Line 3: | Line 3: | ||
<html> | <html> | ||
<body> | <body> | ||
− | + | <section> | |
− | + | <div class="container"> | |
− | + | <div class="timeline"> | |
− | + | <div class="timeline-hline"></div> | |
− | + | <div class="blog-post-item"> | |
− | + | <div class="timeline-entry rounded"> | |
− | + | 18<span>May</span> | |
− | + | <div class="timeline-vline"></div> | |
− | + | </div> | |
− | + | <ul class="blog-post-info list-inline"> | |
− | + | <li><span class="font-lato">May 18, 2016</span></li> | |
− | + | </ul> | |
− | + | <p>Take glycerinated cultures of C58 <i>Agrobacterium</i> | |
− | + | with dsRED from GoldenBraid Collection. Prepare broth | |
− | + | culture (5 mL LB + 5 μL kanamycin + 5 μL Rifampin) 1:1000 | |
− | + | and incubate overnight at 28^C.<br></p> | |
− | + | </div> | |
− | + | <div class="blog-post-item"> | |
− | + | <div class="timeline-entry rounded"> | |
− | + | 19<span>May</span> | |
− | + | <div class="timeline-vline"></div> | |
− | + | </div> | |
− | + | <ul class="blog-post-info list-inline"> | |
− | + | <li><span class="font-lato">May 19, 2016</span></li> | |
− | + | </ul> | |
− | + | <p>Refresh previously made culture by inoculating 10 μL in | |
− | + | a new culture medium.<br></p> | |
− | + | </div> | |
− | + | <div class="blog-post-item"> | |
− | + | <div class="timeline-entry rounded"> | |
− | + | 20<span>May</span> | |
− | + | <div class="timeline-vline"></div> | |
− | + | </div> | |
− | + | <ul class="blog-post-info list-inline"> | |
− | + | <li><span class="font-lato">May 20, 2016</span></li> | |
− | + | </ul> | |
− | + | <p>Agroinfiltration in <i>Nicotiana benthamiana</i> of C58 | |
− | + | with dsRED. href<br></p> | |
− | + | </div> | |
− | + | <div class="blog-post-item"> | |
− | + | <div class="timeline-entry rounded"> | |
− | + | 06<span>Jun</span> | |
− | + | <div class="timeline-vline"></div> | |
− | + | </div> | |
− | + | <ul class="blog-post-info list-inline"> | |
− | + | <li><span class="font-lato">June 06, 2016</span></li> | |
− | + | </ul> | |
− | + | <p></p> | |
− | + | <ul> | |
− | + | <li>Take from the glycerinates of Goldenbraid | |
− | + | Collection:</li> | |
− | + | </ul> | |
− | + | <p></p> | |
− | + | <div class="table-responsive" style= | |
− | + | "width:55%;overflow:inherit"> | |
− | + | <table class="table table-bordered table-striped"> | |
− | + | <tr> | |
− | + | <th>Plasmid</th> | |
− | + | <th>GB Code</th> | |
− | + | </tr> | |
− | + | <tr> | |
− | + | <td>pD6B3 α1</td> | |
− | + | <td>GB0015</td> | |
− | + | </tr> | |
− | + | <tr> | |
− | + | <td>pD6B3 α2</td> | |
− | + | <td>GB0017</td> | |
− | + | </tr> | |
− | + | <tr> | |
− | + | <td>pD6B3 Ω1</td> | |
− | + | <td>GB0019</td> | |
− | + | </tr> | |
− | + | <tr> | |
− | + | <td>pD6B3 Ω2</td> | |
− | + | <td>GB0021</td> | |
− | + | </tr> | |
− | + | <tr> | |
− | + | <td>pUPD2</td> | |
− | + | <td>GB0307</td> | |
− | + | </tr> | |
− | + | </table> | |
− | + | </div> | |
− | + | <p>Prepare liquid culture (3 mL LB + 3 μL antibiotic) | |
− | + | 1:1000. Incubate at 37^C overnight.<br></p> | |
− | + | <ul> | |
− | + | <li>Experiment with snails:</li> | |
− | + | <li style="list-style: none; display: inline"> | |
− | + | <ul> | |
− | + | <li>Two experiments: one with infiltrated | |
− | + | <i>Nicotiana benthamiana</i> and another with | |
− | + | not infiltrated N.benthamiana (negative | |
− | + | control). Lettuce leafs haven’t been correctly | |
− | + | infiltrated and it seems that the expression | |
− | + | level is low.</li> | |
− | + | <li>Let both <i>N. benthamiana</i> leafs with | |
− | + | snails overnight at room temperature in | |
− | + | separated boxes. We will observe if snails eat | |
− | + | the leafs and if appears fluorescence.</li> | |
− | + | </ul> | |
− | + | </li> | |
− | + | </ul> | |
− | + | <p></p> | |
− | + | </div> | |
− | + | <div class="blog-post-item"> | |
− | + | <div class="timeline-entry rounded"> | |
− | + | 15<span>Jun</span> | |
− | + | <div class="timeline-vline"></div> | |
− | + | </div> | |
− | + | <ul class="blog-post-info list-inline"> | |
− | + | <li><span class="font-lato">June 15, 2016</span></li> | |
− | + | </ul> | |
− | + | <p>Experiment is over due to snails haven’t eaten leafs | |
− | + | enough so we have not been able to see | |
− | + | fluorescence.<br></p> | |
− | + | </div> | |
− | + | <div class="blog-post-item"> | |
− | + | <div class="timeline-entry rounded"> | |
− | + | 30<span>Jun</span> | |
− | + | <div class="timeline-vline"></div> | |
− | + | </div> | |
− | + | <ul class="blog-post-info list-inline"> | |
− | + | <li><span class="font-lato">June 30, 2016</span></li> | |
− | + | </ul> | |
− | + | <p>Orange Clemenules DNA Genome Extraction <a href= | |
− | + | "https://2016.igem.org/Team:Valencia_UPV/Notebook/Protocol">protocol</a><br> | |
− | + | </p> | |
− | + | <ul> | |
− | + | <li>Take from the glycerinates of GoldenBraid | |
− | + | Collection:</li> | |
− | + | </ul> | |
− | + | <p></p> | |
− | + | <div class="table-responsive" style= | |
− | + | "width:55%;overflow:inherit"> | |
− | + | <table class="table table-bordered table-striped"> | |
− | + | <tr> | |
− | + | <th>Plasmid</th> | |
− | + | <th>GB Code</th> | |
− | + | </tr> | |
− | + | <tr> | |
− | + | <td>35s:Cas9:nopaline synthase terminator | |
− | + | (Tnos)</td> | |
− | + | <td>GB0639</td> | |
− | + | </tr> | |
− | + | <tr> | |
− | + | <td>Luciferase (Luc) in pUPD2</td> | |
− | + | <td>GB0096</td> | |
− | + | </tr> | |
− | + | <tr> | |
− | + | <td>Tnos in pUPD2</td> | |
− | + | <td>GB0037</td> | |
− | + | </tr> | |
− | + | </table> | |
− | + | </div> | |
− | + | <p></p> | |
− | + | </div> | |
− | + | <div class="blog-post-item"> | |
− | + | <div class="timeline-entry rounded"> | |
− | + | 01<span>Jul</span> | |
− | + | <div class="timeline-vline"></div> | |
− | + | </div> | |
− | + | <ul class="blog-post-info list-inline"> | |
− | + | <li><span class="font-lato">July 01, 2016</span></li> | |
− | + | </ul> | |
− | + | <p>Miniprep of 35s:Cas9:Tnos with E.Z.N.A ®. Plasmid Mini | |
− | + | Kit I, Q(capless) Spin.<br> | |
− | + | Luciferase and nopaline synthase terminator cultures | |
− | + | haven’t succeed. Repeat Luc and Tnos cultures.<br> | |
+ | Primers IG16JUN01 and IG16JUN02 have arrived.<br> | ||
+ | Finish orange DNA Genome Extraction and check DNA | ||
+ | concentration with NanoDrop. Concentration is very low so | ||
+ | extraction will be done again.<br></p> | ||
+ | </div> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class="timeline-entry rounded"> | ||
+ | 02<span>Jul</span> | ||
+ | <div class="timeline-vline"></div> | ||
+ | </div> | ||
+ | <ul class="blog-post-info list-inline"> | ||
+ | <li><span class="font-lato">July 02, 2016</span></li> | ||
+ | </ul> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li>Miniprep with E.Z.N.A ®. Plasmid Mini Kit I, | ||
+ | Q(capless) Spin of:</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <ul> | ||
+ | <li>Luc in pUPD2</li> | ||
+ | <li>Tnos in pUPD2</li> | ||
+ | </ul> | ||
+ | </li> | ||
+ | </ul> | ||
+ | <p>Check orange DNA genome concentration with | ||
+ | NanoDrop.<br></p> | ||
+ | <div class="table-responsive" style= | ||
+ | "width:55%;overflow:inherit"> | ||
+ | <table class="table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <th>Sample</th> | ||
+ | <th>DNA concentration (ng / μL)</th> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>TFL 1</td> | ||
+ | <td>3153.8</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>TFL 2</td> | ||
+ | <td>4527.9</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <p><br> | ||
+ | Perform a PCR to bind linker SAGTI with luciferase:<br></p> | ||
+ | <div class="table-responsive" style= | ||
+ | "width:55%;overflow:inherit"> | ||
+ | <table class="table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <th>Reagent</th> | ||
+ | <th>Volume(μL)</th> | ||
+ | <th>Program</th> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>LuciferasepUPD</td> | ||
+ | <td>1</td> | ||
+ | <td>Temperature</td> | ||
+ | <td>Time</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Buffer HF</td> | ||
+ | <td>10</td> | ||
+ | <td>98^C</td> | ||
+ | <td>5 minutes</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>dNTPs</td> | ||
+ | <td>2</td> | ||
+ | <td>98^C</td> | ||
+ | <td>35x</td> | ||
+ | <td>30 seconds</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>IG16JUN01</td> | ||
+ | <td>2.5</td> | ||
+ | <td>70^C</td> | ||
+ | <td>35x</td> | ||
+ | <td>30 seconds</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>IG16JUN02</td> | ||
+ | <td>2.5</td> | ||
+ | <td>72^C</td> | ||
+ | <td>35x</td> | ||
+ | <td>1 minute 30 seconds</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Taq phusion</td> | ||
+ | <td>0.5</td> | ||
+ | <td>72^C</td> | ||
+ | <td>10 minutes</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>H<sub>2</sub>O milli-Q</td> | ||
+ | <td>31.5</td> | ||
+ | <td>16^C</td> | ||
+ | <td>∞</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <p></p> | ||
+ | </div> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class="timeline-entry rounded"> | ||
+ | 04<span>Jul</span> | ||
+ | <div class="timeline-vline"></div> | ||
+ | </div> | ||
+ | <ul class="blog-post-info list-inline"> | ||
+ | <li><span class="font-lato">July 04, 2016</span></li> | ||
+ | </ul> | ||
+ | <p>Run electrophoresis gel of Clemenules DNA (agarose 1%). | ||
+ | 45 mL agarose gel at 1% 0.45 g of agarose with 45 mL of TAE | ||
+ | 1X. Voltage used is 100 V.<br> | ||
+ | Gleva Rice DNA Genome Extraction <a href= | ||
+ | "https://2016.igem.org/Team:Valencia_UPV/Notebook/Protocol">Protocol</a><br> | ||
+ | Run electrophoresis gel of Luciferase PCR product. 45 mL | ||
+ | agarose gel at 1% 0.45 g of agarose with 45 mL of TAE 1X. | ||
+ | Voltage used is 100 V.<br> | ||
+ | Ligation Reaction of SAGTI:Luciferase into a pUPD2.<br> | ||
+ | Transform <i>E. coli</i> DH5α with it. The method that is | ||
+ | necessary to carry out this procedure is explained in | ||
+ | protocols href<br> | ||
+ | Check DNA concentration with NanoDrop.<br></p> | ||
+ | <div class="table-responsive" style= | ||
+ | "width:55%;overflow:inherit"> | ||
+ | <table class="table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <th>SAMPLE</th> | ||
+ | <th>DNA Concentration(ng / μL)</th> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Rice Gleva 1</td> | ||
+ | <td>22.8</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Rice Gleva 2</td> | ||
+ | <td>17.3</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <p><br></p> | ||
+ | </div> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class="timeline-entry rounded"> | ||
+ | 05<span>Jul</span> | ||
+ | <div class="timeline-vline"></div> | ||
+ | </div> | ||
+ | <ul class="blog-post-info list-inline"> | ||
+ | <li><span class="font-lato">July 05, 2016</span></li> | ||
+ | </ul> | ||
+ | <p>Run electrophoresis gel of Gleva rice DNA. We have | ||
+ | checked that there isn’t DNA.<br> | ||
+ | Repeat: Rice DNA Genome Extraction <a href= | ||
+ | "https://2016.igem.org/Team:Valencia_UPV/Notebook/Protocol">Protocol</a><br> | ||
+ | |||
+ | Check DNA concentration with NanoDrop.<br></p> | ||
+ | <div class="table-responsive" style= | ||
+ | "width:55%;overflow:inherit"> | ||
+ | <table class="table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <th>SAMPLE</th> | ||
+ | <th>DNA Concentration(ng / μL)</th> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Rice Gleva 1</td> | ||
+ | <td>294.9</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Rice Gleva 2</td> | ||
+ | <td>193.7</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <p>Run electrophoresis gel of Gleva rice DNA. It observed | ||
+ | that genome extraction is correctly done.<br> | ||
+ | <br></p> | ||
+ | </div> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class="timeline-entry rounded"> | ||
+ | 06<span>Jul</span> | ||
+ | <div class="timeline-vline"></div> | ||
+ | </div> | ||
+ | <ul class="blog-post-info list-inline"> | ||
+ | <li><span class="font-lato">July 06, 2016</span></li> | ||
+ | </ul> | ||
+ | <p>Take glycerinated cultures from Goldenbraid | ||
+ | Collection:<br></p> | ||
+ | <div class="table-responsive" style= | ||
+ | "width:55%;overflow:inherit"> | ||
+ | <table class="table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <th>GB part</th> | ||
+ | <th>Plasmid</th> | ||
+ | <th>Antibiotic</th> | ||
+ | <th>Number GB</th> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>psgRNA</td> | ||
+ | <td>pUPD</td> | ||
+ | <td>Ampicillin</td> | ||
+ | <td>0645</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>U6-26</td> | ||
+ | <td>pUPD</td> | ||
+ | <td>Ampicillin</td> | ||
+ | <td>1001</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <p><br></p> | ||
+ | </div> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class="timeline-entry rounded"> | ||
+ | 07<span>Jul</span> | ||
+ | <div class="timeline-vline"></div> | ||
+ | </div> | ||
+ | <ul class="blog-post-info list-inline"> | ||
+ | <li><span class="font-lato">July 07, 2016</span></li> | ||
+ | </ul> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li>Miniprep with E.Z.N.A ®. Plasmid Mini Kit I, | ||
+ | Q(capless) Spin of:</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <ul> | ||
+ | <li>psgRNA in pUPD2</li> | ||
+ | <li>U6-26 in pUPD2</li> | ||
+ | </ul> | ||
+ | </li> | ||
+ | </ul> | ||
+ | <p>Primers IG16JUL01, IG16JUL02, IG16JUL03, IG16JUL04, | ||
+ | IG16JUL05, IG16JUL06, IG16JUL07 and IG16JUL08 arrived.<br> | ||
+ | gBlocks of - 35s:5’ region - have arrived.<br> | ||
+ | We perform a PCR of Clemenules Orange and Gleva Rice Genome | ||
+ | Extraction following the <a href= | ||
+ | "https://2016.igem.org/Team:Valencia_UPV/Notebook/Protocol">protocol</a>. | ||
+ | We want to obtain a fragment of the gene TFL of the orange | ||
+ | DNA extraction and the gene Ga20ox of the rice DNA | ||
+ | extraction.<br></p> | ||
+ | <div class="table-responsive" style= | ||
+ | "width:55%;overflow:inherit"> | ||
+ | <table class="table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <th>Sample</th> | ||
+ | <th>Initial concentration(ng/μL)</th> | ||
+ | <th>Final concentration(ng/μL)</th> | ||
+ | <th>Initial volume(μL)</th> | ||
+ | <th>Final volume (μL)</th> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>TFL 1</td> | ||
+ | <td>3153.8</td> | ||
+ | <td>150</td> | ||
+ | <td>4.756</td> | ||
+ | <td>100</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>TFL 2</td> | ||
+ | <td>4527.9</td> | ||
+ | <td>150</td> | ||
+ | <td>3.31</td> | ||
+ | <td>100</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Ga20ox 1</td> | ||
+ | <td>294.9</td> | ||
+ | <td>150</td> | ||
+ | <td>50.8647</td> | ||
+ | <td>100</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Ga20ox 2</td> | ||
+ | <td>193.7</td> | ||
+ | <td>150</td> | ||
+ | <td>77.44</td> | ||
+ | <td>100</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <p><br></p> | ||
+ | <div class="table-responsive" style= | ||
+ | "width:55%;overflow:inherit"> | ||
+ | <table class="table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <th>REAGENT</th> | ||
+ | <th>VOLUME(μL)</th> | ||
+ | <th>PROGRAM</th> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>TFL DNA 1</td> | ||
+ | <td>TEMPERATURE</td> | ||
+ | <td>TIME</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Buffer HF</td> | ||
+ | <td>10</td> | ||
+ | <td>98^C</td> | ||
+ | <td>5 minutes</td> | ||
+ | <td></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>dNTPs</td> | ||
+ | <td>2</td> | ||
+ | <td>98^C</td> | ||
+ | <td>35x</td> | ||
+ | <td>30 seconds</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>IG16JUL01 (TFL_For)</td> | ||
+ | <td>2.5</td> | ||
+ | <td>64^C</td> | ||
+ | <td>35x</td> | ||
+ | <td>30 seconds</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>IG16JUL02 (TFL_Rev)</td> | ||
+ | <td>2.5</td> | ||
+ | <td>72^C</td> | ||
+ | <td>35x</td> | ||
+ | <td>30 seconds</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Taq phusion</td> | ||
+ | <td>0.5</td> | ||
+ | <td>72^C</td> | ||
+ | <td>10 minutes</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>H<sub>2</sub>O milli-Q</td> | ||
+ | <td>31.5</td> | ||
+ | <td>16^C</td> | ||
+ | <td>∞</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <p><br></p> | ||
+ | <div class="table-responsive" style= | ||
+ | "width:55%;overflow:inherit"> | ||
+ | <table class="table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <th>REAGENT</th> | ||
+ | <th>VOLUME(μL)</th> | ||
+ | <th>PROGRAM</th> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Ga20ox DNA</td> | ||
+ | <td>1</td> | ||
+ | <td>TEMPERATURE</td> | ||
+ | <td>TIME</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Buffer HF</td> | ||
+ | <td>10</td> | ||
+ | <td>98^C</td> | ||
+ | <td>5 minutes</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>dNTPs</td> | ||
+ | <td>2</td> | ||
+ | <td>98^C</td> | ||
+ | <td>35x</td> | ||
+ | <td>30 seconds</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>IG16JUL03 (Ga20_for)</td> | ||
+ | <td>2.5</td> | ||
+ | <td>72^C</td> | ||
+ | <td>35x</td> | ||
+ | <td>30 seconds</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>IG16JUL02 (Ga20_rev)</td> | ||
+ | <td>2.5</td> | ||
+ | <td>72^C</td> | ||
+ | <td>35x</td> | ||
+ | <td>30 seconds</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Taq phusion</td> | ||
+ | <td>0.5</td> | ||
+ | <td>72^C</td> | ||
+ | <td>10 minutes</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>H<sub>2</sub>O milli-Q</td> | ||
+ | <td>31.5</td> | ||
