Difference between revisions of "Team:Calgary/Protocols"

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                                 <td>
 
                                 <td>
 
                                     <p>iGEM 2018 distribution kit</p>
 
                                     <p>iGEM 2018 distribution kit</p>
−
                                    <ul>
+
                                <p>ddH<sub>2</sub>O</p>
−
                                        <li>List Item 1</li>
+
−
                                        <li>List Item 2</li>
+
−
                                    </ul>
+
−
                                    <p>ddH₂O</p>
+
 
                                 </td>
 
                                 </td>
 
                             </tr>
 
                             </tr>
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                                 <td>
 
                                 <td>
 
                                     <ol>
 
                                     <ol>
−
                                        <li>Add 10μL of ddH₂O to the desired well</li>
+
                                      <li>Add 10μL of ddH<sub>2</sub>O to the desired well</li>
 
                                         <li>Pipette up and down 3-5 times</li>
 
                                         <li>Pipette up and down 3-5 times</li>
 
                                         <li>Incubate at room temperature for 10 minutes</li>
 
                                         <li>Incubate at room temperature for 10 minutes</li>
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                                 <td>
 
                                 <td>
 
                                     <p>Synthesized DNA from IDT or Genscript</p>
 
                                     <p>Synthesized DNA from IDT or Genscript</p>
−
                                    <p>ddH₂O</p>                           
+
                                  <p>ddH<sub>2</sub>O</p>                           
 
                                 </td>
 
                                 </td>
 
                             </tr>
 
                             </tr>
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                                     <ol>
 
                                     <ol>
 
                                         <li>Centrifuge tube containing the synthesized DNA for 1 minute at 3000g</li>
 
                                         <li>Centrifuge tube containing the synthesized DNA for 1 minute at 3000g</li>
−
                                        <li>Add 20μL ddH₂O</li>
+
                                      <li>Add 20μL ddH<sub>2</sub>O</li>
 
                                         <li>Vortex for 1 minute</li>
 
                                         <li>Vortex for 1 minute</li>
 
                                         <li>Incubate at 50°C for 15 minutes</li>
 
                                         <li>Incubate at 50°C for 15 minutes</li>
Line 258: Line 254:
 
                                               <li>Kanamycin (final concentration of 50μg/mL)</li>                           
 
                                               <li>Kanamycin (final concentration of 50μg/mL)</li>                           
 
                                   </ul>
 
                                   </ul>
−
                                   <p>dH₂O</p>
+
                                   <p>dH<sub>2</sub>O</p>
 
                                   <p>1500mL Erlenmeyer flask</p>
 
                                   <p>1500mL Erlenmeyer flask</p>
 
                                   <p>Stir bar</p>
 
                                   <p>Stir bar</p>
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                                 <td>
 
                                 <td>
 
                                     <ol>
 
                                     <ol>
−
                                         <li>In a 1500mL Erlenmeyer flask, add 10g tryptone, 5 g yeast extract, 10g NaCl and 15g agar. Dissolve solids in 1000mL dH₂O and add a stir bar</li>
+
                                         <li>In a 1500mL Erlenmeyer flask, add 10g tryptone, 5g yeast extract, 10g NaCl and 15g agar. Dissolve solids in 1000mL dH<sub>2</sub>O and add a stir bar</li>
 
                                         <li>Cover flask loosely with aluminum foil, secure with autoclave tape and sterilize by autoclaving</li>
 
                                         <li>Cover flask loosely with aluminum foil, secure with autoclave tape and sterilize by autoclaving</li>
 
                                         <li>Remove agar from autoclave and allow agar to cool until warm to the touch before adding appropriate antibiotic</li>
 
                                         <li>Remove agar from autoclave and allow agar to cool until warm to the touch before adding appropriate antibiotic</li>
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                 </a>
 
