Team:Marburg/Notebook:Template

From 2013.igem.org

(Difference between revisions)
(Blanked the page)
 
(8 intermediate revisions not shown)
Line 1: Line 1:
-
{{:Team:Marburg/Template:Header}}
 
-
{{:Team:Marburg/Template:ContentTitle}}
 
-
Notebook
 
-
{{:Team:Marburg/Template:ContentStart}}
 
-
<html>
 
-
 
-
<!-- Beispiel Allgemein -->
 
-
 
-
<div class="notebooky-entry">
 
-
<h2 class="title">
 
-
<a name="11-11-2012">11.11.2011</a>
 
-
</h2>
 
-
<fieldset class="experiment general">
 
-
<legend><a name="title">Überschrift</a></legend>
 
-
<div class="investigator">
 
-
<span class="inv">Investigator:</span>
 
-
<span class="inv-names">X,Y</span>
 
-
</div>
 
-
<div class="aim">
 
-
<span class="aim">Aim:</span>
 
-
<span class="aim-desc">We attempt to get results.</span>
 
-
</div>
 
-
<div class="exp-content">
 
-
<p>Wichtig ist, dass immer die verwendete Materialien (Plasmide, genomische DNA [aus welchen Stamm],
 
-
Primer) genau benannt und/oder ggf. irgendwo nummeriert werden. Es sollte alles nachvollziehbar sein,
 
-
wann ihr mit welchen Proben was gemacht habt.</p>
 
-
<p></p>
 
-
<p>Auf den folgenden Seiten sind Beispiele, wie wir uns das Notebook vom Aufbau und Detailgrad vorstellen.</p>
 
-
</div>
 
-
</fieldset>
 
-
</div>
 
-
 
-
 
-
 
-
<!-- Beispiel Ligation, Verdau -->
 
-
 
-
<div class="notebooky-entry">
 
-
<h2 class="title">
 
-
<a name="17-04-2013">17.04.2013</a>
 
-
</h2>
 
-
<fieldset class="experiment ligation">
 
-
    <legend><a name="lig">Ligation</a></legend>
 
-
    <div class="investigator">
 
-
<span class="inv">Investigator:</span>
 
-
<span class="inv-names">Franzi, Lucas</span>
 
-
</div>
 
-
    <div class="aim">
 
-
<span class="aim">Aim:</span>
 
-
<span class="aim-desc">Assemble the Bricks 1, 3, 4, 5, 6, 7 and 8 into the vector pSB1C3.</span>
 
-
</div>
 
-
<div class="exp-content">
 
-
<ul class="lig">
 
-
<li>5 µl vector DNA (pSB1C3)</li>
 
-
<li>20 µl insert DNA (1, 3, 4, 5, 6, 7 or 8)</li>
 
-
<li>3 µl 10x T4 DNA ligase buffer</li>
 
-
<li>2 µl T4 DNA ligase</li>
 
-
</ul>
 
-
<p>The samples were incubated for 14 h at 18° C.</p>
 
-
</div>
 
-
</fieldset>
 
-
</div>
 
-
<!-- Beispiel Verdau -->
 
-
<fieldset class="experiment digest">
 
-
    <legend><a name="dig">Digest</a></legend>
 
-
    <div class="investigator">
 
-
<span class="inv">Investigator:</span>
 
-
<span class="inv-names">Christian, Patrick</span>
 
-
</div>
 
-
    <div class="aim">
 
-
<span class="aim">Aim:</span>
 
-
<span class="aim-desc">Digest of pSB1C3-J04450 with <i>Mlu</i>I and <i>Hind</i>III.</span>
 