+ | <td>16^C</td> | ||
+ | <td>∞</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <p>Ligate reaction of 35s:5’ region in pUPD2. Following | ||
+ | <a href= | ||
+ | "https://2016.igem.org/Team:Valencia_UPV/Notebook/Protocol">ligation | ||
+ | protocol</a>, BsmbI enzyme is used in this reaction.<br> | ||
+ | <br></p> | ||
+ | </div> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class="timeline-entry rounded"> | ||
+ | 08<span>Jul</span> | ||
+ | <div class="timeline-vline"></div> | ||
+ | </div> | ||
+ | <ul class="blog-post-info list-inline"> | ||
+ | <li><span class="font-lato">July 08, 2016</span></li> | ||
+ | </ul> | ||
+ | <p>Run electrophoresis gel of TFL and Ga20ox PCR products. | ||
+ | 45 mL agarose gel at 1 % 0.45 g of agarose with 45 mL of | ||
+ | TAE 1X. Voltage used is 120 V.<br> | ||
+ | Transform <i>E. coli</i> with the next part: 35s:5’ region | ||
+ | (electroporation 2.5KV). Plating it and incubate overnight | ||
+ | at 37^C.<br> | ||
+ | Take glycerinated culture for Georgia collaboration. The | ||
+ | part is 35s:GFP:Tnos (α1 and kanamycin).<br> | ||
+ | <br></p> | ||
+ | </div> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class="timeline-entry rounded"> | ||
+ | 09<span>Jul</span> | ||
+ | <div class="timeline-vline"></div> | ||
+ | </div> | ||
+ | <ul class="blog-post-info list-inline"> | ||
+ | <li><span class="font-lato">July 09, 2016</span></li> | ||
+ | </ul> | ||
+ | <p>Miniprep with E.Z.N.A ®. Plasmid Mini Kit I, Q(capless) | ||
+ | Spin of 35s:GFP:Tnos<br> | ||
+ | No colonies have grown in the 35s:5’ region petri dishes. | ||
+ | Repeat transformation procedure, plating again and incubate | ||
+ | overnight at 37^C.<br> | ||
+ | <br></p> | ||
+ | </div> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class="timeline-entry rounded"> | ||
+ | 11<span>Jul</span> | ||
+ | <div class="timeline-vline"></div> | ||
+ | </div> | ||
+ | <ul class="blog-post-info list-inline"> | ||
+ | <li><span class="font-lato">July 11, 2016</span></li> | ||
+ | </ul> | ||
+ | <p>Pick a single E. coli DH5α (35s:5’ region in pUPD2) | ||
+ | colony from the plate that has been incubated overnight. | ||
+ | Inoculate a starter culture of 4 ml of LB medium with 4 μL | ||
+ | of chloramphenicol in a 50 ml tube with the colony and | ||
+ | incubate it overnight at 37^C with shaking.<br> | ||
+ | Check Georgia miniprep concentration with NanoDrop | ||
+ | (35s:GFP:Tnos)<br></p> | ||
+ | <div class="table-responsive" style= | ||
+ | "width:55%;overflow:inherit"> | ||
+ | <table class="table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <th>Sample</th> | ||
+ | <th>DNA Concentration(ng / μL)</th> | ||
+ | <th>DNA Concentration(ng)</th> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>1</td> | ||
+ | <td>105.2</td> | ||
+ | <td>5035.2</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>2</td> | ||
+ | <td>104.6</td> | ||
+ | <td>5035.2</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <p>Targets ligations in pUPD2 (Orange TFL and Rice Ga20ox). | ||
+ | Following <a href= | ||
+ | "https://2016.igem.org/Team:Valencia_UPV/Notebook/Protocol">ligation | ||
+ | protocol</a>, BsmbI enzyme is used in this reaction.<br> | ||
+ | <br></p> | ||
+ | </div> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class="timeline-entry rounded"> | ||
+ | 12<span>Jul</span> | ||
+ | <div class="timeline-vline"></div> | ||
+ | </div> | ||
+ | <ul class="blog-post-info list-inline"> | ||
+ | <li><span class="font-lato">July 12, 2016</span></li> | ||
+ | </ul> | ||
+ | <p>Pick a single E. coli DH5α (target Ga20ox in pUPD2 and | ||
+ | target TFL in pUPD2) colony from the plate that has been | ||
+ | incubated overnight. Inoculate a starter culture of 4 ml of | ||
+ | LB medium with 4 μL of chloramphenicol in a 50 ml tube with | ||
+ | the colony and incubate it 16 hours at 37^C.<br> | ||
+ | Miniprep with E.Z.N.A ®. Plasmid Mini Kit I, Q(capless) | ||
+ | Spin of 35s:5’region in pUPD2<br> | ||
+ | Digestion of minipreps with NotI. Incubate 1 hour at | ||
+ | 37^C<br> | ||
+ | Run electrophoresis gel of the following part: 35s:5’ | ||
+ | region in pUPD2. We remain the samples 1 and 3.<br></p> | ||
+ | <ul> | ||
+ | <li>Miniprep with E.Z.N.A ®. Plasmid Mini Kit I, | ||
+ | Q(capless) Spin of:</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <ul> | ||
+ | <li>Ga20ox PCR in pUPD2</li> | ||
+ | <li>TFL PCR in pUPD2</li> | ||
+ | </ul> | ||
+ | </li> | ||
+ | </ul> | ||
+ | <p>Digestion of minipreps with NotI. Incubate 1 hour at | ||
+ | 37^C.<br></p> | ||
+ | <ul> | ||
+ | <li>Run electrophoresis gel of the same part:</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <ul> | ||
+ | <li>Ga20ox PCR in pUPD2</li> | ||
+ | <li>TFL PCR in pUPD2</li> | ||
+ | </ul> | ||
+ | </li> | ||
+ | </ul> | ||
+ | <p>Ligation using Golden Braid assembly of the device | ||
+ | 35s:5’region:TFL PCR:Luc:Tnos and | ||
+ | 35s:5’region:Ga20oxPCR:Luc:Tnos in α1 plasmid.<br></p> | ||
+ | </div> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class="timeline-entry rounded"> | ||
+ | 13<span>Jul</span> | ||
+ | <div class="timeline-vline"></div> | ||
+ | </div> | ||
+ | <ul class="blog-post-info list-inline"> | ||
+ | <li><span class="font-lato">July 13, 2016</span></li> | ||
+ | </ul> | ||
+ | <p><i>E. coli</i> Transformation with the device | ||
+ | 35s:5’region:TFL PCR:Luc:Tnos and | ||
+ | 35s:5’region:Ga20oxPCR:Luc:Tnos in α1 plasmid.<br> | ||
+ | E. coli plating in plates with Kanamycin (antibiotic). | ||
+ | Incubate overnight at 37^C<br></p> | ||
+ | </div> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class="timeline-entry rounded"> | ||
+ | 14<span>Jul</span> | ||
+ | <div class="timeline-vline"></div> | ||
+ | </div> | ||
+ | <ul class="blog-post-info list-inline"> | ||
+ | <li><span class="font-lato">July 14, 2016</span></li> | ||
+ | </ul> | ||
+ | <p>Pick a single E. coli DH5α (35s:5’ region) colony from | ||
+ | the plate that has been incubated overnight. Inoculate a | ||
+ | starter culture of 4 ml of LB medium with 4 μL of | ||
+ | chloramphenicol in a 50 ml tube with the colony and | ||
+ | incubate it 16 hours at 37^C.<br> | ||
+ | Primers IG16JUL09, IG16JUL10, IG16JUL11, IG16JUL12, | ||
+ | IG16JUL13, IG16JUL14, IG16JUL15 and IG16JUL16 | ||
+ | arrived.<br></p> | ||
+ | <ul> | ||
+ | <li>Ligation using Golden Braid assembly of the next | ||
+ | devices:</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <ul> | ||
+ | <li>35s:5’ region:TFL PCR control | ||
+ | positive:Luc:Tnos</li> | ||
+ | <li>35s:5’ region:Ga20oxPCR control | ||
+ | positive:Luc:Tnos</li> | ||
+ | <li>35s:5’ region:TFL PCR | ||
+ | consensus:Luc:Tnos</li> | ||
+ | <li>35s:5’ region:Ga20ox PCR | ||
+ | consensus:Luc:Tnos</li> | ||
+ | <li>U6-26:sgRNA TFL: psgRNA (scaffold)</li> | ||
+ | <li>U6-26:sgRNA Ga20ox: psgRNA (scaffold)</li> | ||
+ | </ul> | ||
+ | </li> | ||
+ | </ul> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li>Step 1: Annealing of oligonucleotides. Received | ||
+ | primers are at 1uM. It is necessary taking to 10 | ||
+ | uM.</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <ul> | ||
+ | <li>Mix in an Eppendorf:</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <ul> | ||
+ | <li>8 μL of H<sub>2</sub>O milli-Q</li> | ||
+ | <li>1 μL forward primer</li> | ||
+ | <li>1 μL reverse primer</li> | ||
+ | </ul> | ||
+ | </li> | ||
+ | </ul> | ||
+ | </li> | ||
+ | <li>Step 2: Ligation reaction</li> | ||
+ | </ul> | ||
+ | <p></p> | ||
+ | <div class="table-responsive" style= | ||
+ | "width:55%;overflow:inherit"> | ||
+ | <table class="table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <th>Reagent</th> | ||
+ | <th>Volume (μL)</th> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>TFL target control + / Ga20ox target | ||
+ | control + / TFL target consensus / Ga20ox | ||
+ | target consensus</td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>35s:5’ region</td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Luciferase</td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Tnos</td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>α1 plasmid</td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>BSA10X</td> | ||
+ | <td>1.2</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Ligase Buffer</td> | ||
+ | <td>1.2</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>BsaI</td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>T4 ligase</td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>H<sub>2</sub>O milli-Q</td> | ||
+ | <td>2.6</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <p><br></p> | ||
+ | <div class="table-responsive" style= | ||
+ | "width:55%;overflow:inherit"> | ||
+ | <table class="table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <th>Reagent</th> | ||
+ | <th>Volume (μL)</th> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>sgRNA TFL / sgRNA Ga20ox</td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>U6 -26</td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>psgRNA (scaffold)</td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>α1 plasmid</td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>BSA10X</td> | ||
+ | <td>1.2</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Ligase Buffer</td> | ||
+ | <td>1.2</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>BsaI</td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>T4 ligase</td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>H<sub>2</sub>O milli-Q</td> | ||
+ | <td>3.6</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <p><br> | ||
+ | <i>E. coli</i> Transformation with the devices previously | ||
+ | explained.<br> | ||
+ | E. coli plating in 6 plates (6 ligation reactions) with | ||
+ | Kanamycin (antibiotic). Incubate overnight at 37^C.<br></p> | ||
+ | <ul> | ||
+ | <li>Miniprep with E.Z.N.A ®. Plasmid Mini Kit I, | ||
+ | Q(capless) Spin of:</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <ul> | ||
+ | <li>35s:5’ region : TFL PCR : Luc : Tnos | ||
+ | (3α1)</li> | ||
+ | <li>35s:5’ region : Ga20ox PCR : Luc : Tnos | ||
+ | (3α1)</li> | ||
+ | </ul> | ||
+ | </li> | ||
+ | </ul> | ||
+ | <p>Digestion of minipreps with EcoRI. Incubate 1 hour at | ||
+ | 37^C<br></p> | ||
+ | </div> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class="timeline-entry rounded"> | ||
+ | 15<span>Jul</span> | ||
+ | <div class="timeline-vline"></div> | ||
+ | </div> | ||
+ | <ul class="blog-post-info list-inline"> | ||
+ | <li><span class="font-lato">July 15, 2016</span></li> | ||
+ | </ul> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li>Ligation using Golden Braid assembly of the next | ||
+ | devices:</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <ul> | ||
+ | <li>35s:Cas9:Tnos – 35s:5’ region:TFL | ||
+ | PCR:Luc:Tnos</li> | ||
+ | <li>35s:Cas9:Tnos – 35s:5’ region:Ga20ox | ||
+ | PCR:Luc:Tnos</li> | ||
+ | </ul> | ||
+ | </li> | ||
+ | </ul> | ||
+ | <p>E. coli Transformation with the devices previously | ||
+ | explained.<br></p> | ||
+ | <ul> | ||
+ | <li>Run an electrophoresis gel of the products from the | ||
+ | digestion of minipreps. The devices are:</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <ul> | ||
+ | <li>35s:5’ region:TFL PCR:Luc:Tnos (3α1)</li> | ||
+ | <li>35s:5’ region :Ga20ox PCR:Luc:Tnos | ||
+ | (3α1)</li> | ||
+ | </ul> | ||
+ | </li> | ||
+ | </ul> | ||
+ | <p>Sequencing 35s:5’region in pUPD2 → correct<br> | ||
+ | <br></p> | ||
+ | </div> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class="timeline-entry rounded"> | ||
+ | 16<span>Jul</span> | ||
+ | <div class="timeline-vline"></div> | ||
+ | </div> | ||
+ | <ul class="blog-post-info list-inline"> | ||
+ | <li><span class="font-lato">July 16, 2016</span></li> | ||
+ | </ul> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li>Transformations in <i>E. coli</i> DH5α with:</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <ul> | ||
+ | <li>35s:5’ region:TFL PCR:Luc:Tnos (3α1)</li> | ||
+ | <li>35s:5’ region:Ga20ox PCR:Luc:Tnos | ||
+ | (3α1)</li> | ||
+ | </ul> | ||
+ | </li> | ||
+ | </ul> | ||
+ | <p>Plating the last devices in 2 plates with | ||
+ | <i>Agrobacterium</i> C58. Incubate 2 days at 28^C.<br></p> | ||
+ | <ul> | ||
+ | <li>Minipreps (2 samples for each device) with E.Z.N.A | ||
+ | ®. Plasmid Mini Kit I, Q(capless) Spin of:</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <ul> | ||
+ | <li>35s:5’ region:TFL target control | ||
+ | positive:Luc:Tnos</li> | ||
+ | <li>35s:5’ region:Ga20ox target control | ||
+ | positive:Luc:Tnos</li> | ||
+ | <li>35s:5’ region:TFL target | ||
+ | consensus:Luc:Tnos</li> | ||
+ | <li>35s:5’ region:Ga20ox target | ||
+ | consensus:Luc:Tnos</li> | ||
+ | <li>U6-26:sgRNA TFL:psgRNA (scaffold)</li> | ||
+ | <li>U6-26:sgRNA Ga20ox:psgRNA (scaffold)</li> | ||
+ | </ul> | ||
+ | </li> | ||
+ | </ul> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li>Ligation using Golden Braid assembly of the next | ||
+ | devices:</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <ul> | ||
+ | <li>35s:Cas9:Tnos – U6:TFL sgRNA:psgRNA | ||
+ | (scaffold) (Ω1)</li> | ||
+ | <li>35s:Cas9:Tnos – U6: Ga20ox sgRNA:psgRNA | ||
+ | (scaffold) (Ω1)</li> | ||
+ | </ul> | ||
+ | </li> | ||
+ | </ul> | ||
+ | <p></p> | ||
+ | <div class="table-responsive" style= | ||
+ | "width:55%;overflow:inherit"> | ||
+ | <table class="table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <th>Reagent</th> | ||
+ | <th>Volume (μL)</th> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Promotor 35s:Cas9 : Tnos</td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>U6-26:TFL sgRNA:psgRNA / U6-26:Ga20ox | ||
+ | sgRNA:psgRNA</td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>3Ω1</td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>BSA10X</td> | ||
+ | <td>1.2</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Ligase Buffer</td> | ||
+ | <td>1.2</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>BsmbI</td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>T4 ligase</td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>H<sub>2</sub>O milli-Q</td> | ||
+ | <td>4.6</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <p>Digestion of the minipreps with EcoRI which have been | ||
+ | done before. Incubate 1 hour at 37^C. There is a total of | ||
+ | twelve minipreps. It has been followed the Miniprep | ||
+ | {digestion protocol | ||
+ | path:https://2016.igem.org/Team:Valencia_UPV/Notebook/Protocol].<br> | ||
+ | |||
+ | Run electrophoresis gel of the digestion products.<br></p> | ||
+ | <div class="table-responsive" style= | ||
+ | "width:55%;overflow:inherit"> | ||
+ | <table class="table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <th>Lanes</th> | ||
+ | <th>Samples</th> | ||
+ | <th>Verification</th> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>1</td> | ||
+ | <td>1 Kb molecular weight marker</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>2</td> | ||
+ | <td>gRNA Ga20ox 1</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>3</td> | ||
+ | <td>gRNA Ga20ox 2</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>4</td> | ||
+ | <td>Ga20ox consensus 1</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>5</td> | ||
+ | <td>Ga20ox consensus 2</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>6</td> | ||
+ | <td>Ga20ox knock-out 1</td> | ||
+ | <td>-</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>7</td> | ||
+ | <td>Ga20ox knock-out 2</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>8</td> | ||
+ | <td>TFL consensus 1</td> | ||
+ | <td>-</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>9</td> | ||
+ | <td>TFL consensus 2</td> | ||
+ | <td>-</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>10</td> | ||
+ | <td>TFL knock-out 1</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>11</td> | ||
+ | <td>TFL knock-out 2</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>12</td> | ||
+ | <td>TFL gRNA 1</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>13</td> | ||
+ | <td>TFL gRNA 2</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>14</td> | ||
+ | <td>1 Kb molecular weight marker</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li>Pick a single E. coli DH5α colony from the plates | ||
+ | that have been incubated overnight. The devices | ||
+ | are:</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <ul> | ||
+ | <li>35s:TFL Knock-out:Luc:Tnos (4 samples)</li> | ||
+ | <li>U6-26:Ga20ox sgRNA:psgRNA (2 samples)</li> | ||
+ | </ul> | ||
+ | </li> | ||
+ | </ul> | ||
+ | <p>Inoculate a starter culture of 4 ml of LB medium with 4 | ||
+ | μL of kanamycin in a 50 ml tube with the colony and | ||
+ | incubate it 16 hours at 37^C.<br></p> | ||
+ | </div> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class="timeline-entry rounded"> | ||
+ | 17<span>Jul</span> | ||
+ | <div class="timeline-vline"></div> | ||
+ | </div> | ||
+ | <ul class="blog-post-info list-inline"> | ||
+ | <li><span class="font-lato">July 17, 2016</span></li> | ||
+ | </ul> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li>Transformation in DH5α <i>E. coli</i> with:</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <ul> | ||
+ | <li>35s:Cas9:Tnos – U6:TFL sgRNA:psgRNA | ||
+ | (scaffold) (Ω1)</li> | ||
+ | <li>35s:Cas9:Tnos – U6:Ga20ox sgRNA:psgRNA | ||
+ | (scaffold) (Ω1)</li> | ||
+ | </ul> | ||
+ | </li> | ||
+ | </ul> | ||
+ | <p>Plating <i>E. coli</i> transformations in plates with LB | ||
+ | + agar + IPTG + XGal and incubate it overnight at | ||
