Team:Freiburg/Notebook/lab multiple targeting

From 2013.igem.org

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Line 41: Line 41:
</p>
</p>
-
<p class="first_order"><a href="https://2013.igem.org/Team:Freiburg/Notebook/lab_effector"> Effector </a></p>
+
 
-
<p class="first_order"><a href="https://2013.igem.org/Team:Freiburg/Notebook/induction"> Induction </a> </p>
+
<p class="first_order"><a class="active" href="https://2013.igem.org/Team:Freiburg/Notebook/crrna"> Targeting </a></p>
<p class="first_order"><a class="active" href="https://2013.igem.org/Team:Freiburg/Notebook/crrna"> Targeting </a></p>
<p class="second_order_note"> <a class="active" id="link" href="https://2013.igem.org/Team:Freiburg/Notebook/lab_multiple_targeting"> Multiple targeting </a> </p>
<p class="second_order_note"> <a class="active" id="link" href="https://2013.igem.org/Team:Freiburg/Notebook/lab_multiple_targeting"> Multiple targeting </a> </p>
-
<p class="second_order_note"> <a id="link" href="https://2013.igem.org/Team:Freiburg/Notebook/lab_gfp_reporter"> GFP-reporter-plasmid </a> </p>
 
 +
<p class="third_order"> <a href="#may"> May </a> </p>
 +
<p class="third_order"> <a href="#june"> June </a> </p>
 +
<p class="third_order"> <a href="#july"> July </a> </p>
 +
<p class="third_order"> <a href="#august"> August </a> </p>
 +
<p class="third_order"> <a href="#september"> September </a> </p>
-
<p class="first_order"><a href="https://2013.igem.org/Team:Freiburg/Notebook/method"> uniBAss </a></p>
+
<p class="second_order_note"> <a id="link" href="https://2013.igem.org/Team:Freiburg/Notebook/lab_crrna_plasmid"> crRNA-Plasmid </a> </p>
-
<p class="first_order"><a href="https://2013.igem.org/Team:Freiburg/Notebook/modeling"> Modeling </a></p>
+
-
<p class="first_order"><a href="https://2013.igem.org/Team:Freiburg/Notebook/standardisation"> Standardisation </a></p>
+
 +
<p class="second_order_note"> <a id="link" href="https://2013.igem.org/Team:Freiburg/Notebook/lab_gfp_reporter"> GFP-reporter-plasmid </a> </p>
 +
 +
<p class="first_order"><a href="https://2013.igem.org/Team:Freiburg/Notebook/lab_effector"> Effector </a></p>
 +
<p class="first_order"><a href="https://2013.igem.org/Team:Freiburg/Notebook/induction"> Effector Control </a> </p>
 +
<p class="first_order"><a href="https://2013.igem.org/Team:Freiburg/Notebook/modeling"> Modeling </a></p>
 +
<p class="first_order"><a href="https://2013.igem.org/Team:Freiburg/Notebook/method"> uniBAss </a></p>
 +
<p class="first_order"><a href="https://2013.igem.org/Team:Freiburg/Notebook/standardisation"> Standardization </a></p>
 +
<p class="first_order"> <a id="link" href="https://2013.igem.org/Team:Freiburg/protocols"> Material and Methods </a> </p>
Line 355: Line 364:
</div>
</div>
 +
<div>
 +
<p> Program </p>
 +
    <table class="tabelle">
 +
 +
<td> 98°C </td>
 +
                <td> 7min </td>
 +
                <td> Denaturation </td>
 +
      </tr>
 +
      <tr>
 +
<td> 98°C </td>
 +
                <td> 30s </td>
 +
                <td> Denaturation </td>
 +
      </tr>
 +
              <tr>
 +
<td> 67°C </td>
 +
                <td> 30s </td>
 +
                <td> Annealing </td>
 +
      </tr>
 +
              <tr>
 +
<td> 72°C </td>
 +
                <td> 50s </td>
 +
                <td> Elongation </td>
 +
      </tr>
 +
              <tr>
 +
<td> 72°C </td>
 +
                <td> 10min </td>
 +
                <td> final Elongation </td>
 +
      </tr>
 +
              <tr>
 +
<td> 4°C </td>
 +
                <td> hold </td>
 +
      </tr>
 +
              </table>
 +
<p> <em> 30 cycles </em> </p>
 +
</div>
 +
<p> 10µl of each PCR product were load on a gel: <br> 
 +
<table class="gelpic">
 +
<tr>
 +
<td> <img class="gelpic" src="https://static.igem.org/mediawiki/2013/5/5f/Freiburg_2013_projekt7_05-29_colony.png"> </td>
 +
</tr>
 +
<tr>
 +
<td> Products Colony-PCR <br>
 +
left to right:<br>
 +
1: ladder (1kb)<br>
 +
2-7: colonie 1-6 from pIG7001a (gibson assembly 05-28)<br>
 +
8: negativ control<br>
 +
9: positive control (template is pKM006) </td>
 +
</tr>
 +
</table>
 +
PCR did not work </p>
</div>
</div>
 +
<div id="tag">
 +
  <h2> 30.05.13 </h2>
 +
<p> 6 minipreps of pIG7001a: <br>
 +
cancentrations: 196 ng/µl, 175 ng/µl, 195 ng/µl, 133 ng/µl, 203 ng/µl, 197 ng/µl </p>
 +
<h3> Double-Digest of pIG7001a </h3>
 +
<p> used: minipreps of colonies 1-6, NgoMIV, PstI HF </p>
 +
<div id="floatleft">
 +
<table class="tabelle">
 +
<tr>
 +
<th> &micro;l </th>
 +
<th> type </th>
 +
</tr>
 +
<tr>
 +
<td> 5 </td>
 +
<td> DNA </td>
 +
</tr>
 +
<tr>
 +
<td> 1 </td>
 +
<td> NEB-Buffer 4 </td>
 +
</tr>
 +
<tr>
 +
<td> 0.5 </td>
 +
<td> Pst1 HF </td>
 +
</tr>
 +
<tr>
 +
<td> 0.5 </td>
 +
<td> NgoMIV </td>
 +
</tr>
 +
<tr>
 +
<td> Add to 10 &micro;l </td>
 +
<td> H<sub>2</sub>O </td>
 +
</tr>
 +
</table>
 +
</div>
 +
<div id="floatright">
 +
<ul>
 +
<li> Temp.: 37&deg;C </li>
 +
<li> Incubation time: 1h </li>
 +
</ul>
 +
</div>
 +
 +
<p> the whole mix was load on a gel: <br>
 +
<table id="floatleft">
 +
<tr>
 +
<td> <img src="https://static.igem.org/mediawiki/2013/8/8b/Freiburg_2013_projekt7_05-30_double_digest_%28Geneious%29.png"> </td>
 +
</tr>
 +
<tr>
 +
<td> expected bands </td>
 +
 +
</tr>
 +
</table>
 +
<table class="gelpic">
 +
<tr>
 +
<td> <img class="gelpic" src="https://static.igem.org/mediawiki/2013/f/f3/Freiburg_2013_projekt7_05-30_double_digest.Jpg"> </td>
 +
</tr>
 +
<tr>
 +
<td> Products double digest: <br>
 +
pIG7001a (Prep 1-6) with Pst1 and NgoMIV </td>
 +
 +
</tr>
 +
</table>
 +
<div>
 +
<h3> PCR 1 </h3>
 +
<p> colonie 1 was used (oIG7001a) <br>
 +
for Gibson Assembly 2: <br>
 +
<div>
 +
    <table class="tabelle">
 +
      <tr>
 +
