Difference between revisions of "Team:Stony Brook/Notebook/Cancer-W10"

Line 21: Line 21:
 
<div align="center">
 
<div align="center">
 
<h2 > 8/29 </h2>
 
<h2 > 8/29 </h2>
 +
</div>
 +
</div>
 +
 +
<div class="column full_size">
 +
<div align="center">
 +
<h4> AmilCP BioBrick Digests </h4>
 +
<table>
 +
<tr>
 +
<th> Content </th>
 +
<th> Experimental ul </th>
 +
<th> Control ul </th>
 +
</tr>
 +
<tr>
 +
<td> H<sub>2</sub>O </td>
 +
<td> 46.5 </td>
 +
<td> 47.0 </td>
 +
</tr>
 +
<tr>
 +
<td> Cutsmart </td>
 +
<td> 5.0 </td>
 +
<td> 5.0 </td>
 +
</tr>
 +
<tr>
 +
<td> XbaI </td>
 +
<td> 0.5 </td>
 +
<td> X </td>
 +
</tr>
 +
<tr>
 +
<td> DNA </td>
 +
<td> 2.0 </td>
 +
<td> 2.0 </td>
 +
</tr>
 +
</table>
 +
 +
<br>
 +
 +
<h4> PCR of Toggle 1 </h4>
 +
</div>
 +
</div>
 +
 +
<div class="column half_size">
 +
<div align="center">
 +
<table>
 +
<tr>
 +
<th> Contents </th>
 +
<th> ul </th>
 +
</tr>
 +
<td> Phire </td>
 +
<td> 10 </td>
 +
</tr>
 +
<tr>
 +
<td> H<sub>2</sub>O</td>
 +
<td> 8 </td>
 +
</tr>
 +
<tr>
 +
<td> 5 uM F Primer </td>
 +
<td> 1.5 </td>
 +
</tr>
 +
<tr>
 +
<td> 5 uM R Primer </td>
 +
<td> 1.5 </td>
 +
</tr>
 +
<tr>
 +
<td> 100pg/ul Construct </td>
 +
<td> 1.0 </td>
 +
</tr>
 +
</table>
 +
 +
<br>
 +
 +
<ul>
 +
<li> Ran other trials with 2.5, 3.5, 4.5 and 6.5 ul of Forward and Reverse Primers </li>
 +
<li> Water ul was adjusted to compensate: 6, 4, 2 and 0 ul respectively </li>
 +
</ul>
 +
</div>
 +
</div>
 +
 +
<div class="column half_size">
 +
<div align="center">
 +
<table>
 +
<tr>
 +
<th> Phase </th>
 +
<th> Temperature (°C) </th>
 +
<th> Time (sec)</th>
 +
</tr>
 +
<tr>
 +
<td> Initial Denaturation </td>
 +
<td> 98 </td>
 +
<td> 30 </td>
 +
</tr>
 +
<tr>
 +
<td> Denaturation </td>
 +
<td> 98 </td>
 +
<td> 5 </td>
 +
</tr>
 +
<tr>
 +
<td> Annealing </td>
 +
<td> 68 </td>
 +
<td> 5 </td>
 +
</tr>
 +
<tr>
 +
<td> Extension </td>
 +
<td> 72 </td>
 +
<td> 45 </td>
 +
</tr>
 +
<tr>
 +
<td> Final Extension </td>
 +
<td> 72 </td>
 +
<td> 60 </td>
 +
</tr>
 +
</table>
 +
</div>
 +
</div>
 +
 +
<h4> PCR of Toggle 2 </h4>
 +
</div>
 +
</div>
 +
 +
<div class="column half_size">
 +
<div align="center">
 +
<table>
 +
<tr>
 +
<th> Contents </th>
 +
<th> ul </th>
 +
</tr>
 +
<td> Phire </td>
 +
<td> 10 </td>
 +
</tr>
 +
<tr>
 +
<td> H<sub>2</sub>O</td>
 +
<td> 8 </td>
 +
</tr>
 +
<tr>
 +
<td> 5 uM F Primer </td>
 +
<td> 1.5 </td>
 +
</tr>
 +
<tr>
 +
<td> 5 uM R Primer </td>
 +
<td> 1.5 </td>
 +
</tr>
 +
<tr>
 +
<td> 100pg/ul Construct </td>
 +
<td> 1.0 </td>
 +
</tr>
 +
</table>
 +
 +
<br>
 +
 +
<ul>
 +
<li> Ran other trials with 2.5, 3.5, 4.5 and 6.5 ul of Forward and Reverse Primers </li>
 +
<li> Water ul was adjusted to compensate: 6, 4, 2 and 0 ul respectively </li>
 +
</ul>
 +
</div>
 +
</div>
 +
 +
<div class="column half_size">
