the gel on the wrap
 +
    </li>
 +
    <li>Take photographs of the gel by using a trans-illuminator
     </li>
     </li>
   </ul>
   </ul>
 +
  <br>
 +
  <strong>Agarose Concentration Versus Optical Range of DNA Size</strong>
 +
<div class="m_table">
 +
  <table class="materials">
 +
  <tr>
 +
    <td>Agarose Concentration (%)
 +
    </td>
 +
    <td>DNA (kbp)</td>
 +
  </tr>
 +
  <tr>
 +
    <td>0.3</td>
 +
    <td>5-60</td>
 +
  </tr>
 +
  <tr>
 +
    <td>0.6</td>
 +
    <td>1-20</td>
 +
  </tr>
 +
  <tr>
 +
    <td>1.0</td>
 +
    <td>0.3-7</td>
 +
  </tr>
 +
  <tr>
 +
    <td>1.5</td>
 +
    <td>0.2-4</td>
 +
  </tr>
 +
  <tr>
 +
    <td>2.0</td>
 +
    <td>0.1-2</td>
 +
  </tr>
 +
  </table>
 +
</div>
   <br>
   <br>
   </p>
   </p>
</div>
</div>
</div>
</div>
 +
<!--AGE終わり-->
 +
 +
<!-- DNA Refinement 1プロトコル -->
   <div class="scroll">
   <div class="scroll">
-
   </div>
+
   </div>  
-
  <div class="accordion">
+
<div class="accordion">
-
   <h2><a href="javascript:void(0);">Main Culture</a></h2>
+
<!--タイトル-->
 +
   <h2><a href="javascript:void(0);">DNA Refinement 1</a></h2>
 +
<!--タイトル終わり-->
   <div class="ac">
   <div class="ac">
 +
<!--本文-->
   <p class="sentence">
   <p class="sentence">
 +
<!--materials始まり-->
   <strong>Materials</strong>
   <strong>Materials</strong>
 +
<div class="m_table">
   <table class="materials">
   <table class="materials">
-
  <tr>
+
  <tr>
-
     <td>LB medium
+
     <td>DNA sample
     </td>
     </td>
-
     <td>100ml</td>
+
     <td>200μL</td>
-
  </tr>
+
  </tr>
-
  <tr>
+
  <tr>
-
     <td>IPTG
+
     <td>distilled H2O
     </td>
     </td>
-
     <td>10μL</td>
+
     <td>400μL</td>
-
  </tr>
+
  </tr>
-
  <tr>
+
  <tr>
-
     <td>Sample
+
     <td>CH3COONa</td>
 +
    <td>50μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Phe/Chl 
     </td>
     </td>
-
     <td>500μL</td>
+
     <td>700μL</td>
-
  </tr>
+
  </tr>
 +
  <tr>
 +
    <td>Isopropyl alcohol 
 +
    </td>
 +
    <td>750μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>75% Ethanol 
 +
    </td>
 +
    <td>1000μL</td>
 +
  </tr>
   </table>
   </table>
 +
</div>
 +
<!--materials終わり-->
   <br>
   <br>
 +
<!--procedure始まり-->
   <strong>Procedure</strong>
   <strong>Procedure</strong>
   <ul class="procedure">
   <ul class="procedure">
-
     <li>Add samples to LB medium, cultivate at 37°C in shaken culture (120 rpm) until reaching a cell density of OD600 0.5A
+
     <li>Add materials (DNA, H2O, CH3COONa, and Phe/Chl) to sample tube and vortex
 +
    </li>
 +
    <li>Centrifuge at 14,500 rpm for 10 minutes at room temperature
 +
    </li>
 +
    <li>Transfer the supernatant to a new sample tube</li>
 +
    <li>Add 750 μL of isopropyl alcohol to the sample tube and vortex
 +
    </li>
 +
    <li>Centrifuge at 14,500 rpm for 10 minutes at 4°C
 +
    </li>
 +
    <li>Remove isopropyl alcohol gently so that the pellet will not break
 +
    </li>
 +
    <li>Add 1,000 μL of 75% ethanol and centrifuge at 14,500 rpm for 5 minutes at 4°C
     </li>
     </li>
-
     <li>Add IPTG (10 μL) to the sample (25 ml)
+
     <li>Dry it by aspirator for 10 minutes
     </li>
     </li>
-
     <li>Cultivate at 37°C in shaken culture (120 rpm) for 3 hours
+
     <li>Add 25 μL of distilled H2O and mix
     </li>
     </li>
   </ul>
   </ul>
 +
<!--procedure終わり-->
   <br>
   <br>
 +
<!--note始まり-->
   <strong>Note</strong>
   <strong>Note</strong>
   <ul class="note">
   <ul class="note">
-
     <li>
+
     <li>Phe/Chl composition    Phenol:Chloroform:Isoamyl alcohol=25:24:1</li>
 +
  </ul>
 +
<!--note終わり-->
 +
  <br>
 +
  </p>
 +
<!--本文終わり-->
 +
  </div>
 +
  </div>
 +
<!--DNA refinement 1プロトコル終わり-->
 +
 
 +
 
 +
<!-- DNA Refinement 2プロトコル -->
 +
  <div class="scroll">
 +
  </div>
 +
<div class="accordion">
 +
<!--タイトル-->
 +
  <h2><a href="javascript:void(0);">DNA Refinement 2</a></h2>
 +
<!--タイトル終わり-->
 +
  <div class="ac">
 +
<!--本文-->
 +
  <p class="sentence">
 +
<!--materials始まり-->
 +
  <strong>Materials</strong>
 +
<div class="m_table">
 +
  <table class="materials">
 +
  <tr>
 +
    <td>sample
 +
    </td>
 +
    <td>30μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Bacterial Alkaline Phosphatase (BAP)
 +
    </td>
 +
    <td>1μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Low melting agarose gel</td>
 +
    <td></td>
 +
  </tr>
 +
  <tr>
 +
    <td>6×Loading Buffer Double Dye
 +
    </td>
 +
    <td>5μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Distilled water 
 +
    </td>
 +
    <td>200μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Phenol
 +
    </td>
 +
    <td></td>
 +
  </tr>
 +
  <tr>
 +
    <td>Phe/Chl
 +
    </td>
 +
    <td></td>
 +
  </tr>
 +
  <tr>
 +
    <td>Isopropyl alcohol
 +
    </td>
 +
    <td>750μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>5M CH3COONa
 +
    </td>
 +
    <td>50μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>70% Ethanol
 +
    </td>
 +
    <td>1000μL</td>
 +
  </tr>
 +
  </table>
 +
</div>
 +
<!--materials終わり-->
 +
  <br>
 +
<!--procedure始まり-->
 +
  <strong>Procedure</strong>
 +
  <ul class="procedure">
 +
    <li>Add BAP to vector and dephosphorize for 30 minutes at 37°C
 +
    </li>
 +
    <li>Run the electrophoresis with agarose gel
 +
    </li>
 +
    <li>Cut out the targeted band and mix with 200 μL of distilled water in a tube</li>
 +
    <li>Heat the sample for 5 minutes at 65°C
 +
    </li>
 +
    <li>Add the same amount of phenol as the sample and vortex
 +
    </li>
 +
    <li>Centrifuge at 14,500 rpm for 10 minutes at room temperature and apply the supernatant to the new sample tube
 +
    </li>
 +
    <li>Add the same amount of Phe/Chl as the sample and vortex
 +
    </li>
 +
    <li>Centrifuge at 14,500 rpm for 5 minutes at room temperature and apply the supernatant to the sample tube
 +
    </li>
 +
    <li>Add 750 μL of Isopropyl alcohol and 50 μL of CH3COONa and centrifuge at 14,500rpm for 10 minutes at 4°C
 +
    </li>
 +
    <li>Rinse with 70% ethanol at 14,500 rpm 5 minutes at 4°C</li>
 +
    <li>Dry it for 15 minutes</li>
 +
  </ul>
 +
<!--procedure終わり-->
 +
  <br>
 +
  </p>
 +
<!--本文終わり-->
 +
  </div>
 +
  </div>
 +
<!--DNA refinement 2プロトコル終わり-->
 +
 
