Difference between revisions of "Team:NYMU-Taipei/Notebook-Protocol"

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</table>
 
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</div>
 
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<div class="fund">
 
<div class="fund">
 
<h4 style="margin-top:30px; margin-bottom:10px;">Liquid culture:</h4>
 
<h4 style="margin-top:30px; margin-bottom:10px;">Liquid culture:</h4>
 
<li style="list-style-type:decimal;"><p style="font-size:16px;">Aliquot 4 mL of LB medium in a centrifugal tube for each colony.</p></li>
 
<li style="list-style-type:decimal;"><p style="font-size:16px;">Aliquot 4 mL of LB medium in a centrifugal tube for each colony.</p></li>
 
<li style="list-style-type:decimal;"><p style="font-size:16px;">Use a tip and dip it in the LB culture and swirl it around.</p></li>
 
<li style="list-style-type:decimal;"><p style="font-size:16px;">Use a tip and dip it in the LB culture and swirl it around.</p></li>
−
<h4 style="margin-top:30px; margin-bottom:10px;">Draw on 2nd time plate:</h4><br />
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 +
<div class="fund">
 +
<h4 style="margin-top:30px; margin-bottom:10px;">Draw on 2nd time plate:</h4>
 +
 
 
<p style="font-size:16px;">Take out new plates from the fridge and divide them into smaller sections. This is the second-time plate. Make sure to write the date on it. Cross out in red pen any sections you know is wrong after the Colony PCR check</p>
 
<p style="font-size:16px;">Take out new plates from the fridge and divide them into smaller sections. This is the second-time plate. Make sure to write the date on it. Cross out in red pen any sections you know is wrong after the Colony PCR check</p>
−
<h4 style="margin-top:30px; margin-bottom:10px;">Making Gel for gel electrophoresis</h4><br />
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 +
<h4 style="margin-top:30px; margin-bottom:10px; line-height: 24px;">Making Gel for gel electrophoresis</h4>
 
<li style="list-style-type:decimal;"><p style="font-size:16px;">Make either 100mL or 150mL of gel at at time and select a relevant percentage (e.g. 1%, 1.5%, or 2%)</p></li>
 
<li style="list-style-type:decimal;"><p style="font-size:16px;">Make either 100mL or 150mL of gel at at time and select a relevant percentage (e.g. 1%, 1.5%, or 2%)</p></li>
 
<li style="list-style-type:decimal;"><p style="font-size:16px;">Measure out the relevant percentage in agarose (e.g. 1g of agarose for 100mL of 1% gel).</p></li>
 
<li style="list-style-type:decimal;"><p style="font-size:16px;">Measure out the relevant percentage in agarose (e.g. 1g of agarose for 100mL of 1% gel).</p></li>
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<li style="list-style-type:decimal;"><p style="font-size:16px;">Wait at least 15-20 min until using it.</p></li>
 
<li style="list-style-type:decimal;"><p style="font-size:16px;">Wait at least 15-20 min until using it.</p></li>
 
<li style="list-style-type:decimal;"><p style="font-size:16px;">Store in 4°C and away from light.</p></li>
 
<li style="list-style-type:decimal;"><p style="font-size:16px;">Store in 4°C and away from light.</p></li>
−
<h4 style="margin-top:30px; margin-bottom:10px;">Gel electrophoresis</h4><br />
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</div>
 +
 
 +
<div class="fund">
 +
<h4 style="margin-top:30px; margin-bottom:10px;">Gel electrophoresis</h4>
 
<li style="list-style-type:decimal;"><p style="font-size:16px;">Select a relevant % agarose gel based on your own experience</p></li>
 
<li style="list-style-type:decimal;"><p style="font-size:16px;">Select a relevant % agarose gel based on your own experience</p></li>
−
<li style="list-style-type:decimal;"><p style="font-size:16px;"></p>Load 5uL from each tube of Colony PCR, mix it with 1uL of 6x DNA Dye and put it in a well.</li>
+
<li style="list-style-type:decimal;"><p style="font-size:16px;">Load 5uL from each tube of Colony PCR, mix it with 1uL of 6x DNA Dye and put it in a well.</p></li>
−
<li style="list-style-type:decimal;"><p style="font-size:16px;"></p>Load 3uL of marker into a well.</li>
+
<li style="list-style-type:decimal;"><p style="font-size:16px;">Load 3uL of marker into a well.</p></li>
−
<li style="list-style-type:decimal;"><p style="font-size:16px;"></p>Run in the 13x13cm box at 60V or 70V and 400mA for the desired amount of time.</li>
+
<li style="list-style-type:decimal;"><p style="font-size:16px;">Run in the 13x13cm box at 60V or 70V and 400mA for the desired amount of time.</p></li>
 