 +
<div align="center">
 +
<table>
 +
<tr>
 +
<th> Phase </th>
 +
<th> Temperature (°C) </th>
 +
<th> Time (sec)</th>
 +
</tr>
 +
<tr>
 +
<td> Initial Denaturation </td>
 +
<td> 98 </td>
 +
<td> 30 </td>
 +
</tr>
 +
<tr>
 +
<td> Denaturation </td>
 +
<td> 98 </td>
 +
<td> 5 </td>
 +
</tr>
 +
<tr>
 +
<td> Annealing </td>
 +
<td> 68 </td>
 +
<td> 5 </td>
 +
</tr>
 +
<tr>
 +
<td> Extension </td>
 +
<td> 72 </td>
 +
<td> 45 </td>
 +
</tr>
 +
<tr>
 +
<td> Final Extension </td>
 +
<td> 72 </td>
 +
<td> 60 </td>
 +
</tr>
 +
</table>
 +
</div>
 +
</div>
 +
 +
<div class="column full_size">
 +
<div align="center">
 +
<h4> Digests of Toggle parts </h4>
 +
</div>
 +
</div>
 +
 +
<div class="column half_size">
 +
<div align="center">
 +
<h5> Toggle 1 Digest </h5>
 +
<table>
 +
<tr>
 +
<th> Content </th>
 +
<th> Experimental ul </th>
 +
<th> Control ul </th>
 +
</tr>
 +
<tr>
 +
<td> H<sub>2</sub>O </td>
 +
<td> 24</td>
 +
<td> 25 </td>
 +
</tr>
 +
<tr>
 +
<td> Cutsmart </td>
 +
<td> 5.0 </td>
 +
<td> 5.0 </td>
 +
</tr>
 +
<tr>
 +
<td> SpeI </td>
 +
<td> 1.0 </td>
 +
<td> X </td>
 +
</tr>
 +
<tr>
 +
<td> DNA </td>
 +
<td> 25.0 </td>
 +
<td> 25.0 </td>
 +
</tr>
 +
</table>
 +
</div>
 +
</div>
 +
 +
<div class="column half_size">
 +
<div align="center">
 +
<h5> Toggle 1 Digest </h5>
 +
<table>
 +
<tr>
 +
<th> Content </th>
 +
<th> Experimental ul </th>
 +
<th> Control ul </th>
 +
</tr>
 +
<tr>
 +
<td> H<sub>2</sub>O </td>
 +
<td> 24</td>
 +
<td> 25 </td>
 +
</tr>
 +
<tr>
 +
<td> Cutsmart </td>
 +
<td> 5.0 </td>
 +
<td> 5.0 </td>
 +
</tr>
 +
<tr>
 +
<td> XbaI </td>
 +
<td> 1.0 </td>
 +
<td> X </td>
 +
</tr>
 +
<tr>
 +
<td> DNA </td>
 +
<td> 25.0 </td>
 +
<td> 25.0 </td>
 +
</tr>
 +
</table>
 +
</div>
 +
</div>
 +
 +
<div class="column full_size">
 +
<div align="center">
 +
<h4> Linearized pSB1C7 Digest </h4>
 +
<br>
 +
<table>
 +
<tr>
 +
<th> Content </th>
 +
<th> Experimental ul </th>
 +
<th> Control ul </th>
 +
</tr>
 +
<tr>
 +
<td> H<sub>2</sub>O </td>
 +
<td> 16.5</td>
 +
<td> 18.5 </td>
 +
</tr>
 +
<tr>
 +
<td> Cutsmart </td>
 +
<td> 2.5 </td>
 +
<td> 2.5 </td>
 +
</tr>
 +
<tr>
 +
<td> SpeI-HF </td>
 +
<td> 1.0 </td>
 +
<td> X </td>
 +
</tr>
 +
<tr>
 +
<td> XbaI </td>
 +
<td> 1.0 </td>
 +
<td> X </td>
 +
</tr>
 +
<tr>
 +
<td> DNA </td>
 +
<td> 4.0</td>
 +
<td> 4.0 </td>
 +
</tr>
 +
</table>
 +
<br>
 +
<br>
 +
 +
<h4> Ligation of Toggle parts </h4>
 +
<table>
 +
<tr>
 +
<th> Content </th>
 +
<th> ul </th>
 +
</tr>
 +
<tr>
 +
<td> 10X T4 Buffer </td>
 +
<td> 2.0</td>
 +
</tr>
 +
<tr>
 +
<td> Toggle 1 </td>
 +
<td> 5.0 </td>
 +
</tr>
 +
<tr>
 +
<td> Toggle 2 </td>
 +
<td> 10.0 </td>
 +
</tr>
 +
<tr>
 +
<td> H<sub>2</sub>O</td>
 +
<td> 2.0 </td>
 +
</tr>
 +
<tr>
 +
<td> Ligase </td>
 +
<td> 1.0 </td>
 +
</tr>
 +
</table>
 
