Difference between revisions of "Team:NTU-LIHPAO-Taiwan/Notebook"
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− | + | /*-------------------------------------------*/ | |
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/*-------------------Media-------------------*/ | /*-------------------Media-------------------*/ | ||
/*-------------------------------------------*/ | /*-------------------------------------------*/ | ||
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<ul class="main-Content"> | <ul class="main-Content"> | ||
<li> | <li> | ||
− | <span class="title"> | + | <span class="title">Protocols</span> |
<ul class="sub-Content"> | <ul class="sub-Content"> | ||
− | <li><a href="#First1"> | + | <li><a href="#First1">Preparation of Competent Cells (<i>E.coli</i>)</a></li> |
− | <li><a href="#First2"> | + | <li><a href="#First2">DNA Dissolution</a></li> |
− | <li><a href="#First3"> | + | <li><a href="#First3">Agarose Gel Electrophoresis</a></li> |
+ | <li><a href="#First4">Gel Extraction</a></li> | ||
+ | <li><a href="#First5">DNA Ligation</a></li> | ||
+ | <li><a href="#First6">Plasmid DNA Extraction Using Alkaline Lysis Method (<i>E.coli</i>)</a></li> | ||
+ | <li><a href="#First7">Transformation(<i>E.coli</i>)</a></li> | ||
+ | <li><a href="#First8">Protein Extraction</a></li> | ||
+ | <li><a href="#First9">SDS-PAGE</a></li> | ||
+ | <li><a href="#First10">Western Blot</a></li> | ||
+ | <li><a href="#First11">Immunostaining</a></li> | ||
+ | <li><a href="#First12">Thawing Caco-2 cells</a></li> | ||
+ | <li><a href="#First13">Freezing Caco-2 cells</a></li> | ||
+ | <li><a href="#First14">Caco2 Cell passage</a></li> | ||
+ | <li><a href="#First15">Seeding in transwell</a></li> | ||
+ | <li><a href="#First16">Measure TEER</a></li> | ||
</ul> | </ul> | ||
</li> | </li> | ||
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if (i === index) { | if (i === index) { | ||
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} else { | } else { | ||
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<div class="ContentBox"> | <div class="ContentBox"> | ||
<div class="ContentHolder"> | <div class="ContentHolder"> | ||
− | |||
− | + | <div class="Text1" id="First1"><Red>Preparation of Competent Cells (<i>E.coli</i>)</Red></div> | |
+ | <div class="Text2"> | ||
+ | <Green>Materials and Reagents :</Green> | ||
+ | </div> | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part1"> |
+ | <li><i>Escherichia coli</i> DH5α</li> | ||
+ | <li>LB broth</li> | ||
+ | <li>TB buffer</li> | ||
+ | <li>DMSO</li> | ||
+ | <li>Liquid nitrogen</li> | ||
+ | </ol> | ||
</div> | </div> | ||
− | + | <div class="Text2"> | |
− | + | <Green>Equipment :</Green> | |
− | <div class=" | + | </div> |
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part1"> |
+ | <li>Ice</li> | ||
+ | <li>Shaker</li> | ||
+ | <li>Spectrometer</li> | ||
+ | <li>Centrifuge</li> | ||
+ | </ol> | ||
</div> | </div> | ||
+ | <div class="Text2"> | ||
+ | <Green>Procedure :</Green> | ||
+ | </div> | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part2"> |
+ | <li>Inoculate 10μL <i>Escherichia coli</i> DH5α into 10mL LB broth (1:1000)</li> | ||
+ | <li>Grow for 12-16 hours at 37℃ with shaking</li> | ||
+ | <li>Inoculate 500μL <i>Escherichia coli</i> DH5α into 50mL LB broth (1:100)</li> | ||
+ | <li>Grow for 2 hours at 37℃ with shaking to O.D.<Sub>600</Sub>=0.4-0.6</li> | ||
+ | <li>Split the cell into two Falcon tubes, both contain 25 mL <i>Escherichia coli</i> DH5α</li> | ||
+ | <li>Centrifuge at 4℃, 3000rpm(800G) for 10 minutes</li> | ||
+ | <li>Discard the supernatant</li> | ||
+ | <li>Resuspend the cell pellet by gently adding 8.5mL TB buffer (1/3 V)</li> | ||
+ | <li>On ice for 10 minutes</li> | ||
+ | <li>Centrifuge at 4℃, 3000rpm(800G) for 10 minutes</li> | ||
+ | <li>Discard the supernatant using pipetman</li> | ||
+ | <li>Resuspend the cell pellet by gently adding 2mL TB buffer (1/12.5 V)</li> | ||
+ | <li>Add 150μL DMSO (7%)</li> | ||
+ | <li>On ice for 10 minutes</li> | ||
+ | <li>Transfer the cell to new eppendorfs with 60μL per tube</li> | ||
+ | <li>Freeze the cell in liquid nitrogen</li> | ||
+ | <li>Store the cell at -80℃</li> | ||
+ | </ol> | ||
</div> | </div> | ||
− | + | <div class="Text1" id="First2"><Red>DNA Dissolution</Red></div> | |
− | + | <div class="Text2"> | |
− | + | <Green>Materials and Reagents :</Green> | |
− | + | </div> | |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | <div class=" | + | |
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part1"> |
+ | <li>DNA (BioBricks/synthesized)</li> | ||
+ | <li>ddH<Sub>2</Sub>O</li> | ||
+ | </ol> | ||
</div> | </div> | ||
+ | <div class="Text2"> | ||
+ | <Green>Procedure :</Green> | ||
+ | </div> | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part2"> |
+ | <li>Add 10μL ddH<Sub>2</Sub>O</li> | ||
+ | <li>Wait for 1 minute until the DNA dissolve</li> | ||
+ | <li>Pipet several times and transfer the DNA to an eppendorf</li> | ||
+ | </ol> | ||
</div> | </div> | ||
+ | <div class="Text1" id="First3"><Red>Agarose Gel Electrophoresis</Red></div> | ||
+ | <div class="Text2"> | ||
+ | <Green>Materials and Reagents :</Green> | ||
+ | </div> | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part1"> |
− | + | <li>Agarose</li> | |
− | + | <li>1X TAE</li> | |
− | + | <li>Tracking dye</li> | |
− | </div> | + | <li>Marker (1kb/100bp)</li> |
− | + | <li>EtBr</li> | |
− | + | <li>ddH<Sub>2</Sub>O</li> | |
− | + | </ol> | |
+ | </div> | ||
+ | <div class="Text2"> | ||
+ | <Green>Equipment :</Green> | ||
+ | </div> | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part1"> |
+ | <li>Gel tray</li> | ||
+ | <li>Well comb</li> | ||
+ | <li>Electrophoresis tank</li> | ||
+ | <li>UV detector</li> | ||
+ | </ol> | ||
</div> | </div> | ||
− | + | <div class="Text2"> | |
− | + | <Green>Procedure :</Green> | |
− | + | </div> | |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part2"> |
+ | <div class="Text_TitleUnderline">Casting an Agarose Gel (m/v = 1.0% or 1.5%)</div> | ||
+ | <li>Measure out appropriate mass of agarose powder into a serum bottle</li> | ||
+ | <li>Add appropriate volume of 1X TAE</li> | ||
+ | <li>Let agarose solution cool down to acceptable temperature for bare hands</li> | ||
+ | <li>Pour the solution into a gel tray with the well comb in place, and push the bubbles away with a pipette tip</li> | ||
+ | <li>Let sit at room temperature for 30 minutes, until it has completely solidified</li> | ||
+ | <div class="Text_TitleUnderline">Loading Samples and Running the Gel</div> | ||
+ | <li>Place the gel as well as its tray into the electrophoresis tank containing 1X TAE </li> | ||
+ | (Make sure that the surface is higher than the top of the gel and not overflow) | ||
+ | <li>Mix the samples with tracking dye (1/10 V) sufficiently</li> | ||
+ | <li>Load the samples into the each well</li> | ||