-
</div>
 
-
<div class="exp-content">
 
-
<ul class="digest">
 
-
<li>4 µl DNA (pSB1C3-J04450)</li>
 
-
<li>1 µl MluI</li>
 
-
<li>1 µl HindIII</li>
 
-
<li>1,5 µl 10x red buffer</li>
 
-
<li>1,5 µl 10x orange g loading buffer</li>
 
-
<li>6 µl H2O</li>
 
-
</ul>
 
-
<p>The samples were incubated for 4 h at 37° C.</p>
 
-
<table class="gel digest">
 
-
<colgroup>
 
-
<col width="50%" />
 
-
<col width="50%" />
 
-
</colgroup>
 
-
<thead>
 
-
<tr>
 
-
<th colspan="2" class="title">Gel electrophoresis</th>
 
-
</tr>
 
-
</thead>
 
-
<tbody>
 
-
<tr>
 
-
<td>
 
-
<img src="beispiel.png" width="50%" alt="gel-electrophoresis-image" />
 
-
</td>
 
-
<td>
 
-
<p>
 
-
<span class="gel-elc">Gel substances</span>
 
-
<ul class="gel-sub">
 
-
<li>1% Agarose gel</li>
 
-
<li>10 µl RedSafe in 50 ml gel</li>
 
-
<li>x µl Hyper Ladder</li>
 
-
</ul>
 
-
</p>
 
-
<p>
 
-
<span class="exp">Expactations</span>
 
-
<ul class="exp">
 
-
<li>Lane 1: 5300 kbp</li>
 
-
<li>Lane 2: 3300 kbp</li>
 
-
<li>Lane 3: 1300 kbp</li>
 
-
</ul>
 
-
</p>
 
-
<p>We don’t receive all expected fragments. The expected fragment in lane 1 is missing.</p>
 
-
</td>
 
-
</tr>
 
-
<tr>
 
-
<td colspan="2" class="gel-fazit">
 
-
<p>We don’t receive all expected fragments. The expected fragment in lane 1 is missing.</p>
 
-
</td>
 
-
</tr>
 
-
</tbody>
 
-
</table>
 
-
</div>
 
-
</fieldset>
 
-
 
-
<!-- Beispiel Transformation, PCR -->
 
-
 
-
<div class="notebooky-entry">
 
-
<h2 class="title">
 
-
<a name="18-04-2012">18.04.2012</a>
 
-
</h2>
 
-
<fieldset class="experiment transformation">
 
-
    <legend>Transformation</legend>
 
-
    <div class="investigator">
 
-
<span class="inv">Investigator:</span>
 
-
<span class="inv-names">Franzi, Christian</span>
 
-
</div>
 
-
    <div class="aim">
 
-
<span class="aim">Aim:</span>
 
-
<span class="aim-desc">Transformation of the plasmid DNA pB201-40JO in <i>E. coli</i> for amplification.</span>
 
-
</div>
 
-
<div class="exp-content">
 
-
<p>The chemo competent <i>E. coli</i> DH5a cells were transformed with pB201-40JO DNA and plated on dYT-Amp-plates. <br />The plates were incubated over night at 37° C .</p>
 
-
</div>
 
-
</fieldset>
 
-
<!-- PCR -->
 
-
<fieldset class="experiment pcr">
 
-
    <legend><a name="pcr">PCR</a></legend>
 
-
    <div class="investigator">
 
-
<span class="inv">Investigator:</span>
 
-
<span class="inv-names">Patrick, Lucas</span>
 
-
</div>
 
-
    <div class="aim">
 
-
<span class="aim">Aim:</span>
 
-
<span class="aim-desc">Receive <i>Pvu</i>II point-mutation on colonies 3 and 5 of E. coli pB201-40JO.</span>
 