<li style="list-style-type:decimal;"><p style="font-size:16px;">View in the gel viewer machine.</p></li>
 
<li style="list-style-type:decimal;"><p style="font-size:16px;">View in the gel viewer machine.</p></li>
 +
 +
<div class="fund">
 
<h4 style="margin-top:30px; margin-bottom:10px;">Plasmid extraction</h4><br />
 
<h4 style="margin-top:30px; margin-bottom:10px;">Plasmid extraction</h4><br />
 
<p style="font-size:16px;"></p>
 
<p style="font-size:16px;"></p>
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<h3 style="margin-top:30px; margin-bottom:10px;">PCR (Dream Taq or KOD)</h3><br />
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<h3 style="margin-top:30px; margin-bottom:10px;">PCR (Dream Taq or KOD)</h3>
 
<p style="font-size:16px;">Dream Taq:</p>
 
<p style="font-size:16px;">Dream Taq:</p>
  
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<p style="font-size:16px;">KOD:<br />KOD是這種嗎?</p>
 
<p style="font-size:16px;">KOD:<br />KOD是這種嗎?</p>
−
<a href="https://www.merckmillipore.com/TW/zh/product/KOD-Hot-Start-DNA-Polymerase,EMD_BIO-71086?ReferrerURL=https://www.google.com.tw/&bd=1">https://www.merckmillipore.com/TW/zh/product/KOD-Hot-Start-DNA-Polymerase,EMD_BIO-71086?ReferrerURL=https://www.google.com.tw/&bd=1</a>
+
<a href="https://www.merckmillipore.com/TW/zh/product/KOD-Hot-Start-DNA-Polymerase,EMD_BIO-71086?ReferrerURL=https://www.google.com.tw/&bd=1">https://www.merckmillipore.com/TW/zh/product/KOD-Hot-Start-DNA-Polymerase,EMD_BIO-71086?ReferrerURL=https://www.google.com.tw/&bd=1</a><br>
  
 
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   </tr>
 
   </tr>
 
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<br>
 
<h3 style="margin-top:30px; margin-bottom:10px; color:red;">PCR (Dream Taq or KOD)</h3><br />
 
<h3 style="margin-top:30px; margin-bottom:10px; color:red;">PCR (Dream Taq or KOD)</h3><br />
  
−
<h3 style="margin-top:30px; margin-bottom:10px;">Digestion</h3><br />
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<h3 style="margin-top:30px; margin-bottom:10px;">Digestion</h3>
 
<p style="font-size:16px;" color:red;>[Which enzymes we use???]</p>
 
<p style="font-size:16px;" color:red;>[Which enzymes we use???]</p>
 
<p style="font-size:16px;">Insert and backbone:</p>
 
<p style="font-size:16px;">Insert and backbone:</p>

Revision as of 22:24, 17 October 2016

protocol

protocol


E.coli protocol

Two-day efficient cloning cycle

We used an efficient two day cloning cycle split into a "Light" day and a "Heavy" day.

Light Day

The light day consists of Colony PCR and liquid culture of colonies transformed from a previous day.

1. The 3-in-1

First, count the number of colonies you want to check. Then, do the following 3 things sequentially:

  • Liquid culture

  • 2nd time plate

  • Colony PCR

    • (Use the same tip to add the template to these three things)

    2. Make the gel for electrophoresis

    3. Run gel electrophoresis to check the colony PCR product


    Heavy Day


    The heavy day consists of:

  • Previously grown plasmid extraction

  • Plasmid PCR

  • Gel extraction

  • Digestion

  • Ligation

  • Transformation

    • Colony PCR (Thermo DreamTaq®)


  • Make the Colony PCR mix (we use Thermo' DreamTaq) with the mix amount slightly modified:

    • Item uL
    Primer(Forward and reverse) 1
    dNTP (10mM) 1
    10x DreamTaq buffer 5
    Taq Polymerase 0.2
    ddH20 42.8
    Total 50

  • Select a colony using a tip or toothpick.

  • Dip it in a PCR tube and swirl it around.