+ | <li>Load marker (usually in the first and last lane)</li> | ||
+ | <li>Set an appropriate voltage (full/half) and run the gel for 15-20 minutes</li> | ||
+ | <div class="Text_TitleUnderline">Imaging the Gel</div> | ||
+ | <li>Put the gel into a container filled with 1X TAE and EtBr, staining for 5 minutes</li> | ||
+ | <li>Replace EtBr solution with water and destain for 3 minutes</li> | ||
+ | <li>Put the gel in an UV detector and record the result</li> | ||
+ | </ol> | ||
</div> | </div> | ||
+ | <div class="Text1" id="First4"><Red>Gel Extraction</Red></div> | ||
+ | <div class="Text2"> | ||
+ | <Green>Materials and Reagents :</Green> | ||
+ | </div> | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part1"> |
− | </div> | + | <li>Gel/PCR buffer</li> |
+ | <li>W1 buffer</li> | ||
+ | <li>Wash buffer</li> | ||
+ | <li>ddH<Sub>2</Sub>O</li> | ||
+ | </ol> | ||
+ | </div> | ||
+ | <div class="Text2"> | ||
+ | <Green>Equipment :</Green> | ||
+ | </div> | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part1"> |
+ | <li>Cutter knife</li> | ||
+ | <li>Eppendorf</li> | ||
+ | <li>Vortex mixer</li> | ||
+ | <li>Dry bath incubator</li> | ||
+ | <li>DF Column & Collection tube</li> | ||
+ | <li>Mini Centrifuge</li> | ||
+ | <li>Microcentrifuge</li> | ||
+ | </ol> | ||
</div> | </div> | ||
− | + | <div class="Text2"> | |
− | + | <Green>Procedure :</Green> | |
− | + | </div> | |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part2"> |
− | + | <div class="Text_TitleUnderline">Gel Dissociation</div> | |
− | + | <li>Excise the agarose gel slice containing relevant DNA fragments and remove any extra agarose to minimize the size of the gel slice (<300μL)</li> | |
− | + | <li>Transfer the gel slice to an eppendorf</li> | |
− | + | <li>Add 500μL Gel/PCR buffer to the sample and mix by vortex</li> | |
− | + | <li>Incubate at 60℃ for 10-15 minutes to ensure the gel slice has been completely dissolved (invert the tube every 2-3 minutes)</li> | |
− | + | <li>Cool the dissolved sample mixture to room temperature</li> | |
− | + | <div class="Text_TitleUnderline">DNA Binding</div> | |
− | + | <li>Place the DF Column in a 2mL Collection tube</li> | |
− | + | <li>Transfer 800μL of the sample mixture to the DF Column</li> | |
− | + | <li>Discard the flow-through and place the DF Column back in the Collection tube</li> | |
− | + | (If the sample mixture is more than 800μL, repeat the DNA binding step) | |
− | + | <div class="Text_TitleUnderline">Wash</div> | |
− | + | <li>Add 400μL W1 buffer into the DF Column</li> | |
− | + | <li>Spin down for approximately 20 seconds</li> | |
− | + | <li>Discard the flow-through and place the DF Column back in the Collection tube</li> | |
− | + | <li>Add 600μL wash buffer (contains ethanol) into the DF Column</li> | |
− | + | <li>Let stand for 1 minute at room temperature</li> | |
− | + | <li>Spin down for approximately 30 seconds</li> | |
− | + | <li>Discard the flow-through and place the DF Column back in the Collection tube</li> | |
− | + | <li>Centrifuge at 12000 rpm for 3 minutes to dry the column matrix</li> | |
− | < | + | (Can be done twice) |
− | + | <li>Discard the flow-through</li> | |
− | + | <div class="Text_TitleUnderline">DNA Elution</div> | |
− | + | <li>Transfer the dried DF Column to a new eppendorf (cap cut)</li> | |
− | + | <li>Add 30μL of 37℃ ddH2O into the center of the column matrix</li> | |
− | + | <li>Let stand for at least 2 minutes to ensure that ddH2O is completely absorbed</li> | |
− | + | <li>Centrifuge at 12000 rpm for 2 minutes to elute the purified DNA</li> | |
+ | <li>Re-add the subnatant into the center of the column matrix</li> | ||
+ | <li>Centrifuge at 12000 rpm for 2 minutes to elute the purified DNA</li> | ||
+ | </ol> | ||
</div> | </div> | ||
− | + | <div class="Text1" id="First5"><Red>DNA Ligation</Red></div> | |
− | + | <div class="Text2"> | |
− | + | <Green>Materials and Reagents :</Green> | |
− | + | </div> | |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | <div class=" | + | |
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part1"> |
− | </div> | + | <li>DNA (insert & vector)</li> |
+ | <li>Ligation high ver.2</li> | ||
+ | </ol> | ||
+ | </div> | ||
+ | <div class="Text2"> | ||
+ | <Green>Equipment :</Green> | ||
+ | </div> | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part1"> |
+ | <li>Cooling dry bath incubator</li> | ||
+ | </ol> | ||
</div> | </div> | ||
+ | <div class="Text2"> | ||
+ | <Green>Procedure :</Green> | ||
+ | </div> | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part2"> |
− | + | <li> | |
− | + | Table | |
− | + | <table> | |
− | + | <tr> | |
− | + | <th>Components</th> | |
− | + | <th>Volume (μL)</th> | |
− | + | </tr> | |
− | + | <tr> | |
− | + | <td>Insert</td> | |
− | + | <td>x</td> | |
− | + | </tr> | |
− | + | <tr> | |
− | + | <td>Vector</td> | |
− | + | <td>y</td> | |
− | + | </tr> | |
+ | <tr> | ||
+ | <td>Ligation High</td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr class="alt"> | ||
+ | <td>Total</td> | ||
+ | <td>7</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | Molar ratio: insert/vector = 3/1 | ||
+ | <br> x + y = 6</br> | ||
+ | </li> | ||
+ | <li>Gently mix the solution by pipetting up and down</li> | ||
+ | <li>Incubate | ||
+ | <ol class="part3"> | ||
+ | <li>at 16℃ for 2 hours, or</li> | ||
+ | <li>at 37℃ for 1 hour, or</li> | ||
+ | <li>at 4℃ overnight</li> | ||
+ | </ol> | ||
+ | </li> | ||
+ | <li>Proceed with bacterial transformation</li> | ||
+ | </ol> | ||
</div> | </div> | ||
− | + | <div class="Text1" id="First6"><Red>Plasmid DNA Extraction Using Alkaline Lysis Method (<i>E. coli</i>)</Red></div> | |
− | + | <div class="Text2"> | |
+ | <Green>Materials and Reagents :</Green> | ||
+ | </div> | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part1"> |
− | + | <li><i>Escherichia coli</i> DH5α (with plasmid)</li> | |
− | + | <li>LB broth</li> | |
− | + | <li>Resuspension solution (MPI, with RNAase)</li> | |
− | </div> | + | <li>Lysis solution (MPII)</li> |
− | + | <li>Neutralizing solution (MPIII)</li> | |
− | + | <li>Isopropanol</li> | |
− | </div> | + | <li>70% ethanol</li> |
+ | <li>ddH<Sub>2</Sub>O</li> | ||
+ | </ol> | ||
+ | </div> | ||
+ | <div class="Text2"> | ||
+ | <Green>Equipment :</Green> | ||
+ | </div> | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part1"> |
+ | <li>Shaker</li> | ||
+ | <li>Centrifuge</li> | ||
+ | <li>Vortex mixer</li> | ||
+ | </ol> | ||
</div> | </div> | ||
− | + | <div class="Text2"> | |
− | + | <Green>Procedure :</Green> | |
− | < | + | </div> |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part2"> |
+ | <li>Grow bacteria in LB broth with appropriate antibiotics at 37℃ overnight with shaking</li> | ||
+ | <li>Transfer 1.5mL culture to an eppendorf</li> | ||
+ | <li>Centrifuge at 4℃, 5000rpm for 5 minutes</li> | ||
+ | <li>Discard the supernatant</li> | ||
