Difference between revisions of "Team:Stony Brook/Notebook"

 
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</style>
 
<div class="column full_size">
 
<div class="column full_size">
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<p> Document the dates you worked on your project.</p>
 
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</div>
 
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<div class="column half_size">
 
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<h5>What should this page have?</h5>
 
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<ul>
 
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<li>Chronological notes of what your team is doing.</li>
 
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<li> Brief descriptions of daily important events.</li>
 
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<li>Pictures of your progress. </li>
 
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<li>Mention who participated in what task.</li>
 
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</ul>
 
−
 
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</div>
 
−
 
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<div class="column half_size">
 
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<h5>Inspiration</h5>
 
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<p>You can see what others teams have done to organize their notes:</p>
 
−
 
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<ul>
 
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<li><a href="https://2014.igem.org/Team:ATOMS-Turkiye/Notebook">2014 ATOMS-Turkiye</a></li>
 
−
<li><a href="https://2014.igem.org/Team:Tec-Monterrey/ITESM14_project.html#tab_notebook">2014 Tec Monterrey</a></li>
 
−
<li><a href="https://2014.igem.org/Team:Kyoto/Notebook/Magnetosome_Formation#title">2014 Kyoto</a></li>
 
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<li><a href="https://2014.igem.org/Team:Cornell/notebook">2014 Cornell</a></li>
 
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</ul>
 
−
</div>
 
−
 
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<div class="column full_size">
 
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<hr>
 
 
<div align="center">
 
<div align="center">
−
<h1> Week 1 (6/27 - 7/2) </h1>
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<h1> Lab Notebook </h1>
−
<h3 style="color:#B61C1D;"> 6/27 </h3>
+
 
</div>
 
</div>
 
</div>
 
</div>
  
−
<div class="column half_size">
 
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<h5> Cancer Group </h5>
 
−
<ul>
 
−
<li> PCR of 3xHA-TDGF1 construct. 12 cycles </li>
 
−
<li> Gel of PCR Product → PCR was a failure. Band was 300bp. Should have been 750bp</li>
 
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<li> Second PCR of 3xHA-TDGF1 construct. 25 cycles instead of 12 → left overnight </li>
 
−
</ul>
 
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</div>
 
−
 
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<div class="column half_size">
 
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<h5> Vaccine Group </h5>
 
−
<ul>
 
−
<li> Things </li>
 
−
</ul>
 
−
</div>
 
  
 
<div class="column full_size">
 
<div class="column full_size">
 
<div align="center">
 
<div align="center">
−
<h5> Interlab Study </h5>
 
−
<ul>
 
−
<li> Measured LUDOX and H<sub>2</sub>O for plate reader </li>
 
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<li> Transformation of positive and negative controls, test devices 1-3 </li>
 
−
</ul>
 
−
</div>
 
−
</div>
 
  
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<div class="column full_size">
+
<h1> <a id="stuff" href="https://2016.igem.org/Team:Stony_Brook/Notebook/Cancer-W1">Week 1: 6/28 - 7/1 </a> </h1>
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<div align="center">
+
−
<h3 style="color:#B61C1D;"> 6/28</h3>
+
−
</div>
+
−
</div>
+
  
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<div class="column half_size">
 
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<h5> Cancer Group </h5>
 
−
<ul>
 
−
<li> Ran gel on PCR of yesterday's construct → Gel worked </li>
 
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<li> Gel purification of PCR Product → low concentration of DNA found during nanodrop</li>
 
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<li> PCR the construct using a revised method </li>
 
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<li> 2:54pm → ran the gel on the PCR product </li>
 
−
</ul>
 
−
</div>
 
−
 
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<div class="column half_size">
 
−
<h5> Vaccine Group </h5>
 
−
<ul>
 
−
<li> Things </li>
 
−
</ul>
 
−
</div>
 
−
 
−
<div class="column full_size">
 
 
<div align="center">
 
<div align="center">
−
<h5> Interlab Study </h5>
+
<h1> <a id="stuff" href="https://2016.igem.org/Team:Stony_Brook/Notebook/Cancer-W2">Week 2: 7/4 - 7/8 </a> </h1>
−
<ul>
+
−
<li align> Heat and "SB" streaking seems not to have worked</li>
+
−
<li align> No visible red colonies on plate </li>
+
−
</ul>
+
−
</div>
+
 
