| Line 4,666: | Line 4,666: | ||
<div class="modal-body" style="width: 100%; height: 500px;overflow: auto;"> | <div class="modal-body" style="width: 100%; height: 500px;overflow: auto;"> | ||
| − | <p> | + | |
| − | <p> | + | <h3>Miniprep of the 4 pCMM-15 clones from 01.08.19</h3> |
| − | <p> | + | |
| − | <p> | + | <p>- Extract plasmid DNA pCMM-15 of 4 clones using Ozyme <a class="link-inside-page" href="https://files.zymoresearch.com/protocols/_d4208t_d4209_d4210_d4211_d4212_zymopure_plasmid_miniprep.pdf">ZymoPURE™ Plasmid Miniprep Kit.</a></p> |
| + | <br> | ||
| + | |||
| + | <h3>Determination of plasmid concentration with nanodrop</h3> | ||
| + | |||
| + | <p>The concentration of the extracted DNA is measured with the NanoDrop 2000 spectrophotometer (ThermoFisher Scientific) :</p> | ||
| + | <br> | ||
| + | |||
| + | <div class="d-flex justify-content-center"> | ||
| + | <div class="table-responsive"> | ||
| + | <table class="tablenotebook text-center"> | ||
| + | <thead> | ||
| + | <tr> | ||
| + | <th class="th-notebook-aout">Plasmid</th> | ||
| + | <th class="td-notebook" colspan="4">pCMM-15</th> | ||
| + | <th class="td-notebook">pAGM8055</th> | ||
| + | </tr> | ||
| + | </thead> | ||
| + | <tbody> | ||
| + | <tr> | ||
| + | <td class="th-notebook-aout">Colonies</td> | ||
| + | <td class="td-notebook">1</td> | ||
| + | <td class="td-notebook">2</td> | ||
| + | <td class="td-notebook" >3</td> | ||
| + | <td class="td-notebook" >4</td> | ||
| + | <td class="td-notebook" >1</td> | ||
| + | </tr> | ||
| + | <tr > | ||
| + | <td class="th-notebook-aout">DNA concentration (ng/µL)</td> | ||
| + | <td class="td-notebook">1038</td> | ||
| + | <td class="td-notebook" >924</td> | ||
| + | <td class="td-notebook" >920</td> | ||
| + | <td class="td-notebook" >575</td> | ||
| + | <td class="td-notebook" >476</td> | ||
| + | </tr> | ||
| + | </tbody> | ||
| + | </table> | ||
| + | </div> | ||
| + | </div> | ||
| + | <br> | ||
| + | |||
| + | <h3>Quality Control digestion of pCMM-15 </h3> | ||
| + | |||
| + | <p>- Prepare a master mix for 5 reaction :</p> | ||
| + | <br> | ||
| + | |||
| + | <div class="d-flex justify-content-center"> | ||
| + | <div class="table-responsive-sm"> | ||
| + | <table class="tablenotebook text-center"> | ||
| + | <thead> | ||
| + | <tr> | ||
| + | <th class="th-notebook-aout">Reaction mix</th> | ||
| + | <th class="th-notebook-aout">Master mix (µL)<br>pCMM</th> | ||
| + | </tr> | ||
| + | </thead> | ||
| + | <tbody> | ||
| + | <tr > | ||
| + | <td class="td-notebook">Buffer NEB CS (10X) </td> | ||
| + | <td class="td-notebook">5</td> | ||
| + | </tr> | ||
| + | <tr > | ||
| + | <td class="td-notebook">EcoRI-HF</td> | ||
| + | <td class="td-notebook">1.5 </td> | ||
| + | </tr> | ||
| + | <tr > | ||
| + | <td class="td-notebook">Vf/tube</td> | ||
| + | <td class="td-notebook">1.3</td> | ||
| + | </tr> | ||
| + | </tbody> | ||
| + | </table> | ||
| + | </div> | ||
| + | </div> | ||
| + | <br> | ||
| + | |||
| + | <p> - Add 200 ng of DNA (all DNA from samples were diluted 1/10) :</p> | ||
| + | <br> | ||
| + | |||
| + | <div class="d-flex justify-content-center"> | ||
| + | <div class="table-responsive-sm"> | ||
| + | <table class="tablenotebook text-center"> | ||
| + | <thead> | ||
| + | <tr> | ||
| + | <th class="th-notebook-aout">Plasmid</th> | ||
| + | <th class="th-notebook-aout">Conc. DNA<br> (ng/μL)</th> | ||
| + | <th class="th-notebook-aout">Vol. DNA (μL)</th> | ||
| + | </tr> | ||
