Difference between revisions of "Team:Vilnius-Lithuania/LabBook"

 
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         <h1>Description</h1>
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         <h1>Lab Book</h1>
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         <p></p>
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         <h2> Week 1</h2>
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        <p></p>
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<object data="https://static.igem.org/mediawiki/2018/8/81/T--Vilnius-Lithuania--Week_1_Labook.pdf" type="application/pdf" width="100%" height="700px" internalinstanceid="5" title=""><p>It appears you don't have a PDF plugin for this browser, you can <a href="https://static.igem.org/mediawiki/2018/8/81/T--Vilnius-Lithuania--Week_1_Labook.pdf">click here to download the PDF file.</a></object>
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        <h2>What is SynORI?</h2>
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    <h2> Week 2</h2>
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        <p>SynORI stands for synthetic origin of replication. It is a framework designed to make working with single
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<object data="https://static.igem.org/mediawiki/2018/8/89/T--Vilnius-Lithuania--Week_2_Labook.pdf" type="application/pdf" width="100%" height="700px" internalinstanceid="5" title=""><p>It appears you don't have a PDF plugin for this browser, you can <a href="https://static.igem.org/mediawiki/2018/8/89/T--Vilnius-Lithuania--Week_2_Labook.pdf">click here to download the PDF file.</a></object>
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            and multi-plasmid systems precise, easy and on top of that - more functional.</p>
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    <h2> Week 3</h2>
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        <p>The SynORI framework enables scientists to build a multi-plasmid system in a standardized manner by:</p>
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<object data="https://static.igem.org/mediawiki/2018/5/51/T--Vilnius-Lithuania--Week_3_Labook.pdf" type="application/pdf" width="100%" height="700px" internalinstanceid="5" title=""><p>It appears you don't have a PDF plugin for this browser, you can <a href="https://static.igem.org/mediawiki/2018/5/51/T--Vilnius-Lithuania--Week_3_Labook.pdf">click here to download the PDF file.</a></object> 
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        <ol>
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    <h2> Week 4</h2>
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            <li>Selecting the number of plasmid groups</li>
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<object data="https://static.igem.org/mediawiki/2018/6/6e/T--Vilnius-Lithuania--Week_4_Labook.pdf" type="application/pdf" width="100%" height="700px" internalinstanceid="5" title=""> <p>It appears you don't have a PDF plugin for this browser, you can <a href="https://static.igem.org/mediawiki/2018/6/6e/T--Vilnius-Lithuania--Week_4_Labook.pdf">click here to download the PDF file.</a></object>                     
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            <li>Choosing the copy number of each group</li>
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    <h2> Week 5</h2>
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            <li>Picking the type of copy number control (specific to one group or regulating all of them at once).</li>
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<object data="https://static.igem.org/mediawiki/2018/9/9f/T--Vilnius-Lithuania--Week_5_Labook.pdf" type="application/pdf" width="100%" height="700px" internalinstanceid="5" title=""> <p>It appears you don't have a PDF plugin for this browser, you can <a href="https://static.igem.org/mediawiki/2018/9/9f/T--Vilnius-Lithuania--Week_5_Labook.pdf">click here to download the PDF file.</a></object>
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    <h2> Week 6</h2>
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        </ol>
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<object data="https://static.igem.org/mediawiki/2018/f/fe/T--Vilnius-Lithuania--Week_6_Labook.pdf" type="application/pdf" width="100%" height="700px" internalinstanceid="5" title=""> <p>It appears you don't have a PDF plugin for this browser, you can <a href="https://static.igem.org/mediawiki/2018/f/fe/T--Vilnius-Lithuania--Week_6_Labook.pdf">click here to download the PDF file.</a></object>
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        </p>
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    <h2> Week 7</h2>
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    <object data="https://static.igem.org/mediawiki/2018/3/38/T--Vilnius-Lithuania--Week_7_Labook.pdf" type="application/pdf" width="100%" height="700px" internalinstanceid="5" title=""> <p>It appears you don't have a PDF plugin for this browser, you can <a href="https://static.igem.org/mediawiki/2018/3/38/T--Vilnius-Lithuania--Week_7_Labook.pdf">click here to download the PDF file.</a></object>
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        <p></p>
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    <h2> Week 8</h2>