</div>
 
</div>
  
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<div class="column full_size">
 
 
<div align="center">
 
<div align="center">
−
<h3 style="color:#B61C1D;"> 6/29 </h3>
+
<h1> <a id="stuff" href="https://2016.igem.org/Team:Stony_Brook/Notebook/Cancer-W3">Week 3: 7/11 - 7/17 </a> </h1>
−
</div>
+
 
</div>
 
</div>
  
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<div class="column half_size">
 
−
<h5> Cancer Group </h5>
 
−
<ul>
 
−
<li> PCR Not working well → keep trying new methods with different annealing temperatures </li>
 
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<li> Tried 65 and 67 degrees C</li>
 
−
</ul>
 
−
</div>
 
−
 
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<div class="column half_size">
 
−
<h5> Vaccine Group </h5>
 
−
<ul>
 
−
<li> Things </li>
 
−
</ul>
 
−
</div>
 
−
 
−
<div class="column full_size">
 
 
<div align="center">
 
<div align="center">
−
<h5> Interlab Study </h5>
+
<h1> <a id="stuff" href="https://2016.igem.org/Team:Stony_Brook/Notebook/Cancer-W4">Week 4: 7/18 - 7/24</a></h1>
−
<ul>
+
−
<li> FITC started </li>
+
−
<li> Cutting re-inoculated </li>
+
−
<li> Ordered new LUDOX </li>
+
−
</div>
+
 
</div>
 
</div>
  
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<div class="column full_size">
 
 
<div align="center">
 
<div align="center">
−
<h5> Other </h5>
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<h1> <a id="stuff" href="https://2016.igem.org/Team:Stony_Brook/Notebook/Cancer-W5">Week 5: 7/25 - 7/31</a> </h1>
−
<ul>
+
−
<li> College of Arts and Sciences Pre College Summer Institute students stopped by lab </li>
+
−
<li> Spoke to them about information on synthetic biology and iGEM </li>  
+
 
</div>
 
</div>
−
</div>
 
  
−
<div class="column full_size">
 
 
<div align="center">
 
<div align="center">
−
<h3 style="color:#B61C1D;"> 6/30 </h3>
+
<h1>  <a id="stuff" href="https://2016.igem.org/Team:Stony_Brook/Notebook/Cancer-W6">Week 6: 8/1 - 8/7</a></h1>
−
</div>
+
 
</div>
 
</div>
  
−
<div class="column half_size">
 
−
<h5> Cancer Group </h5>
 
−
<ul>
 
−
<li> PCR worked → Test 5 → changed annealing temperature to 66 degrees C + increased the denaturing time </li>
 
−
<li> Nanodropped DNA</li>
 
−
<ul>
 
−
</div>
 
−
 
−
<div class="column half_size">
 
−
<h5> Vaccine Group </h5>
 
−
<ul>
 
−
<li> Things </li>
 
−
</ul>
 
−
</div>
 
−
 
−
<div class="column full_size">
 
 
<div align="center">
 
<div align="center">
−
<h3 style="color:#B61C1D;"> 7/1 </h3>
+
<h1> <a id="stuff" href="https://2016.igem.org/Team:Stony_Brook/Notebook/Cancer-W7">Week 7: 8/8 - 8/14</a></h1>
−
</div>
+
 
</div>
 
</div>
  
−
<div class="column half_size">
 
−
<h5> Cancer Group </h5>
 
−
<ul>
 
−
<li> Digestion of TDGF-1 construct and YFP352GAP vector with two restriction enzymes </li>
 