| + | </thead> | ||
| + | <tbody> | ||
| + | <tr> | ||
| + | <td class="td-notebook">pCMM-15 (1)</td> | ||
| + | <td class="td-notebook">103.8</td> | ||
| + | <td class="td-notebook">1.92</td> | ||
| + | </tr> | ||
| + | <tr > | ||
| + | <td class="td-notebook">pCMM-15 (2)</td> | ||
| + | <td class="td-notebook"> 92.4</td> | ||
| + | <td class="td-notebook">2.16</td> | ||
| + | </tr> | ||
| + | <tr > | ||
| + | <td class="td-notebook">pCMM-15 (3)</td> | ||
| + | <td class="td-notebook">92</td> | ||
| + | <td class="td-notebook">2.17</td> | ||
| + | </tr> | ||
| + | <tr > | ||
| + | <td class="td-notebook">pCMM-15 (4)</td> | ||
| + | <td class="td-notebook">57.5</td> | ||
| + | <td class="td-notebook">3.48</td> | ||
| + | </tr> | ||
| + | <tr > | ||
| + | <td class="td-notebook">pAGM8055</td> | ||
| + | <td class="td-notebook">47.6</td> | ||
| + | <td class="td-notebook">8.28</td> | ||
| + | </tr> | ||
| + | </tbody> | ||
| + | </table> | ||
| + | </div> | ||
| + | </div> | ||
| + | <br> | ||
| + | |||
| + | <p>- Add qsp 10 μL of water.<br> | ||
| + | - Incubate at 37°C during 110 min.</p> | ||
| + | |||
| + | <h2>DNA gel electrophoresis</h2> | ||
| + | |||
| + | <p>Prepare the agarose gel 1% in TAE buffer :<br> | ||
| + | - 0,2 g of agarose powder is dissolved in 20 mL of TAE buffer 0,5X by heating the solution in the microwave.<br> | ||
| + | - 7 μL of Ethidium bromide (EtBr) solution is added.<br> | ||
| + | - The solution is casted on an electrophoresis gel mould and let it solidify at room temperature.<br> | ||
| + | Prepare the samples :<br> | ||
| + | - DNA samples : 10 μL of DNA + 2 μL of NEBTM Gel Loading Dye, Purple (6X)<br> | ||
| + | - Ladder : 3 μL of NEB 1kb plus DNA ladder<br> | ||
| + | - Run the gel for 40 min at 100V.</p> | ||
| + | |||
| + | <h2>Results</h2> | ||
| + | |||
| + | <center><img src="https://2019.igem.org/wiki/images/3/34/T--Sorbonne_U_Paris--gel10NB.png" style="width:100%; cursor:zoom-in" data-toggle="modal" data-target=".gel10NB"></center> | ||
| + | <br> | ||
| + | |||
| + | <p> For the restriction analysis of pCMM-15, we expect three fragments generated against one in the empty vector (see predicted gel from 29/07).<br> | ||
| + | → On the gel, we can see three strips in the samples 1,2 and 3 as expected but we can see only two strip for clone 4, so we can conclude that both transcriptional units were inserted in the corresponding level M plasmid only for clones 1 to 3.</p> | ||
| + | |||
</div> | </div> | ||
</div> | </div> | ||
| Line 4,677: | Line 4,817: | ||
</div> | </div> | ||
<!--------------------END MODAL OR POP UP --------------------------> | <!--------------------END MODAL OR POP UP --------------------------> | ||
| + | <div class="modal gel10NB" tabindex="-1" role="dialog" aria-labelledby="myLargeModalLabel" aria-hidden="true"> | ||
| + | <div class="modal-dialog modal-lg"> | ||
| + | <div class="modal-content"> | ||
| + | <div class="container" ><button type="button" class="close" data-dismiss="modal" aria-label="Close" ><span aria-hidden="true">×</span> </button></div> | ||
| + | <img style="width: 100%;" src="https://2019.igem.org/wiki/images/3/34/T--Sorbonne_U_Paris--gel10NB.png" > | ||
| + | </div> | ||
| + | </div> | ||
| + | </div> | ||
<div id="aoutday3"> <p class="bloc-date-calendrier">3</p> </div> | <div id="aoutday3"> <p class="bloc-date-calendrier">3</p> </div> | ||
| Line 4,701: | Line 4,849: | ||