+ | <li>Add 150μL of resuspension solution (MPI, with RNAase) into each tube, pipet several times, and vortex to completely resuspend the cell pellet</li> | ||
+ | <li>Add 150μL of lysis solution (MPII), gently invert the tubes about 20 times, and then let the sample mixture stand at room temperature for 2 minutes</li> | ||
+ | <li>Add 150μL of neutralizing solution (MPIII) and mix by inverting the tubes about 20 times. Bacterial chromosomal DNA and proteins can be seen as white precipitates</li> | ||
+ | <li>Centrifuge at 4℃, 15000rpm for 15 minutes</li> | ||
+ | <li>Carefully transfer 400μL of the supernatant to a new eppendorf</li> | ||
+ | (Step 8&9 can be done twice) | ||
+ | <li>Add 400μL (same volume as the supernatant) isopropanol, and shake up the tubes as vigorously as one can</li> | ||
+ | <li>Centrifuge at 4℃, 15000rpm for 15 minutes</li> | ||
+ | <li>Discard the supernatant</li> | ||
+ | <li>Add 200μL of 70% ethanol to wash out the salts</li> | ||
+ | <li>Centrifuge at 4℃, 15000rpm for 5 minutes</li> | ||
+ | <li>Discard the supernatant and remove the remains as much as possible with pipetman</li> | ||
+ | <li>Air dry for about 30 minutes</li> | ||
+ | <li>Resuspend the DNA pellet with 20μL ddH<Sub>2</Sub>O</li> | ||
+ | </ol> | ||
</div> | </div> | ||
− | + | <div class="Text1" id="First7"><Red>Transformation (<i>E. coli</i>)</Red></div> | |
− | + | <div class="Text2"> | |
− | + | <Green>Materials and Reagents :</Green> | |
− | + | </div> | |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | <div class=" | + | |
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part1"> |
− | + | <li>Competent cell (<i>Escherichia coli</i> DH5α)</li> | |
− | + | <li>LB plate (Amp+/CP+)</li> | |
− | + | </ol> | |
− | + | </div> | |
− | + | <div class="Text2"> | |
− | + | <Green>Equipment :</Green> | |
− | + | </div> | |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | </div> | + | |
− | + | ||
− | + | ||
− | + | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part1"> |
+ | <li>-80℃ refrigerator</li> | ||
+ | <li>Ice</li> | ||
+ | <li>37℃ incubator</li> | ||
+ | <li>Super optimal broth (SOB) (37℃)</li> | ||
+ | <li>Shaker</li> | ||
+ | </ol> | ||
</div> | </div> | ||
− | + | <div class="Text2"> | |
− | + | <Green>Procedure :</Green> | |
− | <div class=" | + | </div> |
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part2"> |
− | + | <li>Take out the competent cells from -80℃ refrigerator</li> | |
− | + | <li>Thaw the cells on ice for 5 minutes</li> | |
− | + | <li>Add 1μL plasmid DNA into the competent cells, and mix gently by pipetting</li> | |
− | + | <li>On ice for 10 minutes</li> | |
− | + | <li>Heat shock at 37℃ for 3 minutes</li> | |
− | + | <li>On ice for 2 minutes</li> | |
− | + | <li>Add 150μL 37℃ SOB into the mixture</li> | |
+ | <li>Place the tube at 37℃ with shaking for 1 hour(Amp+)/4 hours(CP+) respectively</li> | ||
+ | <li>Spread the cells onto the LB plates (Amp+/ CP+)</li> | ||
+ | <li>Incubate the plates at 37℃ with shaking for 12-16 hours</li> | ||
− | + | </ol> | |
− | + | ||
− | + | ||
− | + | ||
</div> | </div> | ||
+ | <div class="Text1" id="First8"><Red>Protein Extraction</Red></div> | ||
+ | <div class="Text2"> | ||
+ | <Green>Materials and Reagents :</Green> | ||
+ | </div> | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part1"> |
+ | <li>plasmid/ BL21 competent cell</li> | ||
+ | <li>LB plate</li> | ||
+ | <li>LB broth</li> | ||
+ | <li>lysis buffer</li> | ||
+ | </ol> | ||
</div> | </div> | ||
− | + | <div class="Text2"> | |
− | + | <Green>Equipment :</Green> | |
− | + | </div> | |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part1"> |
+ | <li>15/ 50ml conial tube</li> | ||
+ | <li>Shaking incubator</li> | ||
+ | <li>Erlenmeyer flask</li> | ||
+ | <li>Spectrophotometer</li> | ||
+ | <li>Centrifuge</li> | ||
+ | <li>Sonicator</li> | ||
+ | <li>Eppendorf</li> | ||
+ | </ol> | ||
</div> | </div> | ||
− | + | <div class="Text2"> | |
− | + | <Green>Procedure :</Green> | |
− | <div class=" | + | </div> |
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part2"> |
+ | <li>Transform plamid into BL21 (see transformation)</li> | ||
+ | <li>Pick up a single colony and incubate into 2ml LB/CP medium, then agitate them in a shaking incubator at 37℃ overnight</li> | ||
+ | <li>Pour the culture into 100ml LB/CP medium, then agitate until it reach A<sub>600</sub> of 0.6</li> | ||
+ | <li>Pour the culture into 50ml conical tube, and centrifuge at 8000rpm for 10 min</li> | ||
+ | <li>Store the supernate and the pellets in the centrifuge tubes in a -80℃ freezer</li> | ||
+ | <li>Use 6ml lysis buffer(NP-10) to resuspend the cell pellet and transfer into a 15ml centrifuge tube</li> | ||
+ | <li>Lyse the cell with sonication</li> | ||
+ | <li>Centrifuge 15ml conial tube at 9000rpm for 10 min</li> | ||
+ | <li>Store the supernate as coarse extract</li> | ||
+ | </ol> | ||
</div> | </div> | ||
− | + | <div class="Text1" id="First9"><Red>SDS-PAGE</Red></div> | |
− | + | <div class="Text2"> | |
− | + | <Green>Materials and Reagents :</Green> | |
− | + | </div> | |
− | + | ||
− | <div class=" | + | |
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part1"> |
− | + | <li>Solution A (acrylamide/ bis-acrylamide (29:1) 30% solution)</li> | |
− | + | <li>Solution B (Tris (Tris base, 1.5 M) 90.8 gm; TEMED 1.8 ml; pH = 8.8/ 500ml)</li> | |
− | + | <li>Solution C (Tris (Tris base, 0.5 M) 6.0 gm; TEMED 0.4 ml; pH = 6.7/ 100ml)</li> | |
− | + | <li>10% SDS (1kb/100bp)</li> | |
− | + | <li>ddH<Sub>2</Sub>O</li> | |
− | + | <li>APS</li> | |
− | + | <li>Running buffer (1M Tris 12.5 ml; glysine 7.7g/ 500ml)</li> | |
− | + | <li>Sample buffer(5X) (Tris base, 125mM X5; EDTA2•Na, 2mM X 5; SDS(2% X2); β-mercaptoethanol, 5% X5)</li> | |
− | + | <li>Protein marker</li> | |
− | + | </ol> | |
− | + | </div> | |
− | + | <div class="Text2"> | |
− | </div> | + | <Green>Equipment :</Green> |
− | + | </div> | |
− | + | ||
− | <div class=" | + | |
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part1"> |
+ | <li>Gel Caster</li> | ||
+ | <li>Accessories for each gel</li> | ||
+ | <li> (1) One glass plate</li> | ||
+ | <li> (2) One aluminum notched plate</li> | ||
+ | <li> (3) Two 0.75-mm thick spacers</li> | ||
+ | <li> (4) One 0.75-mm thick 10-well comb</li> | ||
+ | <li> (5) One well-locating decal</li> | ||
+ | <li>Power supply</li> | ||
+ | </ol> | ||
</div> | </div> | ||
− | + | <div class="Text2"> | |
− | + | <Green>Procedure :</Green> | |
− | + | </div> | |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part2"> |
+ | <li>Assemble one glass plate and one alumimum plate with two spacers for each gel module</li> | ||
+ | <li>Prepare the SDS gel solution (see the table below). Two 0.75mm mini gels need approximately 10ml separation gel solution and 5ml stacking solution. Add APS solution at the final step</li> | ||
