Difference between revisions of "Team:Stony Brook/Notebook/Cancer-W6"

(Created page with "{{Stony_Brook}} <html> <head> <title> Week 4: 8/1-8/5 </title> </head> <body> <div class="column full_size"> <ul> <hr> </ul> </div> <div class="column_full size"> <div align...")
 
 
(28 intermediate revisions by 2 users not shown)
Line 1: Line 1:
−
{{Stony_Brook}}
+
{{Stony_Brook TryingFailing}}
 
<html>
 
<html>
 
<head>
 
<head>
−
<title> Week 4: 8/1-8/5 </title>
+
<style>
 +
h1 { color: #B61C1D;
 +
}
 +
h2{ color: #B61C1D;
 +
}
 +
h3, h4, h5, h6 {color: black;
 +
}
 +
</style>
 
</head>
 
</head>
 
<body>
 
<body>
  
 
<div class="column full_size">
 
<div class="column full_size">
 +
<div align="center">
 +
<h1>Week 6: 8/1-8/9 </h1>
 +
</div>
 +
</div>
 +
 +
<div align="center">
 +
<br>
 +
<hr>
 +
<br>
 +
</div>
 +
 +
<div class="column full_size">
 +
<div align="center">
 +
<h2 style="color:#B61C1D;"> 8/1 </h2>
 +
</div>
 +
</div>
 +
 +
<div class="column full_size">
 +
<h4> Emmanuel Ligation (193 ng/ul) </h4>
 
<ul>
 
<ul>
 +
<table>
 +
<tr>
 +
<th> Content </th>
 +
<th> Experimental (ul) </th>
 +
<th> Control (ul) </th>
 +
</tr>
 +
<tr>
 +
<td> H<sub>2</sub>O</td>
 +
<td> 38.8 </td>
 +
<td> 39.8 </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> EcoRI-HF </td>
 +
<td> 0.5 </td>
 +
<td> X </td>
 +
</tr>
 +
<tr>
 +
<td> DNA </td>
 +
<td> 5.18 </td>
 +
<td> 5.18 </td>
 +
</tr>
 +
</table>
 +
</ul>
 +
 +
<br>
 +
 +
<h4> Gel run </h4>
 +
<p> Lanes: </p>
 +
<ol>
 +
<li> Ladder </li>
 +
<li> Emmanuel Digest Control </li>
 +
<li> Emmanuel Digest Experimental </li>
 +
</ol>
 +
<ul>
 +
<li> Did not work </li>
 +
</ul>
 +
 +
<br>
 +
 +
<h4> 25 ul Digest of Ryan + Emmanuel (Veronica) Miniprep </h4>
 +
<ul>
 +
<li> Made 17 LB With Ampicillin (600ml)</li>
 +
</ul>
 +
</div>
 +
 +
<div class="column half_size">
 +
<div align="center">
 +
<h5> Ryan - 446.4 ng/ul </h5>
 +
<ul>
 +
<table>
 +
<tr>
 +
<th> Content </th>
 +
<th> Experimental (ul) </th>
 +
<th> Control (ul) </th>
 +
</tr>
 +
<tr>
 +
<td> H<sub>2</sub>O</td>
 +
<td> 20.4 </td>
 +
<td> 21.4 </td>
 +
</tr>
 +
<tr>
 +
<td> Cutsmart </td>
 +
<td> 2.5 </td>
 +
<td> 2.5 </td>
 +
</tr>
 +
<tr>
 +
<td> XbaI </td>
 +
<td> 0.5 </td>
 +
<td> X </td>
 +
</tr>
 +
<tr>
 +
<td> EcoRI-HF </td>
 +
<td> 0.5 </td>
 +
<td> X </td>
 +
</tr>
 +
<tr>
 +
<td> DNA </td>
 +
<td> 1.12</td>
 +
<td> 1.12 </td>
 +
</tr>
 +
</table>
 +
</ul>
 +
</div>
 +
</div>
 +
 +
<div class="column half_size">
 +
<div align="center">
 +
<h5> Emmanuel - 193 ng/ul </h5>
 +
<ul>
 +
<table>
 +
<tr>
 +
<th> Content </th>
 +
<th> Experimental (ul) </th>
 +
<th> Control (ul) </th>
 +
</tr>
 +
<tr>
 +
<td> H<sub>2</sub>O</td>
 +
<td> 18.9 </td>
 +
<td> 19.9 </td>
 +
</tr>
 +
<tr>
 +
<td> Cutsmart </td>
 +
<td> 2.5 </td>
 +
<td> 2.5 </td>
 +
</tr>
 +
<tr>
 +
<td> XbaI </td>
 +
<td> 0.5 </td>
 +
<td> X </td>
 +
</tr>
 +
<tr>
 +
<td> EcoRI-HF </td>
 +
<td> 0.5 </td>
 +
<td> X </td>
 +
</tr>
 +
<tr>
 +
<td> DNA </td>
 +
<td> 2.59</td>
 +
<td> 2.59 </td>
 +
</tr>
 +
</table>
 +
</ul>
 +
</div>
 +
</div>
 +
 +
<div align="center">
 +
<br>
 
