Team:TMU-Tokyo/Notebook

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<div id="template" style="text-align: center; font-weight: bold; font-size: large; color: #f6f6f6; padding: 5px;">
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This is a template page. READ THESE INSTRUCTIONS.
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<div class="container_12">
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<div id="instructions" style="text-align: center; font-weight: normal; font-size: small; color: #f6f6f6; padding: 5px;">
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You are provided with this team page template with which to start the iGEM season.  You may choose to personalize it to fit your team but keep the same "look." Or you may choose to take your team wiki to a different level and design your own wiki.  You can find some examples <a href="https://2008.igem.org/Help:Template/Examples">HERE</a>.
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You <strong>MUST</strong>  have all of the pages listed in the menu below with the names specified.  PLEASE keep all of your pages within your teams namespace. 
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<h1>Plasmid Purification</h1>
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<Hr>
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  <div class="RM">
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QIAprep Spin Miniprep Kit (QIAGEN)<br>
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    Contents ：<br>
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    Buffer P1<br>
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    Buffer P2<br>
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    Buffer PB<br>
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    Buffer EB<br>
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    <li class="reagent">Collection tubes</li>
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  <li class="reagent">Eppendorf Tubes</li>
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  <li class="reagent">Vortex</li>
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  <li class="reagent">Centrifugal machine</li>
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{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"
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        <li class="reagent">Collection tubes</li>
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!align="center"|[[Team:TMU-Tokyo|Home]]
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<li class="reagent">Eppendorf Tubes</li>
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!align="center"|[[Team:TMU-Tokyo/Team|Team]]
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<li class="reagent">Vortex</li>
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!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=TMU-Tokyo Official Team Profile]
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<li class="reagent">Centrifugal machine</li>
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!align="center"|[[Team:TMU-Tokyo/Project|Project]]
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</div>
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!align="center"|[[Team:TMU-Tokyo/Parts|Parts Submitted to the Registry]]
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!align="center"|[[Team:TMU-Tokyo/Modeling|Modeling]]
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!align="center"|[[Team:TMU-Tokyo/Notebook|Notebook]]
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!align="center"|[[Team:TMU-Tokyo/Safety|Safety]]
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!align="center"|[[Team:TMU-Tokyo/Attributions|Attributions]]
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|}
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  <Br>
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  <ol　>
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    <li class="how">Add 2 ml of culture medium of E.coli which cultured in overnights into an Eppendorf
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  tube. Then, centrifuge the tube in room temperature (23~25℃), 130000 rpm for one minute.</li>
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    <li class="how">Add 250 μl Buffer P1 into the tube. Then, stir it with Vortex until deposition disappears.</li> 
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    <li class="how">Add 250 μl Buffer P2 and mix the contents by inverting the tube (Don’t use the Vortex)</li>
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    <li class="how">Add 350 μl Buffer N3 and mix the contents by inverting the tube (Don’t use the Vortex.</li>
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    <li class="how">Centrifuge the tube in room temperature, 13000 rpm for 10 minutes.</li>
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    <li class="how">Move the supernatant by a pipette from the tube to the QIAprep Spin Column. </li>
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    <li class="how">Centrifuge in room temperature, 13000 rpm for 1 minute and throw away the flow through liquid which collected at the bottom of the column.</li>
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    <li class="how">Add 500 μl Buffer PB and centrifuge the tube in room temperature, 13000 rpm for 1 minute. Then, throw away the flow through liquid.</li>
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    <li class="how">Add 500 μl Buffer PE and centrifuge the tube in room temperature, 13000 rpm for 1 minute. Then, throw away the flow through liquid.</li>
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    <li class="how">Set the upper part of the QIAprep Spin Column into another Eppendorf tube.</li>
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    <li class="how">Add 50 μl EB buffer and left it at room temperature for 1 minute.</li>
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    <li class="how">Centrifuge in room temperature, 13000 rpm for 1 minute. The flow through liquid is the plasmid DNA solution.</li>
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  </ol>
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You should make use of the calendar feature on the wiki and start a lab notebook.  This may be looked at by the judges to see how your work progressed throughout the summer.  It is a very useful organizational tool as well.
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<Br>
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<Br>
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<h1>Restriction Enzyme Digestion</h1>
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<Hr>
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Reagents and Materials
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<li class="reagent">Eppendorf tube</li>
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<li class="reagent">milliQ</li>
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<li class="reagent">DNA solution</li>
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<li class="reagent">Digest Buffer</li>
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<li class="reagent">Restriction enzyme</li>
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<br>
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<p>Mix these solutions with the following quantities.</p>
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<table width="700"border="0" cellspacing="10" cellpadding="0"> <tr>
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  <td>
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    <table width="300"border="1" cellspacing="0" cellpadding="0">
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      <caption>Pattern1 </caption>
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        <tr><td>milliQ</td><td>12 µl</td><tr>
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        <tr><td>DNA solution</td><td>5 µl</td><tr>
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        <tr><td>Difest Buffer</td><td>2 µl</td><tr>
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        <tr><td>Restriction enzyme</td><td>1 µl</td><tr>
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        <tr><td>total</td><td>20 µl</td></tr>
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      </table>
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    </td>
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    <td>
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    <table width="300"border="1" cellspacing="0" cellpadding="0">
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      <caption>Pattern 2</caption>
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        <tr><td>milliQ</td><td>12 µl</td><tr>
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        <tr><td>DNA solution</td><td>5 µl</td><tr>
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        <tr><td>Difest Buffer</td><td>2 µl</td><tr>
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        <tr><td>Restriction enzyme ①</td><td>1 µl</td><tr>
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        <tr><td>Restriction enzyme ②</td><td>1 µl</td><tr>
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        <tr><td>total</td><td>20 µl</td><tr> 
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    </table>
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    </td>
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    </tr>
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</table>
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<br>
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<ol>
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<li class="how">Incubate them at 37℃ for 1 hour.</li>
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<li class="how">Incubate them at 60℃ for 15 minutes.</li>
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<ol>
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<br>
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<br>
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<h1>Electrophoresis</h1>
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<hr>
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<br>
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<p>Reagents and Materials</p>
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<li class="reagent">Agarose gel</li>
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<li class="reagent">TAE Buffer</li>
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<li class="reagent">Loading Buffer</li>
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<li class="reagent">DNA solution</li>
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<li class="reagent">Eppendorf tube</li>
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<li class="reagent">Ethidium bromide</li>
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<ol>
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<li class="how">Set gel in the electrophoresis tank anf pour the TAE Buffer into the tank.</li>
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<li class="how">Put DNAsolution and Loading Buffer in the ratio of 1:2 into the Eppendorf tube and mix them.</li>
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  <li class="how">Load samples into wells.</li>
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<li class="how">Do Electrophoresis at 100V for 40min.</li>
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<li class="how">After electrophoresis, soak the gel into water including ethidium bromide for 20min.</li>
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  <li class="how">Observe the bands by ultraviolet radiation.</li>
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</ol>
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<br>
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<br>
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<br>
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</div>