+ | <li>Mix the separation gel solution, and add the solution into the gel module until reaching the designated level. Then add isopropanol on the top of the gel. It takes about 40 min to complete the polymerization step</li> | ||
+ | <li>Remove the isopropanol by using a small strip of filter paper. Fill up the stacking gel solution until reaching the top. Insert comb into the gel solution as soon as possible. It takes 10 min to complete the polymerization step</li> | ||
+ | <li>Remove the comb and set the gel in the cell buffer dam. Pour the running buffer into the inner chamber and keep pouring after overflow until the buffer surface reaches the required level in the outer chamber</li> | ||
+ | <li>Use a micropipette to clean up every single well with the running buffer</li> | ||
+ | <li>Mix protein samples with 1/5 volumes of 5X sample buffer. Heat the mixture at 100oC for 10 min. Let it cool down to room temperature</li> | ||
+ | <li>Load protein sample and the protein marker into the well</li> | ||
+ | <li>Run the electrophoresis at 70V for 20 min, and then 150V for 55 min</li> | ||
+ | <li>Remove the two spacer and lift the glass plate, and remove the stacking gel and the remaining gel is ready for CBR staining and Western blot</li> | ||
+ | </ol> | ||
</div> | </div> | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <table class="Table_Width"> |
+ | <tr> | ||
+ | <th>(Unit: ml)</th> | ||
+ | <th>Separation gel</th> | ||
+ | <th></th> | ||
+ | <th></th> | ||
+ | <th></th> | ||
+ | <th></th> | ||
+ | <th></th> | ||
+ | <th>Stacking gel</th> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Percentage</td> | ||
+ | <td>5%</td> | ||
+ | <td>7.5%</td> | ||
+ | <td>10%</td> | ||
+ | <td>12.5%</td> | ||
+ | <td>15%</td> | ||
+ | <td>20%</td> | ||
+ | <td>4%</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Solution A</td> | ||
+ | <td>16.5</td> | ||
+ | <td>2.5</td> | ||
+ | <td>3.35</td> | ||
+ | <td>4.15</td> | ||
+ | <td>5</td> | ||
+ | <td>6.5</td> | ||
+ | <td>0.66</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Solution B</td> | ||
+ | <td>2.5</td> | ||
+ | <td>2.5</td> | ||
+ | <td>2.5</td> | ||
+ | <td>2.5</td> | ||
+ | <td>2.5</td> | ||
+ | <td>2.5</td> | ||
+ | <td>-</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Solution C</td> | ||
+ | <td>-</td> | ||
+ | <td>-</td> | ||
+ | <td>-</td> | ||
+ | <td>-</td> | ||
+ | <td>-</td> | ||
+ | <td>-</td> | ||
+ | <td>1.24</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>10% SDS</td> | ||
+ | <td>0.1</td> | ||
+ | <td>0.1</td> | ||
+ | <td>0.1</td> | ||
+ | <td>0.1</td> | ||
+ | <td>0.1</td> | ||
+ | <td>0.1</td> | ||
+ | <td>0.05</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>dH<sub>2</sub>O</td> | ||
+ | <td>5.7</td> | ||
+ | <td>4.85</td> | ||
+ | <td>4</td> | ||
+ | <td>3.2</td> | ||
+ | <td>2.35</td> | ||
+ | <td>0.85</td> | ||
+ | <td>2.95</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>APS(10%)</td> | ||
+ | <td>0.05</td> | ||
+ | <td>0.05</td> | ||
+ | <td>0.05</td> | ||
+ | <td>0.05</td> | ||
+ | <td>0.05</td> | ||
+ | <td>0.05</td> | ||
+ | <td>0.1</td> | ||
+ | </tr> | ||
+ | <tr class="alt"> | ||
+ | <td>Total Volume</td> | ||
+ | <td>10</td> | ||
+ | <td>10</td> | ||
+ | <td>10</td> | ||
+ | <td>10</td> | ||
+ | <td>10</td> | ||
+ | <td>10</td> | ||
+ | <td>5</td> | ||
+ | </tr> | ||
+ | </table> | ||
</div> | </div> | ||
+ | <div class="Text1" id="First10"><Red>Western Blot</Red></div> | ||
+ | <div class="Text2"> | ||
+ | <Green>Materials and Reagents :</Green> | ||
+ | </div> | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part1"> |
− | + | <li>Transfer buffer ( Tris 25mM; glycine 0.192M)</li> | |
− | + | <li>Methanol</li> | |
− | + | <li>10 X TBST (1M Tris pH =8.0; Tween 20, 50ml; NaCl 43.5g)</li> | |
− | + | </ol> | |
− | + | </div> | |
− | + | <div class="Text2"> | |
− | + | <Green>Equipment :</Green> | |
− | + | </div> | |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | </div> | + | |
− | + | ||
− | + | ||
− | < | + | |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part1"> |
+ | <li>Semi-dry trnasfer cell</li> | ||
+ | <li>PVDF membrane</li> | ||
+ | <li>Nitrocellulose paper</li> | ||
+ | <li>Square Petri dish</li> | ||
+ | <li>Rotary shaker</li> | ||
+ | </ol> | ||
</div> | </div> | ||
+ | <div class="Text2"> | ||
+ | <Green>Procedure :</Green> | ||
+ | </div> | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part2"> |
+ | <li>Equilibrate the nitrocellulose paper and SDS-PAGE gel by soaking them with transfer buffer</li> | ||
+ | <li>Rinse the PVDF membrane with 100% methanol for a few second and equilibrate it with transfer buffer</li> | ||
+ | <li>Place the elements in the following order onto the semi-dry transfer cell from bottom to top: nitrocellulose paper, PVDF membrane, SDS-PAGE gel, nitrocellulose paper</li> | ||
+ | <li>Set up the current at 0.09A and run for 75 min</li> | ||
+ | </ol> | ||
</div> | </div> | ||
− | + | <div class="Text1" id="First11"><Red>Immunostaining</Red></div> | |
− | + | <div class="Text2"> | |
− | + | <Green>Materials and Reagents :</Green> | |
− | + | </div> | |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part1"> |
− | + | <li>3% milk</li> | |
− | + | <li>Antibody solution</li> | |
− | + | <li>Secondary antibody (anti-mouse HRP)</li> | |
− | + | <li>TBST</li> | |
− | + | <li>Western HRP substrate</li> | |
− | + | </ol> | |
− | + | </div> | |
− | + | <div class="Text2"> | |
− | + | <Green>Equipment :</Green> | |
− | + | </div> | |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | </div> | + | |
− | + | ||
− | + | ||
− | <div class=" | + | |
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part1"> |
+ | <li>Square petri dish</li> | ||
+ | <li>Rotary shaker</li> | ||
+ | <li>UVP Biospectrum</li> | ||
+ | </ol> | ||
</div> | </div> | ||
+ | <div class="Text2"> | ||
+ | <Green>Procedure :</Green> | ||
+ | </div> | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part2"> |
− | + | <li>Put the membrane in the square petri dish block the membrane with the 3% milk/TBST at room temperature for 1hr</li> | |
− | + | <li>Discard the milk and replace it with antibody solution(mouse His-probe Antibody) at 4℃ overnight</li> | |
− | + | <li>Recycle the antibody solution. Wash the membrane with TBST three times, 5 min each</li> | |
− | + | <li>Soak membrane into anti-mouse HRP solution for 1 hr</li> | |
− | + | <li>Discard the anti-mouse HRP solution and wash it with TBST three times, 5 min each</li> | |
− | + | <li>Add HRP substrate on the membrane for 1 min</li> | |
− | + | <li>Soak the membrane into ddH<sub>2</sub>O to remove the substrate</li> | |
− | + | <li>Observe the result with UVP Biospectrum</li> | |
− | + | </ol> | |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
</div> | </div> | ||
+ | <div class="Text1" id="First12"><Red>Thawing Caco-2 cells</Red></div> | ||
+ | <div class="Text2"> | ||
+ | <Green>Materials and Reagents :</Green> | ||
+ | </div> | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part1"> |