<hr>
 
<hr>
 +
<br>
 +
</div>
 +
 +
<div class="column full_size">
 +
<div align="center">
 +
<h2> 8/2 </h2>
 +
</div>
 +
 +
<h4> Miniprep </h4>
 +
<ul>
 +
<li> Miniprep of ligated construct </li>
 +
<li> 10,000rpm for 3 minutes at 25°C </li>
 
</ul>
 
</ul>
 +
 +
<h4> Ran a nanodrop of Minipreps </h4>
 +
<ul>
 +
<table>
 +
<tr>
 +
<th> Content </th>
 +
<th> Concentration (ng/ul) </th>
 +
<th> 260/280 </th>
 +
</tr>
 +
<tr>
 +
<td> Veronica 1 </td>
 +
<td> 311.5 </td>
 +
<td> 1.86 </td>
 +
</tr>
 +
<tr>
 +
<td> Veronica 2 </td>
 +
<td> 43.8 </td>
 +
<td> 1.76 </td>
 +
</tr>
 +
<tr>
 +
<td> Veronica 3</td>
 +
<td> 259 </td>
 +
<td> 1.88 </td>
 +
</tr>
 +
<tr>
 +
<td> Veronica 4 </td>
 +
<td> 296 </td>
 +
<td> 1.88 </td>
 +
</tr>
 +
<tr>
 +
<td> R1 </td>
 +
<td> 176.5 </td>
 +
<td> 1.75 </td>
 +
</tr>
 +
<tr>
 +
<td> Ryan 2 </td>
 +
<td> 277.3 </td>
 +
<td> 1.85 </td>
 +
</tr>
 +
<tr>
 +
<td> Ryan 3 </td>
 +
<td> 301.6 </td>
 +
<td> 1.81 </td>
 +
</tr>
 +
<tr>
 +
<td> Ryan 4 </td>
 +
<td> 366.6 </td>
 +
<td> 1.82 </td>
 +
</tr>
 +
</table>
 +
</ul>
 +
 +
<h4> Ran a gel of miniprepped plasmids </h4>
 +
<ul>
 +
<li> Used 5ul of DNA and 1 ul of dye </li>
 +
</ul>
 +
<p> Lanes: </p>
 +
<ol>
 +
<li> Veronica 1 </li>
 +
<li> Veronica 3 </li>
 +
<li> Veronica 4 </li>
 +
<li> Ladder </li>
 +
<li> Ryan 1 </li>
 +
<li> Ryan 2 </li>
 +
<li> Ryan 3 </li>
 +
<li> Ryan 4 </li>
 +
</ol>
 +
 +
<div align="center">
 +
<h4> Digest of Miniprepped Plasmids </h4>
 +
</div>
 
