Difference between revisions of "Team:Stony Brook/Experiments"

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<li> Monarch PCR & DNA Cleanup Kit </li>
 
<li> Monarch PCR & DNA Cleanup Kit </li>
 
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<br>
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<div align="center">
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<h3> Digestion </h3>
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<ul>
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<li> Add Nuclease free water to a 2ml test tube</li>
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<li> Add 10X buffer for restriction enzymes </li>
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<li> Add restriction Enzymes </li>
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<li> Add DNA using (DNA needed in ng/concentration in ug/ul) = ul </li>
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<li> Make negative controls without the enzymes</li>
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<ul>
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<li> Make up volume with nuclease free water</li>
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</ul>
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<li> Amounts of reagents listed below </li>
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<div align="center">
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<h4> 50ul Reaction </h4>
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<ul>
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<table>
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<tr>
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<th> Content </th>
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<th> ul </th>
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</tr>
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<tr>
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<td> Nuclease-free water </td>
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<td> Bring to volume </td>
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</tr>
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<tr>
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<td> 10X Buffer </td>
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<td> 5</td>
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</tr>
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<tr>
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<td> Restriction Enzymes </td>
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<td> 1 each</td>
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</tr>
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<tr>
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<td> DNA </td>
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<td> Calculate volume for 2ug DNA </td>
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</tr>
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</table>
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</ul>
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</div>
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<div class="column half_size">
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<div align="center">
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<h4> 10ul Reaction </h4>
 +
<ul>
 +
<table>
 +
<tr>
 +
<th> Content </th>
 +
<th> ul </th>
 +
</tr>
 +
<tr>
 +
<td> Nuclease-free water </td>
 +
<td> Bring to volume </td>
 +
</tr>
 +
<tr>
 +
<td> 10X Buffer </td>
 +
<td> 5</td>
 +
</tr>
 +
<tr>
 +
<td> Restriction Enzymes </td>
 +
<td> .5 each</td>
 +
</tr>
 +
<tr>
 +
<td> DNA </td>
 +
<td> Calculate volume for 2ug DNA </td>
 +
</tr>
 +
</table>
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</ul>
 
</div>
 
</div>
  

Revision as of 17:59, 22 July 2016

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Protocols & Experiments

Universal Lab Protocols

Agarose Gel Preparation

  • Add 50mL of 1X TAE buffer to a 500mL erlenmeyer flask
  • Add 0.5g of 1% agarose
  • Microwave for three 20 second intervals and cool slightly
  • Add 1ul Ethidium Bromide
  • Mix and pour into gel box. Add Comb
  • Cool for 30 minutes

YPD Media

  • For liquid media
    • Add 20g of Bacto peptone, 10g of yeast extract and 950mL of water to a flask
    • Autoclave on the liquid setting
    • Add 50mL of 40% glucose and mix
  • For solid media
    • Add same reagents as liquid, plus 24g of Bacto agar
    • Autoclave
    • Stir on a magnetic stir plate and add 50ml of 40% glucose
    • Pour into petri dishes

LB Broth

Add items to flask:

  • 5g Tryptone
  • 2.5g Yeast Extract
  • 5g NaCl
  • H2O filled to 500mL
  • Mix with magnetic stir bar on low heat, autoclave for liquids



Nanodrop

  • Select Nucleic Acid
  • Clean, drop 1ul water, measure
  • Blank
  • Measure with 1ul of substance
  • For PCRs: 260/280 ratio should be near 2

LB Agar

Add items to flask:

  • 5g Tryptone
  • 2.5g Yeast Extract
  • 5g NaCl
  • 7.5g Agar
  • H2O filled to 500mL
  • Mix with magnetic stir bar on low heat, autoclave for liquids



    • NEB Monarch Nucleic Acid Purification Protocols

    The following NEB kits were used and protocols can be found on their website

    • Monarch Plasmid Miniprep Kit
    • Monarch DNA Gel Extraction Kit
    • Monarch PCR & DNA Cleanup Kit

Digestion

  • Add Nuclease free water to a 2ml test tube
  • Add 10X buffer for restriction enzymes
  • Add restriction Enzymes
  • Add DNA using (DNA needed in ng/concentration in ug/ul) = ul
  • Make negative controls without the enzymes
    • Make up volume with nuclease free water
  • Amounts of reagents listed below

50ul Reaction

    Content ul
    Nuclease-free water Bring to volume
    10X Buffer 5
    Restriction Enzymes 1 each
    DNA Calculate volume for 2ug DNA

10ul Reaction

    Content ul
    Nuclease-free water Bring to volume
    10X Buffer 5
    Restriction Enzymes .5 each
    DNA Calculate volume for 2ug DNA

Transformation

  • Thaw competent E. coli cells on ice and pipette 50ul cells into a transformation tube
  • Add 1-5ul containing 1pg-100ng of plasmid DNA and flick tube 4-5 times
  • Place tube on ice for 30 minutes
  • Heat shock at 42°C for 30 seconds
  • Place on ice for 5 minutes
  • Add 950ul room temperature SOC to mixture
  • Incubate at 37°C for 60 minutes at 250rpm
  • Mix and perform several 10-fold serial dilutions in SOC
  • Spread 50-100ul onto a plate and incubate overnight at 37°C

Cancer Group Protocols


Vaccine Group Protocols

Inspiration