− | + | <li>1 ml frozen Caco-2 cells in cryovial</li> | |
− | + | <li>Cell culture medium (MEM (minimum essential medium) (GIBCOTM #41500-034)/2.2g NaHCO3/ 0.11 g sodium pyruvate/20% FBS/1% PSA) </li> | |
− | + | <li>70% ethanol</li> | |
− | + | <li>Trypan blue solution</li> | |
− | + | </ol> | |
− | + | </div> | |
− | + | <div class="Text2"> | |
− | + | <Green>Equipment :</Green> | |
− | + | </div> | |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | </div> | + | |
− | + | ||
− | + | ||
− | <div class=" | + | |
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part1"> |
− | + | <li>Laminar flow hood</li> | |
− | + | <li>Auto pipette</li> | |
− | + | <li>Centrifuge</li> | |
− | + | <li>15 ml centrifuge tubes</li> | |
− | + | <li>10 cm dish</li> | |
− | + | <li>Hemocytometer</li> | |
− | + | <li>Optical microscope</li> | |
− | + | <li>Suction machine</li> | |
− | + | </ol> | |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
</div> | </div> | ||
+ | <div class="Text2"> | ||
+ | <Green>Procedure :</Green> | ||
+ | </div> | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part2"> |
+ | <li>Pre-warm medium in 37˚C water bath</li> | ||
+ | <li>Open a laminar flow hood</li> | ||
+ | <li>Clean materials, reagents and equipments before moving them into the hood</li> | ||
+ | <li>Thawing Caco-2 cells in 37˚C water bath and transfer the cells into a 15ml centrifuge tube</li> | ||
+ | <li>Add 9 ml cell culture medium very slowly</li> | ||
+ | <li>Centrifuge at 1000 rpm for 5 min</li> | ||
+ | <li>Decant the supernate and resuspend cells with 10 ml cell culture medium</li> | ||
+ | <li>Mix 10 ul cell suspension and 10 μl trypan blue solution and count total cell number with a hemocytometer</li> | ||
+ | <li>Add all cell suspension to a 10 cm dish</li> | ||
+ | <li>Write date, cell line and passage number</li> | ||
+ | <li>Put the dish into incubator</li> | ||
+ | </ol> | ||
</div> | </div> | ||
− | + | <div class="Text1" id="First13"><Red>Freezing Caco-2 cells</Red></div> | |
− | + | <div class="Text2"> | |
− | + | <Green>Materials and Reagents :</Green> | |
− | + | </div> | |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | <div class=" | + | |
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part1"> |
− | + | <li>Caco-2 cell in 10 cm dish</li> | |
− | + | <li>Cell culture medium (MEM (minimum essential medium) (GIBCOTM #10370-021)/10% FBS/ 2 mM glutamine</li> | |
− | + | <li>1X PBS (phosphate buffer saline)</li> | |
− | + | <li>0.5% trypsin</li> | |
− | + | <li>Trypan blue solution</li> | |
− | + | <li>70% ethanol</li> | |
− | + | <li>Cell freezing media (50% FBS, 40% cell culture medium, 10% DMSO)</li> | |
− | + | </ol> | |
− | + | </div> | |
− | + | <div class="Text2"> | |
− | + | <Green>Equipment :</Green> | |
− | + | </div> | |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | </div> | + | |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part1"> |
+ | <li>Laminar flow hood</li> | ||
+ | <li>Auto pipette</li> | ||
+ | <li>Centrifuge</li> | ||
+ | <li>15 ml centrifuge tubes</li> | ||
+ | <li>10 cm dish</li> | ||
+ | <li>Hemocytometer</li> | ||
+ | <li>Optical microscope</li> | ||
+ | <li>Suction machine</li> | ||
+ | <li>Cryovials</li> | ||
+ | <li>Freezing apparatus</li> | ||
+ | <li>-80˚C refrigerator</li> | ||
+ | <li>Liquid nitrogen tank</li> | ||
+ | </ol> | ||
</div> | </div> | ||
− | + | <div class="Text2"> | |
− | + | <Green>Procedure :</Green> | |
− | + | </div> | |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part2"> |
− | + | <li>Pre-warm medium in 37˚C water bath</li> | |
− | + | <li>Open a laminar flow hood</li> | |
− | + | <li>Clean materials, reagents and equipments before moving them into the hood</li> | |
− | + | <li>Take a 10 cm dish with Caco-2 cell</li> | |
− | + | <li>Discard the medium with a suction machine</li> | |
− | + | <li>Wash the cells with 5 ml PBS</li> | |
− | + | <li>Add 1 ml 0.5% trypsin and incubate at 37˚C for 7 minutes</li> | |
− | + | <li>Wash out all the cells from the surface of the dish by pipetting the fresh complete culture medium (9 ml) all over the surface</li> | |
− | + | <li>Transfer the cell suspension to a 15 ml centrifuge tube</li> | |
− | + | <li>Mix 10 μl cell suspension and 10 ul trypan blue solution and count total cell number with a hemocytometer</li> | |
− | + | <li>Add about 1x10<sup>6</sup> cells per cryovial, and add cell freezing media</li> | |
− | + | <li>Freeze the cryovials in a controlled rate freezing apparatus, decreasing the temperature approximately 1°C per minute in a -80°C refrigerator for more than 3 hour, then move them into liquid nitrogen tank</li> | |
− | + | </ol> | |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
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− | + | ||
</div> | </div> | ||
+ | <div class="Text1" id="First14"><Red>Caco2 Cell passage</Red></div> | ||
+ | <div class="Text2"> | ||
+ | <Green>Materials and Reagents :</Green> | ||
+ | </div> | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part1"> |
− | + | <li>Caco-2 cell in 10 cm dish</li> | |
− | + | <li>Cell culture medium (MEM (minimum essential medium) (GIBCOTM #10370-021)/10% FBS/ 2 mM glutamine</li> | |
− | + | <li>1X PBS (phosphate buffer saline)</li> | |
− | + | <li>0.5% trypsin</li> | |
− | + | <li>Trypan blue solution</li> | |
− | + | <li>70% ethanol</li> | |
− | + | </ol> | |
− | + | </div> | |
− | + | <div class="Text2"> | |
− | + | <Green>Equipment :</Green> | |
− | + | </div> | |
− | + | ||
− | </div> | + | |
− | + | ||
− | + | ||
− | <div class=" | + | |
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part1"> |
− | + | <li>Laminar flow hood</li> | |
− | + | <li>Auto pipette</li> | |
− | + | <li>Centrifuge</li> | |
+ | <li>15 ml centrifuge tubes</li> | ||
+ | <li>10 cm dish</li> | ||
+ | <li>Hemocytometer</li> | ||
+ | <li>Optical microscope</li> | ||
+ | <li>Suction machine</li> | ||
+ | </ol> | ||
</div> | </div> | ||
+ | <div class="Text2"> | ||
+ | <Green>Procedure :</Green> | ||
+ | </div> | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part2"> |
+ | <li>Pre-warm medium in 37˚C water bath</li> | ||
+ | <li>Open a laminar flow hood</li> | ||
+ | <li>Clean materials, reagents and equipments before moving them into the hood</li> | ||
+ | <li>Take a 10 cm dish with Caco-2 cell</li> | ||
+ | <li>Discard the medium with a suction machine</li> | ||
+ | <li>Wash the cells with 5 ml PBS</li> | ||
+ | <li>Add 1 ml 0.5% trypsin and incubate at 37˚C for 7 minutes</li> | ||
+ | <li>Wash out all the cells from the surface of the dish by pipetting the fresh complete culture medium (9 ml) all over the surface</li> | ||
+ | <li>Transfer the cell suspension to a 15 ml centrifuge tube</li> | ||
+ | <li>Mix 10 ul cell suspension and 10 μl trypan blue solution and count total cell number with a hemocytometer</li> | ||
+ | <li>Transfer appropriate amounts of cell suspension to new dishes (1/4 X)</li> | ||