+ | 37^C.<br></p> | ||
+ | <ul> | ||
+ | <li>Miniprep with E.Z.N.A ®. Plasmid Mini Kit I, | ||
+ | Q(capless) Spin of:</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <ul> | ||
+ | <li>U6-26:Ga20ox sgRNA:psgRNA</li> | ||
+ | <li>35s:5’ region:TFL Knock-out:Luc:Tnos | ||
+ | (3α1)</li> | ||
+ | </ul> | ||
+ | </li> | ||
+ | </ul> | ||
+ | <p>Digestion of the minipreps with EcoRI which have been | ||
+ | done before. Incubate 1 hour at 37^C. There is a total of | ||
+ | six minipreps. It has been followed the Miniprep digestion | ||
+ | protocol href.<br> | ||
+ | Run an electrophoresis gel of the digestion | ||
+ | products.<br></p> | ||
+ | <div class="table-responsive" style= | ||
+ | "width:55%;overflow:inherit"> | ||
+ | <table class="table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <th>Lanes</th> | ||
+ | <th>Samples</th> | ||
+ | <th>Verification</th> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>1</td> | ||
+ | <td>1 Kb molecular weight marker</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>2</td> | ||
+ | <td>gRNA Ga20ox 1</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>3</td> | ||
+ | <td>gRNA Ga20ox 2</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>4</td> | ||
+ | <td>gRNA Ga20ox 3</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>5</td> | ||
+ | <td>gRNA Ga20ox 4</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>6</td> | ||
+ | <td>TFL knock-out 1</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>7</td> | ||
+ | <td>TFL knock-out 2</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>8</td> | ||
+ | <td>1 Kb molecular weight marker</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <p>However, despite the fact that electrophoresis gel have | ||
+ | correctly run, we have decided to repeat the ligation | ||
+ | reactions. We have not get the expected results for a | ||
+ | gRNA.<br></p> | ||
+ | <ul> | ||
+ | <li>Ligation using Golden Braid assembly of the next | ||
+ | devices:</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <ul> | ||
+ | <li>35s:5’ region:TFL target control | ||
+ | positive:Luc:Tnos</li> | ||
+ | <li>35s:5’ region:Ga20ox target control | ||
+ | positive:Luc:Tnos</li> | ||
+ | <li>35s:5’ region:TFL target | ||
+ | consensus:Luc:Tnos</li> | ||
+ | <li>35s:5’ region:Ga20ox target | ||
+ | consensus:Luc:Tnos</li> | ||
+ | <li>U6-26:sgRNA TFL:psgRNA (scaffold)</li> | ||
+ | <li>U6-26:sgRNA Ga20ox:psgRNA (scaffold)</li> | ||
+ | </ul> | ||
+ | </li> | ||
+ | </ul> | ||
+ | <p></p> | ||
+ | <div class="table-responsive" style= | ||
+ | "width:55%;overflow:inherit"> | ||
+ | <table class="table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <th>Reagent</th> | ||
+ | <th>Volume(μL)</th> | ||
+ | <th>Reagent</th> | ||
+ | <th>Volume(μL)</th> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>TFL/Ga20ox gRNA</td> | ||
+ | <td>1</td> | ||
+ | <td>35s:5’region</td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>U6-26</td> | ||
+ | <td>1</td> | ||
+ | <td>TFL/Ga20ox consensus TFL/Ga20ox | ||
+ | knock-out</td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>psgRNA</td> | ||
+ | <td>1</td> | ||
+ | <td>luciferase</td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>3α1</td> | ||
+ | <td>1</td> | ||
+ | <td>Tnos</td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>BSA10X</td> | ||
+ | <td>1.2</td> | ||
+ | <td>3α1</td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Ligase Buffer</td> | ||
+ | <td>1.2</td> | ||
+ | <td>BSA10X</td> | ||
+ | <td>1.2</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>BsaI</td> | ||
+ | <td>1</td> | ||
+ | <td>Ligase Buffer</td> | ||
+ | <td>1.2</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>T4 ligase</td> | ||
+ | <td>1</td> | ||
+ | <td>BsmbI</td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>H<sub>2</sub>O milli-Q</td> | ||
+ | <td>3.6</td> | ||
+ | <td>T4 ligase</td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>H<sub>2</sub>O milli-Q</td> | ||
+ | <td>2.6</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <p><br></p> | ||
+ | </div> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class="timeline-entry rounded"> | ||
+ | 18<span>Jul</span> | ||
+ | <div class="timeline-vline"></div> | ||
+ | </div> | ||
+ | <ul class="blog-post-info list-inline"> | ||
+ | <li><span class="font-lato">July 18, 2016</span></li> | ||
+ | </ul> | ||
+ | <p>Transformation in DH5α <i>E. coli</i> with ligation | ||
+ | products (consensus targets and knock-out targets of TFL | ||
+ | and Ga20ox as well as their gRNAs)<br> | ||
+ | Plating <i>E. coli</i> transformations in plates with LB + | ||
+ | agar + IPTG + XGal and incubate it overnight at | ||
+ | 37^C.<br></p> | ||
+ | <ul> | ||
+ | <li>Pick a single <i>Agrobacterium</i> C58 colony from | ||
+ | the plates that have been incubating since 16/06/2016. | ||
+ | The devices are:</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <ul> | ||
+ | <li>35s:5’ region:TFL PCR:Luc:Tnos (3α1)</li> | ||
+ | <li>35s:5’ region:Ga20ox PCR:Luc:Tnos | ||
+ | (3α1)</li> | ||
+ | </ul> | ||
+ | </li> | ||
+ | </ul> | ||
+ | <p>Incubate it 48 hours at 28^C.<br></p> | ||
+ | </div> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class="timeline-entry rounded"> | ||
+ | 19<span>Jul</span> | ||
+ | <div class="timeline-vline"></div> | ||
+ | </div> | ||
+ | <ul class="blog-post-info list-inline"> | ||
+ | <li><span class="font-lato">July 19, 2016</span></li> | ||
+ | </ul> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li>Pick transformed <i>E. coli</i> colony from the | ||
+ | incubated plates. The devices are:</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <ul> | ||
+ | <li>35s:5’ region:TFL target control | ||
+ | positive:Luc:Tnos</li> | ||
+ | <li>35s:5’ region:Ga20ox target control | ||
+ | positive:Luc:Tnos</li> | ||
+ | <li>35s:5’ region:TFL target | ||
+ | consensus:Luc:Tnos</li> | ||
+ | <li>35s:5’ region:Ga20ox target | ||
+ | consensus:Luc:Tnos</li> | ||
+ | <li>U6-26: sgRNA TFL:psgRNA (scaffold)</li> | ||
+ | <li>U6-26: sgRNA Ga20ox:psgRNA (scaffold)</li> | ||
+ | </ul> | ||
+ | </li> | ||
+ | </ul> | ||
+ | <p>Incubate it overnight at 37^C.<br></p> | ||
+ | </div> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class="timeline-entry rounded"> | ||
+ | 20<span>Jul</span> | ||
+ | <div class="timeline-vline"></div> | ||
+ | </div> | ||
+ | <ul class="blog-post-info list-inline"> | ||
+ | <li><span class="font-lato">July 20, 2016</span></li> | ||
+ | </ul> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li>Miniprep with E.Z.N.A ®. Plasmid Mini Kit I, | ||
+ | Q(capless) Spin of:</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <ul> | ||
+ | <li>35s:5’ region:TFL target | ||
+ | knock-out:Luc:Tnos</li> | ||
+ | <li>35s:5’ region:Ga20ox target control | ||
+ | knock-out:Luc:Tnos</li> | ||
+ | <li>35s:5’ region:TFL target | ||
+ | consensus:Luc:Tnos</li> | ||
+ | <li>35s:5’ region:Ga20ox target | ||
+ | consensus:Luc:Tnos</li> | ||
+ | <li>U6-26:sgRNA TFL:psgRNA (scaffold)</li> | ||
+ | <li>U6-26:sgRNA Ga20ox:psgRNA (scaffold)</li> | ||
+ | </ul> | ||
+ | </li> | ||
+ | </ul> | ||
+ | <p>Digestion of the minipreps with EcoRI which have been | ||
+ | done before. Incubate 1 hour at 37^C. There is a total of | ||
+ | six minipreps. It has been followed the Miniprep {digestion | ||
+ | protocol | ||
+ | path:https://2016.igem.org/Team:Valencia_UPV/Notebook/Protocol].<br> | ||
+ | |||
+ | Run an electrophoresis gel of the digestion products. We | ||
+ | will keep the minipreps with “1”.<br></p> | ||
+ | <div class="table-responsive" style= | ||
+ | "width:55%;overflow:inherit"> | ||
+ | <table class="table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <th>Lanes</th> | ||
+ | <th>Samples</th> | ||
+ | <th>Verification</th> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>1</td> | ||
+ | <td>1 Kb molecular weight marker</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>2</td> | ||
+ | <td>gRNA TFL 1</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>3</td> | ||
+ | <td>gRNA TFL 2</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>4</td> | ||
+ | <td>TFL consensus 1</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>5</td> | ||
+ | <td>TFL consensus 2</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>6</td> | ||
+ | <td>TFL knock-out 1</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>7</td> | ||
+ | <td>TFL knock-out 2</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>8</td> | ||
+ | <td>1 Kb molecular weight marker</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>9</td> | ||
+ | <td>gRNA Ga20ox 1</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>10</td> | ||
+ | <td>gRNA Ga20ox 2</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>11</td> | ||
+ | <td>Ga20ox consensus 1</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>12</td> | ||
+ | <td>Ga20ox consensus 2</td> | ||
+ | <td>-</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>13</td> | ||
+ | <td>Ga20ox knock-out 1</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>14</td> | ||
+ | <td>Ga20ox knock-out 2</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>15</td> | ||
+ | <td>1 Kb molecular weight marker</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li>Ligation using Golden Braid assembly of the next | ||
+ | devices. Is used the restriction enzyme BsmbI.</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <ul> | ||
+ | <li>35s:Cas 9:Tnos – U6-26:TFL | ||
+ | sgRNA:psgRNA</li> | ||
+ | <li>35s:Cas 9:Tnos – U6-26:Ga20ox | ||
+ | sgRNA:psgRNA</li> | ||
+ | </ul> | ||
+ | </li> | ||
+ | </ul> | ||
+ | <p></p> | ||
+ | </div> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class="timeline-entry rounded"> | ||
+ | 21<span>Jul</span> | ||
+ | <div class="timeline-vline"></div> | ||
+ | </div> | ||
+ | <ul class="blog-post-info list-inline"> | ||
+ | <li><span class="font-lato">July 21, 2016</span></li> | ||
+ | </ul> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li>Transformations in <i>E. coli</i> DH5α with:</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <ul> | ||
+ | <li>35s:Cas 9:Tnos – U6-26:TFL | ||
+ | sgRNA:psgRNA</li> | ||
+ | <li>35s:Cas 9:Tnos – U6-26:Ga20ox | ||
+ | sgRNA:psgRNA</li> | ||
+ | </ul> | ||
+ | </li> | ||
+ | </ul> | ||
+ | <p>Incubate 2 hours at 37^C.<br> | ||
+ | Plating <i>E. coli</i> transformation explained before and | ||
+ | incubate it at 37^C overnight.<br> | ||
+ | #<i>Agrobacterium</i> C58 transformation with:<br></p> | ||
+ | <ul> | ||
+ | <li>#35s:5’ region:TFL target knock-out:Luc:Tnos</li> | ||
+ | <li>35s:5’ region:Ga20ox target control | ||
+ | knock-out:Luc:Tnos</li> | ||
+ | <li>35s:5’ region:TFL target consensus:Luc:Tnos</li> | ||
+ | <li>35s:5’ region:Ga20ox target consensus:Luc:Tnos</li> | ||
+ | </ul> | ||
+ | <p>Incubate 48 hours at 28^C.<br> | ||
+ | <br></p> | ||
+ | </div> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class="timeline-entry rounded"> | ||
+ | 22<span>Jul</span> | ||
+ | <div class="timeline-vline"></div> | ||
+ | </div> | ||
+ | <ul class="blog-post-info list-inline"> | ||
+ | <li><span class="font-lato">July 22, 2016</span></li> | ||
+ | </ul> | ||
+ | <p>Sequencing reaction:<br></p> | ||
+ | <div class="table-responsive" style= | ||
+ | "width:55%;overflow:inherit"> | ||
+ | <table class="table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <th>Reagent</th> | ||
+ | <th>Volume (μL)</th> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Primer in order to sequence</td> | ||
+ | <td>3</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Miniprep reaction</td> | ||
+ | <td>5</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>H<sub>2</sub>O milli-Q</td> | ||
+ | <td>6</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <p><br></p> | ||
+ | <div class="table-responsive" style= | ||
+ | "width:55%;overflow:inherit"> | ||
+ | <table class="table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <th>Sequence</th> | ||
+ | <th>Order</th> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>TFL gRNA</td> | ||
+ | <td>210.13.201</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td>Ga20oxgRNA</td> | ||
+ | <td>210.13.202</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <p>Ordered the necessary primers to sequence: TFL | ||
+ | consensus, TFL knockout, Ga20ox consensus and Ga20ox | ||
+ | knockout.<br> | ||
+ | <i>E. coli</i> transformations with 35s:Cas 9:Tnos – | ||
+ | U6-26:TFL sgRNA: psgRNA<br> | ||
+ | Plating the last device in plates with <i>Agrobacterium</i> | ||
+ | C58. Plates contain spec + IPTG + X-Gal. Incubate 2 days at | ||
+ | 28^C.<br> | ||
+ | Pick a single <i>E. coli</i> DH5α (35s:Cas 9:Tnos – | ||
+ | U6-26:TFL sgRNA:psgRNA and 35s:Cas 9:Tnos – U6-26:Ga20ox | ||
+ | sgRNA:psgRNA) colony from the plates that has been | ||
+ | incubated overnight. Inoculate a starter culture of 4 ml of | ||
+ | LB medium with 4 μL of spectinomycin in a 50 ml tube with | ||
+ | the colony and incubate it overnight at 37^C with | ||
+ | shaking.<br> | ||
+ | <br></p> | ||
+ | </div> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class="timeline-entry rounded"> | ||
+ | 23<span>Jul</span> | ||
+ | <div class="timeline-vline"></div> | ||
+ | </div> | ||
+ | <ul class="blog-post-info list-inline"> | ||
+ | <li><span class="font-lato">July 23, 2016</span></li> | ||
+ | </ul> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li>#Minipreps (4 samples for each device) with E.Z.N.A | ||
+ | ®. Plasmid Mini Kit I, Q(capless) Spin of:</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <ul> | ||
+ | <li>#35s:Cas 9:Tnos – U6-26:TFL | ||
+ | sgRNA:psgRNA</li> | ||
+ | <li>35s:Cas 9:Tnos – U6-26:Ga20ox | ||
+ | sgRNA:psgRNA</li> | ||
+ | </ul> | ||
+ | <p></p> | ||
+ | </li> | ||
+ | </ul>Digestion of minipreps with BamHI following digestion | ||
+ | protocol href. Incubate 1 hour at 37^C.<br> | ||
+ | Run an electrophoresis gel of the digestion products. We | ||
+ | will keep the minipreps with the sample number 4 for TFL | ||
+ | sgRNA and the sample number 2 for Ga20ox sgRNA.<br> | ||
+ | Pick a single <i>Agrobacterium</i> C58 (35s:Cas 9:Tnos – | ||
+ | U6-26:TFL sgRNA:psgRNA and 35s:Cas 9:Tnos – U6-26:Ga20ox | ||
+ | sgRNA:psgRNA ) colony from the plates that has been | ||
+ | incubated overnight. Inoculate a starter culture of 5 ml of | ||
+ | LB medium with 5 μL of spectinomycin and kanamycin in a | ||
+ | falcon tube with the colony and incubate it overnight at | ||
+ | 28^C with shaking.<br> | ||
+ | #<i>Agrobacterium</i> C58 transformations with:<br> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li>#35s:Cas 9:Tnos – U6-26:TFL sgRNA:psgRNA</li> | ||
+ | <li style="list-style: none">35s:Cas 9:Tnos – | ||
+ | U6-26:Ga20ox sgRNA:psgRNA<br></li> | ||
+ | </ul> | ||
+ | <p></p> | ||
+ | </div> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class="timeline-entry rounded"> | ||
+ | 24<span>Jul</span> | ||
+ | <div class="timeline-vline"></div> | ||
+ | </div> | ||
+ | <ul class="blog-post-info list-inline"> | ||
+ | <li><span class="font-lato">July 24, 2016</span></li> | ||
+ | </ul> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li>#Store the next cultures at -80^C:</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <ul> | ||
+ | <li>#35s:5’ region in pUPD2 (DH5α) number | ||
+ | 1</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <ul> | ||
+ | <li>#SAGTI: luciferase in pUPD2 (DH5α) | ||
+ | number 2</li> | ||
+ | </ul> | ||
+ | </li> | ||
+ | </ul> | ||
+ | </li> | ||
+ | </ul> | ||
+ | </div> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class="timeline-entry rounded"> | ||
+ | 25<span>Jul</span> | ||
+ | <div class="timeline-vline"></div> | ||
+ | </div> | ||
+ | <ul class="blog-post-info list-inline"> | ||
+ | <li><span class="font-lato">July 25, 2016</span></li> | ||
+ | </ul> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li>Pick a single <i>Agrobacterium</i> C58 (35s:Cas | ||
+ | 9:Tnos – U6-26:TFL sgRNA:psgRNA in 3Ω1 and 35s:Cas | ||
+ | 9:Tnos – U6-26:Ga20ox sgRNA:psgRNA in 3Ω1 ) colony from | ||
+ | the plates that has been incubated overnight. Inoculate | ||
+ | a starter culture of 5 ml of LB medium with 5 μL of | ||
+ | spectinomycin and kanamycin in a falcon tube with the | ||
+ | colony and incubate it overnight at 28^C with | ||
+ | shaking.</li> | ||
+ | <li>Incubate it 48 hours at 28^C</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <ul> | ||
+ | <li>inipreps of <i>Agrobacterium</i> with | ||
+ | E.Z.N.A ®. Plasmid Mini Kit I, Q(capless) Spin | ||
+ | of:</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <ul> | ||
+ | <li>5s:5’ region:TFL target control | ||
+ | positive:Luc:Tnos</li> | ||
+ | <li>35s:5’ region:Ga20ox target control | ||
+ | positive:Luc:Tnos</li> | ||
+ | <li>35s:5’ region:TFL target | ||
+ | consensus:Luc:Tnos</li> | ||
+ | <li>35s:5’ region:Ga20ox target | ||
+ | consensus:Luc:Tnos</li> | ||
+ | </ul> | ||
+ | </li> | ||
+ | </ul> | ||
+ | </li> | ||
+ | <li>Digestion of minipreps with the restriction enzyme | ||
+ | EcoRI. Incubate 1 hour at 37^C.</li> | ||
+ | <li>Run an electrophoresis gel of the digestion | ||
+ | products.</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <div class="table-responsive" style= | ||
+ | "width:55%;overflow:inherit"> | ||
+ | <table class= | ||
+ | "table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <th> | ||
+ | <ul> | ||
+ | <li>Lanes</li> | ||
+ | </ul> | ||
+ | </th> | ||
+ | <th>Samples</th> | ||