<div class="modal-body" style="width: 100%; height: 500px;overflow: auto;"> | <div class="modal-body" style="width: 100%; height: 500px;overflow: auto;"> | ||
| − | <p> | + | |
| − | + | <h3>Determination of plasmid concentration with nanodrop</h3> | |
| − | <p> | + | |
| − | <p> | + | <p>The concentration of the extracted DNA is measured with the NanoDrop 2000 spectrophotometer(ThermoFisher Scientific) :</p> |
| + | <br> | ||
| + | |||
| + | <div class="d-flex justify-content-center"> | ||
| + | <div class="table-responsive"> | ||
| + | <table class="tablenotebook text-center"> | ||
| + | <thead> | ||
| + | <tr> | ||
| + | <th class="th-notebook-aout">Plasmid</th> | ||
| + | <th class="td-notebook" colspan="4">pCMM-15</th> | ||
| + | </tr> | ||
| + | </thead> | ||
| + | <tbody> | ||
| + | <tr> | ||
| + | <td class="th-notebook-aout">Clones</td> | ||
| + | <td class="td-notebook">1</td> | ||
| + | <td class="td-notebook">2</td> | ||
| + | <td class="td-notebook" >3</td> | ||
| + | <td class="td-notebook" >4</td> | ||
| + | </tr> | ||
| + | <tr > | ||
| + | <td class="th-notebook-aout">DNA concentration (ng/µL)</td> | ||
| + | <td class="td-notebook">1038</td> | ||
| + | <td class="td-notebook" >924</td> | ||
| + | <td class="td-notebook" >920</td> | ||
| + | <td class="td-notebook" >575</td> | ||
| + | </tr> | ||
| + | </tbody> | ||
| + | </table> | ||
| + | </div> | ||
| + | </div> | ||
| + | <br> | ||
| + | |||
| + | <h3>Digestion of pCMM-15 to obtain the linear insert for <I>Chlamydomonas</I> transformation (1st part)</h3> | ||
| + | |||
| + | <p>- Prepare a master mix for 2 reaction :</p> | ||
| + | <br> | ||
| + | |||
| + | <div class="d-flex justify-content-center"> | ||
| + | <div class="table-responsive-sm"> | ||
| + | <table class="tablenotebook text-center"> | ||
| + | <thead> | ||
| + | <tr> | ||
| + | <th class="th-notebook-aout">Reaction mix</th> | ||
| + | <th class="th-notebook-aout">Master mix (µL)<br>pCMM</th> | ||
| + | </tr> | ||
| + | </thead> | ||
| + | <tbody> | ||
| + | <tr > | ||
| + | <td class="td-notebook">Buffer NEB CS (10X) </td> | ||
| + | <td class="td-notebook">2</td> | ||
| + | </tr> | ||
| + | <tr > | ||
| + | <td class="td-notebook">EcoRI-HF</td> | ||
| + | <td class="td-notebook">0.6 </td> | ||
| + | </tr> | ||
| + | <tr > | ||
| + | <td class="td-notebook">Vf/tube</td> | ||
| + | <td class="td-notebook">1.3</td> | ||
| + | </tr> | ||
| + | </tbody> | ||
| + | </table> | ||
| + | </div> | ||
| + | </div> | ||
| + | <br> | ||
| + | |||
| + | <p> - Add DNA :</p> | ||
| + | <br> | ||
| + | |||
| + | <div class="d-flex justify-content-center"> | ||
| + | <div class="table-responsive-sm"> | ||
| + | <table class="tablenotebook text-center"> | ||
| + | <thead> | ||
| + | <tr> | ||
| + | <th class="th-notebook-aout">Plasmid</th> | ||
| + | <th class="th-notebook-aout">Conc. DNA<br> (ng/μL)</th> | ||
| + | <th class="th-notebook-aout">Vol. DNA (μL)</th> | ||
| + | </tr> | ||
| + | </thead> | ||
| + | <tbody> | ||
| + | <tr> | ||
| + | <td class="td-notebook">pCMM-15 (1)</td> | ||
| + | <td class="td-notebook">1038</td> | ||
| + | <td class="td-notebook">1.92 (1/10 dilution)</td> | ||
| + | </tr> | ||
| + | <tr > | ||
| + | <td class="td-notebook">pCMM-15 (2)</td> | ||
| + | <td class="td-notebook"> 924</td> | ||
| + | <td class="td-notebook">2.16 (1/10 dilution)</td> | ||
| + | </tr> | ||
| + | <tr > | ||
| + | <td class="td-notebook">pCMM-15 (3)</td> | ||
| + | <td class="td-notebook">920</td> | ||
| + | <td class="td-notebook">2.17 (1/10 dilution)</td> | ||