</div>
 
</div>
 
</div>
 
</div>
Line 35: Line 365:
 
</div>
 
</div>
 
</div>
 
</div>
 +
 +
<div class="column full_size">
 +
<div align="center">
 +
  
 
<div align="center">
 
<div align="center">

Revision as of 02:51, 7 September 2016

Week 10: 8/29 - 9/4

Week 10: 8/29 - 9/4



8/29

AmilCP BioBrick Digests

Content Experimental ul Control ul
H2O 46.5 47.0
Cutsmart 5.0 5.0
XbaI 0.5 X
DNA 2.0 2.0

PCR of Toggle 1

Contents ul
Phire 10
H2O 8
5 uM F Primer 1.5
5 uM R Primer 1.5
100pg/ul Construct 1.0

  • Ran other trials with 2.5, 3.5, 4.5 and 6.5 ul of Forward and Reverse Primers
  • Water ul was adjusted to compensate: 6, 4, 2 and 0 ul respectively
Phase Temperature (°C) Time (sec)
Initial Denaturation 98 30
Denaturation 98 5
Annealing 68 5
Extension 72 45
Final Extension 72 60

PCR of Toggle 2

Contents ul
Phire 10
H2O 8
5 uM F Primer 1.5
5 uM R Primer 1.5
100pg/ul Construct 1.0

  • Ran other trials with 2.5, 3.5, 4.5 and 6.5 ul of Forward and Reverse Primers
  • Water ul was adjusted to compensate: 6, 4, 2 and 0 ul respectively
Phase Temperature (°C) Time (sec)
Initial Denaturation 98 30
Denaturation 98 5
Annealing 68 5
Extension 72 45
Final Extension 72 60

Digests of Toggle parts

Toggle 1 Digest
Content Experimental ul Control ul
H2O 24 25
Cutsmart 5.0 5.0
SpeI 1.0 X
DNA 25.0 25.0
Toggle 1 Digest
Content Experimental ul Control ul
H2O 24 25
Cutsmart 5.0 5.0
XbaI 1.0 X
DNA 25.0 25.0

Linearized pSB1C7 Digest


Content Experimental ul Control ul
H2O 16.5 18.5
Cutsmart 2.5 2.5
SpeI-HF 1.0 X
XbaI 1.0 X
DNA 4.0 4.0


Ligation of Toggle parts

Content ul
10X T4 Buffer 2.0
Toggle 1 5.0
Toggle 2 10.0
H2O 2.0
Ligase 1.0


8/30



9/1



9/2



9/3



9/4