+ | <li>Write date, cell line and passage number</li> | ||
+ | <li>Put the dish into incubator</li> | ||
+ | </ol> | ||
</div> | </div> | ||
− | + | <div class="Text1" id="First15"><Red>Seeding in transwell</Red></div> | |
− | + | <div class="Text2"> | |
− | + | <Green>Materials and Reagents :</Green> | |
− | + | </div> | |
− | + | ||
− | + | ||
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− | + | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part1"> |
− | </div> | + | <li>Caco-2 cell in 10 cm dish</li> |
+ | <li>Cell culture medium (MEM (minimum essential medium) (GIBCOTM #41500-034)/2.2 g NaHCO3/ 0.11 g sodium pyruvate/20% FBS/1% PSA</li> | ||
+ | <li>1X PBS (phosphate buffer saline)</li> | ||
+ | <li>0.5% trypsin</li> | ||
+ | <li>Trypan blue solution</li> | ||
+ | <li>70% ethanol</li> | ||
+ | </ol> | ||
+ | </div> | ||
+ | <div class="Text2"> | ||
+ | <Green>Equipment :</Green> | ||
+ | </div> | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part1"> |
− | + | <li>Laminar flow hood</li> | |
− | + | <li>Auto pipette</li> | |
− | + | <li>Centrifuge</li> | |
− | + | <li>15 ml centrifuge tubes</li> | |
− | + | <li>10 cm dish</li> | |
− | + | <li>Hemocytometer</li> | |
− | + | <li>Optical microscope</li> | |
− | + | <li>Suction machine</li> | |
− | + | <li>6-well plate</li> | |
− | + | <li>Millicell plate insert (PIHP03050)</li> | |
− | + | </ol> | |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
</div> | </div> | ||
+ | <div class="Text2"> | ||
+ | <Green>Procedure :</Green> | ||
+ | </div> | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part2"> |
+ | <li>Open 6-well plate, add 1.5 mL medium to each large well (6 wells) which are going to be used</li> | ||
+ | <li>Add 2 ml PBS/well to other wells</li> | ||
+ | <li>Put transwell in larger well</li> | ||
+ | <li>Take a 10 cm dish with Caco-2 cell</li> | ||
+ | <li>Discard the medium with a suction machine</li> | ||
+ | <li>Wash the cells with 5 ml PBS</li> | ||
+ | <li>Add 1 ml 0.5% trypsin and incubate at 37˚C for 7 minutes</li> | ||
+ | <li>Wash out all the cells from the surface of the dish by pipetting the fresh complete culture medium (9 ml) all over the surface</li> | ||
+ | <li>Transfer the cell suspension to a 15 ml centrifuge tube</li> | ||
+ | <li>Mix 10 ul cell suspension and 10 μl trypan blue solution and count total cell number with a hemocytometer</li> | ||
+ | <li>Cell count: 70/ 2 * orginal volume *100 (*10<sup>4</sup>)= 35 X 10<sup>4</sup> cell/mL (Seeding 42 x 10<sup>4</sup> cell/well)</li> | ||
+ | <li>Write date, cell line and passage number</li> | ||
+ | <li>Put the dish into incubator</li> | ||
+ | </ol> | ||
</div> | </div> | ||
− | + | <div class="Text1" id="First16"><Red>Measure TEER</Red></div> | |
− | + | <div class="Text2"> | |
− | + | <Green>Materials and Reagents :</Green> | |
− | + | </div> | |
− | + | ||
− | + | ||
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− | + | ||
− | + | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part1"> |
− | </div> | + | <li>Caco-2 cells seeded in transwell</li> |
+ | <li>70% ethanol</li> | ||
+ | </ol> | ||
+ | </div> | ||
+ | <div class="Text2"> | ||
+ | <Green>Equipment :</Green> | ||
+ | </div> | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part1"> |
+ | <li>Laminar flow hood</li> | ||
+ | <li>Millicell ERS</li> | ||
+ | </ol> | ||
</div> | </div> | ||
+ | <div class="Text2"> | ||
+ | <Green>Procedure :</Green> | ||
+ | </div> | ||
<div class="Text3"> | <div class="Text3"> | ||
− | < | + | <ol class="part2"> |
− | + | <li>Prepare laminar hood for experiment</li> | |
− | + | <li>To sterilize electrode of Millicell ERS, soak electrode in 70% alcohol for 15 min, and air dry for 15 sec</li> | |
− | < | + | <li>Measure TEER value of each well (n=3)</li> |
− | + | </ol> | |
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</div> | </div> | ||
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Maintained by the iGEM team NTU-LIHPAO-Taiwan ©2015 NTU-LIHPAO-Taiwan | Maintained by the iGEM team NTU-LIHPAO-Taiwan ©2015 NTU-LIHPAO-Taiwan | ||
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Revision as of 21:49, 16 September 2015
-
Protocols
- Preparation of Competent Cells (E.coli)
- DNA Dissolution
- Agarose Gel Electrophoresis
- Gel Extraction
- DNA Ligation
- Plasmid DNA Extraction Using Alkaline Lysis Method (E.coli)
- Transformation(E.coli)
- Protein Extraction
- SDS-PAGE
- Western Blot
- Immunostaining
- Thawing Caco-2 cells
- Freezing Caco-2 cells
- Caco2 Cell passage
- Seeding in transwell
- Measure TEER
- Escherichia coli DH5α
- LB broth
- TB buffer
- DMSO
- Liquid nitrogen
- Ice
- Shaker
- Spectrometer
- Centrifuge
- Inoculate 10μL Escherichia coli DH5α into 10mL LB broth (1:1000)
- Grow for 12-16 hours at 37℃ with shaking
- Inoculate 500μL Escherichia coli DH5α into 50mL LB broth (1:100)
- Grow for 2 hours at 37℃ with shaking to O.D.600=0.4-0.6
- Split the cell into two Falcon tubes, both contain 25 mL Escherichia coli DH5α
- Centrifuge at 4℃, 3000rpm(800G) for 10 minutes
- Discard the supernatant
- Resuspend the cell pellet by gently adding 8.5mL TB buffer (1/3 V)
- On ice for 10 minutes
- Centrifuge at 4℃, 3000rpm(800G) for 10 minutes
- Discard the supernatant using pipetman
- Resuspend the cell pellet by gently adding 2mL TB buffer (1/12.5 V)
- Add 150μL DMSO (7%)
- On ice for 10 minutes
- Transfer the cell to new eppendorfs with 60μL per tube
- Freeze the cell in liquid nitrogen
- Store the cell at -80℃
- DNA (BioBricks/synthesized)
- ddH2O
- Add 10μL ddH2O
- Wait for 1 minute until the DNA dissolve
- Pipet several times and transfer the DNA to an eppendorf
- Agarose
- 1X TAE
- Tracking dye
- Marker (1kb/100bp)
- EtBr
- ddH2O
- Gel tray
- Well comb
- Electrophoresis tank
- UV detector
- Measure out appropriate mass of agarose powder into a serum bottle
- Add appropriate volume of 1X TAE
- Let agarose solution cool down to acceptable temperature for bare hands
- Pour the solution into a gel tray with the well comb in place, and push the bubbles away with a pipette tip
- Let sit at room temperature for 30 minutes, until it has completely solidified
- Place the gel as well as its tray into the electrophoresis tank containing 1X TAE (Make sure that the surface is higher than the top of the gel and not overflow)
- Mix the samples with tracking dye (1/10 V) sufficiently
- Load the samples into the each well
- Load marker (usually in the first and last lane)
- Set an appropriate voltage (full/half) and run the gel for 15-20 minutes
- Put the gel into a container filled with 1X TAE and EtBr, staining for 5 minutes
- Replace EtBr solution with water and destain for 3 minutes
- Put the gel in an UV detector and record the result
Casting an Agarose Gel (m/v = 1.0% or 1.5%)
Loading Samples and Running the Gel
Imaging the Gel
- Gel/PCR buffer
- W1 buffer
- Wash buffer
- ddH2O
- Cutter knife
- Eppendorf
