Difference between revisions of "Team:Northwestern/08 29"

(Created page with "<html> <style> </style> <head> <meta charset="UTF-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-...")
 
 
(4 intermediate revisions by the same user not shown)
Line 20: Line 20:
 
   <article>
 
   <article>
 
     <h1>Monday, August 29<sup>th</sup></h3>
 
     <h1>Monday, August 29<sup>th</sup></h3>
−
     <h2>Agenda:</h2>
+
<h2>Results:</h2>
−
 
+
    <p> While GFP and the Gibson kit positive control had colonies, the gRNA Gibson product (Tet) and positive transformation control (Cam) did not yield colonies.</p>
 +
    <p>The gRNA Gibson has falied grow the past two times we transformed it, so we’re suspicious that it might not be a problem with the Gibson assembly, because the Gibson control has grown on Amp.</p>
 +
    <div class="row">
 +
      <div class="col-xs-6"><img src="https://static.igem.org/mediawiki/2016/0/07/T--Northwestern--08_29_3.jpg" width="1200" height="1600" alt=""/>
 +
        <p><strong>Figure 1:</strong> GFP transformation from iGEM kit</p>
 +
      </div>
 +
      <div class="col-xs-6"><img src="https://static.igem.org/mediawiki/2016/4/4b/T--Northwestern--08_29_5.jpg" width="1200" height="1600" alt=""/>
 +
        <p><strong>Figure 2:</strong> Gibson positive control on Amp</p>
 +
      </div>
 +
    </div>
 +
     <h2>Tasks:</h2>
 +
    <div class="row">
 +
      <div class="col-sm-2">
 +
        <p>Jordan</p>
 +
      </div>
 +
      <div class="col-sm-10">
 +
        <ul>
 +
          <li>Made Cam and Tet plates from the LB Kelly gave us</li>
 +
          <ul>
 +
            <li>Two bottles of 250 mL each</li>
 +
            <li>Added 3.75 grams of Bacto agar to each bottle and autoclaved, cooled to 55&#176;C in water bath</li>
 +
            <li>Added 250 uL of Cam and Tet to respective media</li>
 +
            <li>Poured approximately 20 plates of each</li>
 +
            <li>Wrapped in foil and placed in the fridge </li>
 +
          </ul>
 +
        </ul>
 +
      </div>
 +
    </div>
 +
    <div class="row">
 +
      <div class="col-sm-2">
 +
        <p>Michelle</p>
 +
      </div>
 +
      <div class="col-sm-10">
 +
        <ul>
 +
          <li>Troubleshot transformation plating
 +
            <div class="row">
 +
              <div class="col-xs-12"><img src="https://static.igem.org/mediawiki/2016/e/e5/T--Northwestern--08_29_4.png" width="1204" height="366" alt=""/></div>
 +
            </div>
 +
          </li>
 +
          <li>Started running a western blot on TetR-Cas9 and Assembled Cas9 (in triplicate) with Ben from the Jewett lab</li>
 +
        </ul>
 +
      </div>
 +
    </div>
 +
    <div class="row">
 +
      <div class="col-sm-2">
 +
        <p>Sam</p>
 +
      </div>
 +
      <div class="col-sm-10">
 +
        <ul>
 +
          <li>Worked on questions for Dr. Postelnick</li>
 +
          <li>To do: set up a meeting (or maybe just email?) Dr. Tullman-Ercek</li>
 +
          <ul>
 +
            <li>Ask whether she knows of any good delivery mechanisms to get large proteins to the periplasm</li>
 +
            <li>Cas9 size</li>
 +
            <li>What pathways we’re already trying</li>
 +
          </ul>
 +
        </ul>
 +
      </div>
 +
    </div>
 +
    <div class="row">
 +
      <div class="col-sm-2">
 +
        <p>Tasfia</p>
 +
      </div>
 +