    • PCR run protocol

    Temperature Time  
    94℃ 60s  
    94℃ 15s  
    55℃ 20s 30-35 cycles
    72℃ 1kb/min + 5-10s  
    72℃ 300s  

    Liquid culture:

  • Aliquot 4 mL of LB medium in a centrifugal tube for each colony.

  • Use a tip and dip it in the LB culture and swirl it around.

    • Draw on 2nd time plate:

    Take out new plates from the fridge and divide them into smaller sections. This is the second-time plate. Make sure to write the date on it. Cross out in red pen any sections you know is wrong after the Colony PCR check

    Making Gel for gel electrophoresis

  • Make either 100mL or 150mL of gel at at time and select a relevant percentage (e.g. 1%, 1.5%, or 2%)

  • Measure out the relevant percentage in agarose (e.g. 1g of agarose for 100mL of 1% gel).

  • Fill it up with 1xTAE buffer.

  • Microwave on low, constantly taking it out every so often to swirl and mix it. Keep microwaving until clear. Make sure it is completely clear

  • Cool to a temperature that is still hot but still can be held in your hand. If the gel gets too cold and starts to harden, start microwaving again until clear.

  • Add 5uL of Safe-seeing dye for every 100mL of gel after cooled to the correct tempearature. Mix it well by swirling

  • Pour it onto the molds quickly. Put a cover on it to block out the light.

  • Wait at least 15-20 min until using it.

  • Store in 4°C and away from light.

    • Gel electrophoresis

  • Select a relevant % agarose gel based on your own experience

  • Load 5uL from each tube of Colony PCR, mix it with 1uL of 6x DNA Dye and put it in a well.

  • Load 3uL of marker into a well.

  • Run in the 13x13cm box at 60V or 70V and 400mA for the desired amount of time.

  • View in the gel viewer machine.

    • Plasmid extraction


    PCR (Dream Taq or KOD)

    Dream Taq:

    Item uL
    Primer(Forward and reverse) 0.2
    Template(100ng) ?
    dNTP (10mM) 0.2
    10x DreamTaq buffer 1
    Taq Polymerase 0.04
    ddH20 to 10 uL
    Total 10

    KOD:
    KOD是這種嗎?

    https://www.merckmillipore.com/TW/zh/product/KOD-Hot-Start-DNA-Polymerase,EMD_BIO-71086?ReferrerURL=https://www.google.com.tw/&bd=1
    Item uL
    Primer(Forward and reverse) 0.2
    Template(100ng) ?
    dNTP (10mM) 0.2
    10x KOD buffer 1
    KOD Polymerase 0.04
    Mg2+
    ddH20 to 10 uL
    Total 10

    PCR (Dream Taq or KOD)


    Digestion

    [Which enzymes we use???]

    Insert and backbone:

    Item
    DNA 600 or 1000ng
    10x Buffer 2uL
    Enzyme1 0.6 or 1 uL
    Enzyme2 0.6 or 1 uL
    ddH2O to 20 uL
    Total 20

    Backbone check:
    To check if the backbone is cut.

    Item
    DNA 100ng
    10x Buffer 1 uL
    Enzyme1 or 2 0.1 uL
    ddH2O to 10 uL
    Total 10

    Digest for at least 1hr. Over 2hr is better. EcoRI doesn't have star activity when cut this way (even overnight)

    We run insert digests and backbone digests with backbone check on a gel. Then use GeneAid's gel extraction kit. The modifications in the protocol include:

  • Warm EB to 60-70oC before elution.

  • Always use the Gel (sequencing) protocol for gel extraction.

    • Ligation


    We use Thermo's and NEB's T4 Ligase:

    Item amount
    Vector 8.5uL, total of approximately 100ng of DNA.
    Insert
    ddH2O
    10x Ligase Buffer 1
    T4 Ligase 0.5
    Total 10

    Incubate at room temperature for 2hr then transform 1uL then put the remaining amount in a small bag and put in 4oC overnight in case the transformation fails and retransformation is required.

    Transformation


    We majorly use commercial E. coli DH5α competent cells.

  • Add 1uL of plasmid or ligation mix to 20 uL of competent cells.

  • Put mixture on ice for 30 minutes.

  • Heat shock at 42℃ for 1 min.

  • Put the mixture back on ice for another 20 minutes.

  • Add 200 uL of LB broth to repair the cell wall; incubate at 37oC for 1.5 hr.

  • Plate it on a relevant antibiotic plate.

  • Incubate plate at 37oC overnight.