-
</div>
 
-
<div class="exp-content">
 
-
<table class="pcr">
 
-
<colgroup>
 
-
<col width="15%" />
 
-
<col width="30%" />
 
-
<col width="5%" />
 
-
<col width="20%" />
 
-
<col width="20%" />
 
-
<col width="10%" />
 
-
</colgroup>
 
-
<thead>
 
-
<th>Volume</th>
 
-
<th>Reagent</th>
 
-
<th>&nbsp;</th>
 
-
<th>Temp (°C)</th>
 
-
<th colspan="2">Time</th>
 
-
</thead>
 
-
<tr>
 
-
<td>10 µl</td>
 
-
<td>5x Buffer</td>
 
-
<td>&nbsp;</td>
 
-
<td>95</td>
 
-
<td colspan="2">3 min</td>
 
-
</tr>
 
-
<tr>
 
-
<td>1,5 µl</td>
 
-
<td>Primer fwd 13</td>
 
-
<td>&nbsp;</td>
 
-
<td>95</td>
 
-
<td colspan="2">3 sec</td>
 
-
</tr>
 
-
<tr>
 
-
<td>1,5 µl</td>
 
-
<td>Primer rev 14</td>
 
-
<td>&nbsp;</td>
 
-
<td>58</td>
 
-
<td>30 sec</td>
 
-
<td rowspan="3">x17</td>
 
-
</tr>
 
-
<tr>
 
-
<td>1 µl</td>
 
-
<td>Template</td>
 
-
<td>&nbsp;</td>
 
-
<td>72</td>
 
-
<td>1 min</td>
 
-
</tr>
 
-
<tr>
 
-
<td>36 µl</td>
 
-
<td>H2O</td>
 
-
<td>&nbsp;</td>
 
-
<td>7 min</td>
 
-
<td>3 min</td>
 
-
</tr>
 
-
<tr>
 
-
<td>1 µl Phusion</td>
 
-
<td>Phusion Polymerase</td>
 
-
<td>&nbsp;</td>
 
-
<td>4</td>
 
-
<td colspan="2"><span class="hold">Hold</span></td>
 
-
</tr>
 
-
</table>
 
-
<br />
 
-
<!-- Das Gel-Bild fast gleich wie beim Verdau -->
 
-
<table class="gel pcr">
 
-
<colgroup>
 
-
<col width="50%" />
 
-
<col width="50%" />
 
-
</colgroup>
 
-
<thead>
 
-
<tr>
 
-
<th colspan="2" class="title">Gel electrophoresis</th>
 
-
</tr>
 
-
</thead>
 
-
<tbody>
 
-
<tr>
 
-
<td>
 
-
<img src="beispiel.png" width="50%" alt="gel-electrophoresis-image" />
 
-
</td>
 
-
<td>
 
-
<p>
 
-
<span class="gel-elc">Gel substances</span>
 
-
<ul class="gel-sub">
 
-
<li>1% Agarose gel</li>
 
-
<li>10 µl RedSafe in 50 ml gel</li>
 
-
<li>x µl Hyper Ladder</li>
 
-
</ul>
 
-
</p>
 
-
<p>
 
-
<span class="exp">Expactations</span>
 
-
<ul class="exp">
 
-
<li>Lane 1: 5300 kbp</li>
 
-
<li>Lane 2: 3300 kbp</li>
 
-
<li>Lane 3: 1300 kbp</li>
 
-
</ul>
 
-
</p>
 
-
<p>We don’t receive all expected fragments. The expected fragment in lane 1 is missing.</p>
 
-
</td>
 
-
</tr>
 
-
</tbody>
 
-
</table>
 
-
</div>
 
-
</fieldset>
 
-
 
-
 
-
<!-- Prep Digest -->
 
-
<fieldset class="experiment digest">
 
-
    <legend><a name="dig">Digest</a></legend>
 
-
    <div class="investigator">
 
-
<span class="inv">Investigator:</span>
 
-
<span class="inv-names">Dominik</span>
 
-
</div>
 
-
    <div class="aim">
 
-
<span class="aim">Aim:</span>
 
-
<span class="aim-desc">Digest of pSB1C3-iBB4+iBB11+iBB9, pSB1C3-iBB4+iBB12+iBB9, pSB1C3-iBB6315 and pSB1A3.</span>
 