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        <p>The framework also includes a possibility of adding a selection system that reduces the usage of antibiotics
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<object data="https://static.igem.org/mediawiki/2018/5/57/T--Vilnius-Lithuania--Week_8_Labook.pdf" type="application/pdf" width="100%" height="700px" internalinstanceid="5" title=""> <p>It appears you don't have a PDF plugin for this browser, you can <a href="https://static.igem.org/mediawiki/2018/5/57/T--Vilnius-Lithuania--Week_8_Labook.pdf">click here to download the PDF file.</a></object>
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            (only 1 antibiotic for up to 5 different plasmids!) and an active partitioning system to make sure that low
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    <h2> Week 9</h2>
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            copy number plasmid groups are not lost during the division.
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    <object data="https://static.igem.org/mediawiki/2018/4/4e/T--Vilnius-Lithuania--Week_9_Labook.pdf" type="application/pdf" width="100%" height="700px" internalinstanceid="5" title=""> <p>It appears you don't have a PDF plugin for this browser, you can <a href="https://static.igem.org/mediawiki/2018/4/4e/T--Vilnius-Lithuania--Week_9_Labook.pdf">click here to download the PDF file.</a></object>
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        </p>
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    <h2> Week 10</h2>
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        <p></p>
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    <object data="https://static.igem.org/mediawiki/2018/4/44/T--Vilnius-Lithuania--Week_10_Labook.pdf" type="application/pdf" width="100%" height="700px" internalinstanceid="5" title=""> <p>It appears you don't have a PDF plugin for this browser, you can <a href="https://static.igem.org/mediawiki/2018/4/44/T--Vilnius-Lithuania--Week_10_Labook.pdf">click here to download the PDF file.</a></object>
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        <div class="img-cont">
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    <h2> Week 11</h2>
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            <img src="https://static.igem.org/mediawiki/parts/8/84/Collect.png" alt="img">
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    <object data="https://static.igem.org/mediawiki/2018/d/d9/T--Vilnius-Lithuania--Week_11_Labook.pdf" type="application/pdf" width="100%" height="700px" internalinstanceid="5" title=""> <p>It appears you don't have a PDF plugin for this browser, you can <a href="https://static.igem.org/mediawiki/2018/d/d9/T--Vilnius-Lithuania--Week_11_Labook.pdf">click here to download the PDF file.</a></object>
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            <div class="img-label">
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    <h2> Week 12</h2>
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    <object data="https://static.igem.org/mediawiki/2018/7/75/T--Vilnius-Lithuania--Week_12_Labook.pdf" type="application/pdf" width="100%" height="700px" internalinstanceid="5" title=""> <p>It appears you don't have a PDF plugin for this browser, you can <a href="https://static.igem.org/mediawiki/2018/7/75/T--Vilnius-Lithuania--Week_12_Labook.pdf">click here to download the PDF file.</a></object>
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    <h2> Week 13</h2>
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    <object data="https://static.igem.org/mediawiki/2018/1/16/T--Vilnius-Lithuania--Week_13_Labook.pdf" type="application/pdf" width="100%" height="700px" internalinstanceid="5" title=""> <p>It appears you don't have a PDF plugin for this browser, you can <a href="https://static.igem.org/mediawiki/2018/1/16/T--Vilnius-Lithuania--Week_13_Labook.pdf">click here to download the PDF file.</a></object>
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    <h2> Week 14</h2>
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    <object data="https://static.igem.org/mediawiki/2018/4/4a/T--Vilnius-Lithuania--Week_14_Labook.pdf" type="application/pdf" width="100%" height="700px" internalinstanceid="5" title=""> <p>It appears you don't have a PDF plugin for this browser, you can <a href="https://static.igem.org/mediawiki/2018/4/4a/T--Vilnius-Lithuania--Week_14_Labook.pdf">click here to download the PDF file.</a></object>
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    <h2> Week 15</h2>
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    <object data="https://static.igem.org/mediawiki/2018/a/af/T--Vilnius-Lithuania--Week_15_Labook.pdf" type="application/pdf" width="100%" height="700px" internalinstanceid="5" title=""> <p>It appears you don't have a PDF plugin for this browser, you can <a href="https://static.igem.org/mediawiki/2018/a/af/T--Vilnius-Lithuania--Week_15_Labook.pdf">click here to download the PDF file.</a></object>
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        <h2>Applications</h2>
 
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        <p>
 
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            <h5>Everyday lab work</h5>
 