+ | <th>Verification</th> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>1</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>1 Kb molecular weight marker</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>2</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>Target Ga20ox consensus</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>3</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>Target Ga20ox Knock-out</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>4</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>Target TFL consensus</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>5</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>Target TFL knock-out</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>6</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>1 Kb molecular weight marker</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <p></p> | ||
+ | </li> | ||
+ | <li></li> | ||
+ | </ul> | ||
+ | </div> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class="timeline-entry rounded"> | ||
+ | 26<span>Jul</span> | ||
+ | <div class="timeline-vline"></div> | ||
+ | </div> | ||
+ | <ul class="blog-post-info list-inline"> | ||
+ | <li><span class="font-lato">July 26, 2016</span></li> | ||
+ | </ul> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li>inipreps with E.Z.N.A ®. Plasmid Mini Kit I, | ||
+ | Q(capless) Spin of:</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <ul> | ||
+ | <li>5s:5’ region:TFL PCR:Luc:Tnos in 3α1 | ||
+ | plasmid from C58 <i>Agrobacterium</i></li> | ||
+ | <li>35s:5’ region:Ga20ox PCR:Luc:Tnos in 3α1 | ||
+ | plasmid from C58 <i>Agrobacterium</i></li> | ||
+ | </ul> | ||
+ | </li> | ||
+ | </ul> | ||
+ | <ul> | ||
+ | <li>Digestion of minipreps with the restriction enzyme | ||
+ | EcoRI. Incubate 1 hour at 37^C.</li> | ||
+ | <li>Run an electrophoresis gel of the digestion | ||
+ | products:</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <div class="table-responsive" style= | ||
+ | "width:55%;overflow:inherit"> | ||
+ | <table class= | ||
+ | "table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <th> | ||
+ | <ul> | ||
+ | <li>Lanes</li> | ||
+ | </ul> | ||
+ | </th> | ||
+ | <th>Samples</th> | ||
+ | <th>Verification</th> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>1</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>1 Kb molecular weight marker</td> | ||
+ | <td>correct</td> | ||
+ | <td></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>2</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>35s:5’ region:PCR Ga20ox | ||
+ | :Luc:Tnos</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>3</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>35s:5’ region:PCR TFL | ||
+ | Clemunules:Luc:Tnos</td> | ||
+ | <td>correct</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>6</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>1 Kb molecular weight marker</td> | ||
+ | <td>correct</td> | ||
+ | <td></td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <p></p> | ||
+ | </li> | ||
+ | <li></li> | ||
+ | </ul> | ||
+ | </div> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class="timeline-entry rounded"> | ||
+ | 26<span>Jul</span> | ||
+ | <div class="timeline-vline"></div> | ||
+ | </div> | ||
+ | <ul class="blog-post-info list-inline"> | ||
+ | <li><span class="font-lato">July 26, 2016</span></li> | ||
+ | </ul> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li>equencing products have arrived:</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <ul> | ||
+ | <li>6-26:Ga20ox gRNA:psgRNA in α1 - | ||
+ | correct</li> | ||
+ | <li>U6-26:TFL gRNA:psgRNA in α1 - correct</li> | ||
+ | </ul> | ||
+ | </li> | ||
+ | </ul> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li>inipreps with E.Z.N.A ®.® Plasmid Mini Kit I, | ||
+ | Q(capless) Spin of:</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <ul> | ||
+ | <li>5s:5’ region: Ga20ox PCR : Luc : Tnos in | ||
+ | α1</li> | ||
+ | <li>35s:5’ region: TFL PCR : Luc : Tnos in | ||
+ | α1</li> | ||
+ | </ul> | ||
+ | </li> | ||
+ | </ul> | ||
+ | <ul> | ||
+ | <li>Digestion of minipreps with the restriction enzyme | ||
+ | EcoRI. Incubate 1 hour at 37^.</li> | ||
+ | <li>Run electrophoresis gel of the digestion | ||
+ | products.</li> | ||
+ | <li style="list-style: none; display: inline"> | ||
+ | <div class="table-responsive" style= | ||
+ | "width:55%;overflow:inherit"> | ||
+ | <div class="table-responsive" style= | ||
+ | "width:55%;overflow:inherit"> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class="timeline-entry rounded"> | ||
+ | 27<span>Jul</span> | ||
+ | <div class="timeline-vline"></div> | ||
+ | </div> | ||
+ | <ul class="blog-post-info list-inline"> | ||
+ | <li><span class="font-lato">July | ||
+ | 27, 2016</span></li> | ||
+ | </ul> | ||
+ | <p></p> | ||
+ | </div> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class="timeline-entry rounded"> | ||
+ | 28<span>Jul</span> | ||
+ | <div class="timeline-vline"></div> | ||
+ | </div> | ||
+ | <ul class="blog-post-info list-inline"> | ||
+ | <li><span class="font-lato">July | ||
+ | 28, 2016</span></li> | ||
+ | </ul> | ||
+ | <p></p> | ||
+ | </div> | ||
+ | <div class="table-responsive" style= | ||
+ | "width:55%;overflow:inherit"> | ||
+ | <div class="table-responsive" style= | ||
+ | "width:55%;overflow:inherit"> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class= | ||
+ | "timeline-entry rounded"> | ||
+ | 29<span>Jul</span> | ||
+ | <div class= | ||
+ | "timeline-vline"></div> | ||
+ | </div> | ||
+ | <ul class= | ||
+ | "blog-post-info list-inline"> | ||
+ | <li><span class= | ||
+ | "font-lato">July 29, | ||
+ | 2016</span></li> | ||
+ | </ul> | ||
+ | <p></p> | ||
+ | </div> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class= | ||
+ | "timeline-entry rounded"> | ||
+ | 01<span>Aug</span> | ||
+ | <div class= | ||
+ | "timeline-vline"></div> | ||
+ | </div> | ||
+ | <ul class= | ||
+ | "blog-post-info list-inline"> | ||
+ | <li><span class= | ||
+ | "font-lato">August 01, | ||
+ | 2016</span></li> | ||
+ | </ul> | ||
+ | <p></p> | ||
+ | </div> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class= | ||
+ | "timeline-entry rounded"> | ||
+ | 02<span>Aug</span> | ||
+ | <div class= | ||
+ | "timeline-vline"></div> | ||
+ | </div> | ||
+ | <ul class= | ||
+ | "blog-post-info list-inline"> | ||
+ | <li><span class= | ||
+ | "font-lato">August 02, | ||
+ | 2016</span></li> | ||
+ | </ul> | ||
+ | <p></p> | ||
+ | </div> | ||
+ | <div class="table-responsive" | ||
+ | style="width:55%;overflow:inherit"> | ||
+ | <div class="table-responsive" | ||
+ | style= | ||
+ | "width:55%;overflow:inherit"> | ||
+ | <div class= | ||
+ | "blog-post-item"> | ||
+ | <div class= | ||
+ | "timeline-entry rounded"> | ||
+ | 03<span>Aug</span> | ||
+ | <div class= | ||
+ | "timeline-vline"> | ||
+ | </div> | ||
+ | </div> | ||
+ | <ul class= | ||
+ | "blog-post-info list-inline"> | ||
+ | <li><span class= | ||
+ | "font-lato">August 03, | ||
+ | 2016</span></li> | ||
+ | </ul> | ||
+ | <p></p> | ||
+ | </div> | ||
+ | <div class= | ||
+ | "table-responsive" style= | ||
+ | "width:55%;overflow:inherit"> | ||
+ | <div class= | ||
+ | "table-responsive" | ||
+ | style="width:55%;overflow:inherit"> | ||
+ | <div class= | ||
+ | "table-responsive" | ||
+ | style= | ||
+ | "width:55%;overflow:inherit"> | ||
+ | <div class= | ||
+ | "table-responsive" | ||
+ | style= | ||
+ | "width:55%;overflow:inherit"> | ||
+ | <div class= | ||
+ | "blog-post-item"> | ||
+ | <div class="timeline-entry rounded"> | ||
+ | 04<span>Aug</span> | ||
+ | <div class="timeline-vline"> | ||
+ | </div> | ||
+ | </div> | ||
+ | <ul class="blog-post-info list-inline"> | ||
+ | <li> | ||
+ | <span class="font-lato"> | ||
+ | August | ||
+ | 04, | ||
+ | 2016</span></li> | ||
+ | </ul> | ||
+ | <p></p> | ||
+ | </div> | ||
+ | <div class= | ||
+ | "blog-post-item"> | ||
+ | <div class="timeline-entry rounded"> | ||
+ | 05<span>Aug</span> | ||
+ | <div class="timeline-vline"> | ||
+ | </div> | ||
+ | </div> | ||
+ | <ul class="blog-post-info list-inline"> | ||
+ | <li> | ||
+ | <span class="font-lato"> | ||
+ | August | ||
+ | 05, | ||
+ | 2016</span></li> | ||
+ | </ul> | ||
+ | <p></p> | ||
+ | </div> | ||
+ | <div class= | ||
+ | "table-responsive" | ||
+ | style= | ||
+ | "width:55%;overflow:inherit"> | ||
+ | <div class="table-responsive" | ||
+ | style= | ||
+ | "width:55%;overflow:inherit"> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class="timeline-entry rounded"> | ||
+ | 08<span>Aug</span> | ||
+ | <div class="timeline-vline"> | ||
+ | </div> | ||
+ | </div> | ||
+ | <ul class="blog-post-info list-inline"> | ||
+ | <li> | ||
+ | <span class="font-lato"> | ||
+ | August | ||
+ | 08, | ||
+ | 2016</span></li> | ||
+ | </ul> | ||
+ | <p> | ||
+ | </p> | ||
+ | </div> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class="timeline-entry rounded"> | ||
+ | 09<span>Aug</span> | ||
+ | <div class="timeline-vline"> | ||
+ | </div> | ||
+ | </div> | ||
+ | <ul class="blog-post-info list-inline"> | ||
+ | <li> | ||
+ | <span class="font-lato"> | ||
+ | August | ||
+ | 09, | ||
+ | 2016</span></li> | ||
+ | </ul> | ||
+ | <p> | ||
+ | </p> | ||
+ | </div> | ||
+ | <div class="table-responsive" | ||
+ | style="width:55%;overflow:inherit"> | ||
+ | <div class="table-responsive" | ||
+ | style="width:55%;overflow:inherit"> | ||
+ | <div class="table-responsive" | ||
+ | style="width:55%;overflow:inherit"> | ||
+ | <div class="table-responsive" | ||
+ | style="width:55%;overflow:inherit"> | ||
+ | <div class="table-responsive" | ||
+ | style="width:55%;overflow:inherit"> | ||
+ | <div class="table-responsive" | ||
+ | style="width:55%;overflow:inherit"> | ||
+ | <div class="blog-post-item"> | ||
+ | <div class="timeline-entry rounded"> | ||
+ | 10<span>Aug</span> | ||
+ | <div class="timeline-vline"> | ||
+ | </div> | ||
+ | </div> | ||
+ | <ul class="blog-post-info list-inline"> | ||
+ | <li> | ||
+ | <span class="font-lato"> | ||
+ | August | ||
+ | 10, | ||
+ | 2016</span></li> | ||
+ | </ul> | ||
+ | <p> | ||
+ | </p> | ||
+ | </div> | ||
+ | <div class="table-responsive" | ||
+ | style="width:55%;overflow:inherit"> | ||
+ | <div class="table-responsive" | ||
+ | style="width:55%;overflow:inherit"> | ||
+ | <table class="table table-bordered table-striped"> | ||
+ | </table> | ||
+ | </div> | ||
+ | <table class="table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | devices</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | Volume | ||
+ | (μL)</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | gTS | ||
+ | TFL/ | ||
+ | Ga20ox- | ||
+ | Renilla</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Cas9 | ||
+ | - | ||
+ | gRNA</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | 3 | ||
+ | α | ||
+ | 1 | ||
+ | plasmid</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 1.2</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Bsa | ||
+ | 10x</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 1.2</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Buffer | ||
+ | ligase</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Bsa | ||
+ | I</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | T4 | ||
+ | ligase</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | H20 | ||
+ | milliQ</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 4.6</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <table class="table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Run | ||
+ | electrophoresis | ||
+ | gel | ||
+ | of: | ||
+ | 35s: | ||
+ | 5’ | ||
+ | region: | ||
+ | TFL/Ga20oxPCR: | ||
+ | Luc: | ||
+ | Tnos | ||
+ | – | ||
+ | 35s: | ||
+ | Renilla: | ||
+ | Tnos. | ||
+ | We | ||
+ | keep | ||
+ | the | ||
+ | Miniprep | ||
+ | number | ||
+ | 1.</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Refresh | ||
+ | the | ||
+ | cultures | ||
+ | of | ||
+ | TFL | ||
+ | PCR | ||
+ | (pUPD2) | ||
+ | and | ||
+ | Ga20oxPCR | ||
+ | (pUPD2) | ||
+ | because | ||
+ | we | ||
+ | suspect | ||
+ | that | ||
+ | these | ||
+ | cultures | ||
+ | are | ||
+ | the | ||
+ | correct | ||
+ | ones | ||
+ | but | ||
+ | we | ||
+ | are | ||
+ | not | ||
+ | sure | ||
+ | so | ||
+ | we | ||
+ | want | ||
+ | to | ||
+ | check | ||
+ | them. | ||
+ | The | ||
+ | cultures | ||
+ | that | ||
+ | we | ||
+ | use | ||
+ | to | ||
+ | refresh | ||
+ | were | ||
+ | made | ||
+ | on | ||
+ | 12/07/2016. | ||
+ | It | ||
+ | is | ||
+ | important | ||
+ | to | ||
+ | remember | ||
+ | that | ||
+ | we | ||
+ | need | ||
+ | them | ||
+ | to | ||
+ | assemble | ||
+ | the | ||
+ | gTS | ||
+ | with | ||
+ | the | ||
+ | new | ||
+ | linkers.</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | </li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Miniprep | ||
+ | with | ||
+ | E.Z.N.A | ||
+ | ®.® | ||
+ | Plasmid | ||
+ | Mini | ||
+ | Kit | ||
+ | I, | ||
+ | Q(capless) | ||
+ | Spin | ||
+ | of | ||
+ | TFL | ||
+ | / | ||
+ | Ga20oxPCR | ||
+ | in | ||
+ | pUPD2</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Digestion | ||
+ | of | ||
+ | minipreps | ||
+ | with | ||
+ | NotI. | ||
+ | Incubate | ||
+ | 1 | ||
+ | hour | ||
+ | at | ||
+ | 37^</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Run | ||
+ | electrophoresis | ||
+ | gel | ||
+ | of | ||
+ | Miniprep | ||
+ | products. | ||
+ | We | ||
+ | have | ||
+ | made | ||
+ | a | ||
+ | small | ||
+ | gel | ||
+ | so | ||
+ | we | ||
+ | have | ||
+ | mix | ||
+ | 0.45 | ||
+ | g | ||
+ | of | ||
+ | Agarose | ||
+ | with | ||
+ | 45 | ||
+ | mL | ||
+ | of | ||
+ | TAE | ||
+ | 1X. | ||
+ | Voltage | ||
+ | used | ||
+ | is | ||
+ | 100V. | ||
+ | Both | ||
+ | samples | ||
+ | are | ||
+ | correct.</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Pick | ||
+ | a | ||
+ | single | ||
+ | E. | ||
+ | coli | ||
+ | DH5α | ||
+ | (promoter35s: | ||
+ | 5’ | ||
+ | region: | ||
+ | TFL/Ga20oxcons: | ||
+ | Tnos | ||
+ | - | ||
+ | promoter35s: | ||
+ | Renilla: | ||
+ | Tnos | ||
+ | - | ||
+ | 35s: | ||
+ | Cas9: | ||
+ | Tnos | ||
+ | - | ||
+ | U6: | ||
+ | TFL/Ga20oxgRNA: | ||
+ | psgRNA) | ||
+ | colony | ||
+ | from | ||
+ | the | ||
+ | plate | ||
+ | that | ||
+ | has | ||
+ | been | ||
+ | incubated | ||
+ | overnight. | ||
+ | Inoculate | ||
+ | a | ||
+ | starter | ||
+ | culture | ||
+ | of | ||
+ | 4 | ||
+ | ml | ||
+ | of | ||
+ | LB | ||
+ | medium | ||
+ | with | ||
+ | 4 | ||
+ | μL | ||
+ | of | ||
+ | chloramphenicol | ||
+ | in | ||
+ | a | ||
+ | 50 | ||
+ | ml | ||
+ | tube | ||
+ | with | ||
+ | the | ||
+ | colony | ||
+ | and | ||
+ | incubate | ||
+ | it | ||
+ | overnight | ||
+ | at | ||
+ | 37^ | ||
+ | with | ||
+ | shaking.</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | We | ||
+ | throw | ||
+ | out | ||
+ | from | ||
+ | Golden | ||
+ | Braid | ||
+ | collection | ||
+ | the | ||
+ | glycerinate | ||
+ | number | ||
+ | 1107 | ||
+ | (Cas9 | ||
+ | - | ||
+ | XT1gRNA) | ||
+ | and | ||
+ | 0549 | ||
+ | (35s: | ||
+ | TEV: | ||
+ | Tnos)</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Ligation | ||
+ | reaction | ||
+ | of | ||
+ | 35s: | ||
+ | 5’ | ||
+ | region: | ||
+ | TFL/ | ||
+ | Ga20: | ||
+ | Tnos | ||
+ | - | ||
+ | 35s: | ||
+ | Renilla: | ||
+ | Tnos | ||
+ | + | ||
+ | 35s: | ||
+ | Cas9: | ||
+ | Tnos | ||
+ | - | ||
+ | U6: | ||
+ | TFL/Ga20oxgRNA: | ||
+ | psgRNA</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <table class="table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | 5</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 35s:5’:Ga20cons:Luc:Tnos</td> | ||
+ | <td> | ||
+ | 3α1</td> | ||
+ | <td> | ||
+ | KAN</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | 6</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 35s:5’:Ga20KO:Luc:Tnos</td> | ||
+ | <td> | ||
+ | 3α1</td> | ||
+ | <td> | ||
+ | KAN</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | 7</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 35s:5’:TFLcons:Luc:Tnos</td> | ||
+ | <td> | ||
+ | 3α1</td> | ||
+ | <td> | ||
+ | KAN</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | 8</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 35s:5’:TFLKO:Luc:Tnos</td> | ||
+ | <td> | ||
+ | 3α1</td> | ||
+ | <td> | ||
+ | KAN</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | 9</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 35s:5’:Ga20cons:Luc:Tnos-35s:Ren:Tnos</td> | ||
+ | <td> | ||
+ | 3Ω2</td> | ||
+ | <td> | ||
+ | SPEC</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | 10</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 35s:5’:Ga20KO:Luc:Tnos-35s:Ren:Tnos</td> | ||
+ | <td> | ||
+ | 3Ω2</td> | ||
+ | <td> | ||
+ | SPEC</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | 11</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 35s:5’:Ga20PCR:Luc:Tnos-35s:Ren:Tnos</td> | ||
+ | <td> | ||
+ | 3Ω2</td> | ||
+ | <td> | ||
+ | SPEC</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | 12</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 35s:5’:TFLcons:Luc:Tnos-35s:Ren:Tnos</td> | ||
+ | <td> | ||
+ | 3Ω2</td> | ||
+ | <td> | ||
+ | SPEC</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | 13</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 35s:5’:TFLKO:Luc:Tnos-35s:Ren:Tnos</td> | ||
+ | <td> | ||
+ | 3Ω2</td> | ||
+ | <td> | ||
+ | SPEC</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | 14</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 35s:5’:TFLPCR:Luc:Tnos-35s:Ren:Tnos</td> | ||
+ | <td> | ||
+ | 3Ω2</td> | ||
+ | <td> | ||