</div>
 
</div>
  
−
<div class="column_full size">
+
 
 +
<div class="column half_size">
 
<div align="center">
 
<div align="center">
−
<h2 style="color:#B61C1D;"> 8/1 </h2>
+
<h5> Veronica 1 - 311.5 ng/ul </h5>
 +
<ul>
 +
<table>
 +
<tr>
 +
<th> Content </th>
 +
<th> Experimental (ul) </th>
 +
<th> Control (ul) </th>
 +
</tr>
 +
<tr>
 +
<td> H<sub>2</sub>O</td>
 +
<td> 40.8 </td>
 +
<td> 41.8 </td>
 +
</tr>
 +
<tr>
 +
<td> Cutsmart </td>
 +
<td> 5</td>
 +
<td> 5 </td>
 +
</tr>
 +
<tr>
 +
<td> XbaI </td>
 +
<td> 0.5 </td>
 +
<td> X </td>
 +
</tr>
 +
<tr>
 +
<td> PvuII-HF </td>
 +
<td> 0.5 </td>
 +
<td> X </td>
 +
</tr>
 +
<tr>
 +
<td> DNA </td>
 +
<td> 3.21</td>
 +
<td> 3.21 </td>
 +
</tr>
 +
</table>
 +
</ul>
 +
</div>  
 
