Difference between revisions of "Team:York/Protocols"

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        <h1 style="font-family:Garamond"> Protocols </h1>
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<div id="wrap">
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    <div id="wrap">
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  <ul class="navbar">
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        <ul class="navbar">
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<li><a href="#LB">Growth Media</a></li>
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            <li>
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<li><a href="#">Competent Cells</a>
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                <a href="#LB">Growth Media</a>
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<ul>
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            </li>
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  <li><a href="#">LB Media </a></li>
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            <li>
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  <li><a href="#">LA Media</a></li>
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                <a href="#">Competent Cells</a>
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</ul>        
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                <ul>
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</li>
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                    <li>
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<li><a href="#">Transformations</a>
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                        <a href="#">LB Media </a>
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<ul>
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                    </li>
−
  <li><a href="#" >Gel Electrophoresis</a></li>
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                    <li>
−
  <li><a href="#">Drill Down Report</a></li>
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                        <a href="#">LA Media</a>
−
  <li><a href="#">Ranking Report</a></li>
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                    </li>
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</ul>        
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                </ul>
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</li>
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            </li>
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<li><a href="#">PCR</a>
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            <li>
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<ul>
+
                <a href="#">Transformations</a>
−
  <li><a href="#">Business Dashboard</a></li>
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                <ul>
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  <li><a href="#">Web Pivot Table</a></li>
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                    <li>
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  <li><a href="#">Interactive Report</a></li>
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                        <a href="#" >Gel Electrophoresis</a>
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  <li><a href="#">What-If Analysis</a></li>
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                    </li>
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</ul>        
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                    <li>
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</li>
+
                        <a href="#">Drill Down Report</a>
−
<li><a href="#">Gel Extractions</a>
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                    </li>
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<ul>
+
                    <li>
−
  <li><a href="#">Database CRUD</a></li>
+
                        <a href="#">Ranking Report</a>
−
  <li><a href="#">Database Update</a></li>
+
                    </li>
−
  <li><a href="#">Order Entry</a></li>
+
                </ul>
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  <li><a href="#">Drag-and-Drop Application</a></li>
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            </li>
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</ul>        
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            <li>
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</li>
+
                <a href="#">PCR</a>
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                <ul>
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  </ul>
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                    <li>
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</div>
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                        <a href="#">Business Dashboard</a>
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                    </li>
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<div id="LB">
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                    <li>
−
<h2 style="font-family:Garamond">Lysogeny Broth</h2>
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                        <a href="#">Web Pivot Table</a>
 +
                    </li>
 +
                    <li>
 +
                        <a href="#">Interactive Report</a>
 +
                    </li>
 +
                    <li>
 +
                        <a href="#">What-If Analysis</a>
 +
                    </li>
 +
                </ul>
 +
            </li>
 +
            <li>
 +
                <a href="#">Gel Extractions</a>
 +
                <ul>
 +
                    <li>
 +
                        <a href="#">Database CRUD</a>
 +
                    </li>
 +
                    <li>
 +
                        <a href="#">Database Update</a>
 +
                    </li>
 +
                    <li>
 +
                        <a href="#">Order Entry</a>
 +
                    </li>
 +
                    <li>
 +
                        <a href="#">Drag-and-Drop Application</a>
 +
                    </li>
 +
                </ul>
 +
            </li>
 +
            <li>
 +
                <a href="#Phosphate Assay">Phosphate Assay</a>
 +
            </li>
 +
        </ul>
 +
    </div>
 +
    <div id="LB">
 +
        <h2 style="font-family:Garamond">Lysogeny Broth</h2>
 +
        <h3 style="font-family:Garamond">Materials</h3>
 +
        <ul>
 +
            <li>10g of tryptone</li>
 +
            <li>5g of yeast extract</li>
 +
            <li>10g of NaCl</li>
 +
            <li>1L of Deionized Water</li>
 +
            <li> 1M NaCl </li>
 +
            <li> 1M KOH </li>
 +
        </ul>
 +
        <h3 style="font-family:Garamond">Procedure</h3>
 +
        <ol>
 +
            <li>Use a container with at least double the volume of the liquid that you are making.</li>
 +
            <li>Dissolve 10 g tryptone, 5 g yeast extract, and 10 g NaCl in 950 mL deionized water. </li>
 +
            <li>Adjust the pH of the medium to 7.0 using 1M NaOH or KOH and bring volume up to 1 liter. </li>
 +
            <li>Autoclave. </li>
 +
            <li>Store at room temperature or +4°C.</li>
 +
        </ol>
 +
    </div>
 +
    <div id="phosphate assay">
 +
        <h2> Phosphate Assay</h2>
 +
        <h3> Reagent preparation</h3>
 +
        <ul>
 +
            <li>
 +
                <spam style="font-color:orange">Phosphate Reagent:</spam> 15 ml of colorimetric dye. Ready to use as supplied. Equilibrate to room temperature before use. There may be a small amount of precipitate visible which does not affect the assay performance. Store at room temperature. Actually orange.
  