      <div class="col-sm-10">
 +
        <ul>
 +
          <li>Went to Jewett lab for western blotting TetR-Cas9 and Assembled Cas9</li>
 +
          <li>PCR: Linearization of tet backbone for GFP</li>
 +
          <ul>
 +
            <li>Three 50-uL reactions</li>
 +
            <li>1 uL OneTaq 2X Master Mix</li>
 +
            <li>1 uL DMSO</li>
 +
            <li>1 uL 10 uM forward primer</li>
 +
            <li>1 uL 10 uM reverse primer</li>
 +
            <li>1 uL template</li>
 +
            <ul>
 +
              <li>Template concentration: 28 ng/uL</li>
 +
              <li>Template amounts used:</li>
 +
              <ul>
 +
                <li>28 ng</li>
 +
                <li>2.8 ng</li>
 +
                <li>1.4 ng</li>
 +
              </ul>
 +
            </ul>
 +
            <li>Conditions:
 +
            <div class="row">
 +
                <div class="col-xs-8 col-sm-12"><img src="https://static.igem.org/mediawiki/2016/2/26/T--Northwestern--08_29_2.png" width="1340" height="186" alt=""/></div>
 +
              </div>
 +
            </li>
 +
            <li>Products are DpnI digesting at room temperature overnight</li>
 +
          </ul>
 +
          <li>PCR: Linearization of Cas9 for signal sequences</li>
 +
          <ul>
 +
            <li>We had to rerun the Cas9-Lrz-SS procedure because the gel extractions from the most recent PCR gave us erroneous concentrations and 260 ratios (~555 ng/uL, really high 260/280 and 260/230 ratios) </li>
 +
            <li>25 uL OneTaq 2X Master Mix</li>
 +
            <li>1 uL DMSO </li>
 +
            <li>1 uL 10 μM forward primer</li>
 +
            <li>1 uL 10 uM reverse primer</li>
 +
            <li>1 uL template</li>
 +
            <li>21 uL nuclease-free water </li>
 +
            <li>Two Cas9 template samples used:</li>
 +
            <ul>
 +
              <li>“Cas9 1:3” (concentration ~155 ng/uL)</li>
 +
              <li>“Cas9 miniprep w/ antibiotic” (concentration ~30 ng/uL)</li>
 +
            </ul>
 +
            <li>Four 50-uL reactions with the following template amounts</li>
 +
            <ul>
 +
              <li>“Cas9 1:3”</li>
 +
              <ul>
 +
                <li>15 ng</li>
 +
                <li>1.5 ng</li>
 +
              </ul>
 +
              <li>“Cas9 miniprep w/ antibiotic”</li>
 +
              <ul>
 +
                <li>3.0 ng</li>
 +
                <li>1.5 ng </li>
 +
              </ul>
 +
            </ul>
 +
            <li>Conditions:
 +
              <div class="row">
 +
                <div class="col-xs-8 col-sm-12"><img src="https://static.igem.org/mediawiki/2016/e/e0/T--Northwestern--08_29_1.png" width="1340" height="186" alt=""/></div>
 +
              </div>
 +
            </li>
 +
            <li>Product is in the thermal cycler and will be ready to DpnI digest tomorrow morning</li>
 +
          </ul>
 +
        </ul>
 +
      </div>
 +
    </div>
 +
    <div class="row">
 +
      <div class="col-sm-2">
 +
        <p>Tyler</p>
 +
      </div>
 +
      <div class="col-sm-10">
 +
        <ul>
 +
          <li>PCR: Linearization of mRFP</li>
 +
          <li>Aided in western blotting</li>
 +
          <li>Ordered Gel Kit &amp; SybrSafe </li>
 +
          <li>Troubleshot nanodrop</li>
 +
          <li>Took some plate pics </li>
 +
        </ul>
 +
      </div>
 +
    </div>
 +
  </article>
 