 +
<!--Ligation-->
 +
  <div class="accordion">
 +
  <div class="scroll">
 +
  </div>
 +
  <h2><a href="javascript:void(0);">Ligation</a></h2>
 +
  <div class="ac">
 +
  <p class="sentence">
 +
  <strong>Materials</strong>
 +
  <table class="materials">
 +
  <tr>
 +
    <td>DNA sample
 +
    </td>
 +
    <td>5μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>DNA ligase (Ligation High from Nippon gene)
 +
    </td>
 +
    <td>5μL</td>
 +
  </tr>
 +
  </table>
 +
  <br>
 +
  <strong>Procedure</strong>
 +
  <ul class="procedure">
 +
    <li>Mix DNA sample and DNA ligase in a sample tube gently
 +
    </li>
 +
    <li>Ligation for 15 minutes at room temperature
     </li>
     </li>
   </ul>
   </ul>
Line 299: Line 861:
</div>
</div>
</div>
</div>
 +
<!--Ligation終わり-->
 +
 +
<!--Transformation-->
   <div class="accordion">
   <div class="accordion">
   <div class="scroll">
   <div class="scroll">
   </div>
   </div>
-
   <h2><a href="javascript:void(0);">Transformation (E.coli)</a></h2>
+
   <h2><a href="javascript:void(0);">Transformation (<em>E. coli</em>)</a></h2>
   <div class="ac">
   <div class="ac">
   <p class="sentence">
   <p class="sentence">
Line 308: Line 873:
   <table class="materials">
   <table class="materials">
   <tr>
   <tr>
-
     <td>Sample
+
     <td>DNA Sample
     </td>
     </td>
     <td>10μL</td>
     <td>10μL</td>
Line 315: Line 880:
     <td>Competent cell
     <td>Competent cell
     </td>
     </td>
-
     <td> 20μL</td>
+
     <td> 50μL</td>
     </tr>
     </tr>
   </table>
   </table>
Line 325: Line 890:
     <li>Add 10 μL of sample into thawed competent cells
     <li>Add 10 μL of sample into thawed competent cells
     </li>
     </li>
-
     <li>Cool an Eppendorf tube, which contains competent cells and samples, with ice for one hour, then Heat shock the cells by immersion in pre-hearted water bath at 41°C for 30 seconds
+
     <li>Cool the sample tube, which contains competent cells and DNA samples, with ice for 1 hour, then Heat shock the cells by immersion in pre-hearted water bath at 42°C for 30 seconds
     </li>
     </li>
     <li>Place the tube on ice for 2 minutes to cool it down
     <li>Place the tube on ice for 2 minutes to cool it down
Line 335: Line 900:
     <li>Harvest the cells by centrifuge
     <li>Harvest the cells by centrifuge
     </li>
     </li>
-
     <li>Seed the transformed competent cells onto the agar plate and incubate it at 37°C overnight
+
     <li>Spread the transformed competent cells onto the agar plate and incubate it at 37°C overnight
     </li>
     </li>
   </ul>
   </ul>
Line 342: Line 907:
</div>
</div>
</div>
</div>
 +
<!--Transformation終わり-->
 +
 +
<!--Transformation-->
   <div class="accordion">
   <div class="accordion">
   <div class="scroll">
   <div class="scroll">
   </div>
   </div>
-
   <h2><a href="javascript:void(0);">Pre-culture</a></h2>
+
   <h2><a href="javascript:void(0);">Transformation (<em>S. cerevisiae</em>)</a></h2>
   <div class="ac">
   <div class="ac">
   <p class="sentence">
   <p class="sentence">
Line 352: Line 920:
   <tr>
   <tr>
     <td>Sample
     <td>Sample
 +
    </td>
 +
    <td>5μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Competent cells
 +
    </td>
 +
    <td> 95μL</td>
 +
    </tr>
 +
  <tr>
 +
    <td>YPD plate containing G418
 +
    </td>
 +
    <td></td>
 +
    </tr>
 +
  </table>
 +
  <br>
 +
  <strong>Procedure</strong>
 +
  <ul class="procedure">
 +
    <li>Cool down a cuvette for 5 minutes on ice
 +
    </li>
 +
    <li>Harvest the yeast cells by centrifuge at 4 °C
 +
    </li>
 +
    <li>Suspend the cells in 20 ml of cold 1M sorbitol and harvest by centrifuge at 4 °C (2times)
 +
    </li>
 +
    <li>Suspend the cells in 500μL of cold 1M sorbitol
 +
    </li>
 +
    <li>Mix DNA sample (5 μL) and the cell suspension (95 μL) in a cold cuvette
 +
    </li>
 +
    <li>Electroporate under the following conditions: 200 Ω, 25 μF and 1.5 kV
 +
    </li>
 +
    <li>Immediately inoculate on YPD plates containing G418
 +
    </li>
 +
    <li>Incubate at 30 °C for 2 days
 +
    </li>
 +
  </ul>
 +
  <br>
 +
  </p>
 +
</div>
 +
</div>
 +
<!--Transformation終わり-->
 +
 +
<!--Preculture-->
 +
  <div class="accordion">
 +
  <div class="scroll">
 +
  </div>
 +
  <h2><a href="javascript:void(0);">Preculture</a></h2>
 +
  <div class="ac">
 +
  <p class="sentence">
 +
  <strong>Materials</strong>
 +
<div class="m_table">
 +
  <table class="materials">
 +
  <tr>
 +
    <td>Sample (<em>E. coli</em> cells )
     </td>
     </td>
     <td></td>
     <td></td>
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td>Medium
+
     <td>Medium (LB medium with appropriate antibiotics)
     </td>
     </td>
     <td>20ml</td>
     <td>20ml</td>
   </tr>  
   </tr>  
   </table>
   </table>
 +
</div>
   <br>
   <br>
   <strong>Procedure</strong>
   <strong>Procedure</strong>
   <ul class="procedure">
   <ul class="procedure">
-
     <li>Scrape samples from the agar plate and inoculate them on medium
+
     <li>Scrape samples from the agar plate and inoculate them in liquid media
     </li>
     </li>
-
     <li>Cultivate at 37°C in a shaken culture overnight
+
     <li>Cultivate overnight (37℃, 120 rpm)
     </li>
     </li>
   </ul>
   </ul>
Line 373: Line 994:
</div>
</div>
</div>
</div>
 +
<!--Preculture終わり-->
 +
 +
<!--Main Culture-->
 +
  <div class="scroll">
 +
  </div>
 +
  <div class="accordion">
 +
  <h2><a href="javascript:void(0);">Main Culture</a></h2>
 +
  <div class="ac">
 +
  <p class="sentence">
 +
  <strong>Materials</strong>
 +
<div class="m_table">
 +
  <table class="materials">
 +
  <tr>
 +
    <td>LB medium
 +
    </td>
 +
    <td>100ml</td>
 +
  </tr>
 +
  <tr>
 +
  <td>IPTG</td>
 +
  <td>10μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Sample
 +
    </td>
 +
    <td>500μL</td>
 +
  </tr>
 +
  </table>
 +
</div>
 +
  <br>
 +
  <strong>Procedure</strong>
 +
  <ul class="procedure">
 +
    <li>Add samples to LB medium and cultivate (37°C, 120 rpm) until reaching a cell density of OD600=0.5</li>
 +
    <li>Add IPTG (10 μL) to the medium (25 ml)</li>
 +
    <li>Further cultivation for 3 hours
 +
    </li>
 +
  </ul>
 +
  <br>
 +
  </p>
 +
</div>
 +
</div>
 +
<!--Main Culture終わり-->
 +
 +
<!--Protein Extraction-->
   <div class="accordion">
   <div class="accordion">
   <div class="scroll">
   <div class="scroll">
   </div>
   </div>
-
   <h2><a href="javascript:void(0);">Protein Extraction (E.coli)</a></h2>
+
   <h2><a href="javascript:void(0);">Protein Extraction (<em>E. coli</em>)</a></h2>
   <div class="ac">
   <div class="ac">
   <p class="sentence">
   <p class="sentence">
   <strong>Materials</strong>
   <strong>Materials</strong>
 +
<div class="m_table">
   <table class="materials">
   <table class="materials">
   <tr>
   <tr>
Line 387: Line 1,052:
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td colspan="2">Fast Break Cell Lysis Reagent, 10X (Promega)
+
     <td colspan="2">FastBreak Cell Lysis Reagent, 10X (Promega)
     </td>
     </td>
   </tr>
   </tr>
Line 399: Line 1,064:
   </tr>
   </tr>
   </table>
   </table>
 +
</div>
   <br>
   <br>
   <strong>Procedure</strong>
   <strong>Procedure</strong>
Line 406: Line 1,072:
     <li>Add potassium phosphate buffer, then mix and remove medium completely
     <li>Add potassium phosphate buffer, then mix and remove medium completely
     </li>
     </li>
-
     <li>Add Fast Break Cell Lysis Reagent, 10X at the ratio of Fast Break Buffer Cell Lysis Readent,10X: Samples=1:9 and extract protein for 15 minutes at room temperature
+
     <li>Add FastBreak Cell Lysis Reagent, 10X at the ratio of FastBreak Buffer Cell Lysis Reagent,10X: Samples=1:9 and extract protein for 15 minutes at room temperature
     </li>
     </li>
   </ul>
   </ul>
Line 413: Line 1,079:
</div>
</div>
</div>
</div>
 +
<!--Protein Extraction終わり-->
 +
 +
<!--Protein Extraction-->
   <div class="accordion">
   <div class="accordion">
   <div class="scroll">
   <div class="scroll">
   </div>
   </div>
-
   <h2><a href="javascript:void(0);">Colony Sweep</a></h2>
+
   <h2><a href="javascript:void(0);">Protein Extraction (<em>S. cerevisiae</em>)</a></h2>
   <div class="ac">
   <div class="ac">
   <p class="sentence">
   <p class="sentence">
   <strong>Materials</strong>
   <strong>Materials</strong>
 +
<div class="m_table">
   <table class="materials">
   <table class="materials">
   <tr>
   <tr>
-
     <td colspan="2">Sample
+
     <td>Glass Beads
     </td>
     </td>
 +
    <td></td>
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td>Phe-Chl
+
     <td colspan="2">50 mM potassium phosphate buffer (pH6.8)
     </td>
     </td>
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td>Cracking solution
+
     <td colspan="2">SDS sample buffer
     </td>
     </td>
   </tr>
   </tr>
   </table>
   </table>
 +
</div>
   <br>
   <br>
   <strong>Procedure</strong>
   <strong>Procedure</strong>
   <ul class="procedure">
   <ul class="procedure">
-
     <li>Dispense cracking solution (50 μL) each into Eppendorf tubes
+
     <li>Harvest yeast cells by centrifuge at 3,000 rpm for 4 minutes at room temperature
 +
    </li>   
 +
<li>Wash cells once with potassium phosphate buffer
     </li>
     </li>
-
     <li>Collect the sample and suspend it into cracking solution
+
     <li>Cool down the sample tube on ice for 1 minute
     </li>
     </li>
-
     <li>Incubate at 65°C for 10 minutes
+
     <li>Add the same amount of glass beads as the sample then add 20 μL of potassium phosphate buffer and mix
     </li>
     </li>
-
     <li>Add Phe-Chl and BPB pigment and vortex
+
     <li>Disrupt the cells by FastPrep 24 (MP Biochemicals) for 45 seconds at speed 4.5
     </li>
     </li>
-
     <li>Centrifuge at 14,000 rpm for 5 minutes
+
     <li>Cool down the sample tube on ice for 1 minute
     </li>
     </li>
-
     <li>Check the bands by agar gel electrophoresis
+
     <li>Add 80 µl of potassium phosphate buffer, cool it down and centrifuge for 5 minutes at 14,500 rpm at 4°C
 +
    </li>
 +
    <li>Transfer 40 µl of the supernatant and mix with 8 µl of SDS sample buffer
 +
    </li>
 +
    <li>Treat the sample with heat for 5 minutes at 100˚C
     </li>
     </li>
   </ul>
   </ul>
Line 454: Line 1,132:
</div>
</div>
</div>
</div>
 +
<!--Protein Extraction終わり-->
 +
 +
<!--Colony Sweep-->
   <div class="accordion">
   <div class="accordion">
   <div class="scroll">
   <div class="scroll">
   </div>
   </div>
-
   <h2><a href="javascript:void(0);">AGE</a></h2>
+
   <h2><a href="javascript:void(0);">Colony Sweep</a></h2>
   <div class="ac">
   <div class="ac">
   <p class="sentence">
   <p class="sentence">
   <strong>Materials</strong>
   <strong>Materials</strong>
 +
<div class="m_table">
   <table class="materials">
   <table class="materials">
   <tr>
   <tr>
-
     <td>{Sample}
+
     <td colspan="2">Sample
     </td>
     </td>
-
    <td>5μL</td>
 