−
<h3 style="font-family:Garamond">Materials</h3>
+
            </li>
−
<ul>
+
            <li>
−
<li>10g of tryptone</li>
+
                <span style="font-color:orange">Phosphate Standard: </span>500uL of 10mM Phosphate standard. Ready to use as supplied. Equilibrate to room temperature before use. Store at room temperature. Actually Clear.
−
<li>5g of yeast extract</li>
+
            </li>
−
<li>10g of NaCl</li>
+
        </ul>
−
<li>1L of Deionized Water</li>
+
        <h3> Standard preparation</h3>
−
<li> 1M NaCl </li>
+
        <h4>Materials</h4>
−
<li> 1M KOH </li>
+
        <ul>
−
</ul>
+
            <li>
 +
                <span style="color:green">Phosphate Standard
 +
               
 +
                </li>
 +
                <li>
 +
                    <span style="color:blue">Phosphate Reagent
  
−
<h3 style="font-family:Garamond">Procedure</h3>
+
                    </li>
−
<ol>
+
                    <li>Distilled Water</li>
−
<li>Use a container with at least double the volume of the liquid that you are making.</li>
+
                </ul>
−
<li>Dissolve 10 g tryptone, 5 g yeast extract, and 10 g NaCl in 950 mL deionized water. </li>
+
            </h4>
−
<li>Adjust the pH of the medium to 7.0 using 1M NaOH or KOH and bring volume up to 1 liter. </li>
+
            <h4>Procedure</h4>
−
<li>Autoclave. </li>
+
            <ol>
−
<li>Store at room temperature or +4°C.</li>
+
                <li> Dilute 5ul of supplied Phosphate Standard into 495ul of dH2O in a 1.5ml Eppie. Label ‘S’ </li>
−
</ol>
+
                <li> Make further dilutions to construct the curve. Suggested values are below. Make these in 1.5ml Eppies</li>
−
</div>
+
            </ol>
−
</div class>
+
            <table>
 +
                <tr>
 +
                    <td>Volume S/ ul</td>
 +
                    <td>Volume dH2O/ ul</td>
 +
                    <td>Concentration/ nMol/200ul(well)</td>
 +
                </tr>
 +
                <tr>
 +
                    <td>0</td>
 +
                    <td>600</td>
 +
                    <td>0</td>
 +
                </tr>
 +
                <tr>
 +
                    <td>30</td>
 +
                    <td>570</td>
 +
                    <td>1</td>
 +
                </tr>
 +
                <tr>
 +
                    <td>60</td>
 +
                    <td>540</td>
 +
                    <td>2</td>
 +
                </tr>
 +
                <tr>
 +
                    <td>90</td>
 +
                    <td>510</td>
 +
                    <td>3</td>
 +
                </tr>
 +
                <tr>
 +
                    <td>120</td>
 +
                    <td>480</td>
 +
                    <td>4</td>
 +
                </tr>
 +
                <tr>
 +
                    <td>150</td>
 +
                    <td>450</td>
 +
                    <td>5</td>
 +
                </tr>
 +
            </table>
 +
            <ol>
 +
                <li>Pipette 200ul of each curve sample into a well.</li>
 +
                <li>Add 30ul of Phosphate Reagent to each well</li>
 +
                <li>Leave to equilibrate for 30 mins at room temperature. N.B the reagent is light sensitive so store in a dark room while equilbrating</li>
 +
            </ol>
 +
            <h3>Sample preparation</h3>
 +
            <p>N.B. Make sure our sample is diluted to ensure the readings are within the standard value range.</p>
 +
            <p>
 +
                <u>Steps for cell (adherent or suspension) samples:</u>
 +
            </p>
 +
            <ol>
 +
                <li>Harvest the amount of cells necessary for each assay (initial recommendation = 2 x 10^6 cells).</li>
 +
                <li>Wash cells with cold TBS (kept in 4oC fridge, stable for 3 months). </li>
 +
                <li>Resuspend the cell pellet in 150 µL of Assay Buffer (TBS) on ice. </li>
 +
                <li>Homogenize cells quickly by pipetting up and down a few times. </li>
 +
                <li>Sonicate cells for 50 seconds 3X at high setup (one cycle = 30 s sonication – 10 s break – 10 s sonication – 10 s break). </li>
 +
                <li>Centrifuge sample for 15 minutes at 4°C at top speed using a cold microcentrifuge to remove any insoluble material. </li>
 +
                <li>Collect supernatant and transfer to a clean tube. </li>
 +
            </ol>
 +
            <ul>
 +
                <li>Keep on ice</li>
 +
            </ul>
 +
            <p>
 +
                <u>Tris-Buffered Saline (TBS) Recipe</u>
 +
            </p>
 +
            <ol>
 +
                <li>50 mM Tris-Cl, pH 7.5</li>
 +
                <li>150 mM NaCl</li>
 +
                <li>To prepare, dissolve 6.05 g and 8.76 g NaCl in 800 mL of H2O. </li>
 +
                <li>Adjust pH to 7.5 with 1 M HCl </li>
 +
                <li>Tris Make volume up to 1 L with H2O.</li>
 +
                <p>N.B. TBS is stable at 4°C for 3 mo.</p>
 +
            </ol>
 +
            <h3>Assay procedure and detection</h3>
 +
            <p> Equilibrate all materials and prepared reagents to room temperature prior to use. It is recommended to assay all standards, controls and samples in duplicate.</p>
 +
            <p>Set up Reaction wells: </p>
 +
            <ol>
 +
                <li>Standard wells = 200 µL standard dilution. </li>
 +
                <li>Sample wells = 1 – 100 µL samples (adjust volume to 200 µL/well with ddH2O). </li>
 +
                <li>Background control sample wells = 1 – 100 samples (adjust volume to 200 µL/well with ddH2O). </li>
 +
                <li>Add 30 µL of Phosphate Reagent to standard, sample and background control wells. </li>
 +
                <li>Mix and incubate at room temperature for 30 minutes protected from light. </li>
 +
                <li>Measure output at OD = 650 nm on a microplate reader.</li>
 +
            </ol>
 +
        </div>
 +
    </div>