−
<li> Will ligate later </li>
 
−
</ul>
 
−
<table border=1>
 
−
<tr>
 
−
<td></td>
 
−
<td>TDGF-1 Construct (Phire PCR 128.2 ng/mL)</td>
 
−
<td>YEP352GAP Vector (343.2 ng/mL)</td>
 
−
</tr>
 
−
<tr>
 
−
<td>Total Reaction Volume</td>
 
−
<td>50 uL</td>
 
−
<td>50 uL</td>
 
−
</tr>
 
−
<tr>
 
−
<td>Nuclease Free Water</td>
 
−
<td>27.4 uL</td>
 
−
<td>37.2 uL</td>
 
−
</tr>
 
−
<tr>
 
−
<td>10x Cutsmart Buffer</td>
 
−
<td>5 uL</td>
 
−
<td>5uL</td>
 
−
</tr>
 
−
<tr>
 
−
<td>xho1</td>
 
−
<td>1 uL</td>
 
−
<td>1 uL</td>
 
−
</tr>
 
−
<tr>
 
−
<td>Pvu II</td>
 
−
<td>1 uL</td>
 
−
<Td>1 uL</td>
 
−
</tr>
 
−
<tr>
 
−
<td>DNA</td>
 
−
<td>15.6 uL</td>
 
−
<td>5.8 uL</td>
 
−
</tr>
 
−
</table>
 
−
</div>
 
−
 
−
<div class="column half_size">
 
−
<h5> Vaccine Group </h5>
 
−
<ul>
 
−
<li> Things </li>
 
−
</ul>
 
−
</div>
 
−
 
−
<div class="column full_size">
 
 
<div align="center">
 
<div align="center">
−
<h3 style="color:#B61C1D;">7/2 </h3>
+
<h1> <a id="stuff"href="https://2016.igem.org/Team:Stony_Brook/Notebook/Cancer-W8">Week 8: 8/15 - 8/21</a> </h1>
−
</div>
+
 
</div>
 
</div>
  
−
<div class="column half_size">
 
−
<h5> Cancer Group </h5>
 
−
<ul>
 
−
<li> Running yesterday's digestion on gel </li>
 
−
</ul>
 
−
</div>
 
−
 
−
<div class="column full_size">
 
 
<div align="center">
 
<div align="center">
−
<h1> Week 2 (7/5-7/8) </h1>
+
<h1> <a id="stuff" href="https://2016.igem.org/Team:Stony_Brook/Notebook/Cancer-W9">Week 9: 8/22 - 8/28</a></h1>
−
<h3 style="color:#B61C1D;">7/5 </h3>
+
−
</dv>
+
 
</div>
 
</div>
  
−
<div class="column half_size">
 
−
<h5> Cancer Group </h5>
 
−
<ul>
 
−
<li> Ran the PCR'ed construct on a gel with Phire Polymerase → It didn't work
 
−
</ul>
 
−
</div>
 
−
 
−
<div class="column half_size">
 
−
<h5> Vaccine Group </h5>
 
−
<ul>
 
−
<li> Things </li>
 
−
</ul>
 
−
</div>
 
−
 
−
<div class="column full_size">
 
 
<div align="center">
 
<div align="center">
−
<h3 style="color:#B61C1D;">7/6 </h3>
+
<h1> <a id="stuff" href="https://2016.igem.org/Team:Stony_Brook/Notebook/Cancer-W10"> Week 10: 8/29 - 9/4 </a> </h1>
−
</div>
+
 
</div>
 
</div>
  
−
<div class="column half_size">
 
−
<h5> Cancer group </h5>
 
−
<ul>
 
−
<li> Ran the construct with PCR on gel → it worked </li>
 
−
<li> Tasnia stabbed our gel </li>
 
−
<li> Interlab study continues </li>
 
−
</ul>
 
−
</div>
 
−
 
−
<div class="column half_size">
 
−
<h5> Vaccine Group </h5>
 
−
<ul>
 
−
<li> Things </li>
 
−
</ul>
 
−
</div>
 
−
 
−
<div class="column full_size">
 
 
<div align="center">
 
<div align="center">
−
<h3 style="color:#B61C1D;">7/7 </h3>
+
<h1> <a id="stuff" href="https://2016.igem.org/Team:Stony_Brook/Notebook/Cancer-W11"> Week 11: 9/5 - 9/11 </a> </h1>  
−
</div>
+
</div>  
−
</div>
+
  
