Difference between revisions of "Team:US AFRL CarrollHS/Experiments"

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<li>Thaw 50 µL vial of BL21 cells on ice</li>
 
<li>Thaw 50 µL vial of BL21 cells on ice</li>
 
<li>Inoculate 2µL DNA into 50µL BL21 cells</li>
 
<li>Inoculate 2µL DNA into 50µL BL21 cells</li>
−
<ul class="real">
+
<ul id="real">
 
<li>incubate on ice for 30 minutes</li>
 
<li>incubate on ice for 30 minutes</li>
 
<li>heat shock at 42℃ for 10 seconds</li>
 
<li>heat shock at 42℃ for 10 seconds</li>
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</ul>
 
</ul>
 
<li>Inoculate 250µL LB into vial</li>
 
<li>Inoculate 250µL LB into vial</li>
−
<ul class="real">
+
<ul id="real">
 
<li>incubate at 37℃ with shaking for 1.5 hours</li>
 
<li>incubate at 37℃ with shaking for 1.5 hours</li>
 
</ul>
 
</ul>
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<li>Inoculate 50 µL JM109 cells into Falcon tube</li>
 
<li>Inoculate 50 µL JM109 cells into Falcon tube</li>
 
<li>Inoculate 2µL DNA into 50µL JM109 cells</li>
 
<li>Inoculate 2µL DNA into 50µL JM109 cells</li>
−
<ul class="real">
+
<ul id="real">
 
<li>incubate on ice for 20m</li>
 
<li>incubate on ice for 20m</li>
 
<li>heat shock at 42℃ for 45 seconds</li>
 
<li>heat shock at 42℃ for 45 seconds</li>
 
</ul>
 
</ul>
 
<li>Inoculate 950µL LB into vial</li>
 
<li>Inoculate 950µL LB into vial</li>
−
<ul class="real">
+
<ul id="real">
 
<li>incubate at 37℃ with shaking for 1.5 hours</li>
 
<li>incubate at 37℃ with shaking for 1.5 hours</li>
 
</ul>
 
</ul>
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<li>Use ethanol-wiped scalpel to excise appropriate bands</li>
 
<li>Use ethanol-wiped scalpel to excise appropriate bands</li>
 
<li>Mix and incubate at 50°C for 10 min</li>
 
<li>Mix and incubate at 50°C for 10 min</li>
−
<ul class="real">
+
<ul id="real">
 
<li>Vortex every 2 mins until gel slice is completely dissolved</li>
 
<li>Vortex every 2 mins until gel slice is completely dissolved</li>
 
</ul>
 
</ul>
 
<li>Place nucleospin column into 2mL collection tube</li>
 
<li>Place nucleospin column into 2mL collection tube</li>
−
<ul class="real">
+
<ul id="real">
 
<li>Add sample</li>
 
<li>Add sample</li>
 
<li>Centrifuge at 11,000 xg for 1 minute</li>
 
<li>Centrifuge at 11,000 xg for 1 minute</li>
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  </ul>
 
  </ul>
 
<li>Add 700 mL Buffer NT3</li>
 
<li>Add 700 mL Buffer NT3</li>
−
<ul class="real">
+
<ul id="real">
 
<li>Centrifuge at 11,000 xg for 1 minute</li>
 
<li>Centrifuge at 11,000 xg for 1 minute</li>
 
<li>Discard throughflow and place column back in same tube</li>
 
<li>Discard throughflow and place column back in same tube</li>
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<li>Repeat step 4</li>
 
<li>Repeat step 4</li>
 
<li>Centrifuge at 11,000 xg for another minute</li>
 
<li>Centrifuge at 11,000 xg for another minute</li>
−
<ul class="real">
+
<ul id="real">
 
<li>To remove buffer</li>
 
<li>To remove buffer</li>
−
<ul class="real">
+
<ul id="real">
 
<li>Discard throughflow</li>
 
<li>Discard throughflow</li>
 
<li>Centrifuge at 11,00 xg for add minute</li>
 
<li>Centrifuge at 11,00 xg for add minute</li>
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</ul>
 