<th> Fragment 1 </th>
 +
                <td> pIG7001a </td>
 +
                <td> oIG7004-F </td>
 +
                <td> oIG7004-R </td>
 +
                <td> 2274 bp </td>
 +
      </tr>
 +
      <tr>
 +
<th> Fragment 2 </th>
 +
                <td> pIG7001a </td>
 +
                <td> oIG7005-F </td>
 +
                <td> oIG7005-R </td>
 +
                <td> 2248 bp </td>
 +
      </tr>
 +
              <tr>
 +
<th> Fragment 3 </th>
 +
                <td> GW1-Peredox_mCherry-NLS </td>
 +
                <td> oIG7006-F </td>
 +
                <td> oIG7006-R </td>
 +
                <td> 741 bp </td>
 +
      </tr>
 +
  </table>
 +
  </div>
 +
for Gibson Assembly 3:<br>
 +
<div>
 +
    <table class="tabelle">
 +
      <tr>
 +
<th> Fragment 1 </th>
 +
                <td> pIG7001a </td>
 +
                <td> oIG7004-F </td>
 +
                <td> oIG7004-R </td>
 +
                <td> 2274 bp </td>
 +
      </tr>
 +
      <tr>
 +
<th> Fragment 2 </th>
 +
                <td> pIG7001a </td>
 +
                <td> oIG7005-F </td>
 +
                <td> oIG7005-R </td>
 +
                <td> 2248 bp </td>
 +
      </tr>
 +
              <tr>
 +
<th> Fragment 3 </th>
 +
                <td> pFucci-G1-Orange </td>
 +
                <td> oIG7007-F </td>
 +
                <td> oIG7007-R </td>
 +
                <td> 659 bp </td>
 +
      </tr>
 +
  </table>
 +
  </div>
 +
for Gibson Assembly 4:<br>
 +
<div>
 +
    <table class="tabelle">
 +
      <tr>
 +
<th> Fragment 1 </th>
 +
                <td> pIG7001a </td>
 +
                <td> oIG7004-F </td>
 +
                <td> oIG7004-R </td>
 +
                <td> 2274 bp </td>
 +
      </tr>
 +
      <tr>
 +
<th> Fragment 2 </th>
 +
                <td> pIG7001a </td>
 +
                <td> oIG7005-F </td>
 +
                <td> oIG7005-R </td>
 +
                <td> 2248 bp </td>
 +
      </tr>
 +
              <tr>
 +
<th> Fragment 3 </th>
 +
                <td> pDS47-BFP-dGEM-trunc </td>
 +
                <td> oIG7008-F </td>
 +
                <td> oIG7008-R </td>
 +
                <td> 679 bp </td>
 +
      </tr>
 +
  </table>
 +
  </div>
 +
 +
<div id="floatleft">
 +
<table class="tabelle">
 +
<tr>
 +
<th> &micro;l </th>
 +
<th> type </th>
 +
</tr>
 +
<tr>
 +
<td> 4 </td>
 +
<td> Q5-HF Reaction Buffer </td>
 +
</tr>
 +
<tr>
 +
<td> 0,5 </td>
 +
<td> Template </td>
 +
</tr>
 +
<tr>
 +
<td> 1 </td>
 +
<td> each Primer </td>
 +
</tr>
 +
 +
<tr>
 +
<td> 5 </td>
 +
<td> dNTPs </td>
 +
</tr>
 +
 +
<tr>
 +
<td> 0.5 </td>
 +
<td> Q5-HF Polymerase </td>
 +
</tr>
 +
<tr>
 +
<td> Add to 20 </td>
 +
<td> H<sub>2</sub>O </td>
 +
</tr>
 +
</table>
 +
</div>
 +
<div id="$floatright">
 +
<ul>
 +
<li> Gibson 1 program was used </li>
 +
</ul>
 +
</div>
 +
<p> 5µl of each product were load on a gel <br>
 +
<table class="gelpic">
 +
<tr>
 +
<td> <img class="gelpic" src="https://static.igem.org/mediawiki/2013/b/b1/Freiburg_2013_projekt7_05-30_PCR1.Jpg.png"> </td>
 +
</tr>
 +
<tr>
 +
<td> Products of PCR 1 </td>
 +
 +
</tr>
 +
</table>
 +
<p> Product 3 from Gibson 2 is missing → 0,2 µl extra plasmid template was added for PCR 2 </p>
 +
 +
</div>
 +
 +
<div>
 +
<h3> PCR 2 </h3>
 +
 +
<p> for gibson assembly 2, 3, and 4 <br>
 +
template: products from 1. PCR </p>
 +
 +
<div id="floatleft">
 +
<table class="tabelle">
 +
<tr>
 +
<th> &micro;l </th>
 +
<th> type </th>
 +
</tr>
 +
<tr>
 +
<td> 4 </td>
 +
<td> Q5-HF Reaction Buffer </td>
 +
</tr>
 +
<tr>
 +
<td> 2 </td>
 +
<td> Template </td>
 +
</tr>
 +
<tr>
 +
<td> 1 </td>
 +
<td> each Primer </td>
 +
</tr>
 +
 +
<tr>
 +
<td> 5 </td>
 +
<td> dNTPs </td>
 +
</tr>
 +
 +
<tr>
 +
<td> 0.5 </td>
 +
<td> Q5-HF Polymerase </td>
 +
</tr>
 +
<tr>
 +
<td> Add to 20 </td>
 +
<td> H<sub>2</sub>O </td>
 +
</tr>
 +
</table>
 +
</div><div id="$floatright">
 +
<ul>
 +
<li> Gibson 2 program was used </li>
 +
</ul>
 +
</div>
 +
 +
<p> concetration of PCR products: <br>
 +
Gibson 2: 1415 ng/µl, 1417 ng/µl, 1315 ng/µl<br>
 +
Gibson 3: 2874 ng/µl, 1436 ng/µl, 337 ng/µl<br>
 +
Gibson 4: 324 ng/µl, 325 ng/µl, 2047 ng/µl<br> </p>
 +
 +
<p> 5µl of each PCR product were load on a gel </p>
 +
 +
<table class="gelpic">
 +
<tr>
 +
<td> <img class="gelpic" src="https://static.igem.org/mediawiki/2013/9/95/Freiburg_2013_projekt7_05-30_PCR2.Jpg"> </td>
 +
</tr>
 +
<tr>
 +
<td> Products of PCR 2 </td>
 +
 +
</tr>
 +
</table>
 +
</div>
 +
<div>
 +
<h3> Gibson Assembly </h3>
 +
<p> volumes were calculated with excel sheet with concentration and length:<br>
 +
used volumes:<br>
 +
Gibson 2: 0,3 µl, 0,3 µl, 0,1 µl<br>
 +
Gibson 3: 0,15 µl, 0,3 µl, 0,4 µl<br>
 +
Gibson 4: 1,4 µl, 1,4 µl, 0,1 µl<br>
 +
1h in 1 aliquot of Gibson mix (according to protocol)<br>
 +
→ pIG7002a, heat shock transfection in E. coli (according to protocol)<br>
 +
→ pIG7003a, heat shock transfection in E. coli (according to protocol)<br>
 +
→ pIG7004a, heat shock transfection in E. coli (according to protocol)<br> </p>
 +
</div>
 +
 +
 +
 +
 +
<div id="tag">
 +
  <h2> 31.05.13 </h2>
 +
<h3> Digest of pIG7001a </h3>
 +
<p> used: colonie 1 (pIG7001a), NcoI, PstI HF, XbaI </p>
 +
 +
<div id="floatleft">
 +
<table class="tabelle">
 +
<tr>
 +
<th> &micro;l </th>
 +
<th> type </th>
 +
</tr>
 +
<tr>
 +
<td> 5 </td>
 +
<td> DNA </td>
 +
</tr>
 +
<tr>
 +
<td> 1 </td>
 +
<td> NEB-Buffer 4 </td>
 +
</tr>
 +
<tr>
 +
<td> 0,5 </td>
 +
<td> XbaI </td>
 +
</tr>
 +
<tr>
 +
<td> 0,1 </td>
 +
<td> BSA </td>
 +
</tr>
 +
<tr>
 +
<td> Add to 10&micro;l </td>
 +
<td> H<sub>2</sub>O </td>
 +
</tr>
 +
</table>
 +
</div>
 +
<div id="floatleft">
 +
<table class="tabelle">
 +
<tr>
 +
<th> &micro;l </th>
 +
<th> type </th>
 +
</tr>
 +
<tr>
 +
<td> 5 </td>
 +