- Vortex mixer
- Dry bath incubator
- DF Column & Collection tube
- Mini Centrifuge
- Microcentrifuge
- Excise the agarose gel slice containing relevant DNA fragments and remove any extra agarose to minimize the size of the gel slice (<300μL)
- Transfer the gel slice to an eppendorf
- Add 500μL Gel/PCR buffer to the sample and mix by vortex
- Incubate at 60℃ for 10-15 minutes to ensure the gel slice has been completely dissolved (invert the tube every 2-3 minutes)
- Cool the dissolved sample mixture to room temperature
- Place the DF Column in a 2mL Collection tube
- Transfer 800μL of the sample mixture to the DF Column
- Discard the flow-through and place the DF Column back in the Collection tube (If the sample mixture is more than 800μL, repeat the DNA binding step)
- Add 400μL W1 buffer into the DF Column
- Spin down for approximately 20 seconds
- Discard the flow-through and place the DF Column back in the Collection tube
- Add 600μL wash buffer (contains ethanol) into the DF Column
- Let stand for 1 minute at room temperature
- Spin down for approximately 30 seconds
- Discard the flow-through and place the DF Column back in the Collection tube
- Centrifuge at 12000 rpm for 3 minutes to dry the column matrix (Can be done twice)
- Discard the flow-through
- Transfer the dried DF Column to a new eppendorf (cap cut)
- Add 30μL of 37℃ ddH2O into the center of the column matrix
- Let stand for at least 2 minutes to ensure that ddH2O is completely absorbed
- Centrifuge at 12000 rpm for 2 minutes to elute the purified DNA
- Re-add the subnatant into the center of the column matrix
- Centrifuge at 12000 rpm for 2 minutes to elute the purified DNA
Gel Dissociation
DNA Binding
Wash
DNA Elution
- DNA (insert & vector)
- Ligation high ver.2
- Cooling dry bath incubator
-
Table
Components Volume (μL) Insert x Vector y Ligation High 1 Total 7
x + y = 6 - Gently mix the solution by pipetting up and down
- Incubate
- at 16℃ for 2 hours, or
- at 37℃ for 1 hour, or
- at 4℃ overnight
- Proceed with bacterial transformation
- Escherichia coli DH5α (with plasmid)
- LB broth
- Resuspension solution (MPI, with RNAase)
- Lysis solution (MPII)
- Neutralizing solution (MPIII)
- Isopropanol
- 70% ethanol
- ddH2O
- Shaker
- Centrifuge
- Vortex mixer
- Grow bacteria in LB broth with appropriate antibiotics at 37℃ overnight with shaking
- Transfer 1.5mL culture to an eppendorf
- Centrifuge at 4℃, 5000rpm for 5 minutes
- Discard the supernatant
- Add 150μL of resuspension solution (MPI, with RNAase) into each tube, pipet several times, and vortex to completely resuspend the cell pellet
- Add 150μL of lysis solution (MPII), gently invert the tubes about 20 times, and then let the sample mixture stand at room temperature for 2 minutes
- Add 150μL of neutralizing solution (MPIII) and mix by inverting the tubes about 20 times. Bacterial chromosomal DNA and proteins can be seen as white precipitates
- Centrifuge at 4℃, 15000rpm for 15 minutes
- Carefully transfer 400μL of the supernatant to a new eppendorf (Step 8&9 can be done twice)
- Add 400μL (same volume as the supernatant) isopropanol, and shake up the tubes as vigorously as one can
- Centrifuge at 4℃, 15000rpm for 15 minutes
- Discard the supernatant
- Add 200μL of 70% ethanol to wash out the salts
- Centrifuge at 4℃, 15000rpm for 5 minutes
- Discard the supernatant and remove the remains as much as possible with pipetman
- Air dry for about 30 minutes
- Resuspend the DNA pellet with 20μL ddH2O
- Competent cell (Escherichia coli DH5α)
- LB plate (Amp+/CP+)
- -80℃ refrigerator
- Ice
- 37℃ incubator
- Super optimal broth (SOB) (37℃)
- Shaker
- Take out the competent cells from -80℃ refrigerator
- Thaw the cells on ice for 5 minutes
- Add 1μL plasmid DNA into the competent cells, and mix gently by pipetting
- On ice for 10 minutes
- Heat shock at 37℃ for 3 minutes
- On ice for 2 minutes
- Add 150μL 37℃ SOB into the mixture
- Place the tube at 37℃ with shaking for 1 hour(Amp+)/4 hours(CP+) respectively
- Spread the cells onto the LB plates (Amp+/ CP+)
- Incubate the plates at 37℃ with shaking for 12-16 hours
- plasmid/ BL21 competent cell
- LB plate
- LB broth
- lysis buffer
- 15/ 50ml conial tube
- Shaking incubator
- Erlenmeyer flask
- Spectrophotometer
- Centrifuge
- Sonicator
- Eppendorf
- Transform plamid into BL21 (see transformation)
- Pick up a single colony and incubate into 2ml LB/CP medium, then agitate them in a shaking incubator at 37℃ overnight
- Pour the culture into 100ml LB/CP medium, then agitate until it reach A600 of 0.6
- Pour the culture into 50ml conical tube, and centrifuge at 8000rpm for 10 min
- Store the supernate and the pellets in the centrifuge tubes in a -80℃ freezer
- Use 6ml lysis buffer(NP-10) to resuspend the cell pellet and transfer into a 15ml centrifuge tube
- Lyse the cell with sonication
- Centrifuge 15ml conial tube at 9000rpm for 10 min
- Store the supernate as coarse extract
- Solution A (acrylamide/ bis-acrylamide (29:1) 30% solution)
- Solution B (Tris (Tris base, 1.5 M) 90.8 gm; TEMED 1.8 ml; pH = 8.8/ 500ml)
- Solution C (Tris (Tris base, 0.5 M) 6.0 gm; TEMED 0.4 ml; pH = 6.7/ 100ml)
- 10% SDS (1kb/100bp)
- ddH2O
- APS
- Running buffer (1M Tris 12.5 ml; glysine 7.7g/ 500ml)
- Sample buffer(5X) (Tris base, 125mM X5; EDTA2•Na, 2mM X 5; SDS(2% X2); β-mercaptoethanol, 5% X5)
- Protein marker
- Gel Caster
- Accessories for each gel
- (1) One glass plate
- (2) One aluminum notched plate
- (3) Two 0.75-mm thick spacers
- (4) One 0.75-mm thick 10-well comb
- (5) One well-locating decal
- Power supply
- Assemble one glass plate and one alumimum plate with two spacers for each gel module
- Prepare the SDS gel solution (see the table below). Two 0.75mm mini gels need approximately 10ml separation gel solution and 5ml stacking solution. Add APS solution at the final step
- Mix the separation gel solution, and add the solution into the gel module until reaching the designated level. Then add isopropanol on the top of the gel. It takes about 40 min to complete the polymerization step
- Remove the isopropanol by using a small strip of filter paper. Fill up the stacking gel solution until reaching the top. Insert comb into the gel solution as soon as possible. It takes 10 min to complete the polymerization step
- Remove the comb and set the gel in the cell buffer dam. Pour the running buffer into the inner chamber and keep pouring after overflow until the buffer surface reaches the required level in the outer chamber
- Use a micropipette to clean up every single well with the running buffer
- Mix protein samples with 1/5 volumes of 5X sample buffer. Heat the mixture at 100oC for 10 min. Let it cool down to room temperature
- Load protein sample and the protein marker into the well
- Run the electrophoresis at 70V for 20 min, and then 150V for 55 min
- Remove the two spacer and lift the glass plate, and remove the stacking gel and the remaining gel is ready for CBR staining and Western blot