</ul>
 
<li>Add 25 mL prewarmed (50°C) Buffer NE</li>
 
<li>Add 25 mL prewarmed (50°C) Buffer NE</li>
−
<ul class="real">
+
<ul id="real">
 
<li>Incubate at 50°C for 5 min</li>
 
<li>Incubate at 50°C for 5 min</li>
 
<li>Centrifuge at 50 xg for 1 minute</li>
 
<li>Centrifuge at 50 xg for 1 minute</li>
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<ol>
 
<ol>
 
<li>Aliquot 1 ml media into 1.5 mL tubes</li>
 
<li>Aliquot 1 ml media into 1.5 mL tubes</li>
−
<ul class="real">
+
<ul id="real">
 
     <li>Place in 42°C waterbath</li>
 
     <li>Place in 42°C waterbath</li>
 
</ul>
 
</ul>
 
<li>Prechill labelled 14 mL round-bottom falcon tubes</li>
 
<li>Prechill labelled 14 mL round-bottom falcon tubes</li>
−
<ul class="real">
+
<ul id="real">
 
   <li>Add mL cell culture to tube</li>
 
   <li>Add mL cell culture to tube</li>
 
   <li>Add appropriate amount of ligase rxh (2-2.5 L)</li>  
 
   <li>Add appropriate amount of ligase rxh (2-2.5 L)</li>  
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</ul>
 
</ul>
 
<li>Heat shock cells by placing at 42℃ for 45 seconds in waterbath </li>
 
<li>Heat shock cells by placing at 42℃ for 45 seconds in waterbath </li>
−
<ul class="real">
+
<ul id="real">
 
   <li>Place on ice for 2 minutes</li>
 
   <li>Place on ice for 2 minutes</li>
 
</ul>
 
</ul>
 
<li>Add 950 mL preheated media to each tube</li>
 
<li>Add 950 mL preheated media to each tube</li>
−
<ul class="real">
+
<ul id="real">
 
<li>Incubate at 37℃ with 215 rpm shaking for 1.5 hr -> 20 minutes</li>
 
<li>Incubate at 37℃ with 215 rpm shaking for 1.5 hr -> 20 minutes</li>
 
</ul>
 
</ul>
 
<h3>Plating</h3>
 
<h3>Plating</h3>
 
<li>Plate on LB-antibiotic plates</li>
 
<li>Plate on LB-antibiotic plates</li>
−
<ul class="real">
+
<ul id="real">
 
<li>Plate 100 ml for 1x transformation</li>  
 
<li>Plate 100 ml for 1x transformation</li>  
 
<li>Plate 100 mL 9x centrifuge remaining transformation at 2000 xg for 5 minutes and resuspended pellet in 100 L media </li>
 
<li>Plate 100 mL 9x centrifuge remaining transformation at 2000 xg for 5 minutes and resuspended pellet in 100 L media </li>
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<ol>
 
<ol>
 
<li>Follow LB Agar Recipe </li>
 
<li>Follow LB Agar Recipe </li>
−
   <ul class="real">
+
   <ul id="real">
 
   <li>Make sure to put stirring bar in water</li>
 
   <li>Make sure to put stirring bar in water</li>
 
   <li>Needed to make into homogenous gel</li>
 
   <li>Needed to make into homogenous gel</li>
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   </ul>
 
   </ul>
 
<li>Put into Autoclave </li>
 
<li>Put into Autoclave </li>
−
   <ul class="real">
+
   <ul id="real">
 
   <li>Lid should not be too tight</li>
 
   <li>Lid should not be too tight</li>
 
   </ul>
 
   </ul>
 
<li>Put in ice bath42°C</li>
 
<li>Put in ice bath42°C</li>
−
   <ul class="real">
+
   <ul id="real">
 
   <li>Cool till not burning hand</li>
 
   <li>Cool till not burning hand</li>
 
   <li>Put on stirring plate</li>
 
   <li>Put on stirring plate</li>
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<li>Put sterilized plates in Lamenia shield</li>
 