<td> DNA </td>
 +
</tr>
 +
<tr>
 +
<td> 1 </td>
 +
<td> NEB-Buffer 4 </td>
 +
</tr>
 +
<tr>
 +
<td> 0,5 </td>
 +
<td> NcoI HF </td>
 +
</tr>
 +
<tr>
 +
<td> Add to 10&micro;l </td>
 +
<td> H<sub>2</sub>O </td>
 +
</tr>
 +
</table>
 +
</div>
 +
<div id="floatleft">
 +
<table class="tabelle">
 +
<tr>
 +
<th> &micro;l </th>
 +
<th> type </th>
 +
</tr>
 +
<tr>
 +
<td> 5 </td>
 +
<td> DNA </td>
 +
</tr>
 +
<tr>
 +
<td> 1 </td>
 +
<td> NEB-Buffer 4 </td>
 +
</tr>
 +
<tr>
 +
<td> 0,5 </td>
 +
<td> PstI HF </td>
 +
</tr>
 +
<tr>
 +
<td> Add to 10&micro;l </td>
 +
<td> H<sub>2</sub>O </td>
 +
</tr>
 +
</table>
 +
</div>
 +
<div id="floatleft">
 +
<ul>
 +
<li> Temp.: 37&deg;C </li>
 +
<li> Incubation time: 1h </li>
 +
</ul>
 +
</div>
 +
 +
<table id="floatleft">
 +
<tr>
 +
<td> <img src="https://static.igem.org/mediawiki/2013/9/95/Freiburg_2013_projekt7_05-31_Digest_%28Geneious%29.png"> </td>
 +
</tr>
 +
<tr>
 +
<td> expected bands </td>
 +
 +
</tr>
 +
</table>
 +
<table class="gelpic">
 +
<tr>
 +
<td> <img class="gelpic" src="https://static.igem.org/mediawiki/2013/7/70/Freiburg_2013_projekt7_05-31_3x_digest.Jpg"> </td>
 +
</tr>
 +
<tr>
 +
<td> pIG7001a digest <br>
 +
left to right:<br>
 +
1: ladder (1kb)<br>
 +
2: XbaI <br>
 +
3: NcoI <br>
 +
4: PstI <br>
 +
5: negative control </td>
 +
</tr>
 +
</table>
 +
<p> XbaI did only cut once instead of twice, NcoI and PstI cut as expected </p>
 +
 +
<h3> Sequencing of pIG7001a(1) </h3>
 +
<p> GATC-Watch-box: 706894 <br>
 +
→ Sequence of pIG7001a ok </p>
 +
</div>
 +
 +
<div id="june">
 +
<p id="h2">
 +
June
 +
</p>
 +
</div>
 +
 +
 +
<div id="tag">
 +
  <h2> 01.06.13 </h2>
 +
<p> Repetition of gibson assembly 2,3,4 with old PCR products new 2. PCR only for fragment 3 of gibson 3 –> contamination with plasmid template </p>
 +
 +
<h3> PCR 2 (fragment 3 / gibson 3) </h3>
 +
<p> same protocol was used 5µl of PCR product were load on gel </p>
 +
 +
<table class="gelpic">
 +
<tr>
 +
<td> <img class="gelpic" src="https://static.igem.org/mediawiki/2013/b/b7/Freiburg_2013_projekt7_06-01_PCR.Jpg"> </td>
 +
</tr>
 +
<tr>
 +
<td> Products of PCR 2 <br>
 +
Fragment 3, Gibson 3 </td>
 +
</tr>
 +
</table>
 +
 +
<h3> Gibson Assembly </h3>
 +
 +
<p>
 +
volumes were calculated with excel sheet only by length: <br>
 +
used volumes:<br>
 +
Gibson 2: 1,5 µl, 1,5 µl, 0,5 µl<br>
 +
Gibson 3: 1,5 µl, 1,5 µl, 0,5 µl<br>
 +
Gibson 4: 1,5 µl, 1,5 µl, 1,0 µl<br>
 +
<br>
 +
→ pIG7002a, heat shock transfection in E. coli (according to protocol)<br>
 +
→ pIG7003a, heat shock transfection in E. coli (according to protocol)<br>
 +
→ pIG7004a, heat shock transfection in E. coli (according to protocol)<br> </p>
 +
 +
</div>
 +
 +
<div id="tag">
 +
  <h2> 02.06.13 </h2>
 +
 +
<p> 6 colonys each (pIG7002a,pIG7003a, pIG7004a) were picked and plated <br>
 +
2 colonys control were picked and plated </p>
 +
 +
<div id="tag">
 +
  <h2> 03.06.13 </h2>
 +
 +
<h3> Doubledigest of pIG7002a, pIG7003a, pIG7004a </h3>
 +
<p> PstI and HindIII </p>
 +
<table id="floatleft">
 +
<tr>
 +
<td> <img class="gelpic" src="https://static.igem.org/mediawiki/2013/c/cc/Freiburg_2013_projekt7_06-03_double_digest_%28Geneious%29.png"> </td>
 +
</tr>
 +
<tr>
 +
<td> Expected bands </td>
 +
</tr>
 +
</table>
 +
<table class="gelpic">
 +
<tr>
 +
<td> <img class="gelpic" src="https://static.igem.org/mediawiki/2013/c/c4/Freiburg_2013_projekt7_06-03_double_digest_1.jpg"> </td>
 +
</tr>
 +
<tr>
 +
<td> Digest of pIG7002a, pIG7003a, pIG7004a with PstI and HindIII </td>
 +
</tr>
 +
</table>
 +
 +
 +
<div id="floatleft">
 +
<ul>
 +
<li>  For pIG7002a only the plasmid form colony 4 shows expected bands. </li>
 +
<li> No colony from pIG7003a is positive. </li>
 +
                <li> Only the plasmid from colony 4 of pIG7004a shows the expected bands.  </li>
 +
</ul>
 +
</div>
 +
 +
<h3> Sequencing of pIG7002a (4) and pIG7004a (4) </h3>
 +
<p> GATC-Watch-box: 707852 <br>
 +
→ Sequence of pIG7002a ok <br>
 +
→ Frameshift in pIG7004a ok </p>
 +
</div>
 +
 +
<div id="tag">
 +
  <h2> 04.06.13 </h2>
 +
<p> 6 Minipreps of 6 new colonys with pIG7003a: (7)-(12) </p>
 +
<h3> Doubledigest of pIG7003a </h3>
 +
<p> PstI and HindIII </p>
 +
 +
<table class="gelpic">
 +
<tr>
 +
<td> <img class="gelpic" src="https://static.igem.org/mediawiki/2013/1/1c/Freiburg_2013_projekt7_06-04_double_digest.jpg"> </td>
 +
</tr>
 +
<tr>
 +
<td> Digest of pIG7003a (7)-(12) </td>
 +
</tr>
 +
</table>
 +
 +
<div id="tag">
 +
  <h2> 05.06.13 </h2>
 +
<h3> Sequencing of pIG7003a (12) </h3>
 +
<p> → Sequence of pIG7003a (12) not ok: mito-sequence missing </p>
 +
 +
<div id="tag">
 +
  <h2> 06.06.13 </h2>
 +
<p> 6 colonys od pIG7004a were picked and plated </p>
 +
 +
<div id="tag">
 +
  <h2> 07.06.13 </h2>
 +
 +
<p> 6 Minipreps of 6 new colonies of pIG7004a (7)-(12) </p>
 +
<h3> Doubledigest of pIG7004a </h3>
 +
<p> PstI and HindIII </p>
 +
 +
<h3> Sequencing of pIG7004a (7) </h3>
 +
<p> → Sequence of pIG7004a (7) ok </p>
 +
 +
<div id="tag">
 +
  <h2> 11.06.13 </h2>
 +
<p> 12 colonys od pIG7003a were picked and plated </p>
 +
 +
<div id="tag">
 +
  <h2> 12.06.13 </h2>
 +
<p> 12 Minipreps of 12 new colonys with pIG7003a(13) - (24) </p>
 +
<h3> Doubledigest of pIG7003a </h3>
 +
<p> BamHI and AflII </p>
 +
 +
<table class="gelpic">
 +
<tr>
 +
<td> <img class="gelpic" src="https://static.igem.org/mediawiki/2013/d/de/Freiburg_2013_projekt7_06-12_double_digest.jpg"> </td>
 +
</tr>
 +
<tr>
 +
<td> Digest of pIG7003a (13)-(24) with BamHI and AflII </td>
 +
</tr>
 +
</table>
 +
<h3> Sequencing results of pIG7001(1), pIG7002(4), pIG7004(7) </h3>
 +
<p> → tetO13 sequence is not complete in pIG7001(1), pIG7002(4) and pIG7004(7) </p>
 +
<h3> Sequencing of pIG7003a(13) and (14) </h3>