Revision as of 14:22, 24 July 2015

Protocols

Lysogeny Broth

Materials

  • 10g of tryptone
  • 5g of yeast extract
  • 10g of NaCl
  • 1L of Deionized Water
  • 1M NaCl
  • 1M KOH

Procedure

  1. Use a container with at least double the volume of the liquid that you are making.
  2. Dissolve 10 g tryptone, 5 g yeast extract, and 10 g NaCl in 950 mL deionized water.
  3. Adjust the pH of the medium to 7.0 using 1M NaOH or KOH and bring volume up to 1 liter.
  4. Autoclave.
  5. Store at room temperature or +4°C.

Phosphate Assay

Reagent preparation

  • Phosphate Reagent: 15 ml of colorimetric dye. Ready to use as supplied. Equilibrate to room temperature before use. There may be a small amount of precipitate visible which does not affect the assay performance. Store at room temperature. Actually orange.
  • Phosphate Standard: 500uL of 10mM Phosphate standard. Ready to use as supplied. Equilibrate to room temperature before use. Store at room temperature. Actually Clear.

Standard preparation

Materials

  • Phosphate Standard
  • Phosphate Reagent
  • Distilled Water

Procedure

  1. Dilute 5ul of supplied Phosphate Standard into 495ul of dH2O in a 1.5ml Eppie. Label ‘S’
  2. Make further dilutions to construct the curve. Suggested values are below. Make these in 1.5ml Eppies
Volume S/ ul Volume dH2O/ ul Concentration/ nMol/200ul(well)
0 600 0
30 570 1
60 540 2
90 510 3
120 480 4
150 450 5
  1. Pipette 200ul of each curve sample into a well.
  2. Add 30ul of Phosphate Reagent to each well
  3. Leave to equilibrate for 30 mins at room temperature. N.B the reagent is light sensitive so store in a dark room while equilbrating

Sample preparation

N.B. Make sure our sample is diluted to ensure the readings are within the standard value range.

Steps for cell (adherent or suspension) samples:

  1. Harvest the amount of cells necessary for each assay (initial recommendation = 2 x 10^6 cells).
  2. Wash cells with cold TBS (kept in 4oC fridge, stable for 3 months).
  3. Resuspend the cell pellet in 150 µL of Assay Buffer (TBS) on ice.
  4. Homogenize cells quickly by pipetting up and down a few times.
  5. Sonicate cells for 50 seconds 3X at high setup (one cycle = 30 s sonication – 10 s break – 10 s sonication – 10 s break).
  6. Centrifuge sample for 15 minutes at 4°C at top speed using a cold microcentrifuge to remove any insoluble material.
  7. Collect supernatant and transfer to a clean tube.
  • Keep on ice

Tris-Buffered Saline (TBS) Recipe

  1. 50 mM Tris-Cl, pH 7.5
  2. 150 mM NaCl
  3. To prepare, dissolve 6.05 g and 8.76 g NaCl in 800 mL of H2O.
  4. Adjust pH to 7.5 with 1 M HCl
  5. Tris Make volume up to 1 L with H2O.

    6. N.B. TBS is stable at 4°C for 3 mo.

Assay procedure and detection

Equilibrate all materials and prepared reagents to room temperature prior to use. It is recommended to assay all standards, controls and samples in duplicate.

Set up Reaction wells:

  1. Standard wells = 200 µL standard dilution.
  2. Sample wells = 1 – 100 µL samples (adjust volume to 200 µL/well with ddH2O).
  3. Background control sample wells = 1 – 100 samples (adjust volume to 200 µL/well with ddH2O).
  4. Add 30 µL of Phosphate Reagent to standard, sample and background control wells.
  5. Mix and incubate at room temperature for 30 minutes protected from light.
  6. Measure output at OD = 650 nm on a microplate reader.