<li>Put sterilized plates in Lamenia shield</li>
 
<li>Using micropipette put .5 mL of chlor. And amp. agar solution</li>
 
<li>Using micropipette put .5 mL of chlor. And amp. agar solution</li>
−
   <ul class="real">
+
   <ul id="real">
 
   <li>1000x dilution</li>
 
   <li>1000x dilution</li>
 
   <li>Amp. has to be defrosted in dark drawer</li>
 
   <li>Amp. has to be defrosted in dark drawer</li>
 
   </ul>
 
   </ul>
 
<li>Pour solution into plates</li>
 
<li>Pour solution into plates</li>
−
   <ul class="real">
+
   <ul id="real">
 
   <li>Thin layer fill bottom</li>
 
   <li>Thin layer fill bottom</li>
 
   <li>Take lid slightly off to prevent condensation</li>
 
   <li>Take lid slightly off to prevent condensation</li>
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<ol>
 
<ol>
 
<li>Example for 18 mL LB add</li>
 
<li>Example for 18 mL LB add</li>
−
<ul class="real">
+
<ul id="real">
 
   <li>18 L20 mg/ L Kanamycin (antibiotic)</li>
 
   <li>18 L20 mg/ L Kanamycin (antibiotic)</li>
 
   <li>18 L 50 mg/ L ampicillin</li>
 
   <li>18 L 50 mg/ L ampicillin</li>
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<li>Aliquot 3.5 mL into labelled round bottom falcon tubes</li>
 
<li>Aliquot 3.5 mL into labelled round bottom falcon tubes</li>
 
<li>Using sterile toothpicks- pick a single colony forming unit (cfu) and inoculate tube</li>
 
<li>Using sterile toothpicks- pick a single colony forming unit (cfu) and inoculate tube</li>
−
   <ul class="real">
+
   <ul id="real">
 
   <li>Incubate overnight at 37°C with 215 rpm shaking</li>
 
   <li>Incubate overnight at 37°C with 215 rpm shaking</li>
 
   </ul>
 
   </ul>
 
<li>To 100 mL 60% glycerol stock, add 300mL overnight culture to appropriately labelled tube</li>
 
<li>To 100 mL 60% glycerol stock, add 300mL overnight culture to appropriately labelled tube</li>
−
   <ul class="real">
+
   <ul id="real">
 
   <li>Store at -80°C</li>
 
   <li>Store at -80°C</li>
 
   </ul>
 
   </ul>
 
<li>Pellet remaining cells by centrifugation in 1.5 mL tube at 13,2000 rpm for 1 min</li>
 
<li>Pellet remaining cells by centrifugation in 1.5 mL tube at 13,2000 rpm for 1 min</li>
−
   <ul class="real">
+
   <ul id="real">
 
   <li>Discard supernatant and repeat</li>
 
   <li>Discard supernatant and repeat</li>
 
   </ul>
 
   </ul>
 
<li>Resuspend pellet in Buffer P1 250 mL </li>
 
<li>Resuspend pellet in Buffer P1 250 mL </li>
−
   <ul class="real">
+
   <ul id="real">
 
   <li>Add 250 L Buffer, P2 and mix by inverting 10x</li>
 
   <li>Add 250 L Buffer, P2 and mix by inverting 10x</li>
 
   <li>Add 350 L Buffer N3 and immediately mix by inverting 10x</li>
 
   <li>Add 350 L Buffer N3 and immediately mix by inverting 10x</li>
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<li>Centrifuge at 13, 200 rpm for 10 minute</li>
 