 +
<p> →Sequence of pIG7003a (13) not ok: promotor and mito sequences missing, tetO13 not complete <br>
 +
→Sequence of pIG7003a (14) not ok: mko missing, tetO 13 not complete </p>
 +
 +
<div id="tag">
 +
  <h2> 13.06.13 </h2>
 +
<p> Repetition of Gibson assembly 3 with new pcr products </p>
 +
<h3> PCR 1 </h3>
 +
 +
<table class="tabelle">
 +
      <tr>
 +
<th> Fragment 1 </th>
 +
                <td> pIG7001a </td>
 +
                <td> oIG7004-F </td>
 +
                <td> oIG7004-R </td>
 +
                <td> 2274 bp </td>
 +
      </tr>
 +
      <tr>
 +
<th> Fragment 2 </th>
 +
                <td> pIG7001a </td>
 +
                <td> oIG7005-F </td>
 +
                <td> oIG7005-R </td>
 +
                <td> 2248 bp </td>
 +
      </tr>
 +
              <tr>
 +
<th> Fragment 3 </th>
 +
                <td> pFucci-G1-Orange </td>
 +
                <td> oIG7007-F </td>
 +
                <td> oIG7007-R </td>
 +
                <td> 659 bp </td>
 +
      </tr>
 +
  </table>
 +
 +
<p> PCR program </p>
 +
<div>
 +
    <table class="tabelle">
 +
 +
<td> 98°C </td>
 +
                <td> 5min </td>
 +
                <td> Denaturation </td>
 +
      </tr>
 +
      <tr>
 +
<td> 98°C </td>
 +
                <td> 30s </td>
 +
                <td> Denaturation </td>
 +
      </tr>
 +
              <tr>
 +
<td> 60°C </td>
 +
                <td> 30s </td>
 +
                <td> Annealing </td>
 +
      </tr>
 +
              <tr>
 +
<td> 72°C </td>
 +
                <td> 40s/kb </td>
 +
                <td> Elongation </td>
 +
      </tr>
 +
              <tr>
 +
<td> 72°C </td>
 +
                <td> 10min </td>
 +
                <td> final Elongation </td>
 +
      </tr>
 +
              <tr>
 +
<td> 4°C </td>
 +
                <td> hold </td>
 +
      </tr>
 +
              </table>
 +
<p> <em> 15 cycles </em> </p>
 +
  </div>
 +
<p> no products visible --> PCR did not work </p>
 +
 +
<div id="tag">
 +
  <h2> 14.06.13 </h2>
 +
 +
<p> Repetition of Gibson assembly 3 with new pcr products </p>
 +
<h3> PCR 1 </h3>
 +
 +
<table class="tabelle">
 +
      <tr>
 +
<th> Fragment 1 </th>
 +
                <td> pIG7001a </td>
 +
                <td> oIG7004-F </td>
 +
                <td> oIG7004-R </td>
 +
                <td> 2274 bp </td>
 +
      </tr>
 +
      <tr>
 +
<th> Fragment 2 </th>
 +
                <td> pIG7001a </td>
 +
                <td> oIG7005-F </td>
 +
                <td> oIG7005-R </td>
 +
                <td> 2248 bp </td>
 +
      </tr>
 +
              <tr>
 +
<th> Fragment 3 </th>
 +
                <td> pFucci-G1-Orange </td>
 +
                <td> oIG7007-F </td>
 +
                <td> oIG7007-R </td>
 +
                <td> 659 bp </td>
 +
      </tr>
 +
  </table>
 +
 +
<p> PCR program </p>
 +
<div>
 +
    <table class="tabelle">
 +
 +
<td> 98°C </td>
 +
                <td> 5min </td>
 +
                <td> Denaturation </td>
 +
      </tr>
 +
      <tr>
 +
<td> 98°C </td>
 +
                <td> 30s </td>
 +
                <td> Denaturation </td>
 +
      </tr>
 +
              <tr>
 +
<td> 60°C </td>
 +
                <td> 30s </td>
 +
                <td> Annealing </td>
 +
      </tr>
 +
              <tr>
 +
<td> 72°C </td>
 +
                <td> 35s/kb </td>
 +
                <td> Elongation </td>
 +
      </tr>
 +
              <tr>
 +
<td> 72°C </td>
 +
                <td> 10min </td>
 +
                <td> final Elongation </td>
 +
      </tr>
 +
              <tr>
 +
<td> 4°C </td>
 +
                <td> hold </td>
 +
      </tr>
 +
              </table>
 +
<p> <em> 20 cycles </em> </p>
 +
  </div>
 +
 +
<h3> PCR 2 </h3>
 +
<p> template: products of PCR 1 </p>
 +
<p> PCR program </p>
 +
<div>
 +
    <table class="tabelle">
 +
 +
<td> 98°C </td>
 +
                <td> 5min </td>
 +
                <td> Denaturation </td>
 +
      </tr>
 +
      <tr>
 +
<td> 98°C </td>
 +
                <td> 30s </td>
 +
                <td> Denaturation </td>
 +
      </tr>
 +
              <tr>
 +
<td> 60°C </td>
 +
                <td> 30s </td>
 +
                <td> Annealing </td>
 +
      </tr>
 +
              <tr>
 +
<td> 72°C </td>
 +
                <td> 35s/kb </td>
 +
                <td> Elongation </td>
 +
      </tr>
 +
              <tr>
 +
<td> 72°C </td>
 +
                <td> 10min </td>
 +
                <td> final Elongation </td>
 +
      </tr>
 +
              <tr>
 +
<td> 4°C </td>
 +
                <td> hold </td>
 +
      </tr>
 +
              </table>
 +
<p> <em> 20 cycles </em> </p>
 +
  </div>
 +
<p> all products visible </p>
 +
 +
<h3> Gibson Assembly </h3>
 +
 +
<p> volumes were calculated with excel sheet with concentration and length: <br>
 +
used volumes:<br>
 +
Gibson: 0,88µl, 0,88µl, 0,2µl 1h in 1 aliquot of Gibson mix (according to protocol)<br>
 +
→ pIG7003a, heat shock transfection in E. coli (according to protocol) <br> </p>
 +
 +
<div id="tag">
 +
  <h2> 15.06.13 </h2>
 +
<p> 3 colonys of pIG7003a were picked and plated </p>
 +
 +
<div id="tag">
 +
  <h2> 17.06.13 </h2>
 +
<p> 3 Minipreps of 3 colonys (pIG7003a(25)-(27)) </p>
 +
<h3> Doubledigest of pIG7003a </h3>
 +
<p> BamHI and AflII </p>
 +
 +
<table class="gelpic">
 +
<tr>
 +
<td> <img class="gelpic" src="https://static.igem.org/mediawiki/2013/9/9b/Freiburg_2013_projekt7_06-17_double_digest.Jpg"> </td>
 +
</tr>
 +
<tr>
 +
<td> Digest of pIG7003a (25)-(27) with BamHI and AflII </td>
 +
</tr>
 +
</table>
 +
 +
 +
<h3> Restrictiondigest of pIG7001a, pIG7002a, pIG7004a, pKM006 </h3>
 +
<p> EcoRV and NruI </p>
 +
 +
<table class="gelpic">
 +
<tr>
 +
<td> <img class="gelpic" src="https://static.igem.org/mediawiki/2013/e/eb/Freiburg_2013_projekt7_06-17_Restrictiondigest.png"> </td>