                 </a>
 
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                 <div id="collapseSixteen" class="collapse" aria-labelledby="headingSixteen" data-parent="#accordion">
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                    <div class="card-body row">
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                        <table style="width: 100%">
 +
                            <tr>
 +
                                <td>
 +
                                    <h5>Materials</h5>
 +
                                </td>
 +
                                <td>
 +
                                    <p>Material 1</p>
 +
                                    <p>Material 2</p>
 +
                                  <p>Material 3</p>
 +
                                  <ul>
 +
                                          <li>Sub-bullet 1</li>
 +
                                          <li>Sub-bullet 2</li>
 +
                                          <li>Sub-bullet 3</li>                                   
 +
                                  </ul>
 +
                                </td>
 +
                            </tr>
 +
                            <tr>
 +
                                <td>
 +
                                    <h5>Protocol</h5>
 +
                                </td>
 +
                                <td>
 +
                                    <ol>
 +
                                        <li>Step 1</li>
 +
                                      <li>Step 2</li>
 +
                                      <li>Step 3</li>                                     
 +
                                    </ol>
 +
                                </td>
 +
                            </tr>
 +
                        </table>
 +
                        <br>
 +
                    </div>
 +
                </div>
 +
            </div>
 +
          <div class="card">
 +
                <a id="toggle17" class="remove-underline rotate-icon collapsed" href="#" data-toggle="collapse"
 +
                    data-target="#collapseSeventeen">
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                    <div class="card-header" id="headingSeventeen">
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                        <i id="icon17" class="fas fa-plus accordion-icon" aria-hidden="true"></i>
 +
                        <h3>
 +
                            Protocol Name
 +
                        </h3>
 +
                    </div>
 +
                </a>
 +
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                    <div class="card-body row">
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                        <table style="width: 100%">
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                            <tr>
 +
                                <td>
 +
                                    <h5>Materials</h5>
 +
                                </td>
 +
                                <td>
 +
                                    <p>Material 1</p>
 +
                                    <p>Material 2</p>
 +
                                  <p>Material 3</p>
 +
                                  <ul>
 +
                                          <li>Sub-bullet 1</li>
 +
                                          <li>Sub-bullet 2</li>
 +
                                          <li>Sub-bullet 3</li>                                   
 +
                                  </ul>
 +
                                </td>
 +
                            </tr>
 +
                            <tr>
 +
                                <td>
 +
                                    <h5>Protocol</h5>
 +
                                </td>
 +
                                <td>
 +
                                    <ol>
 +
                                        <li>Step 1</li>
 +
                                      <li>Step 2</li>
 +
                                      <li>Step 3</li>                                     
 +
                                    </ol>
 +
                                </td>
 +
                            </tr>
 +
                        </table>
 +
                        <br>
 +
                    </div>
 +
                </div>
 +
            </div>
 +
          <div class="card">
 +
                <a id="toggle18" class="remove-underline rotate-icon collapsed" href="#" data-toggle="collapse"
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                    data-target="#collapseEighteen">
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                    <div class="card-header" id="headingEighteen">
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                        <i id="icon18" class="fas fa-plus accordion-icon" aria-hidden="true"></i>
 +
                        <h3>
 +
                            Protocol Name
 +
                        </h3>
 +
                    </div>
 +
                </a>
 +
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                    <div class="card-body row">
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                            <tr>
 +
                                <td>
 +
                                    <h5>Materials</h5>
 +
                                </td>
 +
                                <td>
 +
                                    <p>Material 1</p>
 +
                                    <p>Material 2</p>
 +
                                  <p>Material 3</p>
 +
                                  <ul>
 +
                                          <li>Sub-bullet 1</li>
 +
                                          <li>Sub-bullet 2</li>
 +
                                          <li>Sub-bullet 3</li>                                   
 +
                                  </ul>
 +
                                </td>
 +
                            </tr>
 +
                            <tr>
 +
                                <td>
 +
                                    <h5>Protocol</h5>
 +
                                </td>
 +
                                <td>
 +
                                    <ol>
 +
                                        <li>Step 1</li>
 +
                                      <li>Step 2</li>
 +
                                      <li>Step 3</li>                                     
 +
                                    </ol>
 +
                                </td>
 +
                            </tr>
 +
                        </table>
 +
                        <br>
 +
                    </div>
 +
                </div>
 +
            </div>
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          <div class="card">
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                <a id="toggle19" class="remove-underline rotate-icon collapsed" href="#" data-toggle="collapse"
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                    data-target="#collapseNineteen">
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                        <i id="icon19" class="fas fa-plus accordion-icon" aria-hidden="true"></i>
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                        <h3>
 +
                            Protocol Name
 +
                        </h3>
 +
                    </div>
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                </a>
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                     <div class="card-body row">
 