| + | </tr> | ||
| + | <tr > | ||
| + | <td class="td-notebook">pCMM-15 (4)</td> | ||
| + | <td class="td-notebook">575</td> | ||
| + | <td class="td-notebook">3.48 (1/10 dilution)</td> | ||
| + | </tr> | ||
| + | |||
| + | </tbody> | ||
| + | </table> | ||
| + | </div> | ||
| + | </div> | ||
| + | |||
| + | <p>- Add qsp 10 μL of water.<br> | ||
| + | - Incubate at 37°C for 1h.</p> | ||
| + | <br> | ||
| + | |||
| + | <h3><i>Chlamydomonas</I> culture dilution</h3> | ||
| + | |||
| + | <p>The initial cell culture of Chlamydomonas (UVM7) is saturated with a concentration of 15.10^6 cells/mL : <br> | ||
| + | Prepare cell culture of 1.10^6 cells/mL for optimal growth. For that, add 13,3 mL of initial cell culture in a 250 mL flask containing 200 mL of TAP medium.</p> | ||
| + | |||
</div> | </div> | ||
</div> | </div> | ||
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<div class="modal-body" style="width: 100%; height: 500px;overflow: auto;"> | <div class="modal-body" style="width: 100%; height: 500px;overflow: auto;"> | ||
| − | <p> | + | |
| − | + | <h3>Quality Control digestion of pCMM-15 (2nd part)</h3> | |
| − | <p> | + | |
| − | <p> | + | <h2>DNA gel electrophoresis </h2> |
| + | |||
| + | <p>Prepare the agarose gel 0,8% in TAE buffer :<br> | ||
| + | - 0,16 g of agarose powder is dissolved in 20 mL of TAE buffer 0,5X by heating the solution in the microwave.<br> | ||
| + | - 7 μL of Ethidium bromide (EtBr) solution is added.<br> | ||
| + | - The solution is casted on an electrophoresis gel mould and let solidify at room temperature.<br> | ||
| + | Prepare the samples :<br> | ||
| + | - DNA samples : 10 μL of DNA + 2 μL of PromegaTM Gel Loading Dye (6X)<br> | ||
| + | - Ladder : 1µL PromegaTM 200bp DNA step ladder + 1µL PromegaTM Gel Loading Dye (6X)<br> | ||
| + | - Run the gel for 25 min at 100V.</p> | ||
| + | |||
| + | <h2> Results </h2> | ||
| + | |||
| + | <p>We expect three fragments generated against one in the empty vector (see predicted gel from 29/07).<br> | ||
| + | → On the gel, we can see three strips in pCMM15 digestion as expected, so we can conclude that the insert (high size) is separated from the plasmid backbone (low size).</p> | ||
| + | <br> | ||
| + | |||
| + | <h3>Extraction of the insert of pCMM-15</h3> | ||
| + | |||
| + | <p>- To isolate the insert, cut the agarose gel under blue light in. | ||
| + | - Extract plasmid DNA pCMM-15 of 4 clones using Macherey-Nagel <a class="link-inside-page" href="https://www.mn-net.com/Portals/8/attachments/Redakteure_Bio/Protocols/DNA%20clean-up/UM_PCRcleanup_Gelex_NSGelPCR.pdf">NucleoSpinTM Gel and PCR Clean-up kit.</a></p> | ||
| + | <br> | ||
| + | |||
| + | <h3>Determination of insert concentration with nanodrop</h3> | ||
| + | |||
| + | <p>The concentration of the extracted DNA is measured with the NanoDrop 2000 spectrophotometer(ThermoFisher Scientific) :</p> | ||
| + | <br> | ||
| + | |||
| + | <div class="d-flex justify-content-center"> | ||
| + | <div class="table-responsive-sm"> | ||
| + | <table class="tablenotebook text-center"> | ||
| + | <thead> | ||
| + | <tr> | ||
| + | <th class="th-notebook-aout">Plasmid</th> | ||
| + | <th class="td-notebook" colspan="2">pCMM-15</th> | ||
| + | </tr> | ||
| + | </thead> | ||
| + | <tbody> | ||
| + | <tr> | ||
| + | <td class="th-notebook-aout">DNA concentration (ng/µL)</td> | ||
| + | <td class="td-notebook">41.5</td> | ||
| + | </tr> | ||
| + | </tbody> | ||
| + | </table> | ||