<li>Centrifuge at 13, 200 rpm for 10 minute</li>
 
<li>Pipet supernatant into labelled QIA prep spin column</li>
 
<li>Pipet supernatant into labelled QIA prep spin column</li>
−
   <ul class="real">
+
   <ul id="real">
 
   <li>Centrifuge at 13, 200 rpm for 1 minute</li>
 
   <li>Centrifuge at 13, 200 rpm for 1 minute</li>
 
   <li>Discard thoroughflow </li>
 
   <li>Discard thoroughflow </li>
 
   </ul>
 
   </ul>
 
<li>Wash column by adding .5 mL Buffer PB *regular for low copy number plasmids*</li>
 
<li>Wash column by adding .5 mL Buffer PB *regular for low copy number plasmids*</li>
−
   <ul class="real">
+
   <ul id="real">
 
   <li>Centrifuge at 13, 200 rpm for 1 minute</li>
 
   <li>Centrifuge at 13, 200 rpm for 1 minute</li>
 
   <li>Discard thoroughflow </li>
 
   <li>Discard thoroughflow </li>
 
   </ul>
 
   </ul>
 
<li>Wash by adding .75 mL Buffer PE</li>
 
<li>Wash by adding .75 mL Buffer PE</li>
−
   <ul class="real">
+
   <ul id="real">
 
   <li>Centrifuge at 13, 200 rpm for 1 minute</li>
 
   <li>Centrifuge at 13, 200 rpm for 1 minute</li>
 
   <li>Discard thoroughflow </li>
 
   <li>Discard thoroughflow </li>
Line 279: Line 279:
 
   </ul>
 
   </ul>
 
<li>Place spin column in a clean, labelled 1.5 mL tube </li>
 
<li>Place spin column in a clean, labelled 1.5 mL tube </li>
−
   <ul class="real">
+
   <ul id="real">
 
   <li>Add 50 LEB to center of column & let stand for 1 minute at room temperature</li>
 
   <li>Add 50 LEB to center of column & let stand for 1 minute at room temperature</li>
 
   <li>Centrifuge at 12,000 rpm for 1 minute</li>
 
   <li>Centrifuge at 12,000 rpm for 1 minute</li>

Revision as of 19:49, 29 October 2017


Experiments

Transformations

BI21 Cells:

  1. Thaw 50 µL vial of BL21 cells on ice
  2. Inoculate 2µL DNA into 50µL BL21 cells
    • incubate on ice for 30 minutes
    • heat shock at 42℃ for 10 seconds
    • incubate on ice for 5m
  3. Inoculate 250µL LB into vial
    • incubate at 37℃ with shaking for 1.5 hours
  4. Plate 1x/9x

JM109 Cells:

  1. Thaw vial of JM109 cells on ice
  2. Label 14 mL Falcon tube & plane on ice
  3. Inoculate 50 µL JM109 cells into Falcon tube
  4. Inoculate 2µL DNA into 50µL JM109 cells
    • incubate on ice for 20m
    • heat shock at 42℃ for 45 seconds
  5. Inoculate 950µL LB into vial
    • incubate at 37℃ with shaking for 1.5 hours
  6. Plate 1x/9x


Electrophoresis/Gel Protocols

1% Agarose Electrophoresis Gel

  1. Add 0.35 g agarose to 35 mL 1x TAE in 100mL conical flask
  2. Heat in microwave for 35 seconds
  3. Swirl and heat in microwave for 25 seconds
  4. Swirl and heat in microwave for 15 seconds
  5. Swirl and heat in microwave for 7 seconds
  6. Swirl and ensure no ‘floaties’
  7. Cool outside of conical flask with water until ‘hand not’
  8. Pour into gel mold and add well comb