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td colspan="2">Agarose gel
+
     <td>Phenol/Chloroform water-saturated solution (Phe/Chl)
     </td>
     </td>
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td>2X Loading Buffer Triple Dye (NIPPON GENE)
+
     <td>Cracking solution 3% w/v SDS, 50 mM Tris-base, pH12.6
     </td>
     </td>
-
    <td>5μL</td>
 
-
  </tr>
 
-
  <tr>
 
-
    <td>1X TAE Buffer
 
-
    </td>
 
-
    <td></td>
 
   </tr>
   </tr>
   </table>
   </table>
 +
</div>
   <br>
   <br>
   <strong>Procedure</strong>
   <strong>Procedure</strong>
   <ul class="procedure">
   <ul class="procedure">
-
     <li>Set an agarose gel on an electrophoresis chamber
+
     <li>Dispense cracking solution (50 μL) each into sample tubes
     </li>
     </li>
-
     <li>Add 1X TAE buffer to the electrophoresis chamber
+
     <li>Collect the sample and suspend it into cracking solution
-
    <br>
+
-
    <strong>Note</strong>: Do not generate bubbles under the gel
+
     </li>
     </li>
-
     <li>Add 2X loading buffer to electrophoresis samples
+
     <li>Incubate at 65°C for 10 minutes
     </li>
     </li>
-
     <li>Apply samples on agarose gel wells
+
     <li>Add Phe/Chl and BPB pigment and vortex
     </li>
     </li>
-
     <li>Set an appropriate voltage and run the electrophoresis
+
     <li>Centrifuge at 14,000 rpm for 5 minutes
     </li>
     </li>
-
     <li>Stop the electrophoresis when the BPB reaches 2/3 of the gel
+
     <li>Apply the samples (upper layer) to agarose gel with loading dye
     </li>
     </li>
-
     <li>Soak the gel in ethidium bromide and dye it for 20 minutes
+
     <li>Check the bands by agar gel electrophoresis
     </li>
     </li>
-
     <li>Place plastic cooking wrap on the trans-illuminator and irradiate UV to the gel on the wrap
+
 
 +
  </ul>
 +
  <br>
 +
  </p>
 +
</div>
 +
</div>
 +
<!--Colony Sweep終わり-->
 +
 
 +
<!-- SDS-PAGEプロトコル -->
 +
  <div class="scroll">
 +
  </div>
 +
<div class="accordion">
 +
<!--タイトル-->
 +
  <h2><a href="javascript:void(0);">SDS-PAGE</a></h2>
 +
<!--タイトル終わり-->
 +
  <div class="ac">
 +
<!--本文-->
 +
  <p class="sentence">
 +
<!--materials始まり-->
 +
  <strong>Materials</strong>
 +
<div class="m_table">
 +
  <table class="materials">
 +
  <tr>
 +
    <td>Sample
 +
    </td>
 +
    <td></td>
 +
  </tr>
 +
  <tr>
 +
    <td>Separating Gel
 +
    </td>
 +
    <td></td>
 +
  </tr>
 +
  <tr>
 +
    <td>Stacking Gel</td>
 +
    <td></td>
 +
  </tr>
 +
    </table>
 +
</div>
 +
<!--materials終わり-->
 +
  <br>
 +
<!--procedure始まり-->
 +
  <strong>Procedure</strong>
 +
  <ul class="procedure">
 +
     <li>Place stacking gel on separating gel
     </li>
     </li>
-
     <li>Take photographs of the gel by using a trans-illuminator
+
     <li>Rinse the wells of gel with distilled water
 +
    </li>
 +
    <li>Load prepared samples into wells
 +
    </li>
 +
    <li>Run the electrophoresis (25 mA for 75 min)
 +
    </li>
 +
    <li>Check the bands with CBB stain
     </li>
     </li>
   </ul>
   </ul>
 +
<!--procedure終わり-->
   <br>
   <br>
-
  <strong>Agarose Concentration Versus Optical Range of DNA Size</strong>
+
<!--Separating Gel始まり-->
 +
  <strong>Separating Gel</strong>
 +
<div class="m_table">
 +
  <table class="materials">
 +
  <tr>
 +
    <td>Acylamide (%)
 +
    </td>
 +
    <td>7.5</td>
 +
    <td>10</td>
 +
    <td>12.5</td>
 +
    <td>15</td>
 +
    <td>17.5</td>
 +
  </tr>
 +
  <tr>
 +
    <td>MilliQ H2O (ml)
 +
    </td>
 +
    <td>3.89</td>
 +
    <td>3.22</td>
 +
    <td>2.55</td>
 +
    <td>1.87</td>
 +
    <td>1.2</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Acrylamide/Bis-acrylamide (30%/0.8% w/v)</td>
 +
    <td>1.99</td>
 +
    <td>2.7</td>
 +
    <td>3.38</td>
 +
    <td>4.04</td>
 +
    <td>4.7</td>
 +
  </tr>
 +
  <tr>
 +
    <td>1.5M Tris-HCl(pH8.8) (ml)</td>
 +
    <td>2</td>
 +
    <td>2</td>
 +
    <td>2</td>
 +
    <td>2</td>
 +
    <td>2</td>
 +
  </tr>
 +
  <tr>
 +
    <td>10% (w/v)SDS (μL) </td>
 +
    <td>80</td>
 +
    <td>80</td>
 +
    <td>80</td>
 +
    <td>80</td>
 +
    <td>80</td>
 +
  </tr>
 +
  <tr>
 +
    <td>10% (w/v) ammonium persulfate (AP) (μL)</td>
 +
    <td>27</td>
 +
    <td>27</td>
 +
    <td>27</td>
 +
    <td>27</td>
 +
    <td>27</td>
 +
  </tr>
 +
  <tr>
 +
    <td>TEMED (μL)</td>
 +
    <td>4</td>
 +
    <td>4</td>
 +
    <td>4</td>
 +
    <td>4</td>
 +
    <td>4</td>
 +
  </tr>
 +
    </table>
 +
</div>
 +
<!--Separating Gel終わり-->
 +
  <br>
 +
<!--Stacking Gel始まり-->
 +
  <strong>Stacking Gel</strong>
 +
<div class="m_table">
 +
  <table class="materials">
 +
  <tr>
 +
    <td>MilliQ H2O (ml)
 +
    </td>
 +
    <td>2.89</td>
 +
  </tr>
 +
  <tr>
 +
    <td>30% (w/v) acrylamide (ml)</td>
 +
    <td>0.79</td>
 +
  </tr>
 +
  <tr>
 +
    <td>0.5M Tris-HCl(pH6.8) (ml)</td>
 +
    <td>1.25</td>
 +
  </tr>
 +
  <tr>
 +
    <td>10% SDS (μL) (ml)</td>
 +
    <td>50</td>
 +
  </tr>
 +
<tr>
 +
    <td>10% APS (μL) (ml)</td>
 +
    <td>17</td>
 +
  </tr>
 +
<tr>
 +
    <td>TEMED (μl) (ml)</td>
 +
    <td>5</td>
 +
  </tr>
 +
    </table>
 +
</div>
 +
<!--Stacking Gel終わり-->
 +
  <br>
 +
  </p>
 +
<!--本文終わり-->
 +
  </div>
 +
  </div>
 +
<!--SDS-PAGEプロトコル終わり-->
 +
 
