Difference between revisions of "Team:EPF Lausanne/Notebook/Ecoli"
| Line 174: | Line 174: | ||
<h2>Results</h2> | <h2>Results</h2> | ||
<img src="https://static.igem.org/mediawiki/2015/6/6e/10.05_pcr_pdcas9.jpg" align="center"> | <img src="https://static.igem.org/mediawiki/2015/6/6e/10.05_pcr_pdcas9.jpg" align="center"> | ||
| − | <p><small>After testing many parameters, we were able to amplify the plasmid succesfully, as seen on gel above.</br>For further steps sample from lane 1 was used. It was prepared with HF buffer and the following thermocycling settings:</small></p> | + | <p><small>After testing many parameters, we were able to amplify the plasmid succesfully, as seen on gel above (Date: 05/10/15).</br>For further steps sample from lane 1 was used. It was prepared with HF buffer and the following thermocycling settings:</small></p> |
<table width="70%" align="center"> | <table width="70%" align="center"> | ||
<tr> | <tr> | ||
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<td> </td> | <td> </td> | ||
<td>98°C</td> | <td>98°C</td> | ||
| − | <td | + | <td>40 seconds</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
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<td>Denaturation</td> | <td>Denaturation</td> | ||
<td>98°C</td> | <td>98°C</td> | ||
| − | <td | + | <td>15 seconds</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
<td> </td> | <td> </td> | ||
<td>Annealing</td> | <td>Annealing</td> | ||
| − | <td | + | <td>59°C</td> |
| − | <td | + | <td>22 seconds</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
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<td>Extension</td> | <td>Extension</td> | ||
<td>72°C</td> | <td>72°C</td> | ||
| − | <td | + | <td>2 minutes 30 seconds</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 210: | Line 210: | ||
<td> </td> | <td> </td> | ||
<td>72°C</td> | <td>72°C</td> | ||
| − | <td | + | <td>7 minutes</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
Revision as of 13:58, 4 August 2015
E. Coli Laboratory Notebook
Assemble pdCas9-w: Open pdCas9 by PCR
We received plasmid pdCas9 in bacteria. We did a Miniprep (cf. Protocols) on overnight cultures to isolate it.pdCas9 is a plasmid containing dCas9 under a Tetracyclin inducible promoter and a Chloramphenicol resistance gene, available on Addgene under the name pdCas9-bacteria.
Materials and method
- 20 µl Phusion PCR (cf. Protocols) with 1 ng pdCas9 testing parameters such as HF vs. GC buffer, annealing temperatures and extension times
- PCR product purification (cf. Protocols)
- Agarose gel electrophoresis of purified PCR products
Results
After testing many parameters, we were able to amplify the plasmid succesfully, as seen on gel above (Date: 05/10/15).For further steps sample from lane 1 was used. It was prepared with HF buffer and the following thermocycling settings:
| Step | Temperature | Time | |
|---|---|---|---|
| Initial Denaturation | 98°C | 40 seconds | |
| 25 cycles | Denaturation | 98°C | 15 seconds |
| Annealing | 59°C | 22 seconds | |
| Extension | 72°C | 2 minutes 30 seconds | |
| Final Extension | 72°C | 7 minutes | |
| Hold | 4°C |
Assemble pdCas9-w: Extract w subunit from pWJ66 by PCR
We received plasmid pWJ66 in bacteria. We did a Miniprep (cf. Protocols) on overnight cultures to isolate it.pWJ66 is a plasmid containing dCas9 fused at its C-terminal to the w subunit of RNA polymerase as well as a tracrRNA gene and a CRISPR array gene, available on Addgene. We will extract the w subunit to fuse it to our own dCas9.
Materials and method
- 20 µl Phusion PCR (cf. Protocols) with 1 ng pdCas9 testing parameters such as HF vs. GC buffer, annealing temperatures and extension times
- PCR product purification (cf. Protocols)
- Agarose gel electrophoresis of purified PCR products
Results