 +
</tr>
 +
<tr>
 +
<td> Restrictiondigest with EcoRV and NruI <br>
 +
left to right:<br>
 +
1:pIG7001a<br>
 +
2:pIG7002a<br>
 +
3:pIG7004a<br>
 +
4:pKM006 <br> </td>
 +
</tr>
 +
</table>
 +
<div>
 +
<ul>
 +
<li> Bands are to weak for quadruple ligation with pKM006  </li>
 +
 +
</ul>
 +
</div>
 +
<h3> Gibson Assembly </h3>
 +
<p> Repetition of the Gibson Assembly from 14.06.2013 <br>
 +
used volumes (products from PCR2):<br>
 +
Gibson: 0,88µl, 0,88µl, 0,2µl 1h in 1 aliquot of Gibson mix (according to protocol)<br>
 +
→ pIG7003a, heat shock transfection in E. coli (according to protocol) <br> </p>
 +
 +
<div id="tag">
 +
  <h2> 18.06.13 </h2>
 +
<div>
 +
<h3> Gibson Assembly </h3>
 +
<p> no colonies on Gibson plate from 17.06.2013 → Repetition of the Gibson Assembly from 14.06.2013 <br>
 +
used volumes (products from PCR2):<br>
 +
Gibson: 0,9µl, 0,9µl, 0,4µl 1h in 1 aliquot of Gibson mix (according to protocol)<br>
 +
→ pIG7003a, heat shock transfection in E. coli (according to protocol)<br> </p>
 +
</div>
 +
<div>
 +
<h3> Restrictiondigest of pIG7001a, pIG7002a, pIG7004a, pKM006 </h3>
 +
<p> Repetition of the restrictiondigest from 17.06.2013 <br>
 +
EcoRV and NruI </p>
 +
 +
<table class="gelpic">
 +
<tr>
 +
<td> <img class="gelpic" src="https://static.igem.org/mediawiki/2013/3/37/Freiburg_2013_projekt7_06-18_Restrictiondigest.png"> </td>
 +
</tr>
 +
<tr>
 +
<td> Restrictiondigest with EcoRV and NruI <br>
 +
left to right:<br>
 +
1:pIG7001a<br>
 +
2:pIG7002a<br>
 +
3:pIG7004a<br>
 +
4:pKM006 <br> </td>
 +
</tr>
 +
</table>
 +
<div>
 +
<ul>
 +
<li> Bands for the backbones (big fragments) are cut out of pIG7001a, pIG7002a and pIG7004a lane <br> and tet013 (small fragment) is cut out of the pKM006 lanes </li>
 +
<li>→ Gelextraction of gel slices (according to protocoll)<br>
 +
concentrations:<br>
 +
pIG7001a= 13 ng/µl<br>
 +
pIG7002a= 10 ng/µl<br>
 +
pIG7004a= 14 ng/µl<br>
 +
pKM006= 1,3-1,5 ng/µl  </li>
 +
 +
</ul>
 +
</div>
 +
 +
<h3> Ligation of pIG7001a, pIG7002a and pIG7004a </h3>
 +
<div>
 +
    <table class="tabelle">
 +
 +
<td> Insert </td>
 +
                <td> pKM006 </td>
 +
                <td> 11µl </td>
 +
      </tr>
 +
      <tr>
 +
<td> Backbone </td>
 +
                <td> pIG7001a; pIG7002a; pIG7004a </td>
 +
                <td> 11µl </td>
 +
      </tr>
 +
              <tr>
 +
<td> 10x Puffer </td>
 +
                <td> 2,5µl </td>
 +
      </tr>
 +
              <tr>
 +
<td> T4 DNA Ligase </td>
 +
                <td> 1µl </td>
 +
              </tr>
 +
              </table>
 +
</div>
 +
<div>
 +
<ul>
 +
<li> Incubation for 15 minutes (RT) </li>
 +
</ul>
 +
</div>
 +
<p> → pIG7001b, pIG7002b, pIG7004b, heat shock transfection in E. coli (according to protocol) <br>
 +
used: 5µl Ligationmix for 50µl TOP10 cells </p>
 +
</div>
 +
 +
<div id="tag">
 +
  <h2> 19.06.13 </h2>
 +
<p>5 colonies picked and plated for pIG7003a (Gibson) <br>
 +
6 colonies each picked and plated for pIG7001b, pIG7002b, pIG7004b(Ligation) </p>
 +
<h3> Seeding of HELAs </h3>
 +
 +
<p> for transfection <br>
 +
<ul> <li> count: 22*10^4 cells/ml </li>
 +
<li> used volume (24 well plate): 0,5 ml/well </li>
 +
<li> used concentration (24 well plate): 8*10^4 cells/well → 8*10^4[cells/ml] / 0,5[ml] =16*10^4 [cells/ml] </li>
 +
<li> 12 wells needed → 6ml total needed </li>
 +
</ul>
 +
 +
<p> calculation: <br>
 +
c1*v1=c2*v2 <br>
 +
v1=(c2*v2)/c1 <br>
 +
v1=(16*10^4 [cells/ml] * 6 [ml])/ 22*10^4 [cells/ml] <br>
 +
v1=4,3 ml <br>
 +
→ 4,3 ml cells + 1,7 ml medium <br> </p>
 +
 +
 +
<h3> Inoculation of liquid cultures </h3>
 +
<p> for MIDIprep with pIG7001a, pIG7002a, pIG7004a <br>
 +
used: 100ml LB-medium,100µl kanamycin </p>
 +
 +
<div id="tag">
 +
  <h2> 20.06.13 </h2>
 +
 +
<p> Miniprep of 5 colonies with pIG7003a(28-32) <br>
 +
Miniprep of 6 colonies each with pIG7001b(1-6), pIG7002b(1-6), pIG7004b(1-6)<br>
 +
 +
Midiprep of pIG7001a, pIG7002a, pIG7004a → no template<br> </p>
 +
 +
<h3> Doubledigest of pIG7003a </h3>
 +
<p> BamHI and AflII </p>
 +
 +
 +
<table class="gelpic">
 +
<tr>
 +
<td> <img class="gelpic" src="https://static.igem.org/mediawiki/2013/2/2d/Freiburg_2013_projekt7_06-20_Doubledigest_pIG7003a.png"> </td>
 +
</tr>
 +
<tr>
 +
<td> Doubledigest with BamHI and AflII </td>
 +
</tr>
 +
</table>
 +
 +
 +
<h3> Doubledigest of pIG7001b, pIG7002b, pIG7004b </h3>
 +
<p> EcoRV and PstI </p>
 +
 +
<table class="gelpic">
 +
<tr>
 +
<td> <img class="gelpic" src="https://static.igem.org/mediawiki/2013/5/57/Freiburg_2013_projekt7_06-20_Doubledigest_pIG7001a%2C_2a%2C_4a.png"> </td>
 +
</tr>
 +
<tr>
 +
<td> Doubledigest with EcoRV and Pst </td>
 +
</tr>
 +
</table>
 +
 +
<h3>Sequencing of pIG7003a (29) and (30)</h3>
 +
<p>→ Sequence not ok, mito sequence missing</p>
 +
 +
<h3>Transfection of HELAs</h3>
 +
<p>with pIG7001a, pIG7002a and pIG7004a + pSAM200 (according to protocol)<br>
 +
→ no fluorescence visable</p>
 +
 +
<div id="tag">
 +
  <h2> 21.06.13 </h2>
 +
<h3> Doubledigest of pIG7001b, pIG7002b, pIG7004b </h3>
 +
<p> EcoRI and PstI </p>
 +
<table class="gelpic">
 +
<tr>
 +
<td> <img class="gelpic" src="https://static.igem.org/mediawiki/2013/e/e0/Freiburg_2013_projekt7_06-21_Doubledigest_pIG7001a%2C_2a%2C_4a.png"> </td>
 +
</tr>
 +
<tr>
 +
<td> Doubledigest with EcoRI and Pst </td>
 +
</tr>
 +
</table>
 +
 +
<div id="tag">
 +
  <h2> 22.06.13 </h2>
 +
<p>Repetition of Gibson Assembly for pIG7003a with new strategy</p>
 +
<h3>PCR</h3>
 +
<table class="tabelle">
 +
      <tr>
 +
<th> Fragment 1 </th>
 +
                <td> pIG7001a </td>
 +
                <td> oIG7004-F </td>
 +
                <td> oIG7004-R </td>