+ | SPEC</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | 15</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | U6:Ga20sgRNA:psgRNA</td> | ||
+ | <td> | ||
+ | 3α1</td> | ||
+ | <td> | ||
+ | KAN</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | 16</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | U6:TFLsgRNA:psgRNA</td> | ||
+ | <td> | ||
+ | 3α1</td> | ||
+ | <td> | ||
+ | KAN</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | 17</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 35s:Cas9:Tnos-U6:Ga20gRNA:psgRNA</td> | ||
+ | <td> | ||
+ | 3Ω1</td> | ||
+ | <td> | ||
+ | SPEC</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | 18</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 35s:Cas9:Tnos-U6:TFLgRNA:psgRNA</td> | ||
+ | <td> | ||
+ | 3Ω1</td> | ||
+ | <td> | ||
+ | SPEC</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | 19</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | Ga20PCR</td> | ||
+ | <td> | ||
+ | pUPD2</td> | ||
+ | <td> | ||
+ | CAM</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | 20</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | TFLPCR</td> | ||
+ | <td> | ||
+ | pUPD2</td> | ||
+ | <td> | ||
+ | CAM</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <table class="table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Transform | ||
+ | the | ||
+ | products | ||
+ | of | ||
+ | ligation | ||
+ | in | ||
+ | DH5 | ||
+ | α. | ||
+ | Incubate | ||
+ | it | ||
+ | at | ||
+ | 37^ | ||
+ | during | ||
+ | 2 | ||
+ | hours.</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | We | ||
+ | store | ||
+ | at | ||
+ | -80^:</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <table class="table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Promoter35s</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | pNos</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | TFLKO</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | Ga20KO</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | TFLPCRXT1</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | Ga20PCRXT1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | TFLPCROK</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | Ga20PCROK</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | TFLconsOK</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | Ga20consOK</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <table class="table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | U6:Ga20oxgRNA: | ||
+ | psgRNA | ||
+ | - | ||
+ | 35s: | ||
+ | Cas9: | ||
+ | Tnos | ||
+ | - | ||
+ | Miniprep | ||
+ | number | ||
+ | 2 | ||
+ | was | ||
+ | empty. | ||
+ | We | ||
+ | have | ||
+ | resuspended | ||
+ | it | ||
+ | with | ||
+ | 40 | ||
+ | μL | ||
+ | of | ||
+ | H20 | ||
+ | milliQ | ||
+ | and | ||
+ | we | ||
+ | have | ||
+ | checked | ||
+ | the | ||
+ | DNA | ||
+ | concentration | ||
+ | with | ||
+ | the | ||
+ | Nanodrop. | ||
+ | The | ||
+ | results | ||
+ | show | ||
+ | us | ||
+ | that | ||
+ | the | ||
+ | DNA | ||
+ | concentration | ||
+ | in | ||
+ | the | ||
+ | Eppendorf | ||
+ | was | ||
+ | 140 | ||
+ | ng/ | ||
+ | μL | ||
+ | so | ||
+ | we | ||
+ | have | ||
+ | used | ||
+ | it.</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Miniprep | ||
+ | with | ||
+ | E.Z.N.A | ||
+ | ®.® | ||
+ | Plasmid | ||
+ | Mini | ||
+ | Kit | ||
+ | I, | ||
+ | Q(capless) | ||
+ | Spin | ||
+ | of | ||
+ | 35s: | ||
+ | 5’ | ||
+ | region: | ||
+ | TFL/Ga20oxPCR: | ||
+ | Luc: | ||
+ | Tnos | ||
+ | – | ||
+ | 35s: | ||
+ | Renilla: | ||
+ | Tnos</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Transform | ||
+ | in | ||
+ | C58 | ||
+ | <i> | ||
+ | Agrobacterium</i> | ||
+ | 35s: | ||
+ | Renilla | ||
+ | : | ||
+ | Tnos | ||
+ | (3 | ||
+ | α2)</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Plating | ||
+ | promoter35s: | ||
+ | Renilla: | ||
+ | Tnos | ||
+ | (3α2)</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Luciferase | ||
+ | assay</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <table class="table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | devices</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | Volume | ||
+ | (μL)</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | 35s | ||
+ | : | ||
+ | 5’ | ||
+ | region: | ||
+ | Ga20/TFL | ||
+ | KO: | ||
+ | Luc: | ||
+ | Tnos | ||
+ | - | ||
+ | 35s: | ||
+ | Renilla: | ||
+ | Tnos | ||
+ | - | ||
+ | 35s: | ||
+ | hCas9: | ||
+ | Tnos: | ||
+ | U6: | ||
+ | Ga20/TFL | ||
+ | gRNA: | ||
+ | psgRNA</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | 35s | ||
+ | : | ||
+ | 5’ | ||
+ | region: | ||
+ | Ga20/TFL | ||
+ | cons: | ||
+ | Luc: | ||
+ | Tnos | ||
+ | - | ||
+ | 35s: | ||
+ | Renilla: | ||
+ | Tnos | ||
+ | - | ||
+ | 35s: | ||
+ | hCas9: | ||
+ | Tnos: | ||
+ | U6: | ||
+ | Ga20/TFL | ||
+ | gRNA: | ||
+ | psgRNA</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | 3 | ||
+ | α | ||
+ | 1 | ||
+ | plasmid</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 1.2</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Bsa | ||
+ | 10X</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 1.2</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Buffer | ||
+ | ligase</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Bsa | ||
+ | I</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | T4 | ||
+ | ligase</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | H20 | ||
+ | milliQ</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 4.6</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <table class="table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li> | ||
+ | nfiltration | ||
+ | cultures:</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li> | ||
+ | 5s: | ||
+ | Luc: | ||
+ | Tnos</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | Laboratory | ||
+ | controls</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | </li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | Pnos: | ||
+ | Luc: | ||
+ | Tnos</td> | ||
+ | <td> | ||
+ | Laboratory | ||
+ | controls</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | </li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | gTS | ||
+ | TFL | ||
+ | KO | ||
+ | + | ||
+ | Cas9 | ||
+ | - | ||
+ | XT1:XT2</td> | ||
+ | <td> | ||
+ | Positive | ||
+ | controls</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | </li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | gTSGa20oxKO | ||
+ | + | ||
+ | Cas9 | ||
+ | - | ||
+ | XT1:XT2</td> | ||
+ | <td> | ||
+ | Positive | ||
+ | controls</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | </li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | gTS | ||
+ | TFL | ||
+ | PCR | ||
+ | + | ||
+ | Cas9 | ||
+ | - | ||
+ | XT1:XT2</td> | ||
+ | <td> | ||
+ | Negative | ||
+ | controls</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | </li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | gTS | ||
+ | Ga20oxPCR | ||
+ | + | ||
+ | Cas9 | ||
+ | - | ||
+ | XT1:XT2</td> | ||
+ | <td> | ||
+ | Negative | ||
+ | controls</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | </li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | gTS | ||
+ | TFL | ||
+ | PCR | ||
+ | + | ||
+ | Cas9 | ||
+ | - | ||
+ | TFLgRNA</td> | ||
+ | <td> | ||
+ | Samples</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | </li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | gTS | ||
+ | TFL | ||
+ | cons | ||
+ | + | ||
+ | Cas9 | ||
+ | - | ||
+ | TFLgRNA</td> | ||
+ | <td> | ||
+ | Samples</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | </li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | gTS | ||
+ | Ga20oxPCR | ||
+ | + | ||
+ | Cas9 | ||
+ | - | ||
+ | Ga20gRNA</td> | ||
+ | <td> | ||
+ | Samples</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | </li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | gTS | ||
+ | Ga20oxcons | ||
+ | + | ||
+ | Cas9 | ||
+ | - | ||
+ | Ga20gRNA</td> | ||
+ | <td> | ||
+ | Samples</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Transplant | ||
+ | agroinfiltrated | ||
+ | plants | ||
+ | (<i>Nicotiana | ||
+ | benthamiana</i>)</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Pick | ||
+ | up | ||
+ | 6 | ||
+ | disks | ||
+ | per | ||
+ | each | ||
+ | plant | ||
+ | in | ||
+ | order | ||
+ | to | ||
+ | carry | ||
+ | out | ||
+ | the | ||
+ | luciferase | ||
+ | assay | ||
+ | on | ||
+ | 09/08</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Ligate | ||
+ | reaction | ||
+ | of:</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <table class="table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | device</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | Volume | ||
+ | of | ||
+ | culture | ||
+ | (mL)</td> | ||
+ | <td> | ||
+ | Volume | ||
+ | of | ||
+ | Agroinfiltration | ||
+ | solution | ||
+ | (mL)</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Cas9 | ||
+ | - | ||
+ | TFL | ||
+ | gRNA</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 0.7</td> | ||
+ | <td> | ||
+ | 9.3</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Cas | ||
+ | 9 | ||
+ | - | ||
+ | Ga20oxgRNA</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 0.7</td> | ||
+ | <td> | ||
+ | 9.3</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Cas | ||
+ | 9 | ||
+ | - | ||
+ | XT1: | ||
+ | XT2</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 0.59</td> | ||
+ | <td> | ||
+ | 9.41</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | TFL | ||
+ | KO</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 0.67</td> | ||
+ | <td> | ||
+ | 9.33</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | TFL | ||
+ | PCR</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 0.73</td> | ||
+ | <td> | ||
+ | 9.27</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Ga20oxconsensus</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 0.71</td> | ||
+ | <td> | ||
+ | 9.28</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Pnos</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 0.68</td> | ||
+ | <td> | ||
+ | 9.32</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | 35s | ||
+ | : | ||
+ | Luc</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 0.78</td> | ||
+ | <td> | ||
+ | 9.22</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Ga20oxPCR</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 0.74</td> | ||
+ | <td> | ||
+ | 9.26</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | TFL | ||
+ | consensus</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 0.71</td> | ||
+ | <td> | ||
+ | 9.29</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Ga20ox- | ||
+ | KO</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 0.73</td> | ||
+ | <td> | ||
+ | 9.27</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <table class="table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Miniprep | ||
+ | with | ||
+ | E.Z.N.A | ||
+ | ®.® | ||
+ | Plasmid | ||
+ | Mini | ||
+ | Kit | ||
+ | I, | ||
+ | Q(capless) | ||
+ | Spin | ||
+ | of | ||
+ | TMV | ||
+ | CDS</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Transform | ||
+ | DH5 | ||
+ | α | ||
+ | <i> | ||
+ | E. | ||
+ | coli</i> | ||
+ | with | ||
+ | the | ||
+ | device | ||
+ | 35s | ||
+ | : | ||
+ | 5’ | ||
+ | region: | ||
+ | PCR | ||
+ | PCR: | ||
+ | Luc: | ||
+ | Tnos | ||
+ | - | ||
+ | 35s: | ||
+ | Renilla: | ||
+ | Tnos. | ||
+ | After | ||
+ | incubating | ||
+ | 2 | ||
+ | hours, | ||
+ | it | ||
+ | must | ||
+ | be | ||
+ | plated.</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Refresh | ||
+ | C58 | ||
+ | <i> | ||
+ | <i> | ||
+ | Agrobacterium</i> | ||
+ | tumefaciens</i> | ||
+ | cultures | ||
+ | with | ||
+ | the | ||
+ | aim | ||
+ | of | ||
+ | infiltrating | ||
+ | in | ||
+ | N.benthamiana | ||
+ | on | ||
+ | 05/08.</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Pick | ||
+ | a | ||
+ | single | ||
+ | E. | ||
+ | coli | ||
+ | DH5α | ||
+ | (35S | ||
+ | : | ||
+ | 5’ | ||
+ | region: | ||
+ | KO/cons | ||
+ | target: | ||
+ | Luc:Tnos | ||
+ | - | ||
+ | promoter35s: | ||
+ | renilla: | ||
+ | Tnos) | ||
+ | colony | ||
+ | from | ||
+ | the | ||
+ | plate | ||
+ | that | ||
+ | has | ||
+ | been | ||
+ | incubated | ||
+ | overnight. | ||
+ | Inoculate | ||
+ | a | ||
+ | starter | ||
+ | culture | ||
+ | of | ||
+ | 4 | ||
+ | ml | ||
+ | of | ||
+ | LB | ||
+ | medium | ||
+ | with | ||
+ | 4 | ||
+ | μL | ||
+ | of | ||
+ | spectinomycin | ||
+ | in | ||
+ | a | ||
+ | 50 | ||
+ | ml | ||
+ | tube | ||
+ | with | ||
+ | the | ||
+ | colony | ||
+ | and | ||
+ | incubate | ||
+ | it | ||
+ | overnight | ||
+ | at | ||
+ | 37^ | ||
+ | with | ||
+ | shaking.Sequencing | ||
+ | TMV | ||
+ | empty | ||
+ | vector | ||
+ | with | ||
+ | the | ||
+ | primer | ||
+ | D09OCT01 | ||
+ | (10 | ||
+ | uM). | ||
+ | 5μL | ||
+ | of | ||
+ | Miniprep | ||
+ | and | ||
+ | 9μL | ||
+ | of | ||
+ | primer | ||
+ | (dilution | ||
+ | 1:3). | ||
+ | Sequencing | ||
+ | code | ||
+ | of | ||
+ | 210.13.300 | ||
+ | and | ||
+ | 210.13.301.</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Pick | ||
+ | a | ||
+ | single | ||
+ | E. | ||
+ | coli | ||
+ | DH5α | ||
+ | (promoter35s: | ||
+ | 5’ | ||
+ | region: | ||
+ | TFL/Ga20oxPCR: | ||
+ | Luc: | ||
+ | Tnos | ||
+ | - | ||
+ | promoter35s: | ||
+ | Renilla: | ||
+ | Tnos | ||
+ | ) | ||
+ | colony | ||
+ | from | ||
+ | the | ||
+ | plate | ||
+ | that | ||
+ | has | ||
+ | been | ||
+ | incubated | ||
+ | overnight. | ||
+ | Inoculate | ||
+ | a | ||
+ | starter | ||
+ | culture | ||
+ | of | ||
+ | 4 | ||
+ | ml | ||
+ | of | ||
+ | LB | ||
+ | medium | ||
+ | with | ||
+ | 4 | ||
+ | μL | ||
+ | of | ||
+ | kanamycin | ||
+ | in | ||
+ | a | ||
+ | 50 | ||
+ | ml | ||
+ | tube | ||
+ | with | ||
+ | the | ||
+ | colony | ||
+ | and | ||
+ | incubate | ||
+ | it | ||
+ | overnight | ||
+ | at | ||
+ | 37^ | ||
+ | with | ||
+ | shaking.</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li> | ||
+ | iniprep | ||
+ | with | ||
+ | E.Z.N.A | ||
+ | ®.® | ||
+ | Plasmid | ||
+ | Mini | ||
+ | Kit | ||
+ | I, | ||
+ | Q(capless) | ||
+ | Spin | ||
+ | of:</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li> | ||
+ | 5s: | ||
+ | 5’ | ||
+ | region: | ||
+ | TFL | ||
+ | PCR: | ||
+ | Luc: | ||
+ | Tnos | ||
+ | - | ||
+ | promoter35s: | ||
+ | Renilla: | ||
+ | Tnos</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | </li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 35s: | ||
+ | 5’ | ||
+ | region: | ||
+ | Ga20oxPCR: | ||
+ | Luc: | ||
+ | Tnos | ||
+ | - | ||
+ | promoter35s: | ||
+ | Renilla: | ||
+ | Tnos</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | </li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 35s: | ||
+ | 5’ | ||
+ | region: | ||
+ | Ga20oxconsensus: | ||
+ | Luc: | ||
+ | Tnos | ||
+ | - | ||
+ | promoter35s: | ||
+ | Renilla: | ||
+ | Tnos</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | </li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 35s: | ||
+ | 5’ | ||
+ | region: | ||
+ | Ga20oxKO: | ||
+ | Luc: | ||
+ | Tnos | ||
+ | - | ||
+ | promoter35s: | ||
+ | Renilla: | ||
+ | Tnos</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Digestion | ||
+ | of | ||
+ | minipreps | ||
+ | with | ||
+ | EcoRV. | ||
+ | Incubate | ||
+ | 1 | ||
+ | hour | ||
+ | at | ||
+ | 37^</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Run | ||
+ | electrophoresis | ||
+ | gel | ||
+ | of | ||
+ | the | ||
+ | digestion | ||
+ | products: | ||
+ | TFLK01, | ||
+ | TFLK02, | ||
+ | TFLcons01, | ||
+ | TFLcons02, | ||
+ | GAK01, | ||
+ | GAK02, | ||
+ | GAcons01, | ||
+ | GAcons02.</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Prepare | ||
+ | the | ||
+ | Agroinfiltration | ||
+ | with | ||
+ | the | ||
+ | correct | ||
+ | protocol.</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Centrifuge | ||
+ | the | ||
+ | cultures | ||
+ | at | ||
+ | 3000 | ||
+ | rpm | ||
+ | during | ||
+ | 15 | ||
+ | minutes. | ||
+ | We | ||
+ | discard | ||
+ | the | ||
+ | supernatant | ||
+ | and | ||
+ | it | ||
+ | is | ||
+ | necessary | ||
+ | to | ||
+ | resuspend | ||
+ | in | ||
+ | 5mL | ||
+ | of | ||
+ | Agroinfiltration | ||
+ | solution. | ||
+ | Let | ||
+ | shaking | ||
+ | it | ||
+ | a | ||
+ | RT | ||
+ | during | ||
+ | 2 | ||
+ | hours. | ||
+ | OD’s | ||
+ | measurement</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <table class= | ||
+ | "table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Reagent</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | Volume(μL)</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | 35s:5’region: | ||
+ | TFL/Ga20oxPCR: | ||
+ | Luc: | ||
+ | Tnos</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Promoter35s: | ||
+ | Renilla: | ||
+ | Tnos</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | pUPD2</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | BSA10X</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 1.2</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Ligase | ||
+ | Buffer</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 1.2</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | BsmbI</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | T4 | ||
+ | ligase</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | H<sub>2</sub>O | ||
+ | milli-Q</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 4.6</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <table class= | ||