-
</div>
 
-
<div class="exp-content">
 
-
<p><ul class="digest">
 
-
<li>1000 ng Plasmid (pSB1C3-iBB4+iBB11+iBB9, pSB1C3-iBB4+iBB12+iBB9)</li>
 
-
<li>0.5 µl EcoRI</li>
 
-
<li>0.5 µl SpeI</li>
 
-
<li>2 µl CutSmart</li>
 
-
<li>ad 20 µl ddH2O</li>
 
-
</ul>
 
-
 
-
<p><ul class="digest">
 
-
<li>1000 ng Plasmid (pSB1C3-iBB6315)</li>
 
-
<li>0.5 µl XbaI</li>
 
-
<li>0.5 µl PstI</li>
 
-
<li>2 µl CutSmart</li>
 
-
<li>ad 20 µl ddH2O</li>
 
-
</ul>
 
-
 
-
<p><ul class="digest">
 
-
<li>1000 ng Plasmid (pSB1A3)</li>
 
-
<li>0.5 µl EcoRI</li>
 
-
<li>0.5 µl PstI</li>
 
-
<li>2 µl CutSmart</li>
 
-
<li>ad 20 µl ddH2O</li>
 
-
</ul>
 
-
 
-
<p>The samples were incubated for 1 h at 37° C.</p>
 
-
<table class="gel digest">
 
-
<colgroup>
 
-
<col width="50%" />
 
-
<col width="50%" />
 
-
</colgroup>
 
-
<thead>
 
-
<tr>
 
-
<th colspan="2" class="title">Gel electrophoresis</th>
 
-
</tr>
 
-
</thead>
 
-
<tbody>
 
-
<tr>
 
-
<td>
 
-
<img src="beispiel.png" width="50%" alt="gel-electrophoresis-image" />
 
-
</td>
 
-
<td>
 
-
<p>
 
-
<span class="gel-elc">Gel substances</span>
 
-
<ul class="gel-sub">
 
-
<li>1% Agarose gel</li>
 
-
<li>10 µl RedSafe in 50 ml gel</li>
 
-
<li>x µl Hyper Ladder</li>
 
-
</ul>
 
-
</p>
 
-
<p>
 
-
<span class="exp">Expactations</span>
 
-
<ul class="exp">
 
-
<li>Lane 1: 5300 kbp</li>
 
-
<li>Lane 2: 3300 kbp</li>
 
-
<li>Lane 3: 1300 kbp</li>
 
-
</ul>
 
-
</p>
 
-
<p>All expected fragments were present. The relevant fragments were cut from the gel and then purified via “Qiagen Gel Extraction Kit” (Qiagen, Düsseldorf).</p>
 
-
</td>
 
-
</tr>
 
-
</tbody>
 
-
</table>
 
-
</div>
 
-
</fieldset>
 
-
 
-
<!-- Inoculation -->
 
-
<fieldset class="experiment inoculation">
 
-
    <legend><a name="ino">Inoculation</a></legend>
 
-
    <div class="investigator">
 
-
<span class="inv">Investigator:</span>
 
-
<span class="inv-names">Dominik</span>
 
-
</div>
 
-
    <div class="aim">
 
-
<span class="aim">Aim:</span>
 
-
<span class="aim-desc">inoculation of colonies for plasmid preparation</span>
 
-
</div>
 
-
<div class="exp-content">
 
-
<p>4 colonies of pSB1A3-iBB395146 and 4 colonies of pSB1A3-iBB496315 were inoculated in 5 ml LB medium containing ampicillin.</p>
 
-
</div>
 
-
</fieldset>
 
-
 
-
<!-- Sequencing -->
 
-
<fieldset class="experiment sequencing">
 
-
    <legend>Sequencing</legend>
 
-
    <div class="investigator">
 
-
<span class="inv">Investigator:</span>
 
-
<span class="inv-names">Dominik</span>
 
-
</div>
 
-
    <div class="aim">
 
-
<span class="aim">Aim:</span>
 
-
<span class="aim-desc">Complete sequencing of pSB1A3-iBB496315.</span>
 
-
</div>
 
-
<div class="exp-content">
 
-
<p>8 new sequencing samples were sent out.</p>
 
-
</div>
 
-
</fieldset>
 
-
 
-
<!-- Compis -->
 
-
<fieldset class="experiment competent cells">
 
-
    <legend>Competent cells</legend>
 
-
    <div class="investigator">
 
-
<span class="inv">Investigator:</span>
 
-
<span class="inv-names">Dominik</span>
 
-
</div>
 
-
    <div class="aim">
 
-
<span class="aim">Aim:</span>
 
-
<span class="aim-desc">Overnight culture for making new aliquots of competent cells.</span>
 
-
</div>
 
-
<div class="exp-content">
 
-
<p>For making new aliquots of <i>E. coli</i> DH5α cells 50 ml LB medium were inoculated with 500 µl of an <i>E. coli</i> DH5α culture.</p>
 
-
</div>
 
-
</fieldset>
 
-
 
-
 
-
<!-- Miniprep -->
 
-
<fieldset class="experiment miniprep">
 
-
    <legend><a name="min">Miniprep</a></legend>
 
-
    <div class="investigator">
 
-
<span class="inv">Investigator:</span>
 
-
<span class="inv-names">Dominik</span>
 
-
</div>
 
-
    <div class="aim">
 
-
<span class="aim">Aim:</span>
 
-
<span class="aim-desc">preparation of the plasmids pSB1A3-iBB10+iBB9, pSB1A3-iBB11+iBB9, pSB1A3-iBB12+iBB9 and pSB1A3-iBB13+iBB9.</span>
 
-
</div>
 
-
<div class="exp-content">
 
-
<p>The plasmids were isolated with the “QIAprep Spin Miniprep Kit” (Qiagen, Düsseldorf) according to the producer instructions.</p>
 
-
</div>
 
-
</fieldset>
 
-
 
-
 
-
</div>
 
-
 
-
</html>
 
-
 
-
{{:Team:Marburg/Template:ContentEnd}}
 
-
{{:Team:Marburg/Template:Footer}}
 

Latest revision as of 09:09, 4 October 2013