(Unit: ml) | Separation gel | Stacking gel | |||||
---|---|---|---|---|---|---|---|
Percentage | 5% | 7.5% | 10% | 12.5% | 15% | 20% | 4% |
Solution A | 16.5 | 2.5 | 3.35 | 4.15 | 5 | 6.5 | 0.66 |
Solution B | 2.5 | 2.5 | 2.5 | 2.5 | 2.5 | 2.5 | - |
Solution C | - | - | - | - | - | - | 1.24 |
10% SDS | 0.1 | 0.1 | 0.1 | 0.1 | 0.1 | 0.1 | 0.05 |
dH2O | 5.7 | 4.85 | 4 | 3.2 | 2.35 | 0.85 | 2.95 |
APS(10%) | 0.05 | 0.05 | 0.05 | 0.05 | 0.05 | 0.05 | 0.1 |
Total Volume | 10 | 10 | 10 | 10 | 10 | 10 | 5 |
- Transfer buffer ( Tris 25mM; glycine 0.192M)
- Methanol
- 10 X TBST (1M Tris pH =8.0; Tween 20, 50ml; NaCl 43.5g)
- Semi-dry trnasfer cell
- PVDF membrane
- Nitrocellulose paper
- Square Petri dish
- Rotary shaker
- Equilibrate the nitrocellulose paper and SDS-PAGE gel by soaking them with transfer buffer
- Rinse the PVDF membrane with 100% methanol for a few second and equilibrate it with transfer buffer
- Place the elements in the following order onto the semi-dry transfer cell from bottom to top: nitrocellulose paper, PVDF membrane, SDS-PAGE gel, nitrocellulose paper
- Set up the current at 0.09A and run for 75 min
- 3% milk
- Antibody solution
- Secondary antibody (anti-mouse HRP)
- TBST
- Western HRP substrate
- Square petri dish
- Rotary shaker
- UVP Biospectrum
- Put the membrane in the square petri dish block the membrane with the 3% milk/TBST at room temperature for 1hr
- Discard the milk and replace it with antibody solution(mouse His-probe Antibody) at 4℃ overnight
- Recycle the antibody solution. Wash the membrane with TBST three times, 5 min each
- Soak membrane into anti-mouse HRP solution for 1 hr
- Discard the anti-mouse HRP solution and wash it with TBST three times, 5 min each
- Add HRP substrate on the membrane for 1 min
- Soak the membrane into ddH2O to remove the substrate
- Observe the result with UVP Biospectrum
- 1 ml frozen Caco-2 cells in cryovial
- Cell culture medium (MEM (minimum essential medium) (GIBCOTM #41500-034)/2.2g NaHCO3/ 0.11 g sodium pyruvate/20% FBS/1% PSA)
- 70% ethanol
- Trypan blue solution
- Laminar flow hood
- Auto pipette
- Centrifuge
- 15 ml centrifuge tubes
- 10 cm dish
- Hemocytometer
- Optical microscope
- Suction machine
- Pre-warm medium in 37˚C water bath
- Open a laminar flow hood
- Clean materials, reagents and equipments before moving them into the hood
- Thawing Caco-2 cells in 37˚C water bath and transfer the cells into a 15ml centrifuge tube
- Add 9 ml cell culture medium very slowly
- Centrifuge at 1000 rpm for 5 min
- Decant the supernate and resuspend cells with 10 ml cell culture medium
- Mix 10 ul cell suspension and 10 μl trypan blue solution and count total cell number with a hemocytometer
- Add all cell suspension to a 10 cm dish
- Write date, cell line and passage number
- Put the dish into incubator
- Caco-2 cell in 10 cm dish
- Cell culture medium (MEM (minimum essential medium) (GIBCOTM #10370-021)/10% FBS/ 2 mM glutamine
- 1X PBS (phosphate buffer saline)
- 0.5% trypsin
- Trypan blue solution
- 70% ethanol
- Cell freezing media (50% FBS, 40% cell culture medium, 10% DMSO)
- Laminar flow hood
- Auto pipette
- Centrifuge
- 15 ml centrifuge tubes
- 10 cm dish
- Hemocytometer
- Optical microscope
- Suction machine
- Cryovials
- Freezing apparatus
- -80˚C refrigerator
- Liquid nitrogen tank
- Pre-warm medium in 37˚C water bath
- Open a laminar flow hood
- Clean materials, reagents and equipments before moving them into the hood
- Take a 10 cm dish with Caco-2 cell
- Discard the medium with a suction machine
- Wash the cells with 5 ml PBS
- Add 1 ml 0.5% trypsin and incubate at 37˚C for 7 minutes
- Wash out all the cells from the surface of the dish by pipetting the fresh complete culture medium (9 ml) all over the surface
- Transfer the cell suspension to a 15 ml centrifuge tube
- Mix 10 μl cell suspension and 10 ul trypan blue solution and count total cell number with a hemocytometer
- Add about 1x106 cells per cryovial, and add cell freezing media
- Freeze the cryovials in a controlled rate freezing apparatus, decreasing the temperature approximately 1°C per minute in a -80°C refrigerator for more than 3 hour, then move them into liquid nitrogen tank
- Caco-2 cell in 10 cm dish
- Cell culture medium (MEM (minimum essential medium) (GIBCOTM #10370-021)/10% FBS/ 2 mM glutamine
- 1X PBS (phosphate buffer saline)
- 0.5% trypsin
- Trypan blue solution
- 70% ethanol
- Laminar flow hood
- Auto pipette
- Centrifuge
- 15 ml centrifuge tubes
- 10 cm dish
- Hemocytometer
- Optical microscope
- Suction machine
- Pre-warm medium in 37˚C water bath
- Open a laminar flow hood
- Clean materials, reagents and equipments before moving them into the hood
- Take a 10 cm dish with Caco-2 cell
- Discard the medium with a suction machine
- Wash the cells with 5 ml PBS
- Add 1 ml 0.5% trypsin and incubate at 37˚C for 7 minutes
- Wash out all the cells from the surface of the dish by pipetting the fresh complete culture medium (9 ml) all over the surface
- Transfer the cell suspension to a 15 ml centrifuge tube
- Mix 10 ul cell suspension and 10 μl trypan blue solution and count total cell number with a hemocytometer
- Transfer appropriate amounts of cell suspension to new dishes (1/4 X)
- Write date, cell line and passage number
- Put the dish into incubator
- Caco-2 cell in 10 cm dish
- Cell culture medium (MEM (minimum essential medium) (GIBCOTM #41500-034)/2.2 g NaHCO3/ 0.11 g sodium pyruvate/20% FBS/1% PSA
- 1X PBS (phosphate buffer saline)
- 0.5% trypsin
- Trypan blue solution
- 70% ethanol
- Laminar flow hood
- Auto pipette
- Centrifuge
- 15 ml centrifuge tubes
- 10 cm dish
- Hemocytometer
- Optical microscope
- Suction machine
- 6-well plate
- Millicell plate insert (PIHP03050)
- Open 6-well plate, add 1.5 mL medium to each large well (6 wells) which are going to be used
- Add 2 ml PBS/well to other wells
- Put transwell in larger well
- Take a 10 cm dish with Caco-2 cell
- Discard the medium with a suction machine
- Wash the cells with 5 ml PBS
- Add 1 ml 0.5% trypsin and incubate at 37˚C for 7 minutes
- Wash out all the cells from the surface of the dish by pipetting the fresh complete culture medium (9 ml) all over the surface
- Transfer the cell suspension to a 15 ml centrifuge tube
- Mix 10 ul cell suspension and 10 μl trypan blue solution and count total cell number with a hemocytometer
- Cell count: 70/ 2 * orginal volume *100 (*104)= 35 X 104 cell/mL (Seeding 42 x 104 cell/well)
- Write date, cell line and passage number
- Put the dish into incubator
- Caco-2 cells seeded in transwell
- 70% ethanol
- Laminar flow hood
- Millicell ERS
- Prepare laminar hood for experiment
- To sterilize electrode of Millicell ERS, soak electrode in 70% alcohol for 15 min, and air dry for 15 sec
- Measure TEER value of each well (n=3)
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