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Revision as of 17:29, 16 October 2018

Team:Calgary/Notebook - 2018.igem.org

PROTOCOLS



Below are the protocols used by the team.


Materials

iGEM 2018 distribution kit

ddH2O
Protocol
  1. Add 10μL of ddH2O to the desired well
  2. Pipette up and down 3-5 times
  3. Incubate at room temperature for 10 minutes
  4. Transform cells with 1μL of rehydrated DNA as per transformation protocol. Store the remaining amount at -20°C

Materials

Synthesized DNA from IDT or Genscript

ddH2O
Protocol
  1. Centrifuge tube containing the synthesized DNA for 1 minute at 3000g
  2. Add 20μL ddH2O
  3. Vortex for 1 minute
  4. Incubate at 50°C for 15 minutes
  5. Briefly centrifuge. Store at -20°C

Materials

Luria-Bertani broth with agar:

  • 10% (w/v) tryptone
  • 5% (w/v) NaCl
  • 10% (w/v) yeast extract
  • 15% (w/v) agar

Appropriate antibiotic:

  • Ampicillin (final concentration of 100μg/mL)
  • Chloramphenicol (final concentration of 25μg/mL)
  • Kanamycin (final concentration of 50μg/mL)

dH2O

1500mL Erlenmeyer flask

Stir bar

Aluminum foil
Protocol
  1. In a 1500mL Erlenmeyer flask, add 10g tryptone, 5g yeast extract, 10g NaCl and 15g agar. Dissolve solids in 1000mL dH2O and add a stir bar
  2. Cover flask loosely with aluminum foil, secure with autoclave tape and sterilize by autoclaving
  3. Remove agar from autoclave and allow agar to cool until warm to the touch before adding appropriate antibiotic
  4. Stir on hot plate and magnetic stirrer for 30 seconds
  5. Pour agar into plates using aseptic technique

Materials

Luria-Bertani agar plate with appropriate antibiotic (if required)

Overnight culture of desired bacteria

70% ethanol

Spreading rod
Protocol
  1. Using aseptic technique, pipette 100μL of bacterial culture onto agar plate
  2. Dip spreading rod in 70% ethanol, pass over flame, and allow for excess liquid to burn off. Cool rod on agar, avoiding bacterial culture
  3. Use rod to spread bacterial culture over entire plate, spinning the plate at the same time
  4. Dip spreading rod in 70% ethanol, pass over flame, and allow excess liquid to burn off
  5. Incubate plates at 37°C overnight or until growth is observed

Materials

Escherichia coli DH5-α cells

Luria-Bertani broth

125mm culture tubes

250mL Erlenmeyer flasks

50mL Falcon tubes, pre-chilled

1M KCl

1M MgSO4

100mM CaCl2

100mM CaCl2, 10% glycerol

0.5mL microcentrifuge tubes, pre-chilled
Protocol
  1. Inoculate 2mL of Luria-Bertani broth with E. coli DH5-α cells and incubate overnight at 37°C, shaking at 200 rpm
  2. Subculture 1mL of the E.coli overnight culture in 49mL fresh Luria-Bertani broth in a 250mL Erlenmeyer flask with 500μL 1M MgSO4 and 50μL 1M KCl
  3. Incubate at 37°C, shaking at 200 rpm until the subculture reaches OD600 of 0.4-0.6
  4. Chill on ice for at least 10 minutes
  5. Spin down cells in 50mL pre-chilled Falcon tube at 2500g for 8 minutes at 4°C
  6. Resuspend cells in 10mL cold 100mM CaCl2, gently mix and place on ice for 10 minutes
  7. Centrifuge at 2500g for 8 minutes at 4°C
  8. Resuspend cells in 500μL cold 100mM CaCl2, 10% glycerol and place on ice for 10 minutes
  9. Separate cells into 50μL aliquots in pre-chilled 0.5mL microcentrifuge tubes and store at -80°C