 +
                <td> 2274 bp </td>
 +
      </tr>
 +
      <tr>
 +
<th> Fragment 2 </th>
 +
                <td> pIG7001a </td>
 +
                <td> oIG7005-F </td>
 +
                <td> oIG7005-R </td>
 +
                <td> 2248 bp </td>
 +
      </tr>
 +
              <tr>
 +
<th> Fragment 3 </th>
 +
                <td> pFucci-G1-Orange </td>
 +
                <td> oIG7007-F </td>
 +
                <td> oIG7007-R </td>
 +
                <td> 659 bp </td>
 +
      </tr>
 +
  </table>
 +
 +
<p> PCR program </p>
 +
<div>
 +
    <table class="tabelle">
 +
 +
<td> 98°C </td>
 +
                <td> 5min </td>
 +
                <td> Denaturation </td>
 +
      </tr>
 +
      <tr>
 +
<td> 98°C </td>
 +
                <td> 30s </td>
 +
                <td> Denaturation </td>
 +
      </tr>
 +
              <tr>
 +
<td> 60°C </td>
 +
                <td> 30s </td>
 +
                <td> Annealing </td>
 +
      </tr>
 +
              <tr>
 +
<td> 72°C </td>
 +
                <td> 35s/kb </td>
 +
                <td> Elongation </td>
 +
      </tr>
 +
              <tr>
 +
<td> 72°C </td>
 +
                <td> 10min </td>
 +
                <td> final Elongation </td>
 +
      </tr>
 +
              <tr>
 +
<td> 4°C </td>
 +
                <td> hold </td>
 +
      </tr>
 +
              </table>
 +
<p> <em> 15 cycles </em> </p>
 +
  </div>
 +
 +
<table class="gelpic">
 +
<tr>
 +
<td> <img class="gelpic" src="https://static.igem.org/mediawiki/2013/8/84/Freiburg_2013_projekt7_06-21_gelex1.png"> </td>
 +
</tr>
 +
<tr>
 +
<td> Gelextraction </td>
 +
</tr>
 +
</table>
 +
 +
<div id="tag">
 +
  <h2> 23.06.13 </h2>
 +
<p>4 colonies are picked and plated</p>
 +
 +
 +
<div id="tag">
 +
  <h2> 24.06.13 </h2>
 +
<p>Miniprep of pIG7003a(1-4)</p>
 +
<h3>Doubledigest of pIG7003a (1-4)</h3>
 +
<p>EcoRV and NruI</p>
 +
<table class="gelpic">
 +
<tr>
 +
<td> <img class="gelpic" src="https://static.igem.org/mediawiki/2013/e/ec/Freiburg_2013_projekt7_06-24_restrictiondigest.png"> </td>
 +
</tr>
 +
<tr>
 +
<td> Restrictiondigest with EcoRV and NruI <br>
 +
left to right<br>
 +
1:Marker<br>
 +
2,3,4,5:pIG7003a(1-4) </td>
 +
</tr>
 +
</table>
 +
<h3> Sequencing of pIG7003a(4)</h3>
 +
<p>→ Sequence not ok, mito Sequence missing</p>
 +
 +
 +
<div id="tag">
 +
  <h2> 27.06.13 </h2>
 +
<h3> Gelextraction </h3>
 +
<table class="gelpic">
 +
<tr>
 +
<td> <img class="gelpic" src="https://static.igem.org/mediawiki/2013/a/a3/Freiburg_2013_projekt7_06-27-1_restrictiondigest.png"> </td>
 +
</tr>
 +
<tr>
 +
<td> Restrictiondigest with EcoRV and NruI <br>
 +
left to right<br>
 +
1:Marker<br>
 +
2,3:pIG7002a<br>
 +
4,5:pIG7004a </td>
 +
</tr>
 +
</table>
 +
<p> Bands for the backbones are cut out </p>
 +
 +
<table class="gelpic">
 +
<tr>
 +
<td> <img class="gelpic" src="https://static.igem.org/mediawiki/2013/d/d0/Freiburg_2013_projekt7_06-27-2_restrictiondigest.png"> </td>
 +
</tr>
 +
<tr>
 +
<td> Restrictiondigest with EcoRV and NruI <br>
 +
left to right<br>
 +
1:Marker<br>
 +
2,3:pKM006 </td>
 +
</tr>
 +
</table>
 +
<p> Bands for tetO13 are cut out </p>
 +
 +
<div id="july">
 +
<p id="h2">
 +
July
 +
</p>
 +
</div>
 +
<div id="tag">
 +
  <h2> 13.07.13 </h2>
 +
<p>Repetition of the restrictiondigest (pIG7001a, pIG7002a, pIG7004a and pKM006) <br>
 +
EcoRV and NruI<br>
 +
Bands for the backbones (big fragments) are cut out of pIG7001a, pIG7002a and pIG7004a lane and tet013 (small fragment) is cut out of the pKM006 lanes</p>
 +
 +
<div id="tag">
 +
  <h2> 15.07.13 </h2>
 +
<h3> Ligation of pIG7001b, pIG7002b and pIG7004b </h3>
 +
 +
<div id="floatleft">
 +
<table class="tabelle">
 +
      <tr>
 +
<th> Insert </th>
 +
                <td> pKM006 </td>
 +
                <td> 11µl </td>
 +
              </tr>
 +
      <tr>
 +
<th> Backbone </th>
 +
                <td> pIG7001a; pIG7002a; pIG7004a </td>
 +
                <td> 11µl </td>
 +
              </tr>
 +
              <tr>
 +
<th> 10xBuffer </th>
 +
                <td>  </td>
 +
                <td> 2,5µl </td>
 +
      </tr>
 +
              <tr>
 +
<th> T4 DNA Ligase </th>
 +
                <td> </td>
 +
                <td> 1µl </td>
 +
      </tr>
 +
  </table>
 +
</div>
 +
<div id="floatright">
 +
<ul>
 +
<li> incubation for 15 minutes (RT)
 +
</ul>
 +
</div>
 +
<p>→ pIG7001b, pIG7002b, pIG7004b, heat shock transfection in E. coli (according to protocol) <br>
 +
used: 5µl Ligationmix for 50µl TOP10 cells</p>
 +
 +
<div id="tag">
 +
  <h2> 16.07.13 </h2>
 +
<p>-2 colonies picked and plated for pIG7001b, pIG7002b and pIG7004b in liquid culture<br>
 +
Miniprep of pIG7001b (1-2), pIG7002b (1-2), pIG7004b (1-2)</p>
 +
 +
<div id="tag">
 +
  <h2> 18.07.13 </h2>
 +
<h3>Doubledigest of pIG7001b(1-2), pIG7002b(1-2), pIG7004b(1-2)</h3>
 +
<p>EcoRV and NheI</p>
 +
 +
<table class="gelpic">
 +
<tr>
 +
<td> <img class="gelpic" src="https://static.igem.org/mediawiki/2013/9/99/Freiburg_2013_projekt7_07-18_testdigest.png"> </td>
 +
</tr>
 +
<tr>
 +
<td> Restrictiondigest with EcoRV and NheI <br>
 +
left to right<br>
 +
1:pIG7001b(1) <br>
 +
2:pIG7001b(2)<br>
 +
3:pIG7002b(1)<br>
 +
4:pIG7002b(2)<br>
 +
5:pIG7004b(1)<br>
 +
6:pIG7004b(2)</td>
 +
</tr>
 +
</table>
 +
 +
<h3>Sequencing of pIG7001b(2), pIG7002b(2), pIG7004b(2)</h3>
 +
<p> → Sequence ok </p>
 +
 +
<div id="tag">
 +
  <h2> 19.07.13 </h2>
 +
<p> Changing of the target cassett in two constructs (pIG7002b and pIG7004b)<br>
 +
→ every construct can be targeted seperately</p>
 +
<h3>PCR</h3>
 +
<p> amplifying the 400bp cassett out of the opposite construct (pIG7002 insert for pIG7004b backbone; pIG7004 insert for pIG7002b backbone)</p>
 +
 +
<table class="tabelle">
 +
      <tr>
 +
<th> Fragment 1 </th>