 +
<!--Western Brotting-->
 +
  <div class="accordion">
 +
  <div class="scroll">
 +
  </div>
 +
  <h2><a href="javascript:void(0);">Western Blotting</a></h2>
 +
  <div class="ac">
 +
  <p class="sentence">
 +
  <strong>Materials</strong>
 +
<div class="m_table">
   <table class="materials">
   <table class="materials">
   <tr>
   <tr>
-
     <td>Agarose Gel (%)
+
     <td>BufferⅠ
     </td>
     </td>
-
     <td>DNA (kbp)</td>
+
     <td> 0.3 M Tris base, 20% MetOH (pH 10.9)</td>
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td>0.3</td>
+
     <td>BufferⅡ
-
     <td>5-60</td>
+
    </td>
 +
     <td>25 mM Tris base, 20% MetOH</td>
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td>0.6</td>
+
     <td>BufferⅢ
-
     <td>1-20</td>
+
    </td>
 +
     <td>25 mM Tris base, 0.05 mM Boric acid, 20% MetOH (pH 9.5)</td>
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td>1.0</td>
+
     <td>PBS
-
     <td>0.3-7</td>
+
    </td>
 +
     <td>137 mM NaCl, 8.1 mM Na2HPO4 (12H2O), 2.68 mM KCl, 1.47 mM KH2PO4</td>
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td>1.5</td>
+
     <td>PBS-S
-
     <td>0.2-4</td>
+
    </td>
 +
     <td>PBS including 0.1% skim milk</td>
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td>2.0</td>
+
     <td>PBS-T
-
     <td>0.1-2</td>
+
    </td>
 +
     <td>PBS including 0.05% Tween20</td>
   </tr>
   </tr>
-
  </table>
 
-
 
-
  <br>
 
-
  </p>
 
-
</div>
 
-
</div>
 
-
  <div class="accordion">
 
-
  <div class="scroll">
 
-
  </div>
 
-
  <h2><a href="javascript:void(0);">PCR</a></h2>
 
-
  <div class="ac">
 
-
  <p class="sentence">
 
-
  <strong>Materials</strong>
 
-
  <table class="materials">
 
   <tr>
   <tr>
-
     <td>Buffer for KOD-FX-NEO</td>
+
     <td>PBS-TS
-
     <td>50μL</td>
+
    </td>
 +
     <td>PBS including 0.1% skim milk & 0.05% Tween20</td>
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td>dNTP</td>
+
     <td>PonceauS (Sigma) </td>
-
     <td>20μL</td>
+
     <td></td>
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td>Primer mix</td>
+
     <td>PVDF membrane (Immobilon Transfer membrane by Millipore)
-
     <td>1.0μL</td>
+
    </td>
 +
     <td>1 sheet</td>
   </tr>
   </tr>
-
   <tr>  
+
   <tr>
-
     <td>Sample</td>
+
     <td>Whatman paper (Whatman 3MM)
-
     <td>0.5μL</td>
+
 
 +
    </td>
 +
     <td></td>
   </tr>
   </tr>
-
   <tr>  
+
   <tr>
-
     <td>KOD-FX-NEO (TOYOBO)</td>
+
     <td>Hybridization bag (Cosmo Bio)
-
     <td>2.0μL</td>
+
    </td>
 +
     <td></td>
   </tr>
   </tr>
-
   <tr>  
+
   <tr>
-
     <td>H2O</td>
+
     <td>Peroxidase Stain Kit (Nacalai Tesque)
-
     <td>26.5μL</td>
+
    </td>
 +
     <td></td>
   </tr>
   </tr>
-
   <tr>  
+
   <tr>
-
     <th>Total</th>
+
     <td>Anti-GST antibody conjugated with HRP (Wako)
-
     <th>100μL</th>  
+
    </td>
 +
     <td></td>
   </tr>
   </tr>
   </table>
   </table>
 +
</div>
   <br>
   <br>
   <strong>Procedure</strong>
   <strong>Procedure</strong>
   <ul class="procedure">
   <ul class="procedure">
-
     <li>Add buffer, dNTP, primer mix, sample, KOD-FX-NEO and distilled water to an Eppendorf tube and mix
+
     <li>Cut the gel in appropriate size
 +
    </li>
 +
    <li>Soak gel in buffer III and shake gently for 15 minutes
 +
    </li>
 +
    <li>Soak the membrane on methanol then transfer it in buffer III
 +
    </li>
 +
    <li>Soak Whatman papers (all in the same size) in Buffer I (2 sheets), Buffer II (1 sheet) and Buffer III (3 sheets) respectively
 +
    </li>
 +
    <li>Wet the surface of the blotter</li>
 +
<li>Put items in the following order: Buffer III paper, gel, membrane, Buffer II paper and Buffer I paper</li>
 +
<li>Blot at the constant current of membrane's area ×2.5 mA for 20 minutes</li>
 +
<li>Dye the membrane with Ponceau S for 5 minutes, rinse it with distilled water and scan it</li>
 +
<li>Shake and wash with PBS-TS (3 minutes ×3times)</li>
 +
<li>The membrane was incubated with anti-GST antibody containing HRP in PBS-S at room temperature for 1 hour</li>
 +
<li>Wash with PBS-T twice (5 minutes/10 minutes)</li>
 +
<li>Wash with PBS twice (5 minutes/5 minutes)</li>
 +
<li>Stain the membrane using Peroxidase Stain Kits</li>
 +
<li>Scan it</li>
 +
</ul>
 +
<br><br></p>
 +
</div>
 +
</div>
 +
<!--Westone Botting終わり-->
 +
 
 +
<!-- LB Brothプロトコル -->
 +
  <div class="scroll">
 +
  </div>
 +
<div class="accordion">
 +
<!--タイトル-->
 +
  <h2><a href="javascript:void(0);">LB Medium</a></h2>
 +
<!--タイトル終わり-->
 +
  <div class="ac">
 +
<!--本文-->
 +
  <p class="sentence">
 +
<!--materials始まり-->
 +
  <strong>Materials</strong>
 +
<div class="m_table">
 +
  <table class="materials">
 +
  <tr>
 +
    <td>Tryptone
 +
    </td>
 +
    <td>final concentration: 1%(w/v)</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Yeast Extract
 +
    </td>
 +
    <td>final concentration: 0.5%(w/v)</td>
 +
  </tr>
 +
  <tr>
 +
    <td>NaCl</td>
 +
    <td>final concentration: 1%(w/v)</td>
 +
  </tr>
 +
  <tr>
 +
    <td colspan="2">5M NaOH
 +
    </td>
 +
  </tr>
 +
  </table>
 +
</div>
 +
<!--materials終わり-->
 +
  <br>
 +
<!--procedure始まり-->
 +
  <strong>Procedure</strong>
 +
  <ul class="procedure">
 +
    <li>Dissolve Tryptone (1.0 g), Yeast Extract (500 mg) and NaCl (1.0 g) in distilled water (90 ml)
 +
    </li>
 +
    <li>Adjust pH to 7.0 by adding 20 μL of 5M NaOH
 +
    </li>
 +
    <li>Fill up to 100 ml with distilled water</li>
 +
    <li>Autoclave
     </li>
     </li>
-
    <li>Clone
 
   </ul>
   </ul>
 +
<!--procedure終わり-->
 +
  <br>
 +
<!--note始まり-->
 +
  <strong>Note</strong>
 +
  <ul class="note">
 +
    <li>To make agar plate, add agar powder at the final concentration of 2 %(w/v) in Procedure 2</li>
 +
  </ul>
 +
<!--note終わり-->
   <br>
   <br>
   </p>
   </p>
-
</div>
+
<!--本文終わり-->
-
</div>
+
  </div>
 +
  </div>
 +
<!--LB Mediumプロトコル終わり-->
 +
 