+ | "table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Ligate | ||
+ | reactions | ||
+ | of | ||
+ | TFL | ||
+ | PCR | ||
+ | and | ||
+ | Ga20ox | ||
+ | PCR | ||
+ | with | ||
+ | Renilla</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <table class= | ||
+ | "table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | 1</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>35S:5’</td> | ||
+ | <td>pUPD2</td> | ||
+ | <td>CAM</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | 2</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | SAGTI:Luc</td> | ||
+ | <td>pUPD2</td> | ||
+ | <td>CAM</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | 3</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 35s:5’:TFLPCR:Luc:Tnos</td> | ||
+ | <td>3α1</td> | ||
+ | <td>KAN</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | 4</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 35s:5’:Ga20PCR:Luc:Tnos</td> | ||
+ | <td>3α1</td> | ||
+ | <td>KAN</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <table class= | ||
+ | "table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li>H5α | ||
+ | <i>E. | ||
+ | coli</i> | ||
+ | transformation | ||
+ | with the | ||
+ | devices:</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li>5S : 5’ | ||
+ | region : | ||
+ | TFL KO : | ||
+ | Luc : Tnos | ||
+ | - | ||
+ | promoter35s: | ||
+ | Renilla:Tnos | ||
+ | in Ω2</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li></li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>35S : 5’ region | ||
+ | : TFL consensus : | ||
+ | Luc : Tnos - | ||
+ | promoter35s: | ||
+ | Renilla:Tnos in | ||
+ | Ω2</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li></li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>35S : 5’ region | ||
+ | : Ga20ox KO : Luc : | ||
+ | Tnos - promoter35s: | ||
+ | Renilla:Tnos in | ||
+ | Ω2</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li></li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>35S : 5’ region | ||
+ | : Ga20ox consensus | ||
+ | : Luc : Tnos - | ||
+ | promoter35s: | ||
+ | Renilla:Tnos in | ||
+ | Ω2</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>E. coli | ||
+ | plating in | ||
+ | plates with | ||
+ | Kanamycin | ||
+ | (antibiotic). | ||
+ | Incubate 16 | ||
+ | hours at | ||
+ | 37^</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li> | ||
+ | inipreps | ||
+ | with | ||
+ | E.Z.N.A ®.® | ||
+ | Plasmid | ||
+ | Mini Kit I, | ||
+ | Q(capless) | ||
+ | Spin | ||
+ | of:</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li> | ||
+ | 5s:5’region:TFL | ||
+ | PCR:Luc:Tnos | ||
+ | in α1</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li></li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td> | ||
+ | 35s:5’region:Ga20oxPCR: | ||
+ | Luc: Tnos in | ||
+ | α1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>Pick a | ||
+ | single E. | ||
+ | coli DH5α | ||
+ | (TMV CDS) | ||
+ | colony from | ||
+ | the plate | ||
+ | that has | ||
+ | been | ||
+ | incubated | ||
+ | overnight. | ||
+ | Inoculate a | ||
+ | starter | ||
+ | culture of | ||
+ | 4 ml of LB | ||
+ | medium with | ||
+ | 4 μL of | ||
+ | kanamycin | ||
+ | in a 50 ml | ||
+ | tube with | ||
+ | the colony | ||
+ | and | ||
+ | incubate it | ||
+ | overnight | ||
+ | at 37^ with | ||
+ | shaking.</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Digestion | ||
+ | of | ||
+ | minipreps | ||
+ | with EcoRI. | ||
+ | Incubate 1 | ||
+ | hour at | ||
+ | 37^</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>Run | ||
+ | electrophoresis | ||
+ | gel of the | ||
+ | devices. We | ||
+ | remain the | ||
+ | samples | ||
+ | 1.</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>Store | ||
+ | at -80^ the | ||
+ | devices of | ||
+ | gTS | ||
+ | PCR</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <table class= | ||
+ | "table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Reagent</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>Volume(μL)</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>TFL | ||
+ | KO/Ga20KO/TFL | ||
+ | cons / | ||
+ | Ga20oxcons</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Promoter35s: | ||
+ | Renilla: | ||
+ | Tnos</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>pUPD2</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>BSA10X</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>1.2</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>Ligase | ||
+ | Buffer</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>1.2</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>BsmbI</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>T4 | ||
+ | ligase</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | H<sub>2</sub>O | ||
+ | milli-Q</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>4.6</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <table class= | ||
+ | "table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li>iniprep with | ||
+ | E.Z.N.A ®.® Plasmid | ||
+ | Mini Kit I, | ||
+ | Q(capless) Spin | ||
+ | of:</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li>5s: TFL PCR : | ||
+ | Luc : Tnos</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li></li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>35s : Ga20ox PCR : Luc | ||
+ | : Tnos</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>Digestion of | ||
+ | minipreps with | ||
+ | EcoRI following | ||
+ | digestion protocol. | ||
+ | Incubate 1 hour at | ||
+ | 37^.</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>Run | ||
+ | electrophoresis gel | ||
+ | of the digestion | ||
+ | products. We will | ||
+ | discard this | ||
+ | culture because the | ||
+ | gel result doesn’t | ||
+ | correspond with | ||
+ | what we | ||
+ | expect.</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li> | ||
+ | Agroinfiltration | ||
+ | procedure with 9 | ||
+ | plants of | ||
+ | N.benthamiana | ||
+ | following the | ||
+ | Agroinfiltration | ||
+ | protocol.</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li></li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>Pick up the | ||
+ | samples of | ||
+ | infiltrated plants. | ||
+ | We keep 3 disks per | ||
+ | plant in a | ||
+ | Eppendorf tube and | ||
+ | we take 2 samples | ||
+ | of each plant.</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>Luciferase | ||
+ | assay is made | ||
+ | following the | ||
+ | correct protocol. | ||
+ | After analyzing all | ||
+ | the data obtained, | ||
+ | it seems that the | ||
+ | system works but we | ||
+ | must optimized it | ||
+ | to increase the | ||
+ | signal range. In | ||
+ | this way, we will | ||
+ | be able to | ||
+ | distinguish signal | ||
+ | from noise.</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li>onclusions | ||
+ | luciferase | ||
+ | assay:</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li>liminate 5’ | ||
+ | region of the | ||
+ | device</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li></li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>Change linker | ||
+ | sequence</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li></li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>Add renilla in | ||
+ | luciferase assay</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li></li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>Change reporter to | ||
+ | +1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li></li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>Use pLess as | ||
+ | control</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li></li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>Use a Wild Type as | ||
+ | control</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li></li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>Insert devices in | ||
+ | cis</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li></li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>Design a consensus | ||
+ | target as longer as the | ||
+ | amplified.</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>Culture refresh | ||
+ | of C58 | ||
+ | <i>Agrobacterium</i> | ||
+ | to infiltrate on | ||
+ | Friday.</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>Pick a single | ||
+ | E. coli DH5α | ||
+ | (35s:5’region:TFL | ||
+ | PCR:Luc:Tnos in α1 | ||
+ | and | ||
+ | 35s:5’region:Ga20oxPCR: | ||
+ | Luc: Tnos in α1) | ||
+ | colony from the | ||
+ | plate that has been | ||
+ | incubated | ||
+ | overnight. | ||
+ | Inoculate a starter | ||
+ | culture of 4 ml of | ||
+ | LB medium with 4 μL | ||
+ | of kanamycin in a | ||
+ | 50 ml tube with the | ||
+ | colony and incubate | ||
+ | it overnight at 37^ | ||
+ | with shaking.</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>Targets | ||
+ | ligations with | ||
+ | Renilla | ||
+ | reporters.</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <table class= | ||
+ | "table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>Device</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>Order</td> | ||
+ | <td>Sequencing</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>TFL PCR</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>210.13.250</td> | ||
+ | <td>SNP in the position 652 of | ||
+ | the target. Position 1 of the | ||
+ | gRNA. GA</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>Ga20ox PCR</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>210.13.253</td> | ||
+ | <td>Same sequence</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>TFL consensus</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>210.13.251</td> | ||
+ | <td>Same sequence</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>TFL KO</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>210.13.252</td> | ||
+ | <td>Same sequence</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>Ga20ox | ||
+ | Consensus</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>210.13.254</td> | ||
+ | <td>Same sequence</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>Ga20ox KO</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>210.13.255</td> | ||
+ | <td>Same sequence</td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <table class= | ||
+ | "table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>Received the necessary | ||
+ | primers to sequence: TFL | ||
+ | consensus, TFL knockout, | ||
+ | Ga20ox consensus and Ga20ox | ||
+ | knockout.</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li>repare | ||
+ | <i>Agrobacterium</i> | ||
+ | cultures: Inoculate a | ||
+ | starter culture of 5 ml of | ||
+ | LB medium with 5 μL of | ||
+ | Kanamycin and 5 μL of | ||
+ | rifampin in a 50 ml tube | ||
+ | with the colony and | ||
+ | incubate it 48 hours at 28^ | ||
+ | with shaking. The devices | ||
+ | are:</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <p></p> | ||
+ | <ul> | ||
+ | <li>5S : 5’Region : TFL | ||
+ | consensus : Luc : Tnos</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li></li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>35S : 5’Region : TFL knockout : | ||
+ | Luc : Tnos</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li></li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>35S : 5’Region :TFL PCR: Luc : | ||
+ | Tnos</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li></li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>35S : 5’Region : Ga20ox | ||
+ | consensus : Luc : Tnos</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li></li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>35S : 5’Region : Ga20ox | ||
+ | knockout : Luc : Tnos</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li></li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>35S : 5’Region :Ga20ox PCR: Luc | ||
+ | : Tnos</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>Sequencing the last | ||
+ | devices to check if these | ||
+ | are correct.</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li></li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>Refresh | ||
+ | <i><i>Agrobacterium</i> | ||
+ | tumefaciens</i> cultures | ||
+ | with the aim of | ||
+ | infiltrating in | ||
+ | N.benthamiana on 29/07</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>Refresh cultures of the | ||
+ | devices 35s: 5’ region: TFL | ||
+ | PCR : Luc : Tnos and 35s : | ||
+ | 5’ region: Ga20ox PCR : Luc | ||
+ | : Tnos in order to prepare | ||
+ | the more Miniprep | ||
+ | reaction.</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>Sequencing results have | ||
+ | arrived.</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | <table class= | ||
+ | "table table-bordered table-striped"> | ||
+ | <tr> | ||
+ | <th> | ||
+ | <ul> | ||
+ | <li>Lanes</li> | ||
+ | </ul> | ||
+ | </th> | ||
+ | <th>Samples</th> | ||
+ | <th>Verification</th> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>1</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>1 Kb molecular weight marker</td> | ||
+ | <td></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>2</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>TFL PCR</td> | ||
+ | <td></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td> | ||
+ | <ul> | ||
+ | <li>3</li> | ||
+ | </ul> | ||
+ | </td> | ||
+ | <td>Ga20ox PCR</td> | ||
+ | <td></td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
+ | </li> | ||
+ | </ul> | ||
+ | </div> | ||
+ | </div> | ||
+ | </div> | ||
+ | </section> | ||
</body> | </body> | ||
+ | |||
</html> | </html> | ||
{{:Team:Valencia_UPV/Templates:footerUPV}} | {{:Team:Valencia_UPV/Templates:footerUPV}} |
Revision as of 18:21, 1 October 2016
- May 18, 2016
Take glycerinated cultures of C58 Agrobacterium
with dsRED from GoldenBraid Collection. Prepare broth
culture (5 mL LB + 5 μL kanamycin + 5 μL Rifampin) 1:1000
and incubate overnight at 28^C.
- May 19, 2016
Refresh previously made culture by inoculating 10 μL in
a new culture medium.
- May 20, 2016
Agroinfiltration in Nicotiana benthamiana of C58
with dsRED. href
- June 06, 2016
- Take from the glycerinates of Goldenbraid Collection:
Plasmid | GB Code |
---|---|
pD6B3 α1 | GB0015 |
pD6B3 α2 | GB0017 |
pD6B3 Ω1 | GB0019 |
pD6B3 Ω2 | GB0021 |
pUPD2 | GB0307 |
Prepare liquid culture (3 mL LB + 3 μL antibiotic)
1:1000. Incubate at 37^C overnight.
- Experiment with snails:
-
- Two experiments: one with infiltrated Nicotiana benthamiana and another with not infiltrated N.benthamiana (negative control). Lettuce leafs haven’t been correctly infiltrated and it seems that the expression level is low.
- Let both N. benthamiana leafs with snails overnight at room temperature in separated boxes. We will observe if snails eat the leafs and if appears fluorescence.
- June 15, 2016
Experiment is over due to snails haven’t eaten leafs
enough so we have not been able to see
fluorescence.
- June 30, 2016
Orange Clemenules DNA Genome Extraction protocol
- Take from the glycerinates of GoldenBraid Collection:
Plasmid | GB Code |
---|---|
35s:Cas9:nopaline synthase terminator (Tnos) | GB0639 |
Luciferase (Luc) in pUPD2 | GB0096 |
Tnos in pUPD2 | GB0037 |
- July 01, 2016
Miniprep of 35s:Cas9:Tnos with E.Z.N.A ®. Plasmid Mini
Kit I, Q(capless) Spin.
Luciferase and nopaline synthase terminator cultures
haven’t succeed. Repeat Luc and Tnos cultures.
Primers IG16JUN01 and IG16JUN02 have arrived.
Finish orange DNA Genome Extraction and check DNA
concentration with NanoDrop. Concentration is very low so
extraction will be done again.
- July 02, 2016
- Miniprep with E.Z.N.A ®. Plasmid Mini Kit I, Q(capless) Spin of:
-
- Luc in pUPD2
- Tnos in pUPD2
Check orange DNA genome concentration with
NanoDrop.
Sample | DNA concentration (ng / μL) |
---|---|
TFL 1 | 3153.8 |
TFL 2 | 4527.9 |
Perform a PCR to bind linker SAGTI with luciferase:
Reagent | Volume(μL) | Program | ||
---|---|---|---|---|
LuciferasepUPD | 1 | Temperature | Time | |
Buffer HF | 10 | 98^C | 5 minutes | |
dNTPs | 2 | 98^C | 35x | 30 seconds |
IG16JUN01 | 2.5 | 70^C | 35x | 30 seconds |
IG16JUN02 | 2.5 | 72^C | 35x | 1 minute 30 seconds |
Taq phusion | 0.5 | 72^C | 10 minutes | |
H2O milli-Q | 31.5 | 16^C | ∞ |
- July 04, 2016
Run electrophoresis gel of Clemenules DNA (agarose 1%).
45 mL agarose gel at 1% 0.45 g of agarose with 45 mL of TAE
1X. Voltage used is 100 V.
Gleva Rice DNA Genome Extraction Protocol
Run electrophoresis gel of Luciferase PCR product. 45 mL
agarose gel at 1% 0.45 g of agarose with 45 mL of TAE 1X.
Voltage used is 100 V.
Ligation Reaction of SAGTI:Luciferase into a pUPD2.
Transform E. coli DH5α with it. The method that is
necessary to carry out this procedure is explained in
protocols href
Check DNA concentration with NanoDrop.
SAMPLE | DNA Concentration(ng / μL) |
---|---|
Rice Gleva 1 | 22.8 |
Rice Gleva 2 | 17.3 |
- July 05, 2016
Run electrophoresis gel of Gleva rice DNA. We have
checked that there isn’t DNA.
Repeat: Rice DNA Genome Extraction Protocol
Check DNA concentration with NanoDrop.
SAMPLE | DNA Concentration(ng / μL) |
---|---|
Rice Gleva 1 | 294.9 |
Rice Gleva 2 | 193.7 |
Run electrophoresis gel of Gleva rice DNA. It observed
that genome extraction is correctly done.
- July 06, 2016
Take glycerinated cultures from Goldenbraid
Collection:
GB part | Plasmid | Antibiotic | Number GB |
---|---|---|---|
psgRNA | pUPD | Ampicillin | 0645 |
U6-26 | pUPD | Ampicillin | 1001 |
- July 07, 2016
- Miniprep with E.Z.N.A ®. Plasmid Mini Kit I, Q(capless) Spin of:
-
- psgRNA in pUPD2
- U6-26 in pUPD2
Primers IG16JUL01, IG16JUL02, IG16JUL03, IG16JUL04,
IG16JUL05, IG16JUL06, IG16JUL07 and IG16JUL08 arrived.
gBlocks of - 35s:5’ region - have arrived.