<footer id="nav">
 
<footer id="nav">
 
       <div class="row">
 
       <div class="row">
 
         <div class="col-sm-4"><a href="https://2016.igem.org/Team:Northwestern/08_28"><img src="https://static.igem.org/mediawiki/2016/c/c6/T--Northwestern--backarrow.png" height="15" width="15"/> yesterday</a></div>
 
         <div class="col-sm-4"><a href="https://2016.igem.org/Team:Northwestern/08_28"><img src="https://static.igem.org/mediawiki/2016/c/c6/T--Northwestern--backarrow.png" height="15" width="15"/> yesterday</a></div>
−
         <div class="col-sm-4"><a href="https://2016.igem.org/Team:Northwestern/Notebook">back to calender </a></div>
+
         <div class="col-sm-4"><a href="https://2016.igem.org/Team:Northwestern/Notebook">back to calendar </a></div>
 
         <div class="col-sm-4"><a href="https://2016.igem.org/Team:Northwestern/08_30">tomorrow <img src="https://static.igem.org/mediawiki/2016/6/65/T--Northwestern--forwardarrow.png" height="15" width="15"/></a></div>
 
         <div class="col-sm-4"><a href="https://2016.igem.org/Team:Northwestern/08_30">tomorrow <img src="https://static.igem.org/mediawiki/2016/6/65/T--Northwestern--forwardarrow.png" height="15" width="15"/></a></div>
 
       </div>
 
       </div>
 
     </footer>
 
     </footer>
−
  </article>
+
 
 
<script type="text/javascript" src="https://2016.igem.org/Team:Northwestern/libraries/jquery?action=raw&ctype=text/javascript"></script>
 
<script type="text/javascript" src="https://2016.igem.org/Team:Northwestern/libraries/jquery?action=raw&ctype=text/javascript"></script>
 
         <script type="text/javascript" src="https://2016.igem.org/Team:Northwestern/libraries/bootstrap?action=raw&ctype=text/javascript"></script>
 
         <script type="text/javascript" src="https://2016.igem.org/Team:Northwestern/libraries/bootstrap?action=raw&ctype=text/javascript"></script>

Latest revision as of 15:33, 18 October 2016

Notebook

Monday, August 29th

Results:

While GFP and the Gibson kit positive control had colonies, the gRNA Gibson product (Tet) and positive transformation control (Cam) did not yield colonies.

The gRNA Gibson has falied grow the past two times we transformed it, so we’re suspicious that it might not be a problem with the Gibson assembly, because the Gibson control has grown on Amp.

Figure 1: GFP transformation from iGEM kit

Figure 2: Gibson positive control on Amp

Tasks:

Jordan

  • Made Cam and Tet plates from the LB Kelly gave us
    • Two bottles of 250 mL each
    • Added 3.75 grams of Bacto agar to each bottle and autoclaved, cooled to 55°C in water bath
    • Added 250 uL of Cam and Tet to respective media
    • Poured approximately 20 plates of each
    • Wrapped in foil and placed in the fridge

Michelle

  • Troubleshot transformation plating
  • Started running a western blot on TetR-Cas9 and Assembled Cas9 (in triplicate) with Ben from the Jewett lab

Sam

  • Worked on questions for Dr. Postelnick
  • To do: set up a meeting (or maybe just email?) Dr. Tullman-Ercek
    • Ask whether she knows of any good delivery mechanisms to get large proteins to the periplasm
    • Cas9 size
    • What pathways we’re already trying

Tasfia

  • Went to Jewett lab for western blotting TetR-Cas9 and Assembled Cas9
  • PCR: Linearization of tet backbone for GFP
    • Three 50-uL reactions
    • 1 uL OneTaq 2X Master Mix
    • 1 uL DMSO
    • 1 uL 10 uM forward primer
    • 1 uL 10 uM reverse primer
    • 1 uL template
      • Template concentration: 28 ng/uL
      • Template amounts used:
        • 28 ng
        • 2.8 ng
        • 1.4 ng
    • Conditions:
    • Products are DpnI digesting at room temperature overnight
  • PCR: Linearization of Cas9 for signal sequences
    • We had to rerun the Cas9-Lrz-SS procedure because the gel extractions from the most recent PCR gave us erroneous concentrations and 260 ratios (~555 ng/uL, really high 260/280 and 260/230 ratios)
    • 25 uL OneTaq 2X Master Mix
    • 1 uL DMSO
    • 1 uL 10 μM forward primer
    • 1 uL 10 uM reverse primer
    • 1 uL template
    • 21 uL nuclease-free water
    • Two Cas9 template samples used:
      • “Cas9 1:3” (concentration ~155 ng/uL)
      • “Cas9 miniprep w/ antibiotic” (concentration ~30 ng/uL)
    • Four 50-uL reactions with the following template amounts
      • “Cas9 1:3”
        • 15 ng
        • 1.5 ng
      • “Cas9 miniprep w/ antibiotic”
        • 3.0 ng
        • 1.5 ng
    • Conditions:
    • Product is in the thermal cycler and will be ready to DpnI digest tomorrow morning

Tyler

  • PCR: Linearization of mRFP
  • Aided in western blotting
  • Ordered Gel Kit & SybrSafe
  • Troubleshot nanodrop
  • Took some plate pics