 +
<!--YPD Broth-->
   <div class="accordion">
   <div class="accordion">
   <div class="scroll">
   <div class="scroll">
   </div>
   </div>
-
   <h2><a href="javascript:void(0);">Ligation</a></h2>
+
   <h2><a href="javascript:void(0);">YPD Medium</a></h2>
   <div class="ac">
   <div class="ac">
   <p class="sentence">
   <p class="sentence">
 +
<div class="m_table">
   <strong>Materials</strong>
   <strong>Materials</strong>
   <table class="materials">
   <table class="materials">
   <tr>
   <tr>
-
     <td colspan="2">DNA sample (cut out from the gel)
+
     <td>Peptone 
     </td>
     </td>
 +
    <td>final concentration: 2%(w/v)</td>
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td>Distilled water
+
     <td>Yeast extract
     </td>
     </td>
-
     <td>5μL</td>
+
     <td>final concentration: 1%(w/v)</td>
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td>DNA ligase
+
     <td>Glucose
     </td>
     </td>
-
     <td>5μL</td>
+
     <td>final concentration: 2%(w/v)</td>
   </tr>
   </tr>
   </table>
   </table>
 +
</div>
   <br>
   <br>
   <strong>Procedure</strong>
   <strong>Procedure</strong>
   <ul class="procedure">
   <ul class="procedure">
-
     <li>Add DNA sample, distilled water and DNA ligase into a micro test tube and vortex
+
     <li>Dissolve peptone (2.0 g), yeast extract (1.0 g) and glucose (2.0 g) to distilled water (90 ml)
     </li>
     </li>
-
     <li>Ligation for 5minutes at room temperature
+
     <li>Fill up to 100 ml with distilled water
 +
    </li>
 +
    <li>Sterilize by autoclave
 +
    </li>
 +
  </ul>
 +
  <br>
 +
  <strong>Note</strong>
 +
  <ul class="note">
 +
    <li>To make agar plate, add agar powder (final concentration: 2.0%) at procedure 1.
     </li>
     </li>
   </ul>
   </ul>
Line 623: Line 1,549:
</div>
</div>
</div>
</div>
 +
<!--YPD Broth終わり-->
 +
 +
<!-- SD Brothプロトコル -->
 +
  <div class="scroll">
 +
  </div>
 +
<div class="accordion">
 +
<!--タイトル-->
 +
  <h2><a href="javascript:void(0);">SD Medium</a></h2>
 +
<!--タイトル終わり-->
 +
  <div class="ac">
 +
<!--本文-->
 +
  <p class="sentence">
 +
<!--materials始まり-->
 +
  <strong>Materials</strong>
 +
<div class="m_table">
 +
  <table class="materials">
 +
  <tr>
 +
    <td>Yeast nitrogen base
 +
    </td>
 +
    <td>0.67%(w/v)</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Glucose
 +
    </td>
 +
    <td>2% (w/v)</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Adenine</td>
 +
    <td>0.004% (w/v)</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Histidine
 +
    </td>
 +
    <td>0.002% (w/v)</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Leucine
 +
    </td>
 +
    <td>0.006% (w/v)</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Lysine
 +
    </td>
 +
    <td>0.003% (w/v)</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Methionine
 +
    </td>
 +
    <td>0.002% (w/v)</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Tryptophan
 +
    </td>
 +
    <td>0.004% (w/v)</td>
 +
  </tr>
 +
  </table>
 +
</div>
 +
<!--materials終わり-->
 +
  <br>
 +
<!--procedure始まり-->
 +
  <strong>Procedure</strong>
 +
  <ul class="procedure">
 +
    <li>Dissolve yeast nitrogen base (6.7 g), adenine (40 mg), histidine (20 mg), leucine (60 mg), lysine (30mg), tryptophan (40mg) and methionine (20mg) into 40 ml of distilled H2O, and then fill up to 50 ml with H2O.
 +
    </li>
 +
    <li>Dissolve glucose (20.0 g) into 40 ml of distilled H2O, and then fill up to 50 ml with H2O.
 +
    </li>
 +
    <li>Sterilize each solution by autoclave.</li>
 +
    <li>Mix solutions after cooling it down.
 +
    </li>
 +
  </ul>
 +
<!--procedure終わり-->
 +
  <br>
 +
<!--note始まり-->
 +
  <strong>Note</strong>
 +
  <ul class="note">
 +
    <li> Autoclave glucose and agar plate separately from other materials</li>
 +
  </ul>
 +
<!--note終わり-->
 +
  <br>
 +
  </p>
 +
<!--本文終わり-->
 +
  </div>
 +
  </div>
 +
<!--LB Mediumプロトコル終わり-->
 +
<!--PCR-1-->
   <div class="accordion">
   <div class="accordion">
   <div class="scroll">
   <div class="scroll">
   </div>
   </div>
-
   <h2><a href="javascript:void(0);">Western Blotting</a></h2>
+
   <h2><a href="javascript:void(0);">No. 1 Inverse PCR</a></h2>
   <div class="ac">
   <div class="ac">
   <p class="sentence">
   <p class="sentence">
-
  <strong>Materials</strong>
+
    <ul class="procedure">
 +
    <li>Prepare PCR primers (10 pmol/μL) and template plasmid (50 ng/μL)</li>
 +
    <li>Prepare the PCR reaction mixture as follows:
 +
<div class="m_table">
   <table class="materials">
   <table class="materials">
   <tr>
   <tr>
-
     <td>BufferⅠ
+
     <td>PCR grade water</td>
-
    </td>
+
     <td>35μL</td>
-
     <td></td>
+
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td>BufferⅡ
+
     <td>10×Buffer for iPCR</td>
-
    </td>
+
     <td>5μL</td>
-
     <td></td>
+
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td>BufferⅢ
+
     <td>2 mM dNTPs</td>
-
    </td>
+
     <td>5μL</td>
-
     <td></td>
+
   </tr>
   </tr>
-
   <tr>
+
   <tr>  
-
     <td>Distilled water
+
     <td>Primer A (10 pmol/μL)</td>
-
    </td>
+
     <td>1.5μL</td>
-
     <td>2ml</td>
+
   </tr>
   </tr>
 +
  <tr>
 +
    <td>Primer B (10 pmol/μL)</td>
 +
    <td>1.5μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Plasmid Template DNA (50ng/μL)</td>
 +
    <td>1μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>KOD-Plus-DNA Polymerase</td>
 +
    <td>1μL</td>
 +
  </tr>
 +
  <tr>
 +
    <th>Total</th>
 +
    <th>50μL</th>
 +
  </tr>
 +
  </table>
 +
</div><br>
 +
    </li>
 +
    <li>Perform PCR reaction as follows: <strong>PCR Profile for KOD-FX-NEO</strong>
 +
<div class="m_table">
 +
  <table class="materials">
   <tr>
   <tr>
-
     <td>PBS
+
     <td>94.0°C</td>
-
     </td>
+
     <td>98.0°C</td>
-
     <td></td>
+
    <td>68.0°C</td>
 +
     <td>4.0°C</td>
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td>PBS-S
+
     <td>2 minutes</td>
-
     </td>
+
     <td>10 seconds</td>
-
     <td></td>
+
    <td>7 minutes</td>
 +
     <td>Hold</td>
   </tr>
   </tr>
 +
  <tr>
 +
    <td>1 cycle</td>
 +
    <td colspan="2" style="background-color:rgba(0,0,0,0.1);">20 cycles</td>
 +
    <td>1 cycle</td>
 +
  </tr>
 +
  </table>
 +
  </div><br> 
 +
  </li>
 +
  <li> [Optional] The control reaction is as follows:
 +
<div class="m_table">
 +
  <table class="materials">
   <tr>
   <tr>
-
     <td>PBS-T
+
     <td>PCR grade water</td>
-
    </td>
+
     <td>35μL</td>
-
     <td></td>
+
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td>PBS-TS
+
     <td>10×Buffer for iPCR</td>
-
    </td>
+
     <td>5μL</td>
-
     <td></td>
+
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td>PonceauS
+
     <td>2 mM dNTPs</td>
-
    </td>
+
     <td>5μL</td>
-
     <td></td>
+
   </tr>
   </tr>
 +
  <tr>
 +
    <td>Control Primer #1（10 pmol/μL）</td>
 +
    <td>1.5μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Control Primer #2（10 pmol/μL）</td>
 +
    <td>1.5μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>Control Plasmid pAK119M （50 ng/μL）</td>
 +
    <td>1μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>KOD -Plus- (1 U/μL) </td>
 +
    <td>1μL</td>
 +
  </tr>
 +
  <tr>
 +
    <th>Total</th>
 +
    <th>50μL</th>
 +
  </tr>
 +
  </table>
 +
</div>
 +
<br><br>
 +
<div class="m_table">
 +
  <table class="materials">
   <tr>
   <tr>
-
     <td>PVDF membrane
+
     <td>94.0°C</td>
-
     </td>
+
     <td>98.0°C</td>
-
     <td>1 sheet</td>
+
     <td>98.0°C</td>
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td>Whatman paper
+
     <td>2 minutes</td>
-
     </td>
+
     <td>10 seconds</td>
-
     <td>6 sheets</td>
+
     <td>5 minutes</td>
   </tr>
   </tr>
 +
  <tr>
 +
    <td>1 cycle</td>
 +
    <td colspan="2" style="background-color:rgba(0,0,0,0.1);">5 cycles</td>
 +
  </tr>
 +
  </table>
 +
</div>
 +
  </li>
 +
  </ul>
 +
  <br>
 +
  </p>
 +
  </div>
 +
  </div>
 +
 +
  <div class="accordion">
 +
  <div class="scroll">
 +
  </div>
 +
  <h2><a href="javascript:void(0);">No. 2 <em>Dpn</em>1 digestion of the template plasmid</a></h2>
 +
  <div class="ac">
 +
　<ul class="procedure">
 +
　<li>Add 2 μL of <em>Dpn</em>1 restriction enzyme (10 U/μL) to 50 μL PCR reaction from
 +
step 1.</li>
 +
  <li>Gently and thoroughly mix each reaction mixture by pipetting</li>
 +
  <li>Spin down the reaction mixture and incubate at 37°C for 1 hr to digest the
 +
template plasmid</li>
 +
  </ul>
 +
  <p class="sentence">
 +
（Optional） Gel electrophoresis<br>
 +
To confirm PCR amplification, we recommend agarose gel electrophoresis analysis.
 +
However, in the case of 5 or less cycles of amplification, it may be only possible to
 +
detect a faint band or no band at all. If only a faint or no band is detected, please
 +
proceed to the next step. <br><br>
 +
  </p>
 +
</div>
 +
</div>
 +
 +
  <div class="accordion">
 +
  <div class="scroll">
 +
  </div>
 +
  <h2><a href="javascript:void(0);">No. 3 Self-ligation of the PCR Product</a></h2>
 +
  <div class="ac">
 +
  <p class="sentence">
 +
    <ul class="procedure">
 +
    <li>Prepare the kination/ligation reaction mixture using a fresh tube as follows:<br>
 +
<div class="m_table">
 +
  <table class="materials">
   <tr>
   <tr>
-
     <td>Hybridization bag
+
     <td><em>Dpn</em>1- treated PCR product </td>
-
    </td>
+
     <td>2μL</td>
-
     <td>1</td>
+
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td>Peroxidase Stain Kit
+
     <td>PCR grade water </td>
-
    </td>
+
     <td>7μL</td>
-
     <td>one drop for each</td>
+
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td>antiglutathione S - transferase (和光純薬工業株式会社製)
+
     <td>Ligation high</td>
-
     </td>
+
     <td>5μL</td>
 +
  </tr>
 +
  <tr>
 +
    <td>T4 Polynucleotide Kinase </td>
     <td>1μL</td>
     <td>1μL</td>
 +
  </tr>
 +
  <tr>
 +
    <th>Total Volum</th>
 +
    <th>15μL</th>
   </tr>
   </tr>
   </table>
   </table>
 +
</div><br>
 +
    </li>
 +
    <li>
 +
Gently and thoroughly mix each reaction mixture by pipetting
 +
  </li>
 +
  <li>Centrifuge the reaction mixture and incubate each reaction at 16°C for 1 hr
 +
  </li>
 +
  </ul>
   <br>
   <br>
-
   <strong>Procedure</strong>
+
   <br>
 +
  </p>
 +
  </div>
 +
  </div>
 +
   