−
<div class="column half_size">
 
−
<h5> Cancer group </h5>
 
−
<ul>
 
−
<li> Nanodrops were pretty low (84-120 ng/nl) </li>
 
−
<li> 11:46am PCR'ed the highest nanodrop result in tube #1 → PCR successful </li>
 
−
<li> 2:33pm → attempt to digest with remaining non-PCR product → removed from incubator at 5:00pm </li>
 
−
<li> Made a gel → ran PCR </li>
 
−
</ul>
 
−
</div>
 
  
−
<div class="column half_size">
 
−
<h5> Vaccine Group </h5>
 
−
<ul>
 
−
<li> Things </li>
 
−
</ul>
 
−
</div>
 
−
 
−
<div class="column full_size">
 
 
<div align="center">
 
<div align="center">
−
<h1> Week 3 (7/11-7//15) </h1>
+
<h1> <a id="stuff" href="https://2016.igem.org/Team:Stony_Brook/Notebook/Cancer-W14"> Week 12: 9/26 - 10/2 </a> </h1>
−
<h3 style="color:#B61C1D;"> 7/11 </h3>
+
−
</div>
+
 
</div>
 
</div>
  
−
<div class="column half_size">
 
−
<h5> Cancer group </h5>
 
−
<ul>
 
−
<li> Ran PCR on the construct (5x) → gel did not work </li>
 
−
<li> PCR'ed 84.2 ng/ml construct </li>
 
−
<li> 5 replicates made using Phire </li>
 
−
<li>Thermocycler Program</li>
 
−
</ul>
 
−
<br>
 
−
<table>
 
−
<tr>
 
−
<td colspan=3 align=center>Thermocycler Program</td>
 
−
<tr>
 
−
<td>Step</td>
 
−
<td>Temperature (Degrees C)</td>
 
−
<td>Duration (seconds)</td>
 
−
</tr>
 
−
<tr>
 
−
<td>1</td>
 
−
<td>98</td>
 
−
<td>30</td>
 
−
</tr>
 
−
<tr>
 
−
<td>2</td>
 
−
<td>98</td>
 
−
<td>20</td>
 
−
</tr>
 
−
<tr>
 
−
<td>3</td>
 
−
<td>66</td>
 
−
<td>5</td>
 
−
</tr>
 
−
<tr>
 
−
<td>4</td>
 
−
<td>72</td>
 
−
<td>30</td>
 
−
</tr>
 
−
<tr>
 
−
<td>5</td>
 
−
<td>72</td>
 
−
<td>60</td>
 
−
</tr>
 
−
<tr>
 
−
<td>6</td>
 
−
<td>4</td>
 
−
<td>Hold</td>
 
−
</tr>
 
−
<tr>
 
−
<td colspan=3>After step 4, return to step 2. Repeat steps 2-4 thirty-five times before continuing to step 5 and on.</td>
 