 +
                <td> pIG7002b </td>
 +
                <td> oIG7009-F </td>
 +
                <td> oIG7009-R </td>
 +
                <td> 400bp </td>
 +
              </tr>
 +
              <tr>
 +
<th> Fragment 2 </th>
 +
                <td> pIG7004b </td>
 +
                <td> oIG7011-F </td>
 +
                <td> oIG7011-R </td>
 +
                <td> 400bp </td>
 +
              </tr>
 +
</table>
 +
<p> PCR program </p>
 +
<div>
 +
    <table class="tabelle">
 +
 +
<td> 98°C </td>
 +
                <td> 5min </td>
 +
                <td> Denaturation </td>
 +
      </tr>
 +
      <tr>
 +
<td> 95°C </td>
 +
                <td> 30s </td>
 +
                <td> Denaturation </td>
 +
      </tr>
 +
              <tr>
 +
<td> 60°C </td>
 +
                <td> 30s </td>
 +
                <td> Annealing </td>
 +
      </tr>
 +
              <tr>
 +
<td> 72°C </td>
 +
                <td> 30s/kb </td>
 +
                <td> Elongation </td>
 +
      </tr>
 +
              <tr>
 +
<td> 72°C </td>
 +
                <td> 10min </td>
 +
                <td> final Elongation </td>
 +
      </tr>
 +
              <tr>
 +
<td> 4°C </td>
 +
                <td> hold </td>
 +
      </tr>
 +
              </table>
 +
<p> <em> 15 cycles </em> </p>
 +
  </div>
 +
<p>→ PCR product 2 and 4</p>
 +
 +
<div id="tag">
 +
  <h2> 22.07.13 </h2>
 +
<h3>Restrictiondigest of pIG7002b, pIG7004b, PCR product 2 and PCR product 4</h3>
 +
<table class="tabelle">
 +
      <tr>
 +
<th> DNA </th>
 +
                <th> Enzyme </th>
 +
              <tr>
 +
              <tr>
 +
<td> pIG7002b </td>
 +
                <td> NruI and NheI </td>
 +
              </tr>
 +
              <tr>
 +
<td> pIG7004b </td>
 +
                <td> PstI and NheI </td>
 +
              </tr>
 +
              <tr>
 +
<td> PCR product 2 </td>
 +
                <td> PstI and NheI </td>
 +
              </tr>
 +
              <tr>
 +
<td> PCR product 4 </td>
 +
                <td> NheI </td>
 +
              </tr>
 +
</table>
 +
<p> Restricted DNA was load on gel:</p>
 +
 +
<table class="gelpic">
 +
<tr>
 +
<td> <img class="gelpic" src="https://static.igem.org/mediawiki/2013/b/be/Freiburg_2013_projekt7_07-22_restictiondigest.png"> </td>
 +
</tr>
 +
<tr>
 +
<td> Restrictiondigest with EcoRV and NheI <br>
 +
left to right<br>
 +
1:pIG7002b <br>
 +
2:PCR product 2<br>
 +
3:pIG7004b(1)<br>
 +
4:PCR product 4</td>
 +
</tr>
 +
</table>
 +
<p> → no bands for both PCR products visible, pIG7002b and pIG7004b: restricted DNA band not differentiable from not restricted </p>
 +
 +
<div id="tag">
 +
  <h2> 23.07.13 </h2>
 +
<p> - Repetition of PCR (19.07.) and Restriction (22.07.) </p>
 +
<table class="tabelle">
 +
      <tr>
 +
<th> Fragment 1 </th>
 +
                <td> pIG7002b </td>
 +
                <td> oIG7009-F </td>
 +
                <td> oIG7009-R </td>
 +
                <td> 400bp </td>
 +
              </tr>
 +
              <tr>
 +
<th> Fragment 2 </th>
 +
                <td> pIG7004b </td>
 +
                <td> oIG7011-F </td>
 +
                <td> oIG7011-R </td>
 +
                <td> 400bp </td>
 +
              </tr>
 +
</table>
 +
<p> PCR program </p>
 +
<div>
 +
    <table class="tabelle">
 +
 +
<td> 95°C </td>
 +
                <td> 30s </td>
 +
                <td> Denaturation </td>
 +
      </tr>
 +
      <tr>
 +
<td> 95°C </td>
 +
                <td> 30s </td>
 +
                <td> Denaturation </td>
 +
      </tr>
 +
              <tr>
 +
<td> 60°C </td>
 +
                <td> 30s </td>
 +
                <td> Annealing </td>
 +
      </tr>
 +
              <tr>
 +
<td> 68°C </td>
 +
                <td> 30s/kb </td>
 +
                <td> Elongation </td>
 +
      </tr>
 +
              <tr>
 +
<td> 68°C </td>
 +
                <td> 5min </td>
 +
                <td> final Elongation </td>
 +
      </tr>
 +
              <tr>
 +
<td> 4°C </td>
 +
                <td> hold </td>
 +
      </tr>
 +
              </table>
 +
<p> <em> 30 cycles </em> </p>
 +
  </div>
 +
<p>→ PCR product 2 and 4</p>
 +
 +
<div id="tag">
 +
  <h2> 24.07.13 </h2>
 +
<p> Doubledigest of PCR product 2 and 4<br>
 +
- bands for both PCR products visible </p>
 +
 +
<h3>Restrictiondigest of pIG7002b, pIG7004b, PCR product 2 and PCR product 4</h3>
 +
<table class="tabelle">
 +
      <tr>
 +
<th> DNA </th>
 +
                <th> Enzyme </th>
 +
              <tr>
 +
              <tr>
 +
<td> pIG7002b </td>
 +
                <td> NruI and NheI </td>
 +
              </tr>
 +
              <tr>
 +
<td> pIG7004b </td>
 +
                <td> PstI and NheI </td>
 +
              </tr>
 +
              <tr>
 +
<td> PCR product 2 </td>
 +
                <td> PstI and NheI </td>
 +
              </tr>
 +
              <tr>
 +
<td> PCR product 4 </td>
 +
                <td> NheI </td>
 +
              </tr>
 +
</table>
 +
<p> Restricted DNA was load on gel:</p>
 +
 +
<table class="gelpic">
 +
<tr>
 +
<td> <img class="gelpic" src="https://static.igem.org/mediawiki/2013/a/ab/Freiburg_2013_projekt7_07-24-1_restrictiondigest.png"> </td>
 +
</tr>
 +
<tr>
 +
<td> Restrictiondigest <br>
 +
left to right<br>
 +
1:Marker <br>
 +
2:PCR product 2<br>
 +
3:PCR product 4</td>
 +
</tr>
 +
</table>
 +
<table class="gelpic">
 +
<tr>
 +
<td> <img class="gelpic" src="https://static.igem.org/mediawiki/2013/5/5d/Freiburg_2013_projekt7_07-24-2_restrictiondigest.png"> </td>
 +
</tr>
 +
<tr>
 +
<td> Restrictiondigest<br>
 +
left to right<br>
 +
1:Marker <br>
 +
2:pIG7002b<br>
 +
3:pIG7004b</td>
 +
</tr>
 +
</table>
 +
<p> Bands are cut out <br>
 +
Gelextraction concentrations:<br>
 +
pIG7002b: 10,7 ng/µl<br>
 +
pIG7004b: 31 ng/µl<br>