 +
  <div class="accordion">
 +
  <div class="scroll">
 +
  </div>
 +
  <h2><a href="javascript:void(0);">No. 4 Transformation</a></h2>
 +
  <div class="ac">
 +
  <p class="sentence">
 +
Standard <em>E. coli</em> strains can be used as the transformation host. Both
 +
electrocompetent and chemically competent <em>E. coli</em> cells can be used. The
 +
following protocol is a standard protocol using chemically prepared competent <em>E.
 +
coli</em> cells. <br>
   <ul class="procedure">
   <ul class="procedure">
-
    <li>Cut the gel in appropriate size
+
  <li>Gently thaw the competent cells （100 μL） on ice. </li>
-
    </li>
+
  <li>Add 10 μL of reaction mixture from Step 3 to the competent cells, swirl gently  
-
    <li>Add BufferⅢ and gel then shake it gently
+
and incubate for 30 min on ice.</li>
-
    </li>
+
  <li>Incubate for 30 seconds at 42°C and then place on ice for 2 min</li>
-
    <li>Soak the membrane on ethanol then soak it in BufferⅢ and percolate
+
  <li>Add 900 μL of SOC medium and incubate at 37°C for 1 hr with shaking.  
-
    </li>
+
</li>
-
    <li>2, 1, 3 Whatman papers (all in the same size) on BufferⅠ, BufferⅡ, BufferⅢ respectively. wet the surface of the blotter
+
  <li>Plate appropriate volumes (10~200 μL) of transformed <em>E. coli</em> solution on agar
-
    </li>
+
plates containing the appropriate antibiotic for the plasmid vector. </li>
-
    <li>Blot at the constant current of membrane's area ×2.5 mA</li>
+
  <li>Incubate the plates at 37°C for ~16 hr.</li>
-
<li>Dye the membrane with Ponceau S for 5 minutes rinse it with distilled water and scan it</li>
+
  </ul>
-
<li>Shake and wash with PBS-TS (3 minutes ×3 times)</li>
+
<br>
-
<li>Put the membrane in a hybridization bag add PBS-S antiglutathione S-transferase and shake it for one hour at room temperature </li>
+
<br>
-
<li>Shake and wash with PBS-T twice (5 min/10 min)</li>
+
</p>
-
<li>Shake and wash with PBS twice (5 min/5 min)</li>
+
</div>
-
<li>Add one drip of 3 Peroxidase Stain Kits and distilled water</li>
+
</div>
-
<li>Scan it</li>
+
 
-
</ul>
+
  <div class="accordion">
-
<br><strong>Reagent</strong>
+
  <div class="scroll">
-
<ul class="materials">
+
  </div>
-
<li>BufferⅠ: bring to 300 ml with Tris base 10.9g, MetOH60ml/H2O</li>
+
  <h2><a href="javascript:void(0);">No. 5 Analysis of Transfomants</a></h2>
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<li>BufferⅡ: bring to 300 ml with Tris base 0.9g, MetOH60ml/H2O</li>
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<li>BufferⅢ: bring to 300 ml with Tris base 0.91g, Boric acid10.5mg, MetOH60ml/H2O</li>
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<li>PBS-S: PBS with 1% SkimMilk</li>
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A typical mutagenesis efficiency of this kit is greater than 80%. Therefore, analysis
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<li>PBS-T: PBS with 0.05% Tween20</li>
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of 4-8 clones is typically appropriate for sequence verification. <br><br></p></div></div>
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<li>PBS-TS: PBS with 0.05% Tween20+1% SkimMilk</li>
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Latest revision as of 03:36, 18 October 2014

notebook

Protocol

Miniprep

Materials

Buffer 1 250μL
Buffer 2 250μL
Buffer 3 350μL
Buffer 4 500μL
Buffer 5 700μL
Distilled water 100μL
Sample

Procedure
  • Suspend the sample in buffer 1 (1.5 ml sample tube)
  • Add buffer 2 to the sample and mix it
  • Add buffer 3 to the sample and mix it
  • Centrifuge for 5 minutes at 13,000 rpm and apply the supernatants to the column
  • Add buffer 4 and centrifuge for 1 minute at 13,000 rpm then throw away the filter paper
  • Add buffer 5 and centrifuge for 1 minute at 13,000 rpm then throw away the filter paper
  • Centrifuge again for 1 minute at 13,000 rpm
  • Place the column on a new sample tube and add 100 μL distilled water
  • Centrifuge for 1 minute at 6,000 rpm

Recipes for Buffer
Buffer 1 (Suspension Buffer) 50 mM Tris-HCl and 10 mM EDTA, pH 8.0 (25°C) 50 μg/ml RNase A
Buffer 2 (Lysis Buffer) 0.2 M NaOH and 1% SDS
Buffer 3 (Neutralization and Binding Buffer) 4 M guanidine hydrochloride and 0.5 M potassium acetate, pH 4.2
Buffer 4 (Wash Buffer) 5 M guanidine hydrochloride, 20 mM Tris-HCl, pH 6.6 (25°C) [final conentrations after addition of ethanol] with 38% ethanol
Buffer 5 (Wash Buffer) 20 mM NaCl, 2 mM Tris-HCl, pH 7.5 (25°C) [final conentrations after addition of ethanol] with 80% ethanol

PCR-1

Materials

Buffer for KOD-FX-NEO 50μL
dNTP 20μL
Primer mix 1.0μL
Template DNA 0.5μL
KOD-FX-NEO (TOYOBO) 2.0μL
H2O 26.5μL
Total 100μL

Procedure
  • Add buffer, dNTP, primer mix, Template DNA, KOD-FX-NEO and distilled water to an Eppendorf tube and mix
  • Place the PCR tubes into the PCR machine and set the program