−
</tr>
 
−
</table>
 
  
−
<table>
 
−
<tr>
 
−
<td>Water</td>
 
−
<td>19.5 uL</td>
 
−
</tr>
 
−
<tr>
 
−
<td>Phire Polymerase</td>
 
−
<td>25 uL</td>
 
−
</tr>
 
−
<tr>
 
−
<td>Template</td>
 
−
<td>0.5 uL</td>
 
−
</tr>
 
−
<tr>
 
−
<td>Forward Primer</td>
 
−
<td>2.5 uL</td>
 
−
</tr>
 
−
<tr>
 
−
<td>Reverse Primer</td>
 
−
<td>2.5 uL</td>
 
−
</tr>
 
−
</table>
 
  
−
<ul>
 
−
<li> Restreaking of YEP352GAP transformed cells for miniprep</li>
 
−
<li> Restreaking placed in incubator at 12am</li>
 
 
</div>
 
</div>
−
 
−
<div class="column half_size">
 
−
<h5> Vaccine Group </h5>
 
−
<ul>
 
−
<li> Stuff & Things </li>
 
−
</ul>
 
−
</div>
 
−
 
−
<div class="column full_size">
 
−
<div align="center">
 
−
<h3 style="color:#B61C1D;"> 7/12 </h3>
 
−
</div>
 
−
</div>
 
−
 
−
<div class="column half_size">
 
−
<h5> Cancer group </h5>
 
−
<ul>
 
−
<li> Made gel for electrophoresis of PCR construct → it didn't work </li>
 
−
<li>Thermocycler Program: Same as PCR from 7/11</li>
 
−
</ul>
 
−
<br>
 
−
<table>
 
−
<tr>
 
−
<td>Q5 Rx Buffer</td>
 
−
<td>10 uL</td>
 
−
</tr>
 
−
<tr>
 
−
<td>10nM dNTPs</td>
 
−
<td>1 uL</td>
 
−
</tr>
 
−
<tr>
 
−
<td>10 uM Forward Primer</td>
 
−
<td>2.5 uL</td>
 
−
</tr>
 
−
<tr>
 
−
<td>10 uM Reverse Primer</td>
 
−
<td>2.5 uL</td>
 
−
</tr>
 
−
<tr>
 
−
<td>Template (Q5 PCR Pw.1 for 6/30/16)</td>
 
−
<td>0.5 uL</td>
 
−
</tr>
 
−
<tr>
 
−
<td>Q5 Polymerase</td>
 
−
<td>2.5 uL</td>
 
−
</tr>
 
−
<tr>
 
−
<td>Water</td>
 
−
<td>33 uL</td>
 
−
</tr>
 
−
</table>
 
−
<ul>
 
−
<li> LB liquid culture (3ml with 3ul of ampicillin) </li>
 
−
<li> Loaded 10ul Ladder DNA. </li>
 
−
<li> Loaded 1ul dye + 5ul PCR product </li>
 
−
<li> Ran gel at 115V </li>
 
−
<li> Checked gel ladder → faint, no band for the PCR product </li>
 
−
<li> Made new gel, loaded with the same amount of reagents as before → ran at 90V → No ladder band </li>
 
−
<li> Ran it again at 115V → visible ladder, no PCR band </li>
 
−
<li> Preparing a gel to run ladder and construct that previously showed a strong band → used this to diagnose a problem with gel setup. Ran TDGF1 152.9 Phire Child. Lane 1 is ladder, Lane 2 is that construct (10ul) with 2ul of dye </li>
 
−
<li> Setup new PCR using the 6/30/16 PCR construct </li>
 
−
</ul>
 
−
<ol>
 
−
<li> 98°C → 30sec </li>
 
−
<li> 98°C → 20sec </li>
 
−
<li> 66°C → 5sec </li>
 
−
<li> 72°C → 30sec </li>
 
−
<li> 72°C → 1min </li>
 
−
<li> 4°C → hold </li>
 
−
</ol>
 
−
</div>
 
−
 
−
<div class="column half_size">
 
−
<h5> Vaccine Group </h5>
 
−
<ul>
 
−
<li> Stuff & Things </li>
 
−
</ul>
 
−
</div>
 
−
 
−
<div class="column full_size">
 
−
<div align="center">
 
−
<h3 style="color:#B61C1D;">7/13 </h3>
 
−
</div>
 
−
</div>
 
−
 
−
<div class="column half_size">
 
−
<h5> Cancer group </h5>
 
−
<ul>
 
−
<li> Ran 5ul of PCR with ladder, cancer construct and vaccine construct → to diagnose problem with gel </li>
 