Materials

Chemically competent E. coli DH5-α aliquots

DNA for transformation

Luria-Bertani broth with and without appropriate antibiotic

Agar plate with appropriate antibiotic
Protocol
  1. Thaw aliquot of competent E. coli DH5-α cells on ice
  2. Add 0.3-1μg DNA to cells (maximum 5μL), flick gently to mix, and place on ice for 45 minutes
  3. Heat shock at 42°C for 1 minute
  4. Place on ice for 5 minutes
  5. Add 250μL plain Luria-Bertani medium to aliquot of cells
  6. Incubate cells at 37°C, shaking at 200 rpm for 60 to 90 minutes
  7. Plate 100μL of resuspended culture on agar plate with appropriate antibiotic and spread
  8. Incubate plates at 37°C overnight or until desired growth is observed

Materials

Overnight culture of transformed bacteria

Sterile 1.5mL microcentrifuge tubes

Sterile 50% glycerol
Protocol
  1. Using aseptic technique, pipette 0.5mL of 50% sterile glycerol into a 1.5mL microcentrifuge tube
  2. Using aseptic technique, add 0.5 mL of overnight culture
  3. Pipette up and down gently to mix
  4. Store at -80°C

Materials

Overnight culture of bacteria

Resuspension buffer (stored at 4°C)

  • 50mM Tris-HCl, pH 8
  • 10mM EDTA
  • 100μg/mL RNase A

Lysis buffer

  • 200mM NaOH
  • 1% (v/v) SDS

Precipitation buffer

  • 3M CH3CO3K, pH 5.5

Isopropanol

70% ethanol, ice cold

2mL microcentrifuge tubes

1.5mL microcentrifuge tubes

ddH2O
Protocol
  1. Transfer 2mL of the overnight culture to a 2mL microcentrifuge tube and pellet the cells by spinning at 3500g for 1 minute. Discard supernatant, and repeat as necessary
  2. Resuspend pellet in 300μL Resuspension buffer
  3. Add 300μL Lysis buffer. Invert gently
  4. Quickly add 300μL Precipitation buffer. Invert gently
  5. Centrifuge at 14,000g for 10 minutes at room temperature
  6. Retain supernatant in a clean 1.5mL microcentrifuge tube
  7. Add 650μL isopropanol. Gently invert and incubate at room temperature for 10 minutes
  8. Centrifuge at 14,000g for 10 minutes at  4°C. Discard supernatant
  9. Wash pellet with 500μL cold 70% ethanol (do not resuspend)
  10. Centrifuge at 14,000g for 5 minutes at 4°C. Discard supernatant
  11. Dry pellet in vacufuge for 30 to 60 minutes
  12. Resuspend pellet in ddH2O and store at - 20°C

Materials

DNA

Restriction enzymes

10X appropriate buffer

ddH2O

0.2mL PCR tubes

(Optional) Antarctic phosphatase

(Optional) 10X Antarctic phosphatase buffer
Protocol
  1. Add the following into a 0.2mL PCR tube:
    • 1-3μg DNA
    • 1μL restriction enzyme 1
    • 1μL restriction enzyme 2
    • 2μL 10X appropriate buffer
    • (Optional) 2μL Antarctic phosphatase
    • (Optional) 2μL 10X Antarctic phosphatase buffer
  2. Incubate at 37°C for one to three hours
  3. Deactivate restriction enzymes via heat shock by incubating tube at 80°C for 20 minutes

Materials

**CRISPY BOIS fill out**

Material 2

Material 3

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Protocol
  1. Step 1
  2. Step 2
  3. Step 3

Materials

TAE buffer:

  • 40mM Tris, pH 7.6
  • 20mM CH3COOH
  • 1mM EDTA

Agarose

250mL Erlenmeyer flask

RedSafe nucleic acid staining solution

Gel casting tray and comb

6X loading dye

DNA sample
Protocol
  1. For a 1% gel, add 1g agarose to 100mL TAE buffer in a 250mL Erlenmeyer flask and microwave until agarose is fully dissolved
  2. Allow flask to cool until warm to the touch before adding 4μL RedSafe nucleic acid staining solution. Gently swirl to mix
  3. Pour agarose into assembled gel casting tray. Remove any bubbles with a pipette tip and place comb in gel
  4. Allow gel to solidify and transfer to a gel running apparatus filled with TAE buffer
  5. Load samples of DNA containing 6X loading dye
  6. Run gel at 100V for 30 minutes or until loading dye is ⅔ way down the gel

Materials

TAE buffer:

  • 40mM Tris, pH 7.6
  • 20mM CH3COOH
  • 1mM EDTA

Low melting point agarose

250mL Erlenmeyer flask

RedSafe nucleic acid staining solution

Gel casting tray and comb

6X loading dye

Razor blade

UV-safe mask and shield

1.5mL microcentrifuge tubes
Protocol
  1. For a 1% gel, add 0.3g low melting point agarose to 30mL TAE buffer in a 250mL Erlenmeyer flask and microwave until agarose is fully dissolved
  2. Allow flask to cool until warm to the touch before adding 1.5μL RedSafe nucleic acid staining solution. Gently swirl to mix
  3. Pour agarose into assembled gel casting tray. Remove any bubbles with a pipette tip and place comb in gel
  4. Allow gel to solidify and transfer to a gel running apparatus filled with TAE buffer
  5. Load samples of DNA containing 6X loading dye
  6. Run gel at 80 V for 30 minutes or until loading dye is 1/2 way down the gel
  7. Remove the gel from casting tray and place it on a UV-light viewer. While using a UV-protecting face mask and shield, turn on the UV light and use razor blade to excise out the desired DNA bands (as quickly as possible as UV-light damages the DNA). Place each band into individual 1.5mL microcentrifuge tubes
  8. Melt the gel at 65°C for 5 minutes for ligation

Materials

**Crispy bois fill in**

Material 2

Material 3

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  • Sub-bullet 3
Protocol
  1. Step 1
  2. Step 2
  3. Step 3

Materials

Digested vector DNA

Digested insert DNA

10X DNA ligase buffer

T4 DNA ligase

ddH2O

0.2mL PCR tubes
Protocol
  1. Add to a 0.2mL PCR tube:
    • digested vector DNA
    • Appropriate amount of digested insert DNA to give desired insert:vector molar ratio
    • 0.5μL T4 DNA ligase
    • 2μL 10X T4 DNA ligase buffer
    • ddH2O to a total volume of 20μL
  2. Incubate tube at room temperature for 2 hours
  3. Use 3-10μL to transform cells, store at -20°C

Materials

Transformed bacterial colony on agar plate

10X Taq DNA polymerase

10X Taq polymerase buffer

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Protocol
  1. Step 1
  2. Step 2
  3. Step 3

Materials

Material 1

Material 2

Material 3

  • Sub-bullet 1
  • Sub-bullet 2
  • Sub-bullet 3
Protocol
  1. Step 1
  2. Step 2
  3. Step 3

Materials

Material 1

Material 2

Material 3

  • Sub-bullet 1
  • Sub-bullet 2
  • Sub-bullet 3
Protocol
  1. Step 1
  2. Step 2
  3. Step 3

Materials

Material 1

Material 2

Material 3

  • Sub-bullet 1
  • Sub-bullet 2
  • Sub-bullet 3
Protocol
  1. Step 1
  2. Step 2
  3. Step 3

Materials

Material 1

Material 2

Material 3

  • Sub-bullet 1
  • Sub-bullet 2
  • Sub-bullet 3
Protocol
  1. Step 1
  2. Step 2
  3. Step 3