PCR Profile for KOD-FX-NEO
Predenature Denature Annealing Extension Final Extension
98.0°C KOD-FX-NEO 98.0°C 51.0°C 68.0°C 68.0°C
2 minutes 10 seconds 30 seconds 1 minute 2 minutes
1 cycle 30 cycles 1 cycle

PCR Primer Design
Lot.No Oligo Base Number Sequence
T14F190235 pGEX6P-2F1 30 CACACAGGAACTAGTATTCATGTCCCCTAT
T14F190236 pGEX6P-2F2 30 GGATCTGGAAGTTCTGTTCCACTAGTCCCT
T14F190237 pGEX6P-2R 29 TCATCACCGAAACGCTCGAGGCAGATCGT


PCR-2

Materials

Taq Buffer 50μL
dNTP 20μL
Primer mix 1.0μL
Template DNA 0.5μL
Taq polymerase 2.0μL
H2O 26.5μL
Total 100μL

Procedure
  • Add buffer, dNTP, primer mix, Template DNA, Taq polymerase and distilled water to an Eppendorf tube and mix
  • Place the PCR tubes into the PCR machine and set the program

PCR Profile for KOD-FX-NEO
Predenature Denature Annealing Extension Final Extension
98.0°C Taq polymerase 95.0°C 53.0°C 72.0°C 72.0°C
30 seconds 30 seconds 45 seconds 2 minutes 1 minute
1 cycle 30 cycles 1 cycle


PCR Primer Design
　　
Lot.No Oligo Base Number Sequence
T14H280166 Terpinene3-suffix-Spe1 30 CAGTCAGTCACGAACTAGTTTAAGGATGGG
T14H280167 Terpinene3-prefix-Xba1 30 CCGGGTTCTAGATGGCTGCATCCACTACTT
T14H180317 Terpinene3-mutagenesis-FP 28 TTGGAGTTCTTGCAGGATTCTCCCGATA
T14H180318 Terpinene3-mutagenesis-RP 26 GGCCTCCTTTGTTATTGGATTTGCTG

Restriction Digest

Materials

DNA sample 6μL
Buffer 1μL
Restriction Enzyme 0.5μL
Distilled water 2.5μL

Procedure
  • Add all materials to a tube and mix them gently
  • Incubate at 37˚C for the enzyme reaction for 15 minutes


AGE

Materials

Sample 5μL
Agarose gel
2X Loading Buffer Triple Dye (NIPPON GENE) 5μL
1X TAE Buffer

Procedure
  • Set an agarose gel on an electrophoresis chamber
  • Add 1X TAE buffer to the electrophoresis chamber
    Note: Do not generate bubbles under the gel
  • Add 2X loading buffer to electrophoresis samples
  • Apply samples on agarose gel wells
  • Set an appropriate voltage (100 V) and run the electrophoresis
  • Stop the electrophoresis when the BPB reaches 2/3 of the gel
  • Soak the gel in EtBr (ethidium bromide) solution and dye it for 20 minutes
  • Place plastic cooking wrap on the trans-illuminator and irradiate UV to the gel on the wrap
  • Take photographs of the gel by using a trans-illuminator

Agarose Concentration Versus Optical Range of DNA Size
Agarose Concentration (%) DNA (kbp)
0.3 5-60
0.6 1-20
1.0 0.3-7
1.5 0.2-4
2.0 0.1-2

DNA Refinement 1

Materials

DNA sample 200μL
distilled H2O 400μL
CH3COONa 50μL
Phe/Chl 700μL
Isopropyl alcohol 750μL
75% Ethanol 1000μL

Procedure
  • Add materials (DNA, H2O, CH3COONa, and Phe/Chl) to sample tube and vortex
  • Centrifuge at 14,500 rpm for 10 minutes at room temperature
  • Transfer the supernatant to a new sample tube
  • Add 750 μL of isopropyl alcohol to the sample tube and vortex
  • Centrifuge at 14,500 rpm for 10 minutes at 4°C
  • Remove isopropyl alcohol gently so that the pellet will not break
  • Add 1,000 μL of 75% ethanol and centrifuge at 14,500 rpm for 5 minutes at 4°C
  • Dry it by aspirator for 10 minutes
  • Add 25 μL of distilled H2O and mix

Note
  • Phe/Chl composition Phenol:Chloroform:Isoamyl alcohol=25:24:1

DNA Refinement 2

Materials

sample 30μL
Bacterial Alkaline Phosphatase (BAP) 1μL
Low melting agarose gel
6×Loading Buffer Double Dye 5μL
Distilled water 200μL
Phenol
Phe/Chl
Isopropyl alcohol 750μL
5M CH3COONa 50μL
70% Ethanol 1000μL

Procedure
  • Add BAP to vector and dephosphorize for 30 minutes at 37°C
  • Run the electrophoresis with agarose gel
  • Cut out the targeted band and mix with 200 μL of distilled water in a tube
  • Heat the sample for 5 minutes at 65°C
  • Add the same amount of phenol as the sample and vortex
  • Centrifuge at 14,500 rpm for 10 minutes at room temperature and apply the supernatant to the new sample tube
  • Add the same amount of Phe/Chl as the sample and vortex
  • Centrifuge at 14,500 rpm for 5 minutes at room temperature and apply the supernatant to the sample tube
  • Add 750 μL of Isopropyl alcohol and 50 μL of CH3COONa and centrifuge at 14,500rpm for 10 minutes at 4°C
  • Rinse with 70% ethanol at 14,500 rpm 5 minutes at 4°C
  • Dry it for 15 minutes

Ligation

Materials

DNA sample 5μL
DNA ligase (Ligation High from Nippon gene) 5μL

Procedure
  • Mix DNA sample and DNA ligase in a sample tube gently
  • Ligation for 15 minutes at room temperature

Transformation (E. coli)

Materials

DNA Sample 10μL
Competent cell 50μL

Procedure
  • Thaw the competent cells on ice
  • Add 10 μL of sample into thawed competent cells
  • Cool the sample tube, which contains competent cells and DNA samples, with ice for 1 hour, then Heat shock the cells by immersion in pre-hearted water bath at 42°C for 30 seconds
  • Place the tube on ice for 2 minutes to cool it down
  • At a clean bench, add 1.0 ml of LB medium into the tube and suspend it
  • Incubate the tube at 37°C for 35 minutes
  • Harvest the cells by centrifuge
  • Spread the transformed competent cells onto the agar plate and incubate it at 37°C overnight

Transformation (S. cerevisiae)

Materials

Sample 5μL
Competent cells 95μL
YPD plate containing G418

Procedure
  • Cool down a cuvette for 5 minutes on ice
  • Harvest the yeast cells by centrifuge at 4 °C
  • Suspend the cells in 20 ml of cold 1M sorbitol and harvest by centrifuge at 4 °C (2times)
  • Suspend the cells in 500μL of cold 1M sorbitol
  • Mix DNA sample (5 μL) and the cell suspension (95 μL) in a cold cuvette
  • Electroporate under the following conditions: 200 Ω, 25 μF and 1.5 kV
  • Immediately inoculate on YPD plates containing G418
  • Incubate at 30 °C for 2 days

Preculture

Materials

Sample (E. coli cells )
Medium (LB medium with appropriate antibiotics) 20ml

Procedure
  • Scrape samples from the agar plate and inoculate them in liquid media
  • Cultivate overnight (37℃, 120 rpm)

Main Culture

Materials

LB medium 100ml
IPTG 10μL
Sample 500μL

Procedure
  • Add samples to LB medium and cultivate (37°C, 120 rpm) until reaching a cell density of OD600=0.5
  • Add IPTG (10 μL) to the medium (25 ml)
  • Further cultivation for 3 hours

Protein Extraction (E. coli)

Materials

Sample
FastBreak Cell Lysis Reagent, 10X (Promega)
50mM potassium phosphate buffer (=pH6.8)
SDS sample buffer

Procedure
  • Separate samples into two and harvest by centrifuge
  • Add potassium phosphate buffer, then mix and remove medium completely
  • Add FastBreak Cell Lysis Reagent, 10X at the ratio of FastBreak Buffer Cell Lysis Reagent,10X: Samples=1:9 and extract protein for 15 minutes at room temperature

Protein Extraction (S. cerevisiae)

Materials

Glass Beads
50 mM potassium phosphate buffer (pH6.8)
SDS sample buffer

Procedure
  • Harvest yeast cells by centrifuge at 3,000 rpm for 4 minutes at room temperature
  • Wash cells once with potassium phosphate buffer
  • Cool down the sample tube on ice for 1 minute
  • Add the same amount of glass beads as the sample then add 20 μL of potassium phosphate buffer and mix
  • Disrupt the cells by FastPrep 24 (MP Biochemicals) for 45 seconds at speed 4.5
  • Cool down the sample tube on ice for 1 minute
  • Add 80 µl of potassium phosphate buffer, cool it down and centrifuge for 5 minutes at 14,500 rpm at 4°C
  • Transfer 40 µl of the supernatant and mix with 8 µl of SDS sample buffer
  • Treat the sample with heat for 5 minutes at 100˚C