−
<li> Miniprep of Dean vector (3ml LB culture) </li>
 
−
<li> Purification of PCR product → nanodropped 16.4ug/ul </li>
 
−
<li> Nanodrop of: </li>
 
−
</ul>
 
−
<ol>
 
−
<li> Yellow 7/13 construct NEB purified → 16.4ng/ml</li>
 
−
<li> Blue gel purification → 48.7ng/ul</li>
 
−
<li> Pink PCR purification 7/13 → 102.2ng/ul</li>
 
−
<li>7/13 -RK Vector 1 → 48.2ng/ul</li>
 
−
<li> 7/13 -RK Vector 2 → 96.3ng/ul</li>
 
−
</ol>
 
−
</div>
 
−
 
−
<div class="column half_size">
 
−
<h5> Vaccine Group </h5>
 
−
<ul>
 
−
<li> Things </li>
 
−
</ul>
 
−
</div>
 
−
 
−
<div class="column full_size">
 
−
<div align="center">
 
−
<h3 style="color:#B61C1D;"> 7/14</h3>
 
−
</div>
 
−
</div>
 
−
 
−
<div class="column half_size">
 
−
<h5> Cancer group </h5>
 
−
<ul>
 
−
<li>Things</li>
 
−
</ul>
 
−
</div>
 
−
 
−
<div class="column half_size">
 
−
<h5> Vaccine Group </h5>
 
−
<table>
 
−
<tr>
 
−
<th> Contents of well </th>
 
−
<th> Amount (ul)</th>
 
−
</tr>
 
−
<tr>
 
−
<td> Ladder </td>
 
−
<td> 10 </td>
 
−
</tr>
 
−
<td> AD </td>
 
−
<td> 5 </td>
 
−
</tr>
 
−
<tr>
 
−
<td> AO </td>
 
−
<td> 5 </td>
 
−
</tr>
 
−
<tr>
 
−
<td> AM </td>
 
−
<td> 5 </td>
 
−
</tr>
 
−
<tr>
 
−
<td> AN </td>
 
−
<td> 5 </td>
 
−
</tr>
 
−
<tr>
 
−
<td> Gal-Sunil </td>
 
−
<td> Added 1ul loading dye </td>
 
−
</tr>
 
−
<tr>
 
−
<td> Con-Sunil </td>
 
−
<td> 5 </td>
 
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</tr>
 
−
</table>
 
−
</div>
 
−
<ul>
 
−
<li> Brian and Sunil's Gal promoters worked but both constructs failed</li>
 
−
</ul>
 
−
</div>
 
−
 
−
<div class="column full_size">
 
−
<div align="center">
 
−
<h5> Biobrick ideas </h5>
 
−
<ol>
 
−
<li> Smelly yeast → optimized from e. coli </li>
 
−
<li> Twist on smelly e. coli on e. coli → regulated with quorum sensing</li>
 
−
<li> OmpA/EnvZ recognize osmolarity</li>
 
−
<li>Genetic Circuit</li>
 
−
<li> Shine yellow light → Banana smell. Shine green light → wintergreen </li>
 
−
<li> TetR operator system genetic circuit </li>
 
−
<li> Have cell die at certain wavelength → killswitch </li>
 
−
</ol>
 
−
</div>
 
−
</div>
 
−
 
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<div class="column full_size">
 
−
<div align="center">
 
−
<h3 style="color:#B61C1D;"> 7/15 </h3>
 
−
</div>
 
−
</div>
 
−
 
−
<div class="column half_size">
 
−
<h5> Cancer group </h5>
 
−
<ul>
 
−
<li> Stuff & Things </li>
 
−
</ul>
 
−
</div>
 
−
 
−
<div class="column half_size">
 
−
<h5> Vaccine group </h5>
 
−
<ul>
 
−
<li> Jon and Sunil retrying construct </li>
 
−
<li> Jon used phire at 50°C</li>
 
−
<li> Sunil used Q5. Extension at 72°C for 30 seconds </li>
 
−
</ul>
 
−
<table>
 
−
<tr>
 
−
<th> Polymerase </th>
 
−
<th> Primers (ul) </th>
 
−
<th> Template (ul) </th>
 
−
<th> H<sub>2</sub>O (ul)</th>
 
−
</tr>
 
−
<tr>
 
−
<td> Phire (25ul) </td>
 
−
<td> 2.5 Reverse Construct 2.5 Forward Stitch </td>
 
−
<td> 1.5 </td>
 
−
<td>19.5 </td>
 
−
</tr>
 
−
<tr>
 
−
<td> Q5 (25ul) </td>
 
−
<td> 2.5 Reverse Construct 2.5 Forward Stitch </td>
 
−
<td> 1.5 </td>
 
−
<td> 19.5 </td>
 
−
</tr>
 
−
</table>
 
−
</div>
 
−
 
−
<div class="column full_size">
 
−
<hr>
 
 
</div>
 
</div>
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</html>
 

Latest revision as of 07:53, 19 October 2016

Lab Notebook