We perform a PCR of Clemenules Orange and Gleva Rice Genome
Extraction following the protocol.
We want to obtain a fragment of the gene TFL of the orange
DNA extraction and the gene Ga20ox of the rice DNA
extraction.
Sample | Initial concentration(ng/μL) | Final concentration(ng/μL) | Initial volume(μL) | Final volume (μL) |
---|---|---|---|---|
TFL 1 | 3153.8 | 150 | 4.756 | 100 |
TFL 2 | 4527.9 | 150 | 3.31 | 100 |
Ga20ox 1 | 294.9 | 150 | 50.8647 | 100 |
Ga20ox 2 | 193.7 | 150 | 77.44 | 100 |
REAGENT | VOLUME(μL) | PROGRAM | ||
---|---|---|---|---|
TFL DNA 1 | TEMPERATURE | TIME | ||
Buffer HF | 10 | 98^C | 5 minutes | |
dNTPs | 2 | 98^C | 35x | 30 seconds |
IG16JUL01 (TFL_For) | 2.5 | 64^C | 35x | 30 seconds |
IG16JUL02 (TFL_Rev) | 2.5 | 72^C | 35x | 30 seconds |
Taq phusion | 0.5 | 72^C | 10 minutes | |
H2O milli-Q | 31.5 | 16^C | ∞ |
REAGENT | VOLUME(μL) | PROGRAM | ||
---|---|---|---|---|
Ga20ox DNA | 1 | TEMPERATURE | TIME | |
Buffer HF | 10 | 98^C | 5 minutes | |
dNTPs | 2 | 98^C | 35x | 30 seconds |
IG16JUL03 (Ga20_for) | 2.5 | 72^C | 35x | 30 seconds |
IG16JUL02 (Ga20_rev) | 2.5 | 72^C | 35x | 30 seconds |
Taq phusion | 0.5 | 72^C | 10 minutes | |
H2O milli-Q | 31.5 | 16^C | ∞ |
Ligate reaction of 35s:5’ region in pUPD2. Following
ligation
protocol, BsmbI enzyme is used in this reaction.
- July 08, 2016
Run electrophoresis gel of TFL and Ga20ox PCR products.
45 mL agarose gel at 1 % 0.45 g of agarose with 45 mL of
TAE 1X. Voltage used is 120 V.
Transform E. coli with the next part: 35s:5’ region
(electroporation 2.5KV). Plating it and incubate overnight
at 37^C.
Take glycerinated culture for Georgia collaboration. The
part is 35s:GFP:Tnos (α1 and kanamycin).
- July 09, 2016
Miniprep with E.Z.N.A ®. Plasmid Mini Kit I, Q(capless)
Spin of 35s:GFP:Tnos
No colonies have grown in the 35s:5’ region petri dishes.
Repeat transformation procedure, plating again and incubate
overnight at 37^C.
- July 11, 2016
Pick a single E. coli DH5α (35s:5’ region in pUPD2)
colony from the plate that has been incubated overnight.
Inoculate a starter culture of 4 ml of LB medium with 4 μL
of chloramphenicol in a 50 ml tube with the colony and
incubate it overnight at 37^C with shaking.
Check Georgia miniprep concentration with NanoDrop
(35s:GFP:Tnos)
Sample | DNA Concentration(ng / μL) | DNA Concentration(ng) |
---|---|---|
1 | 105.2 | 5035.2 |
2 | 104.6 | 5035.2 |
Targets ligations in pUPD2 (Orange TFL and Rice Ga20ox).
Following ligation
protocol, BsmbI enzyme is used in this reaction.
- July 12, 2016
Pick a single E. coli DH5α (target Ga20ox in pUPD2 and
target TFL in pUPD2) colony from the plate that has been
incubated overnight. Inoculate a starter culture of 4 ml of
LB medium with 4 μL of chloramphenicol in a 50 ml tube with
the colony and incubate it 16 hours at 37^C.
Miniprep with E.Z.N.A ®. Plasmid Mini Kit I, Q(capless)
Spin of 35s:5’region in pUPD2
Digestion of minipreps with NotI. Incubate 1 hour at
37^C
Run electrophoresis gel of the following part: 35s:5’
region in pUPD2. We remain the samples 1 and 3.
- Miniprep with E.Z.N.A ®. Plasmid Mini Kit I, Q(capless) Spin of:
-
- Ga20ox PCR in pUPD2
- TFL PCR in pUPD2
Digestion of minipreps with NotI. Incubate 1 hour at
37^C.
- Run electrophoresis gel of the same part:
-
- Ga20ox PCR in pUPD2
- TFL PCR in pUPD2
Ligation using Golden Braid assembly of the device
35s:5’region:TFL PCR:Luc:Tnos and
35s:5’region:Ga20oxPCR:Luc:Tnos in α1 plasmid.
- July 13, 2016
E. coli Transformation with the device
35s:5’region:TFL PCR:Luc:Tnos and
35s:5’region:Ga20oxPCR:Luc:Tnos in α1 plasmid.
E. coli plating in plates with Kanamycin (antibiotic).
Incubate overnight at 37^C
- July 14, 2016
Pick a single E. coli DH5α (35s:5’ region) colony from
the plate that has been incubated overnight. Inoculate a
starter culture of 4 ml of LB medium with 4 μL of
chloramphenicol in a 50 ml tube with the colony and
incubate it 16 hours at 37^C.
Primers IG16JUL09, IG16JUL10, IG16JUL11, IG16JUL12,
IG16JUL13, IG16JUL14, IG16JUL15 and IG16JUL16
arrived.
- Ligation using Golden Braid assembly of the next devices:
-
- 35s:5’ region:TFL PCR control positive:Luc:Tnos
- 35s:5’ region:Ga20oxPCR control positive:Luc:Tnos
- 35s:5’ region:TFL PCR consensus:Luc:Tnos
- 35s:5’ region:Ga20ox PCR consensus:Luc:Tnos
- U6-26:sgRNA TFL: psgRNA (scaffold)
- U6-26:sgRNA Ga20ox: psgRNA (scaffold)
- Step 1: Annealing of oligonucleotides. Received primers are at 1uM. It is necessary taking to 10 uM.
-
- Mix in an Eppendorf:
-
- 8 μL of H2O milli-Q
- 1 μL forward primer
- 1 μL reverse primer
- Step 2: Ligation reaction
Reagent | Volume (μL) |
---|---|
TFL target control + / Ga20ox target control + / TFL target consensus / Ga20ox target consensus | 1 |
35s:5’ region | 1 |
Luciferase | 1 |
Tnos | 1 |
α1 plasmid | 1 |
BSA10X | 1.2 |
Ligase Buffer | 1.2 |
BsaI | 1 |
T4 ligase | 1 |
H2O milli-Q | 2.6 |
Reagent | Volume (μL) |
---|---|
sgRNA TFL / sgRNA Ga20ox | 1 |
U6 -26 | 1 |
psgRNA (scaffold) | 1 |
α1 plasmid | 1 |
BSA10X | 1.2 |
Ligase Buffer | 1.2 |
BsaI | 1 |
T4 ligase | 1 |
H2O milli-Q | 3.6 |
E. coli Transformation with the devices previously
explained.
E. coli plating in 6 plates (6 ligation reactions) with
Kanamycin (antibiotic). Incubate overnight at 37^C.
- Miniprep with E.Z.N.A ®. Plasmid Mini Kit I, Q(capless) Spin of:
-
- 35s:5’ region : TFL PCR : Luc : Tnos (3α1)
- 35s:5’ region : Ga20ox PCR : Luc : Tnos (3α1)
Digestion of minipreps with EcoRI. Incubate 1 hour at
37^C
- July 15, 2016
- Ligation using Golden Braid assembly of the next devices:
-
- 35s:Cas9:Tnos – 35s:5’ region:TFL PCR:Luc:Tnos
- 35s:Cas9:Tnos – 35s:5’ region:Ga20ox PCR:Luc:Tnos
E. coli Transformation with the devices previously
explained.
- Run an electrophoresis gel of the products from the digestion of minipreps. The devices are:
-
- 35s:5’ region:TFL PCR:Luc:Tnos (3α1)
- 35s:5’ region :Ga20ox PCR:Luc:Tnos (3α1)
Sequencing 35s:5’region in pUPD2 → correct
- July 16, 2016
- Transformations in E. coli DH5α with:
-
- 35s:5’ region:TFL PCR:Luc:Tnos (3α1)
- 35s:5’ region:Ga20ox PCR:Luc:Tnos (3α1)
Plating the last devices in 2 plates with
Agrobacterium C58. Incubate 2 days at 28^C.
- Minipreps (2 samples for each device) with E.Z.N.A ®. Plasmid Mini Kit I, Q(capless) Spin of:
-
- 35s:5’ region:TFL target control positive:Luc:Tnos
- 35s:5’ region:Ga20ox target control positive:Luc:Tnos
- 35s:5’ region:TFL target consensus:Luc:Tnos
- 35s:5’ region:Ga20ox target consensus:Luc:Tnos
- U6-26:sgRNA TFL:psgRNA (scaffold)
- U6-26:sgRNA Ga20ox:psgRNA (scaffold)
- Ligation using Golden Braid assembly of the next devices:
-
- 35s:Cas9:Tnos – U6:TFL sgRNA:psgRNA (scaffold) (Ω1)
- 35s:Cas9:Tnos – U6: Ga20ox sgRNA:psgRNA (scaffold) (Ω1)
Reagent | Volume (μL) |
---|---|
Promotor 35s:Cas9 : Tnos | 1 |
U6-26:TFL sgRNA:psgRNA / U6-26:Ga20ox sgRNA:psgRNA | 1 |
3Ω1 | 1 |
BSA10X | 1.2 |
Ligase Buffer | 1.2 |
BsmbI | 1 |
T4 ligase | 1 |
H2O milli-Q | 4.6 |
Digestion of the minipreps with EcoRI which have been
done before. Incubate 1 hour at 37^C. There is a total of
twelve minipreps. It has been followed the Miniprep
{digestion protocol
path:https://2016.igem.org/Team:Valencia_UPV/Notebook/Protocol].
Run electrophoresis gel of the digestion products.
Lanes | Samples | Verification |
---|---|---|
1 | 1 Kb molecular weight marker | correct |
2 | gRNA Ga20ox 1 | correct |
3 | gRNA Ga20ox 2 | correct |
4 | Ga20ox consensus 1 | correct |
5 | Ga20ox consensus 2 | correct |
6 | Ga20ox knock-out 1 | - |
7 | Ga20ox knock-out 2 | correct |
8 | TFL consensus 1 | - |
9 | TFL consensus 2 | - |
10 | TFL knock-out 1 | correct |
11 | TFL knock-out 2 | correct |
12 | TFL gRNA 1 | correct |
13 | TFL gRNA 2 | correct |
14 | 1 Kb molecular weight marker | correct |
- Pick a single E. coli DH5α colony from the plates that have been incubated overnight. The devices are:
-
- 35s:TFL Knock-out:Luc:Tnos (4 samples)
- U6-26:Ga20ox sgRNA:psgRNA (2 samples)
Inoculate a starter culture of 4 ml of LB medium with 4
μL of kanamycin in a 50 ml tube with the colony and
incubate it 16 hours at 37^C.
- July 17, 2016
- Transformation in DH5α E. coli with:
-
- 35s:Cas9:Tnos – U6:TFL sgRNA:psgRNA (scaffold) (Ω1)
- 35s:Cas9:Tnos – U6:Ga20ox sgRNA:psgRNA (scaffold) (Ω1)
Plating E. coli transformations in plates with LB
+ agar + IPTG + XGal and incubate it overnight at
37^C.
- Miniprep with E.Z.N.A ®. Plasmid Mini Kit I, Q(capless) Spin of:
-
- U6-26:Ga20ox sgRNA:psgRNA
- 35s:5’ region:TFL Knock-out:Luc:Tnos (3α1)
Digestion of the minipreps with EcoRI which have been
done before. Incubate 1 hour at 37^C. There is a total of
six minipreps. It has been followed the Miniprep digestion
protocol href.
Run an electrophoresis gel of the digestion
products.
Lanes | Samples | Verification |
---|---|---|
1 | 1 Kb molecular weight marker | |
2 | gRNA Ga20ox 1 | correct |
3 | gRNA Ga20ox 2 | correct |
4 | gRNA Ga20ox 3 | correct |
5 | gRNA Ga20ox 4 | correct |
6 | TFL knock-out 1 | correct |
7 | TFL knock-out 2 | correct |
8 | 1 Kb molecular weight marker | correct |
However, despite the fact that electrophoresis gel have
correctly run, we have decided to repeat the ligation
reactions. We have not get the expected results for a
gRNA.
- Ligation using Golden Braid assembly of the next devices:
-
- 35s:5’ region:TFL target control positive:Luc:Tnos
- 35s:5’ region:Ga20ox target control positive:Luc:Tnos
- 35s:5’ region:TFL target consensus:Luc:Tnos
- 35s:5’ region:Ga20ox target consensus:Luc:Tnos
- U6-26:sgRNA TFL:psgRNA (scaffold)
- U6-26:sgRNA Ga20ox:psgRNA (scaffold)
Reagent | Volume(μL) | Reagent | Volume(μL) |
---|---|---|---|
TFL/Ga20ox gRNA | 1 | 35s:5’region | 1 |
U6-26 | 1 | TFL/Ga20ox consensus TFL/Ga20ox knock-out | 1 |
psgRNA | 1 | luciferase | 1 |
3α1 | 1 | Tnos | 1 |
BSA10X | 1.2 | 3α1 | 1 |
Ligase Buffer | 1.2 | BSA10X | 1.2 |
BsaI | 1 | Ligase Buffer | 1.2 |
T4 ligase | 1 | BsmbI | 1 |
H2O milli-Q | 3.6 | T4 ligase | 1 |
H2O milli-Q | 2.6 |
- July 18, 2016
Transformation in DH5α E. coli with ligation
products (consensus targets and knock-out targets of TFL
and Ga20ox as well as their gRNAs)
Plating E. coli transformations in plates with LB +
agar + IPTG + XGal and incubate it overnight at
37^C.
- Pick a single Agrobacterium C58 colony from the plates that have been incubating since 16/06/2016. The devices are:
-
- 35s:5’ region:TFL PCR:Luc:Tnos (3α1)
- 35s:5’ region:Ga20ox PCR:Luc:Tnos (3α1)
Incubate it 48 hours at 28^C.
- July 19, 2016
- Pick transformed E. coli colony from the incubated plates. The devices are:
-
- 35s:5’ region:TFL target control positive:Luc:Tnos
- 35s:5’ region:Ga20ox target control positive:Luc:Tnos
- 35s:5’ region:TFL target consensus:Luc:Tnos
- 35s:5’ region:Ga20ox target consensus:Luc:Tnos
- U6-26: sgRNA TFL:psgRNA (scaffold)
- U6-26: sgRNA Ga20ox:psgRNA (scaffold)
Incubate it overnight at 37^C.
- July 20, 2016
- Miniprep with E.Z.N.A ®. Plasmid Mini Kit I, Q(capless) Spin of:
-
- 35s:5’ region:TFL target knock-out:Luc:Tnos
- 35s:5’ region:Ga20ox target control knock-out:Luc:Tnos
- 35s:5’ region:TFL target consensus:Luc:Tnos
- 35s:5’ region:Ga20ox target consensus:Luc:Tnos
- U6-26:sgRNA TFL:psgRNA (scaffold)
- U6-26:sgRNA Ga20ox:psgRNA (scaffold)
Digestion of the minipreps with EcoRI which have been
done before. Incubate 1 hour at 37^C. There is a total of
six minipreps. It has been followed the Miniprep {digestion
protocol
path:https://2016.igem.org/Team:Valencia_UPV/Notebook/Protocol].
Run an electrophoresis gel of the digestion products. We
will keep the minipreps with “1”.
Lanes | Samples | Verification |
---|---|---|
1 | 1 Kb molecular weight marker | correct |
2 | gRNA TFL 1 | correct |
3 | gRNA TFL 2 | correct |
4 | TFL consensus 1 | correct |
5 | TFL consensus 2 | correct |
6 | TFL knock-out 1 | correct |
7 | TFL knock-out 2 | correct |
8 | 1 Kb molecular weight marker | correct |
9 | gRNA Ga20ox 1 | correct |
10 | gRNA Ga20ox 2 | correct |
11 | Ga20ox consensus 1 | correct |
12 | Ga20ox consensus 2 | - |
13 | Ga20ox knock-out 1 | correct |
14 | Ga20ox knock-out 2 | correct |
15 | 1 Kb molecular weight marker | correct |
- Ligation using Golden Braid assembly of the next devices. Is used the restriction enzyme BsmbI.
-
- 35s:Cas 9:Tnos – U6-26:TFL sgRNA:psgRNA
- 35s:Cas 9:Tnos – U6-26:Ga20ox sgRNA:psgRNA
- July 21, 2016
- Transformations in E. coli DH5α with:
-
- 35s:Cas 9:Tnos – U6-26:TFL sgRNA:psgRNA
- 35s:Cas 9:Tnos – U6-26:Ga20ox sgRNA:psgRNA
Incubate 2 hours at 37^C.
Plating E. coli transformation explained before and
incubate it at 37^C overnight.
#Agrobacterium C58 transformation with:
- #35s:5’ region:TFL target knock-out:Luc:Tnos
- 35s:5’ region:Ga20ox target control knock-out:Luc:Tnos
- 35s:5’ region:TFL target consensus:Luc:Tnos
- 35s:5’ region:Ga20ox target consensus:Luc:Tnos
Incubate 48 hours at 28^C.
- July 22, 2016
Sequencing reaction:
Reagent | Volume (μL) |
---|---|
Primer in order to sequence | 3 |
Miniprep reaction | 5 |
H2O milli-Q | 6 |
Sequence | Order |
---|---|
TFL gRNA | 210.13.201 |
Ga20oxgRNA | 210.13.202 |
Ordered the necessary primers to sequence: TFL
consensus, TFL knockout, Ga20ox consensus and Ga20ox
knockout.
E. coli transformations with 35s:Cas 9:Tnos –
U6-26:TFL sgRNA: psgRNA
Plating the last device in plates with Agrobacterium
C58. Plates contain spec + IPTG + X-Gal. Incubate 2 days at
28^C.
Pick a single E. coli DH5α (35s:Cas 9:Tnos –
U6-26:TFL sgRNA:psgRNA and 35s:Cas 9:Tnos – U6-26:Ga20ox
sgRNA:psgRNA) colony from the plates that has been
incubated overnight. Inoculate a starter culture of 4 ml of
LB medium with 4 μL of spectinomycin in a 50 ml tube with
the colony and incubate it overnight at 37^C with
shaking.
