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

 
(120 intermediate revisions by 3 users not shown)
Line 1: Line 1:
−
{{Stony_Brook}}
+
{{Stony_Brook TryingFailing}}
 
<html>
 
<html>
 +
<head>
 +
<style>
 +
h1 { color: #B61C1D;
 +
font-family: Georgia;
 +
}
 +
h2{ color: #B61C1D;
 +
}
 +
h3, h4, h5, h6 {color: black;
 +
}
 +
h1, h2, h3, h4, h5, h6 { font-family: Georgia;}
 +
#stuff { color:#B61C1D;}
  
−
 
+
</style>
 
<div class="column full_size">
 
<div class="column full_size">
−
 
+
<div align="center">
−
<p> Document the dates you worked on your project.</p>
+
<h1> Lab Notebook </h1>
−
 
+
 
</div>
 
</div>
−
 
−
<div class="column half_size">
 
−
<h5>What should this page have?</h5>
 
−
<ul>
 
−
<li>Chronological notes of what your team is doing.</li>
 
−
<li> Brief descriptions of daily important events.</li>
 
−
<li>Pictures of your progress. </li>
 
−
<li>Mention who participated in what task.</li>
 
−
</ul>
 
−
 
 
</div>
 
</div>
  
−
<div class="column half_size">
 
−
<h5>Inspiration</h5>
 
−
<p>You can see what others teams have done to organize their notes:</p>
 
−
 
−
<ul>
 
−
<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>
 
−
<li><a href="https://2014.igem.org/Team:Cornell/notebook">2014 Cornell</a></li>
 
−
</ul>
 
−
 
−
</div>
 
  
 
<div class="column full_size">
 
<div class="column full_size">
−
<hr>
 
 
<div align="center">
 
<div align="center">
−
<h2> Week 1 (6/27 - 7/2) </h2>
 
−
<h4> 6/27 </h4>
 
−
</div>
 
−
</div>
 
  
−
<div class="column half_size">
+
<h1> <a id="stuff" href="https://2016.igem.org/Team:Stony_Brook/Notebook/Cancer-W1">Week 1: 6/28 - 7/1 </a> </h1>
−
<h5> Cancer Group </h5>
+
−
<ul>
+
−
<li> PCR of 3xHA-TDGF1 construct </li>
+
−
<li> Gel of PCR Product → PCR was a failure </li>
+
−
<li> Second PCR of 3xHA-TDGF1 construct → left overnight </li>
+
−
</ul>
+
−
</div>
+
  
−
<div class="column half_size">
 
−
<h5> Interlab Study </h5>
 
−
<ul>
 
−
<li> Measured LUDOX and water for plate reader </li>
 
−
<li> Transformation of positive and negative controls, test devices 1-3 </li>
 
−
</ul>
 
−
</div>
 
−
 
−
<div class="column full_size">
 
 
<div align="center">
 
<div align="center">
−
<h4> 6/28</h4>
+
<h1> <a id="stuff" href="https://2016.igem.org/Team:Stony_Brook/Notebook/Cancer-W2">Week 2: 7/4 - 7/8 </a> </h1>
−
</div>
+
 
</div>
 
</div>
  
−
<div class="column half_size">
 
−
<h5> Cancer Group </h5>
 
−
<ul>
 
−
<li> Ran gel on PCR of yesterday's construct → Gel worked </li>
 
−
<li> Gel purification of PCR Product → low concentration of DNA found during nanodrop</li>
 
−
<li> PCR the construct using a revised method </li>
 
−
<li> 2:54pm → ran the gel on the PCR product </li>
 
−
</ul>
 
−
</div>
 
−
 
−
<div class="column half_size">
 
−
<h5> Interab Study </h5>
 
−
<ul>
 
−
<li> Heat and "SB" streaking seems not to have worked</li>
 
−
<li> No visible red colonies on plate </li>
 
−
</ul>
 
−
</div>
 
−
 
−
<div class="column full_size">
 
 
<div align="center">
 
<div align="center">
−
<h4> 6/29 </h4>
+
<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>
  
−
<div class="column half_size">
 
−
<h5> Cancer Group </h5>
 
−
<ul>
 
−
<li> PCR Not working well → keep trying new methods with different annealing temperatures </li>
 
−
<li> Tried 65 and 67 degrees C</li>
 
−
</ul>
 
−
</div>
 
−
 
−
<div class="column half_size">
 
−
<h5> Interlab Study </h5>
 
−
<ul>
 
−
<li> FITC started </li>
 
−
<li> Cutting re-inoculated </li>
 
−
<li> Ordered new LUDOX </li>
 
−
</div>
 
−
 
−
<div class="column full_size">
 
 
<div align="center">
 
<div align="center">
−
<h5> Other </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> 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">
−
<h4> 6/30 </h4>
+
<h1> <a id="stuff" href="https://2016.igem.org/Team:Stony_Brook/Notebook/Cancer-W5">Week 5: 7/25 - 7/31</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 full_size">
 
 
<div align="center">
 
<div align="center">
−
<h4> 7/1 </h4>
+
<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> Digestion of TDGF-1 construct and YFP352GAP vector </li>
 
−
<h1> Will add a table to this later </h1>
 
−
</div>
 
−
 
−
<div class="column full_size">
 
 
<div align="center">
 
<div align="center">
−
<h4> 7/2 </h4>
+
<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> Running yesterday's digestion on gel </li>
 
−
</ul>
 
−
</div>
 
−
 
−
<div class="column full_size">
 
 
<div align="center">
 
<div align="center">
−
<h2> Week 2 (7/5-7/8) </h2>
+
<h1> <a id="stuff"href="https://2016.igem.org/Team:Stony_Brook/Notebook/Cancer-W8">Week 8: 8/15 - 8/21</a> </h1>
−
<h4> 7/5 </h4>
+
−
</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">
−
<h4> 7/6 </h4>
+
<h1> <a id="stuff" href="https://2016.igem.org/Team:Stony_Brook/Notebook/Cancer-W9">Week 9: 8/22 - 8/28</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 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">
−
<h4> 7/7 </h4>
+
<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> 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">
−
<h2> Week 3 (7/11-7//15) </h2>
+
<h1> <a id="stuff" href="https://2016.igem.org/Team:Stony_Brook/Notebook/Cancer-W11"> Week 11: 9/5 - 9/11 </a> </h1>  
−
<h4> 7/11 </h4>
+
</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><h1> Insert Table </h1></li>
 
−
<li> Restreaking of YEP352GAP transformed cells for miniprep</li>
 
−
<li> Restreaking placed in incubator at 12am</li>
 
−
</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">
 
<div align="center">
−
<h4> 7/12 </h4>
+
<h1> <a id="stuff" href="https://2016.igem.org/Team:Stony_Brook/Notebook/Cancer-W14"> Week 12: 9/26 - 10/2 </a> </h1>
−
</div>
+
 
</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><h1> Insert table here</h1></li>
 
−
<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">
 
−
<h4> 7/13 </h4>
 
 
</div>
 
</div>
 
</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>
 
−
</ul>
 
−
</div>
 
−
 
−
<div class="column full_size">
 
−
<hr>
 
−
</div>
 
−
</html>
 

Latest revision as of 07:53, 19 October 2016

Lab Notebook