Gel Extraction

  1. Use ethanol-wiped scalpel to excise appropriate bands
  2. Mix and incubate at 50°C for 10 min
    • Vortex every 2 mins until gel slice is completely dissolved
  3. Place nucleospin column into 2mL collection tube
    • Add sample
    • Centrifuge at 11,000 xg for 1 minute
    • Discard throughflow and place column back in same tube
  4. Add 700 mL Buffer NT3
    • Centrifuge at 11,000 xg for 1 minute
    • Discard throughflow and place column back in same tube
  5. Repeat step 4
  6. Centrifuge at 11,000 xg for another minute
    • To remove buffer
      • Discard throughflow
      • Centrifuge at 11,00 xg for add minute
      • Place column in a clean, labelled 1.5 mL tube
  7. Add 25 mL prewarmed (50°C) Buffer NE
    • Incubate at 50°C for 5 min
    • Centrifuge at 50 xg for 1 minute
    • Centrifuge at 11,000 xg for 1 minute

Plasmid Transformation Protocol

  1. Aliquot 1 ml media into 1.5 mL tubes
    • Place in 42°C waterbath
  2. Prechill labelled 14 mL round-bottom falcon tubes
    • Add mL cell culture to tube
    • Add appropriate amount of ligase rxh (2-2.5 L)
    • Incubate in nice for 20 minutes
  3. Heat shock cells by placing at 42℃ for 45 seconds in waterbath
    • Place on ice for 2 minutes
  4. Add 950 mL preheated media to each tube
    • Incubate at 37℃ with 215 rpm shaking for 1.5 hr -> 20 minutes

    Plating

  5. Plate on LB-antibiotic plates
    • Plate 100 ml for 1x transformation
    • Plate 100 mL 9x centrifuge remaining transformation at 2000 xg for 5 minutes and resuspended pellet in 100 L media

Plates Protocol

  1. Follow LB Agar Recipe
    • Make sure to put stirring bar in water
    • Needed to make into homogenous gel
    • Needs to be sterile
  2. Put into Autoclave
    • Lid should not be too tight
  3. Put in ice bath42°C
    • Cool till not burning hand
    • Put on stirring plate
  4. Put sterilized plates in Lamenia shield
  5. Using micropipette put .5 mL of chlor. And amp. agar solution
    • 1000x dilution
    • Amp. has to be defrosted in dark drawer
  6. Pour solution into plates
    • Thin layer fill bottom
    • Take lid slightly off to prevent condensation

QIA Prep Spin Mini Prep Kit

    1. Example for 18 mL LB add
      • 18 L20 mg/ L Kanamycin (antibiotic)
      • 18 L 50 mg/ L ampicillin
    2. Aliquot 3.5 mL into labelled round bottom falcon tubes
    3. Using sterile toothpicks- pick a single colony forming unit (cfu) and inoculate tube
      • Incubate overnight at 37°C with 215 rpm shaking
    4. To 100 mL 60% glycerol stock, add 300mL overnight culture to appropriately labelled tube
      • Store at -80°C
    5. Pellet remaining cells by centrifugation in 1.5 mL tube at 13,2000 rpm for 1 min
      • Discard supernatant and repeat
    6. Resuspend pellet in Buffer P1 250 mL
      • Add 250 L Buffer, P2 and mix by inverting 10x
      • Add 350 L Buffer N3 and immediately mix by inverting 10x
    7. Centrifuge at 13, 200 rpm for 10 minute
    8. Pipet supernatant into labelled QIA prep spin column
      • Centrifuge at 13, 200 rpm for 1 minute
      • Discard thoroughflow
    9. Wash column by adding .5 mL Buffer PB *regular for low copy number plasmids*
      • Centrifuge at 13, 200 rpm for 1 minute
      • Discard thoroughflow
    10. Wash by adding .75 mL Buffer PE
      • Centrifuge at 13, 200 rpm for 1 minute
      • Discard thoroughflow
      • Centrifuge for an addition minute to ensure removal of residual wash buffer
    11. Place spin column in a clean, labelled 1.5 mL tube
      • Add 50 LEB to center of column & let stand for 1 minute at room temperature
      • Centrifuge at 12,000 rpm for 1 minute
      • Store at -20℃