- July 23, 2016
- #Minipreps (4 samples for each device) with E.Z.N.A ®. Plasmid Mini Kit I, Q(capless) Spin of:
-
- #35s:Cas 9:Tnos – U6-26:TFL sgRNA:psgRNA
- 35s:Cas 9:Tnos – U6-26:Ga20ox sgRNA:psgRNA
Run an electrophoresis gel of the digestion products. We will keep the minipreps with the sample number 4 for TFL sgRNA and the sample number 2 for Ga20ox sgRNA.
Pick a single Agrobacterium C58 (35s:Cas 9:Tnos – U6-26:TFL sgRNA:psgRNA and 35s:Cas 9:Tnos – U6-26:Ga20ox sgRNA:psgRNA ) colony from the plates that has been incubated overnight. Inoculate a starter culture of 5 ml of LB medium with 5 μL of spectinomycin and kanamycin in a falcon tube with the colony and incubate it overnight at 28^C with shaking.
#Agrobacterium C58 transformations with:
- #35s:Cas 9:Tnos – U6-26:TFL sgRNA:psgRNA
- 35s:Cas 9:Tnos –
U6-26:Ga20ox sgRNA:psgRNA
- July 24, 2016
- #Store the next cultures at -80^C:
-
- #35s:5’ region in pUPD2 (DH5α) number 1
-
- #SAGTI: luciferase in pUPD2 (DH5α) number 2
- July 25, 2016
- Pick a single Agrobacterium C58 (35s:Cas 9:Tnos – U6-26:TFL sgRNA:psgRNA in 3Ω1 and 35s:Cas 9:Tnos – U6-26:Ga20ox sgRNA:psgRNA in 3Ω1 ) colony from the plates that has been incubated overnight. Inoculate a starter culture of 5 ml of LB medium with 5 μL of spectinomycin and kanamycin in a falcon tube with the colony and incubate it overnight at 28^C with shaking.
- Incubate it 48 hours at 28^C
-
- inipreps of Agrobacterium with E.Z.N.A ®. Plasmid Mini Kit I, Q(capless) Spin of:
-
- 5s:5’ region:TFL target control positive:Luc:Tnos
- 35s:5’ region:Ga20ox target control positive:Luc:Tnos
- 35s:5’ region:TFL target consensus:Luc:Tnos
- 35s:5’ region:Ga20ox target consensus:Luc:Tnos
- Digestion of minipreps with the restriction enzyme EcoRI. Incubate 1 hour at 37^C.
- Run an electrophoresis gel of the digestion products.
-
- Lanes
Samples Verification - 1
1 Kb molecular weight marker correct - 2
Target Ga20ox consensus correct - 3
Target Ga20ox Knock-out correct - 4
Target TFL consensus correct - 5
Target TFL knock-out correct - 6
1 Kb molecular weight marker correct
- July 26, 2016
- inipreps with E.Z.N.A ®. Plasmid Mini Kit I, Q(capless) Spin of:
-
- 5s:5’ region:TFL PCR:Luc:Tnos in 3α1 plasmid from C58 Agrobacterium
- 35s:5’ region:Ga20ox PCR:Luc:Tnos in 3α1 plasmid from C58 Agrobacterium
- Digestion of minipreps with the restriction enzyme EcoRI. Incubate 1 hour at 37^C.
- Run an electrophoresis gel of the digestion products:
-
- Lanes
Samples Verification - 1
1 Kb molecular weight marker correct - 2
35s:5’ region:PCR Ga20ox :Luc:Tnos correct - 3
35s:5’ region:PCR TFL Clemunules:Luc:Tnos correct - 6
1 Kb molecular weight marker correct
- July 26, 2016
- equencing products have arrived:
-
- 6-26:Ga20ox gRNA:psgRNA in α1 - correct
- U6-26:TFL gRNA:psgRNA in α1 - correct
- inipreps with E.Z.N.A ®.® Plasmid Mini Kit I, Q(capless) Spin of:
-
- 5s:5’ region: Ga20ox PCR : Luc : Tnos in α1
- 35s:5’ region: TFL PCR : Luc : Tnos in α1
- Digestion of minipreps with the restriction enzyme EcoRI. Incubate 1 hour at 37^.
- Run electrophoresis gel of the digestion products.
-
27Jul
- July 27, 2016
28Jul- July 28, 2016
29Jul- July 29, 2016
01Aug- August 01, 2016
02Aug- August 02, 2016
03Aug- August 03, 2016
04Aug- August 04, 2016
05Aug- August 05, 2016
08Aug- August 08, 2016
09Aug- August 09, 2016
10Aug- August 10, 2016
- devices
Volume (μL) - gTS TFL/ Ga20ox- Renilla
1 - Cas9 - gRNA
1 - 3 α 1 plasmid
1.2 - Bsa 10x
1.2 - Buffer ligase
1 - Bsa I
1 - T4 ligase
1 - H20 milliQ
4.6 - Run electrophoresis gel of: 35s: 5’ region: TFL/Ga20oxPCR: Luc: Tnos – 35s: Renilla: Tnos. We keep the Miniprep number 1.
- Refresh the cultures of TFL PCR (pUPD2) and Ga20oxPCR (pUPD2) because we suspect that these cultures are the correct ones but we are not sure so we want to check them. The cultures that we use to refresh were made on 12/07/2016. It is important to remember that we need them to assemble the gTS with the new linkers.
- Miniprep with E.Z.N.A ®.® Plasmid Mini Kit I, Q(capless) Spin of TFL / Ga20oxPCR in pUPD2
- Digestion of minipreps with NotI. Incubate 1 hour at 37^
- Run electrophoresis gel of Miniprep products. We have made a small gel so we have mix 0.45 g of Agarose with 45 mL of TAE 1X. Voltage used is 100V. Both samples are correct.
- Pick a single E. coli DH5α (promoter35s: 5’ region: TFL/Ga20oxcons: Tnos - promoter35s: Renilla: Tnos - 35s: Cas9: Tnos - U6: TFL/Ga20oxgRNA: psgRNA) colony from the plate that has been incubated overnight. Inoculate a starter culture of 4 ml of LB medium with 4 μL of chloramphenicol in a 50 ml tube with the colony and incubate it overnight at 37^ with shaking.
- We throw out from Golden Braid collection the glycerinate number 1107 (Cas9 - XT1gRNA) and 0549 (35s: TEV: Tnos)
- Ligation reaction of 35s: 5’ region: TFL/ Ga20: Tnos - 35s: Renilla: Tnos + 35s: Cas9: Tnos - U6: TFL/Ga20oxgRNA: psgRNA
- 5
35s:5’:Ga20cons:Luc:Tnos 3α1 KAN - 6
35s:5’:Ga20KO:Luc:Tnos 3α1 KAN - 7
35s:5’:TFLcons:Luc:Tnos 3α1 KAN - 8
35s:5’:TFLKO:Luc:Tnos 3α1 KAN - 9
35s:5’:Ga20cons:Luc:Tnos-35s:Ren:Tnos 3Ω2 SPEC - 10
35s:5’:Ga20KO:Luc:Tnos-35s:Ren:Tnos 3Ω2 SPEC - 11
35s:5’:Ga20PCR:Luc:Tnos-35s:Ren:Tnos 3Ω2 SPEC - 12
35s:5’:TFLcons:Luc:Tnos-35s:Ren:Tnos 3Ω2 SPEC - 13
35s:5’:TFLKO:Luc:Tnos-35s:Ren:Tnos 3Ω2 SPEC - 14
35s:5’:TFLPCR:Luc:Tnos-35s:Ren:Tnos 3Ω2 SPEC - 15
U6:Ga20sgRNA:psgRNA 3α1 KAN - 16
U6:TFLsgRNA:psgRNA 3α1 KAN - 17
35s:Cas9:Tnos-U6:Ga20gRNA:psgRNA 3Ω1 SPEC - 18
35s:Cas9:Tnos-U6:TFLgRNA:psgRNA 3Ω1 SPEC - 19
Ga20PCR pUPD2 CAM - 20
TFLPCR pUPD2 CAM - Transform the products of ligation in DH5 α. Incubate it at 37^ during 2 hours.
- We store at -80^:
- Promoter35s
pNos - TFLKO
Ga20KO - TFLPCRXT1
Ga20PCRXT1 - TFLPCROK
Ga20PCROK - TFLconsOK
Ga20consOK - U6:Ga20oxgRNA: psgRNA - 35s: Cas9: Tnos - Miniprep number 2 was empty. We have resuspended it with 40 μL of H20 milliQ and we have checked the DNA concentration with the Nanodrop. The results show us that the DNA concentration in the Eppendorf was 140 ng/ μL so we have used it.
- Miniprep with E.Z.N.A ®.® Plasmid Mini Kit I, Q(capless) Spin of 35s: 5’ region: TFL/Ga20oxPCR: Luc: Tnos – 35s: Renilla: Tnos
- Transform in C58 Agrobacterium 35s: Renilla : Tnos (3 α2)
- Plating promoter35s: Renilla: Tnos (3α2)
- Luciferase assay
- devices
Volume (μL) - 35s : 5’ region: Ga20/TFL KO: Luc: Tnos - 35s: Renilla: Tnos - 35s: hCas9: Tnos: U6: Ga20/TFL gRNA: psgRNA
1 - 35s : 5’ region: Ga20/TFL cons: Luc: Tnos - 35s: Renilla: Tnos - 35s: hCas9: Tnos: U6: Ga20/TFL gRNA: psgRNA
1 - 3 α 1 plasmid
1.2 - Bsa 10X
1.2 - Buffer ligase
1 - Bsa I
1 - T4 ligase
1 - H20 milliQ
4.6 - nfiltration cultures:
- 5s: Luc: Tnos
Laboratory controls Pnos: Luc: Tnos Laboratory controls gTS TFL KO + Cas9 - XT1:XT2 Positive controls gTSGa20oxKO + Cas9 - XT1:XT2 Positive controls gTS TFL PCR + Cas9 - XT1:XT2 Negative controls gTS Ga20oxPCR + Cas9 - XT1:XT2 Negative controls gTS TFL PCR + Cas9 - TFLgRNA Samples gTS TFL cons + Cas9 - TFLgRNA Samples gTS Ga20oxPCR + Cas9 - Ga20gRNA Samples gTS Ga20oxcons + Cas9 - Ga20gRNA Samples - Transplant agroinfiltrated plants (Nicotiana benthamiana)
- Pick up 6 disks per each plant in order to carry out the luciferase assay on 09/08
- Ligate reaction of:
- device
Volume of culture (mL) Volume of Agroinfiltration solution (mL) - Cas9 - TFL gRNA
0.7 9.3 - Cas 9 - Ga20oxgRNA
0.7 9.3 - Cas 9 - XT1: XT2
0.59 9.41 - TFL KO
0.67 9.33 - TFL PCR
0.73 9.27 - Ga20oxconsensus
0.71 9.28 - Pnos
0.68 9.32 - 35s : Luc
0.78 9.22 - Ga20oxPCR
0.74 9.26 - TFL consensus
0.71 9.29 - Ga20ox- KO
0.73 9.27 - Miniprep with E.Z.N.A ®.® Plasmid Mini Kit I, Q(capless) Spin of TMV CDS
- Transform DH5 α E. coli with the device 35s : 5’ region: PCR PCR: Luc: Tnos - 35s: Renilla: Tnos. After incubating 2 hours, it must be plated.
- Refresh C58 Agrobacterium tumefaciens cultures with the aim of infiltrating in N.benthamiana on 05/08.
- Pick a single E. coli DH5α (35S : 5’ region: KO/cons target: Luc:Tnos - promoter35s: renilla: Tnos) colony from the plate that has been incubated overnight. Inoculate a starter culture of 4 ml of LB medium with 4 μL of spectinomycin in a 50 ml tube with the colony and incubate it overnight at 37^ with shaking.Sequencing TMV empty vector with the primer D09OCT01 (10 uM). 5μL of Miniprep and 9μL of primer (dilution 1:3). Sequencing code of 210.13.300 and 210.13.301.
- Pick a single E. coli DH5α (promoter35s: 5’ region: TFL/Ga20oxPCR: Luc: Tnos - promoter35s: Renilla: Tnos ) colony from the plate that has been incubated overnight. Inoculate a starter culture of 4 ml of LB medium with 4 μL of kanamycin in a 50 ml tube with the colony and incubate it overnight at 37^ with shaking.
- iniprep with E.Z.N.A ®.® Plasmid Mini Kit I, Q(capless) Spin of:
- 5s: 5’ region: TFL PCR: Luc: Tnos - promoter35s: Renilla: Tnos
35s: 5’ region: Ga20oxPCR: Luc: Tnos - promoter35s: Renilla: Tnos 35s: 5’ region: Ga20oxconsensus: Luc: Tnos - promoter35s: Renilla: Tnos 35s: 5’ region: Ga20oxKO: Luc: Tnos - promoter35s: Renilla: Tnos - Digestion of minipreps with EcoRV. Incubate 1 hour at 37^
- Run electrophoresis gel of the digestion products: TFLK01, TFLK02, TFLcons01, TFLcons02, GAK01, GAK02, GAcons01, GAcons02.
- Prepare the Agroinfiltration with the correct protocol.
- Centrifuge the cultures at 3000 rpm during 15 minutes. We discard the supernatant and it is necessary to resuspend in 5mL of Agroinfiltration solution. Let shaking it a RT during 2 hours. OD’s measurement
- Reagent
Volume(μL) - 35s:5’region: TFL/Ga20oxPCR: Luc: Tnos
1 - Promoter35s: Renilla: Tnos
1 - pUPD2
1 - BSA10X
1.2 - Ligase Buffer
1.2 - BsmbI
1 - T4 ligase
1 - H2O milli-Q
4.6 - Ligate reactions of TFL PCR and Ga20ox PCR with Renilla
- 1
35S:5’ pUPD2 CAM - 2
SAGTI:Luc pUPD2 CAM - 3
35s:5’:TFLPCR:Luc:Tnos 3α1 KAN - 4
35s:5’:Ga20PCR:Luc:Tnos 3α1 KAN - H5α E. coli transformation with the devices:
- 5S : 5’ region : TFL KO : Luc : Tnos - promoter35s: Renilla:Tnos in Ω2
35S : 5’ region : TFL consensus : Luc : Tnos - promoter35s: Renilla:Tnos in Ω2 35S : 5’ region : Ga20ox KO : Luc : Tnos - promoter35s: Renilla:Tnos in Ω2 35S : 5’ region : Ga20ox consensus : Luc : Tnos - promoter35s: Renilla:Tnos in Ω2 - E. coli plating in plates with Kanamycin (antibiotic). Incubate 16 hours at 37^
- inipreps with E.Z.N.A ®.® Plasmid Mini Kit I, Q(capless) Spin of:
- 5s:5’region:TFL PCR:Luc:Tnos in α1
35s:5’region:Ga20oxPCR: Luc: Tnos in α1 - Pick a single E. coli DH5α (TMV CDS) colony from the plate that has been incubated overnight. Inoculate a starter culture of 4 ml of LB medium with 4 μL of kanamycin in a 50 ml tube with the colony and incubate it overnight at 37^ with shaking.
- Digestion of minipreps with EcoRI. Incubate 1 hour at 37^
- Run electrophoresis gel of the devices. We remain the samples 1.
- Store at -80^ the devices of gTS PCR
- Reagent
Volume(μL) - TFL KO/Ga20KO/TFL cons / Ga20oxcons
1 - Promoter35s: Renilla: Tnos
1 - pUPD2
1 - BSA10X
1.2 - Ligase Buffer
1.2 - BsmbI
1 - T4 ligase
1 - H2O milli-Q
4.6 - iniprep with E.Z.N.A ®.® Plasmid Mini Kit I, Q(capless) Spin of:
- 5s: TFL PCR : Luc : Tnos
35s : Ga20ox PCR : Luc : Tnos - Digestion of minipreps with EcoRI following digestion protocol. Incubate 1 hour at 37^.
- Run electrophoresis gel of the digestion products. We will discard this culture because the gel result doesn’t correspond with what we expect.
- Agroinfiltration procedure with 9 plants of N.benthamiana following the Agroinfiltration protocol.
- Pick up the samples of infiltrated plants. We keep 3 disks per plant in a Eppendorf tube and we take 2 samples of each plant.
- Luciferase assay is made following the correct protocol. After analyzing all the data obtained, it seems that the system works but we must optimized it to increase the signal range. In this way, we will be able to distinguish signal from noise.
- onclusions luciferase assay:
- liminate 5’ region of the device
Change linker sequence Add renilla in luciferase assay Change reporter to +1 Use pLess as control Use a Wild Type as control Insert devices in cis Design a consensus target as longer as the amplified. - Culture refresh of C58 Agrobacterium to infiltrate on Friday.
- Pick a single E. coli DH5α (35s:5’region:TFL PCR:Luc:Tnos in α1 and 35s:5’region:Ga20oxPCR: Luc: Tnos in α1) colony from the plate that has been incubated overnight. Inoculate a starter culture of 4 ml of LB medium with 4 μL of kanamycin in a 50 ml tube with the colony and incubate it overnight at 37^ with shaking.
- Targets ligations with Renilla reporters.
- Device
Order Sequencing - TFL PCR
210.13.250 SNP in the position 652 of the target. Position 1 of the gRNA. GA - Ga20ox PCR
210.13.253 Same sequence - TFL consensus
210.13.251 Same sequence - TFL KO
210.13.252 Same sequence - Ga20ox Consensus
210.13.254 Same sequence - Ga20ox KO
210.13.255 Same sequence - Received the necessary primers to sequence: TFL consensus, TFL knockout, Ga20ox consensus and Ga20ox knockout.
- repare Agrobacterium cultures: Inoculate a starter culture of 5 ml of LB medium with 5 μL of Kanamycin and 5 μL of rifampin in a 50 ml tube with the colony and incubate it 48 hours at 28^ with shaking. The devices are:
- 5S : 5’Region : TFL consensus : Luc : Tnos
35S : 5’Region : TFL knockout : Luc : Tnos 35S : 5’Region :TFL PCR: Luc : Tnos 35S : 5’Region : Ga20ox consensus : Luc : Tnos 35S : 5’Region : Ga20ox knockout : Luc : Tnos 35S : 5’Region :Ga20ox PCR: Luc : Tnos - Sequencing the last devices to check if these are correct.
- Refresh Agrobacterium tumefaciens cultures with the aim of infiltrating in N.benthamiana on 29/07
- Refresh cultures of the devices 35s: 5’ region: TFL PCR : Luc : Tnos and 35s : 5’ region: Ga20ox PCR : Luc : Tnos in order to prepare the more Miniprep reaction.
- Sequencing results have arrived.
- Lanes
Samples Verification - 1
1 Kb molecular weight marker - 2
TFL PCR - 3
Ga20ox PCR