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            <p>
 
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                A multi-plasmid system that is easy to assemble and control. With our framework the need to limit your
 
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                research to a particular plasmid copy number just because there are not enough right replicons to
 
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                choose from, is eliminated. With SynORI you can easily create a vector with a desired copy number that
 
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                suits your needs.</li>
 
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            </p>
 
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            <h5>Biological computing</h5>
 
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            <p>
 
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                The ability to choose a wide range of copy number options and their control types will make the
 
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                synthetic biology engineering much more flexible and predictable. Introduction of plasmid copy number
 
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                regulation is equivalent to adding a global parameter to a computer system. It enables the coordination
 
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                of multiple gene group expression.
 
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            </p>
 
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            <h5>Smart assembly of large protein complexes</h5>
 
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            <p>
 
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                The co-expression of multi-subunit complexes using different replicons brings incoherency to an already
 
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                chaotic cell system. This can be avoided by using SynORI, as in this framework every plasmid group uses
 
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                the same type of control, and in addition can act in a group-specific manner.</p>
 
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            <h5>Metabolic engineering</h5>
 
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            <p>
 
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                A big challenge for heterologous expression of multiple gene pathways is to accurately adjust the
 
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                levels of each enzyme to achieve optimal production efficiency. Precise promoter tuning in
 
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                transcriptional control and synthetic ribosome binding sites in translational control are already
 
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                widely used to maintain expression levels. In addition to current approaches, our framework allows a
 
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                simultaneous multiple gene control. Furthermore, an inducible regulation that we offer, can make the
 
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                search for perfect conditions a lot easier.
 
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            </p>
 
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        </p>
 
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        <p>
 
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        </p>
 
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        <table style="width:100%">
 
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<thead>
 
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<td align='center'>Species sign in ODE system</td>
 
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<td align='center'>Species</td>
 
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<td align='center'>Initial concentration (M)</td>
 
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</thead>
 
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<tbody>
 
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<tr>
 
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<td align='center'>A</td>
 
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<td align='center'>pDNA+RNA I+RNAII early</td>
 
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<td align='center'>0</td>
 
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</tr>
 
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<tr>
 
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<td align='center'>B</td>
 
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<td align='center'>pDNA+RNA II short</td>
 
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<td align='center'>0</td>
 
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</tr>
 
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<tr>
 
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<td align='center'>RNAI</td>
 
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<td align='center'>RNA I</td>
 
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<td align='center'>1E-6</td>
 
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</tr>
 
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<tr>
 
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<td align='center'>D</td>
 
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<td align='center'>pDNA+RNA II long</td>
 
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<td align='center'>0</td>
 
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</tr>
 
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<tr>
 
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<td align='center'>E</td>
 
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<td align='center'>pDNA+RNAII primer</td>
 
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<td align='center'>0</td>
 
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</tr>
 
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<tr>
 
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<td align='center'>F</td>
 
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<td align='center'>RNA II long</td>
 
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<td align='center'>0</td>
 
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</tr>
 
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<tr>
 
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<td align='center'>G</td>
 
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<td align='center'>pDNA</td>
 
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<td align='center'>4E-8*</td>
 
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</tr>
 
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<tr>
 
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<td align='center'>H</td>
 
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<td align='center'>pDNA+RNA II+RNA I late</td>
 
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<td align='center'>0</td>
 
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</tr>
 
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<tr>
 
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<td align='center'>RNA II</td>
 
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<td align='center'>RNA II</td>
 
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<td align='center'>0</td>
 
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</tr>
 
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<tr>
 
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<td align='center'>J</td>
 
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<td align='center'>RNAI+RNAII</td>
 
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<td align='center'>0</td>
 
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</tr>
 
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</tbody>
 
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</table>
 
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    </div>
 
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Latest revision as of 19:45, 4 November 2018

Lab Book

Writing a Book

Our team intensively and precisely worked in the lab for 15 weeks from the beginning of summer till the middle of autumn to develop a SynDrop idea. Here is a detailed documentation of our Wet Lab work, including tasks, reagents used and conditions needed during the experiments.

Lab Book

Week 1

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Week 2

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Week 3

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Week 4

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Week 5

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Week 6

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Week 7

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Week 8

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Week 9

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Week 10

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Week 11

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Week 12

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Week 13

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Week 14

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Week 15

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