Revision as of 07:51, 16 September 2013



Plasmid Purification

QIAprep Spin Miniprep Kit (QIAGEN)
Contents ：
Buffer P1
Buffer P2
Buffer PB
Buffer EB
  • Collection tubes
  • Eppendorf Tubes
  • Vortex
  • Centrifugal machine
  • Collection tubes
  • Eppendorf Tubes
  • Vortex
  • Centrifugal machine

  • Add 2 ml of culture medium of E.coli which cultured in overnights into an Eppendorf tube. Then, centrifuge the tube in room temperature (23~25℃), 130000 rpm for one minute.
  • Add 250 μl Buffer P1 into the tube. Then, stir it with Vortex until deposition disappears.
  • Add 250 μl Buffer P2 and mix the contents by inverting the tube (Don’t use the Vortex)
  • Add 350 μl Buffer N3 and mix the contents by inverting the tube (Don’t use the Vortex.
  • Centrifuge the tube in room temperature, 13000 rpm for 10 minutes.
  • Move the supernatant by a pipette from the tube to the QIAprep Spin Column.
  • Centrifuge in room temperature, 13000 rpm for 1 minute and throw away the flow through liquid which collected at the bottom of the column.
  • Add 500 μl Buffer PB and centrifuge the tube in room temperature, 13000 rpm for 1 minute. Then, throw away the flow through liquid.
  • Add 500 μl Buffer PE and centrifuge the tube in room temperature, 13000 rpm for 1 minute. Then, throw away the flow through liquid.
  • Set the upper part of the QIAprep Spin Column into another Eppendorf tube.
  • Add 50 μl EB buffer and left it at room temperature for 1 minute.
  • Centrifuge in room temperature, 13000 rpm for 1 minute. The flow through liquid is the plasmid DNA solution.


    • Restriction Enzyme Digestion

    Reagents and Materials
  • Eppendorf tube
  • milliQ
  • DNA solution
  • Digest Buffer
  • Restriction enzyme

    • Mix these solutions with the following quantities.

    Pattern1
    milliQ12 µl
    DNA solution5 µl
    Difest Buffer2 µl
    Restriction enzyme1 µl
    total20 µl
    Pattern 2
    milliQ12 µl
    DNA solution5 µl
    Difest Buffer2 µl
    Restriction enzyme ①1 µl
    Restriction enzyme ②1 µl
    total20 µl

    1. Incubate them at 37℃ for 1 hour.
    2. Incubate them at 60℃ for 15 minutes.


        3. Electrophoresis


        Reagents and Materials

      1. Agarose gel
      2. TAE Buffer
      3. Loading Buffer
      4. DNA solution
      5. Eppendorf tube
      6. Ethidium bromide
        1. Set gel in the electrophoresis tank anf pour the TAE Buffer into the tank.
        2. Put DNAsolution and Loading Buffer in the ratio of 1:2 into the Eppendorf tube and mix them.
        3. Load samples into wells.
        4. Do Electrophoresis at 100V for 40min.
        5. After electrophoresis, soak the gel into water including ethidium bromide for 20min.
        6. Observe the bands by ultraviolet radiation.



    Retrieved from "http://2013.igem.org/Team:TMU-Tokyo/Notebook"