| + | </div> | ||
| + | </div> | ||
| + | <br> | ||
| + | |||
| + | <h3>Transformation of <I>Chlamydomonas reinhardtii</I></h3> | ||
| + | |||
| + | <p>- Verify into the countness of chlamy swing, and the concentration culture (it must be 1-5.106 cells/mL).<br> | ||
| + | - Aliquote 50 mL of culture in 50 mL falcon tubes 2 times (1 tube = 2 transformations).<br> | ||
| + | - Centrifuge 5 min at 1500 g, RT.<br> | ||
| + | - Discard the supernatant.<br> | ||
| + | - Resuspend each pellet with 500 µL of TAP + 60 mM Sucrose (i.e. concentrating it 100X).<br> | ||
| + | - Aliquote 250 µL of cells into a 0,4 cm gapped cuvette.<br> | ||
| + | - Add 10 ng to 1 g of DNA :</p> | ||
| + | <br> | ||
| + | |||
| + | <div class="d-flex justify-content-center"> | ||
| + | <div class="table-responsive-sm"> | ||
| + | <table class="tablenotebook text-center"> | ||
| + | <thead> | ||
| + | <tr> | ||
| + | <th class="th-notebook-aout">Construct</th> | ||
| + | <th class="th-notebook-aout">Strain</th> | ||
| + | <th class="th-notebook-aout">DNA (ng)</th> | ||
| + | <th class="th-notebook-aout">Vol. DNA (μL)</th> | ||
| + | <th class="th-notebook-aout">Selection</th> | ||
| + | </tr> | ||
| + | </thead> | ||
| + | <tbody> | ||
| + | <tr> | ||
| + | <td class="td-notebook">pl.22</td> | ||
| + | <td class="td-notebook">+ ctrl Hygromycine</td> | ||
| + | <td class="td-notebook">500</td> | ||
| + | <td class="td-notebook">2,7</td> | ||
| + | <td class="td-notebook" rowspan="4">TAP + Hygromycine</td> | ||
| + | </tr> | ||
| + | <tr > | ||
| + | <td class="td-notebook">iMl7</td> | ||
| + | <td class="td-notebook"> - Ctrl Hygromycine</td> | ||
| + | <td class="td-notebook">100</td> | ||
| + | <td class="td-notebook">3</td> | ||
| + | </tr> | ||
| + | <tr > | ||
| + | <td class="td-notebook">pCMM-15</td> | ||
| + | <td class="td-notebook">M1</td> | ||
| + | <td class="td-notebook">100</td> | ||
| + | <td class="td-notebook">2.4</td> | ||
| + | </tr> | ||
| + | <tr > | ||
| + | <td class="td-notebook">pCMM-15</td> | ||
| + | <td class="td-notebook">M2</td> | ||
| + | <td class="td-notebook">200</td> | ||
| + | <td class="td-notebook">4</td> | ||
| + | </tr> | ||
| + | |||
| + | </tbody> | ||
| + | </table> | ||
| + | </div> | ||
| + | </div> | ||
| + | <br> | ||
| + | |||
| + | <p>- Incubate 15 min on ice.<br> | ||
| + | - Place each cuvette in the electroporation machine and use 800V (2000V/cm) and 25 uF with NO shunt resistance.<br> | ||
| + | - Transfer the cells in 10 mL of TAP + Sucrose (60 mM).<br> | ||
| + | - Let the cells recover overnight (at least 16h) while being rotated.</p> | ||
| + | |||
</div> | </div> | ||
</div> | </div> | ||
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<div class="modal-body" style="width: 100%; height: 500px;overflow: auto;"> | <div class="modal-body" style="width: 100%; height: 500px;overflow: auto;"> | ||
| − | < | + | |
| − | + | <h3>Transplantation of <I>Chlamydomonas</I> colonies onto solid medium</h3> | |
| − | < | + | |
| − | < | + | <p>- Centrifuge 3 min at 2000 g.<br> |
| + | - Resuspend in 500 µL TAP.<br> | ||
| + | - Plate onto selective TAP agar/ Hygromycine (15 µg/mL) plates using "hockey stick spreader" under the hood, dim light.<br> | ||
| + | - Transfer the plates in the light.<br> | ||
| + | - Wait about 5 days for the colonies to grow.</p> | ||
| + | |||
</div> | </div> | ||
</div> | </div> | ||
Revision as of 09:26, 5 October 2019
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