</div>
 
</div>
 +
 +
<div class="column half_size">
 +
<div align="center">
 +
<h5> Ryan 4 - 366.6 ng/ul </h5>
 +
<ul>
 +
<table>
 +
<tr>
 +
<th> Content </th>
 +
<th> Experimental (ul) </th>
 +
<th> Control (ul) </th>
 +
</tr>
 +
<tr>
 +
<td> H<sub>2</sub>O</td>
 +
<td> 41.3 </td>
 +
<td> 42.3 </td>
 +
</tr>
 +
<tr>
 +
<td> Cutsmart </td>
 +
<td> 5</td>
 +
<td> 5 </td>
 +
</tr>
 +
<tr>
 +
<td> XbaI </td>
 +
<td> 0.5 </td>
 +
<td> X </td>
 +
</tr>
 +
<tr>
 +
<td> PvuII-HF </td>
 +
<td> 0.5 </td>
 +
<td> X </td>
 +
</tr>
 +
<tr>
 +
<td> DNA </td>
 +
<td> 2.73</td>
 +
<td> 2.73 </td>
 +
</tr>
 +
</table>
 +
</ul>
 +
</div>
 +
</div>
 +
 +
<div align="center">
 +
<br>
 +
<hr>
 +
<br>
 +
</div>
 +
 +
<div class="column full_size">
 +
<div align="center">
 +
<h2 style="color:#B61C1D;"> 8/3 </h2>
 +
</div>
 +
</div>
 +
 +
<h4> Transformations </h4>
 +
<ul>
 +
<li> Transformed R001, J61100, puC19 </li>
 +
<li> 500 uL of SOC used for each transformation </li>
 +
</ul>
 +
 +
<h4>Miniprep of BioBricks from 8/2</h4>
 +
 +
<h4> Gel run ( 6uL of each tube loaded)</h4>
 +
<p> Lanes: </p>
 +
<ol>
 +
<li> 5 uL plasmid</li>
 +
<li> 5 uL plasmid + 5 uL of nuclease free water</li>
 +
<li> 5 uL plasmid + 5 uL water + 2.5 uL of CutSmart Buffer</li>
 +
<li> Ladder </li>
 +
<li> 5 uL plasmid + 5 uL water + 2.5 uL CutSmart + 0.75 uL XhoI </li>
 +
<li> 5 ul plasmid + 5 uL water + 2.5 uL CutSmart + 0.75 uL PvuII</li>
 +
<li> 5 ul plasmid + 6 uL water + 2.5 uL CutSmart + 0.75 uL XhoI + 0.75 uL PvuII</li>
 +
 +
</ol>
 +
<ul>
 +
<li> Did not work </li>
 +
</ul>
 +
 +
<h4>Interlab LB cultures made from plates </h4>
 +
 +
<h4> Developed sequencing primers for construct </h4>
 +
 +
<div align="center">
 +
<br>
 +
<hr>
 +
<br>
 +
</div>
 +
 +
<div class="column full_size">
 +
<div align="center">
 +
<h2 style="color:#B61C1D;"> 8/4 </h2>
 +
</div>
 +
</div>
 +
 +
<h4>Worked on InterLab study </h4>
 +
 +
<h4> Gel ran (done by Emmanuel) </h4>
 +
<p> Lanes: </p>
 +
<ol>
 +
<li> Veronica control (plasmid) </li>
 +
<li> Veronica digest </li>
 +
<li> Ladder </li>
 +
<li>  Ryan digest</li>
 +
<li> Ryan control (plasmid) </li>
 +
 +
</ol>
 +
<ul>
 +
<li> Did not work </li>
 +
</ul>
 +
 +
<h5>PCR of miniprepped project plasmids to determine ligation</h5>
 +
 +
</div>
 +
 +
<div class="column half_size">
 +
<div align="center">
 +
<h5> PCR Contents: </h5>
 +
<ul>
 +
<table>
 +
<tr>
 +
<th> Contents </th>
 +
<th> ul </th>
 +
</tr>
 +
<td> Phire </td>
 +
<td> 10 uL </td>
 +
</tr>
 +
<tr>
 +
<td> H<sub>2</sub>O</td>
 +
<td> 7.5 uL </td>
 +
</tr>
 +
<tr>
 +
<td> 50 uM F Primer </td>
 +
<td> 1 uL </td>
 +
</tr>
 +
<tr>
 +
<td> 50 uM R Primer </td>
 +
<td> 1 uL </td>
 +
</tr>
 +
<tr>
 +
<td> Plasmids: 366.6 ng/uL, 301 ng/uL, 259 ng/uL </td>
 +
<td> 0.5 uL </td>
 +
</tr>
 +
</table>
 +
</ul>
 +
</div>
 +
</div>
 +
 +
<div class="column half_size">
 +
<div align="center">
 +
<h4> PCR Settings: </h4>
 +
<ul>
 +
<table>
 +
<tr>
 +
<th> Phase </th>
 +
<th> Temperature (°C) </th>
 +
<th> Time (sec)</th>
 +
</tr>
 +
<tr>
 +
<td> Initial Denaturation </td>
 +
<td> 98 </td>
 +
<td> 30s </td>
 +
</tr>
 +
<tr>
 +
<td> Denaturation </td>
 +
<td> 98 </td>
 +
<td> 20s </td>
 +
</tr>
 +
<tr>
 +
<td> Annealing </td>
 +
<td> 66 </td>
 +
<td> 5 </td>
 +
</tr>
 +
<tr>
 +
<td> Extension </td>
 +
<td> 72 </td>
 +
<td> 30s </td>
 +
</tr>
 +
<tr>
 +
<td> Final Extension </td>
 +
<td> 72 </td>
 +
<td> 60s </td>
 +
</tr>
 +
</table>
 +
</ul>
 +
</div>
 +
</div>
 +
 +
 +
<div class="column full_size">
 +
<h5>Miniprep of BioBrick LBs made by Noah</h5>
 +
<br>
 +
<br>
 +
<h4> Gel run ( 5uL of each tube loaded)</h4>
 +
<p> Lanes: </p>
 +
<ol>
 +
<li> Ladder </li>
 +
<li> Plasmid PCR 301 ng/uL </li>
 +
<li> Plasmid PCR 259 ng/uL </li>
 +
<li> Plasmid PCR 366.6 ng/uL </li>
 +
 +
</ol>
 +
<ul>
 +
<li> Worked! :) </li>
 +
</ul>
 +
</div>
 +
 +
<div align="center">
 +
<br>
 +
<hr>
 +
<br>
 
</div>
 
</div>

Latest revision as of 15:01, 23 August 2016

Week 6: 8/1-8/9



8/1

Emmanuel Ligation (193 ng/ul)

    Content Experimental (ul) Control (ul)
    H2O 38.8 39.8
    Cutsmart 5.0 5.0
    XbaI 0.5 X
    EcoRI-HF 0.5 X
    DNA 5.18 5.18

Gel run

Lanes:

  1. Ladder
  2. Emmanuel Digest Control
  3. Emmanuel Digest Experimental
  • Did not work

25 ul Digest of Ryan + Emmanuel (Veronica) Miniprep

  • Made 17 LB With Ampicillin (600ml)
Ryan - 446.4 ng/ul
    Content Experimental (ul) Control (ul)
    H2O 20.4 21.4
    Cutsmart 2.5 2.5
    XbaI 0.5 X
    EcoRI-HF 0.5 X
    DNA 1.12 1.12
Emmanuel - 193 ng/ul
    Content Experimental (ul) Control (ul)
    H2O 18.9 19.9
    Cutsmart 2.5 2.5
    XbaI 0.5 X
    EcoRI-HF 0.5 X
    DNA 2.59 2.59


8/2

Miniprep

  • Miniprep of ligated construct
  • 10,000rpm for 3 minutes at 25°C

Ran a nanodrop of Minipreps

    Content Concentration (ng/ul) 260/280
    Veronica 1 311.5 1.86
    Veronica 2 43.8 1.76
    Veronica 3 259 1.88
    Veronica 4 296 1.88
    R1 176.5 1.75
    Ryan 2 277.3 1.85
    Ryan 3 301.6 1.81
    Ryan 4 366.6 1.82

Ran a gel of miniprepped plasmids

  • Used 5ul of DNA and 1 ul of dye

Lanes:

  1. Veronica 1
  2. Veronica 3
  3. Veronica 4
  4. Ladder
  5. Ryan 1
  6. Ryan 2
  7. Ryan 3
  8. Ryan 4

Digest of Miniprepped Plasmids

Veronica 1 - 311.5 ng/ul
    Content Experimental (ul) Control (ul)
    H2O 40.8 41.8
    Cutsmart 5 5
    XbaI 0.5 X
    PvuII-HF 0.5 X
    DNA 3.21 3.21
Ryan 4 - 366.6 ng/ul
    Content Experimental (ul) Control (ul)
    H2O 41.3 42.3
    Cutsmart 5 5
    XbaI 0.5 X
    PvuII-HF 0.5 X
    DNA 2.73 2.73


8/3

Transformations

  • Transformed R001, J61100, puC19
  • 500 uL of SOC used for each transformation

Miniprep of BioBricks from 8/2

Gel run ( 6uL of each tube loaded)

Lanes:

  1. 5 uL plasmid
  2. 5 uL plasmid + 5 uL of nuclease free water
  3. 5 uL plasmid + 5 uL water + 2.5 uL of CutSmart Buffer
  4. Ladder
  5. 5 uL plasmid + 5 uL water + 2.5 uL CutSmart + 0.75 uL XhoI
  6. 5 ul plasmid + 5 uL water + 2.5 uL CutSmart + 0.75 uL PvuII
  7. 5 ul plasmid + 6 uL water + 2.5 uL CutSmart + 0.75 uL XhoI + 0.75 uL PvuII
  • Did not work

Interlab LB cultures made from plates

Developed sequencing primers for construct



8/4

Worked on InterLab study

Gel ran (done by Emmanuel)

Lanes:

  1. Veronica control (plasmid)
  2. Veronica digest
  3. Ladder
  4. Ryan digest
  5. Ryan control (plasmid)
  • Did not work
PCR of miniprepped project plasmids to determine ligation
PCR Contents:
    Contents ul
    Phire 10 uL
    H2O 7.5 uL
    50 uM F Primer 1 uL
    50 uM R Primer 1 uL
    Plasmids: 366.6 ng/uL, 301 ng/uL, 259 ng/uL 0.5 uL

PCR Settings:

    Phase Temperature (°C) Time (sec)
    Initial Denaturation 98 30s
    Denaturation 98 20s
    Annealing 66 5
    Extension 72 30s
    Final Extension 72 60s
Miniprep of BioBrick LBs made by Noah


Gel run ( 5uL of each tube loaded)

Lanes:

  1. Ladder
  2. Plasmid PCR 301 ng/uL
  3. Plasmid PCR 259 ng/uL
  4. Plasmid PCR 366.6 ng/uL
  • Worked! :)