Colony Sweep

Materials

Sample
Phenol/Chloroform water-saturated solution (Phe/Chl)
Cracking solution 3% w/v SDS, 50 mM Tris-base, pH12.6

Procedure
  • Dispense cracking solution (50 μL) each into sample tubes
  • Collect the sample and suspend it into cracking solution
  • Incubate at 65°C for 10 minutes
  • Add Phe/Chl and BPB pigment and vortex
  • Centrifuge at 14,000 rpm for 5 minutes
  • Apply the samples (upper layer) to agarose gel with loading dye
  • Check the bands by agar gel electrophoresis

SDS-PAGE

Materials

Sample
Separating Gel
Stacking Gel

Procedure
  • Place stacking gel on separating gel
  • Rinse the wells of gel with distilled water
  • Load prepared samples into wells
  • Run the electrophoresis (25 mA for 75 min)
  • Check the bands with CBB stain

Separating Gel
Acylamide (%) 7.5 10 12.5 15 17.5
MilliQ H2O (ml) 3.89 3.22 2.55 1.87 1.2
Acrylamide/Bis-acrylamide (30%/0.8% w/v) 1.99 2.7 3.38 4.04 4.7
1.5M Tris-HCl(pH8.8) (ml) 2 2 2 2 2
10% (w/v)SDS (μL) 80 80 80 80 80
10% (w/v) ammonium persulfate (AP) (μL) 27 27 27 27 27
TEMED (μL) 4 4 4 4 4

Stacking Gel
MilliQ H2O (ml) 2.89
30% (w/v) acrylamide (ml) 0.79
0.5M Tris-HCl(pH6.8) (ml) 1.25
10% SDS (μL) (ml) 50
10% APS (μL) (ml) 17
TEMED (μl) (ml) 5

Western Blotting

Materials

BufferⅠ 0.3 M Tris base, 20% MetOH (pH 10.9)
BufferⅡ 25 mM Tris base, 20% MetOH
BufferⅢ 25 mM Tris base, 0.05 mM Boric acid, 20% MetOH (pH 9.5)
PBS 137 mM NaCl, 8.1 mM Na2HPO4 (12H2O), 2.68 mM KCl, 1.47 mM KH2PO4
PBS-S PBS including 0.1% skim milk
PBS-T PBS including 0.05% Tween20
PBS-TS PBS including 0.1% skim milk & 0.05% Tween20
PonceauS (Sigma)
PVDF membrane (Immobilon Transfer membrane by Millipore) 1 sheet
Whatman paper (Whatman 3MM)
Hybridization bag (Cosmo Bio)
Peroxidase Stain Kit (Nacalai Tesque)
Anti-GST antibody conjugated with HRP (Wako)

Procedure
  • Cut the gel in appropriate size
  • Soak gel in buffer III and shake gently for 15 minutes
  • Soak the membrane on methanol then transfer it in buffer III
  • Soak Whatman papers (all in the same size) in Buffer I (2 sheets), Buffer II (1 sheet) and Buffer III (3 sheets) respectively
  • Wet the surface of the blotter
  • Put items in the following order: Buffer III paper, gel, membrane, Buffer II paper and Buffer I paper
  • Blot at the constant current of membrane's area ×2.5 mA for 20 minutes
  • Dye the membrane with Ponceau S for 5 minutes, rinse it with distilled water and scan it
  • Shake and wash with PBS-TS (3 minutes ×3times)
  • The membrane was incubated with anti-GST antibody containing HRP in PBS-S at room temperature for 1 hour
  • Wash with PBS-T twice (5 minutes/10 minutes)
  • Wash with PBS twice (5 minutes/5 minutes)
  • Stain the membrane using Peroxidase Stain Kits
  • Scan it


LB Medium

Materials

Tryptone final concentration: 1%(w/v)
Yeast Extract final concentration: 0.5%(w/v)
NaCl final concentration: 1%(w/v)
5M NaOH

Procedure
  • Dissolve Tryptone (1.0 g), Yeast Extract (500 mg) and NaCl (1.0 g) in distilled water (90 ml)
  • Adjust pH to 7.0 by adding 20 μL of 5M NaOH
  • Fill up to 100 ml with distilled water
  • Autoclave

Note
  • To make agar plate, add agar powder at the final concentration of 2 %(w/v) in Procedure 2

YPD Medium

Materials
Peptone final concentration: 2%(w/v)
Yeast extract final concentration: 1%(w/v)
Glucose final concentration: 2%(w/v)

Procedure
  • Dissolve peptone (2.0 g), yeast extract (1.0 g) and glucose (2.0 g) to distilled water (90 ml)
  • Fill up to 100 ml with distilled water
  • Sterilize by autoclave

Note
  • To make agar plate, add agar powder (final concentration: 2.0%) at procedure 1.

SD Medium

Materials

Yeast nitrogen base 0.67%(w/v)
Glucose 2% (w/v)
Adenine 0.004% (w/v)
Histidine 0.002% (w/v)
Leucine 0.006% (w/v)
Lysine 0.003% (w/v)
Methionine 0.002% (w/v)
Tryptophan 0.004% (w/v)

Procedure
  • Dissolve yeast nitrogen base (6.7 g), adenine (40 mg), histidine (20 mg), leucine (60 mg), lysine (30mg), tryptophan (40mg) and methionine (20mg) into 40 ml of distilled H2O, and then fill up to 50 ml with H2O.
  • Dissolve glucose (20.0 g) into 40 ml of distilled H2O, and then fill up to 50 ml with H2O.
  • Sterilize each solution by autoclave.
  • Mix solutions after cooling it down.

Note
  • Autoclave glucose and agar plate separately from other materials

No. 1 Inverse PCR

  • Prepare PCR primers (10 pmol/μL) and template plasmid (50 ng/μL)
  • Prepare the PCR reaction mixture as follows:
    PCR grade water 35μL
    10×Buffer for iPCR 5μL
    2 mM dNTPs 5μL
    Primer A (10 pmol/μL) 1.5μL
    Primer B (10 pmol/μL) 1.5μL
    Plasmid Template DNA (50ng/μL) 1μL
    KOD-Plus-DNA Polymerase 1μL
    Total 50μL

  • Perform PCR reaction as follows: PCR Profile for KOD-FX-NEO
    94.0°C 98.0°C 68.0°C 4.0°C
    2 minutes 10 seconds 7 minutes Hold
    1 cycle 20 cycles 1 cycle

  • [Optional] The control reaction is as follows:
    PCR grade water 35μL
    10×Buffer for iPCR 5μL
    2 mM dNTPs 5μL
    Control Primer #1（10 pmol/μL） 1.5μL
    Control Primer #2（10 pmol/μL） 1.5μL
    Control Plasmid pAK119M （50 ng/μL） 1μL
    KOD -Plus- (1 U/μL) 1μL
    Total 50μL


    94.0°C 98.0°C 98.0°C
    2 minutes 10 seconds 5 minutes
    1 cycle 5 cycles

No. 2 Dpn1 digestion of the template plasmid

　
    　
  • Add 2 μL of Dpn1 restriction enzyme (10 U/μL) to 50 μL PCR reaction from step 1.
  • Gently and thoroughly mix each reaction mixture by pipetting
  • Spin down the reaction mixture and incubate at 37°C for 1 hr to digest the template plasmid

（Optional） Gel electrophoresis
To confirm PCR amplification, we recommend agarose gel electrophoresis analysis. However, in the case of 5 or less cycles of amplification, it may be only possible to detect a faint band or no band at all. If only a faint or no band is detected, please proceed to the next step.

No. 3 Self-ligation of the PCR Product

  • Prepare the kination/ligation reaction mixture using a fresh tube as follows:
    Dpn1- treated PCR product 2μL
    PCR grade water 7μL
    Ligation high 5μL
    T4 Polynucleotide Kinase 1μL
    Total Volum 15μL

  • Gently and thoroughly mix each reaction mixture by pipetting
  • Centrifuge the reaction mixture and incubate each reaction at 16°C for 1 hr


No. 4 Transformation

Standard E. coli strains can be used as the transformation host. Both electrocompetent and chemically competent E. coli cells can be used. The following protocol is a standard protocol using chemically prepared competent E. coli cells.

  • Gently thaw the competent cells （100 μL） on ice.
  • Add 10 μL of reaction mixture from Step 3 to the competent cells, swirl gently and incubate for 30 min on ice.
  • Incubate for 30 seconds at 42°C and then place on ice for 2 min
  • Add 900 μL of SOC medium and incubate at 37°C for 1 hr with shaking.
  • Plate appropriate volumes (10~200 μL) of transformed E. coli solution on agar plates containing the appropriate antibiotic for the plasmid vector.
  • Incubate the plates at 37°C for ~16 hr.


No. 5 Analysis of Transfomants

A typical mutagenesis efficiency of this kit is greater than 80%. Therefore, analysis of 4-8 clones is typically appropriate for sequence verification.

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