 +
PCR product 2: 14,4 ng/µl<br>
 +
PCR product 4: 3,3 ng/µl</p>
 +
 +
<h3>Ligation</h3>
 +
<p>for pIG7002c</p>
 +
<table class="tabelle">
 +
      <tr>
 +
<th> Stuff </th>
 +
                <th> Amount </th>
 +
              <tr>
 +
              <tr>
 +
<td> restricted pIG7002b </td>
 +
                <td> 5µl </td>
 +
              </tr>
 +
              <tr>
 +
<td> restricted PCR product 4 </td>
 +
                <td> 4µl </td>
 +
              </tr>
 +
              <tr>
 +
<td> T4 Ligase Buffer (10X) </td>
 +
                <td> 2µl </td>
 +
              </tr>
 +
              <tr>
 +
<td> T4 Ligase </td>
 +
                <td> 1µl </td>
 +
              </tr>
 +
              <tr>
 +
<td> water </td>
 +
                <td> 8µl </td>
 +
              </tr>
 +
              <tr>
 +
<td> total </td>
 +
                <td> 20µl </td>
 +
              </tr>
 +
</table>
 +
 +
<p>for pIG7004c</p>
 +
<table class="tabelle">
 +
      <tr>
 +
<th> Stuff </th>
 +
                <th> Amount </th>
 +
              <tr>
 +
              <tr>
 +
<td> restricted pIG7004b </td>
 +
                <td> 1,8µl </td>
 +
              </tr>
 +
              <tr>
 +
<td> restricted PCR product 2 </td>
 +
                <td> 1µl </td>
 +
              </tr>
 +
              <tr>
 +
<td> T4 Ligase Buffer (10X) </td>
 +
                <td> 2µl </td>
 +
              </tr>
 +
              <tr>
 +
<td> T4 Ligase </td>
 +
                <td> 1µl </td>
 +
              </tr>
 +
              <tr>
 +
<td> water </td>
 +
                <td> 14,2µl </td>
 +
              </tr>
 +
              <tr>
 +
<td> total </td>
 +
                <td> 20µl </td>
 +
              </tr>
 +
</table>
 +
 +
<p> incubation for 30 minutes (RT) </p>
 +
<p> → pIG7002c, pIG7004c, heat shock transfection in E. coli (according to protocol) <br>
 +
used: 1µl Ligationmix for 25µl TOP10 cells </p>
 +
 +
<div id="tag">
 +
  <h2> 25.07.13 </h2>
 +
<p> 6 colonies each are picked and plated </p>
 +
 +
 +
<div id="tag">
 +
  <h2> 26.07.13 </h2>
 +
<p> Miniprep of all 12 colonies <br>
 +
Sequencing of the first 3 colonies each </p>
 +
 +
<div id="tag">
 +
  <h2> 27.07.13 </h2>
 +
<p> Sequences not ok <br>
 +
Sequencing of the last 3 colonies each </p>
 +
 +
<div id="tag">
 +
  <h2> 28.07.13 </h2>
 +
<p> Sequences not ok <br>
 +
→ Ligation failed </p>
 +
 +
 +
<div id="august">
 +
<p id="h2">
 +
August
 +
</p>
 +
</div>
-
<h3>12.08.13</h3>
+
<h2>12.08.13</h2>
-
   <h5>Digest of reporter plasmids</h5>
+
   <h3>Digest of reporter plasmids</h3>
  <div id="floatleft">
  <div id="floatleft">
<table class="tabelle">
<table class="tabelle">
Line 444: Line 1,930:
</div>
</div>
-
<h3>13.08.13</h3>
+
<h2>13.08.13</h2>
-
   <h5>Gel run</h5>
+
   <h3>Gel run</h3>
<p>A) Digest of pIG700..</p>
<p>A) Digest of pIG700..</p>
<div id="floathleft">
<div id="floathleft">
<table class="gelpic">
<table class="gelpic">
<tr>  
<tr>  
-
<td> <img class="gelpic" src="https://wiki.uni-freiburg.de/freigemintern/lib/exe/fetch.php?t=1376480056&w=500&h=376&media=wiki:laborbuecher:michael:13.08.13_digest_of_pig700x.jpg"> </td>
+
<td> <img class="gelpic" src="https://static.igem.org/mediawiki/2013/9/94/3_multiple_targeting_laabbook_freiburg_13.Jpg"> </td>
</tr>
</tr>
<tr>
<tr>
Line 462: Line 1,948:
<table class="gelpic">
<table class="gelpic">
<tr>  
<tr>  
-
<td> <img class="gelpic" src="https://wiki.uni-freiburg.de/freigemintern/lib/exe/fetch.php?t=1376480056&w=500&h=376&media=wiki:laborbuecher:michael:13.08.13_digest_of_pig700x_cut.jpg"> </td>
+
<td> <img class="gelpic" src="https://static.igem.org/mediawiki/2013/0/08/4_multiple_targeting_laabbook_freiburg_13.Jpg"> </td>
</tr>
</tr>
<tr>
<tr>
Line 475: Line 1,961:
<table class="gelpic">
<table class="gelpic">
<tr>  
<tr>  
-
<td> <img class="gelpic" src="https://wiki.uni-freiburg.de/freigemintern/lib/exe/fetch.php?t=1376480056&w=500&h=376&media=wiki:laborbuecher:michael:13.08.13_digest_of_pkm60x.jpg"> </td>
+
<td> <img class="gelpic" src="https://static.igem.org/mediawiki/2013/0/02/5_multiple_targeting_laabbook_freiburg_13.Jpg"> </td>
</tr>
</tr>
<tr>
<tr>
Line 487: Line 1,973:
<table class="gelpic">
<table class="gelpic">
<tr>  
<tr>  
-
<td> <img class="gelpic" src="https://wiki.uni-freiburg.de/freigemintern/lib/exe/fetch.php?t=1376480056&w=500&h=376&media=wiki:laborbuecher:michael:13.08.13_digest_of_pkm60x_cut.jpg"> </td>
+
<td> <img class="gelpic" src="https://static.igem.org/mediawiki/2013/8/80/6_multiple_targeting_laabbook_freiburg_13.Jpg"> </td>
</tr>
</tr>
<tr>
<tr>
Line 498: Line 1,984:
<p>All bands are at the expected sizes.</p>
<p>All bands are at the expected sizes.</p>
-
   <h5>Gel extraction</h5>
+
   <h3>Gel extraction</h3>
<p>DNA were purified using <i>High Pure Plasmid Isolation Kit</i> of Roche.</p>
<p>DNA were purified using <i>High Pure Plasmid Isolation Kit</i> of Roche.</p>
<p>Changes to the protocol:  
<p>Changes to the protocol:  
Line 507: Line 1,993:
<p>Yield: 10 ng/µl (pIG700..); 2 ng/µl (pKM60..)</p>
<p>Yield: 10 ng/µl (pIG700..); 2 ng/µl (pKM60..)</p>
-
   <h5>Recombination of cutted parts</h5>
+
   <h3>Recombination of cutted parts</h3>
<div class="floatleft">
<div class="floatleft">
Line 553: Line 2,039:
</div>
</div>
-
   <h5>Trafo</h5>
+
   <h3>Trafo</h3>
<div class="floatleft">
<div class="floatleft">
<ol>
<ol>
Line 567: Line 2,053:
</div>
</div>
-
<h3>14.08.13</h3>
+
<h2>14.08.13</h2>
-
   <h5>Picking of clones</h5>
+
   <h3>Picking of clones</h3>
<p>From each Ligation 7 clones were picked and spread on 1/4 plates.</p>
<p>From each Ligation 7 clones were picked and spread on 1/4 plates.</p>
-
<h3>15.08.13</h3>
+
<h2>15.08.13</h2>
-
   <h5>Miniprep</h5>
+
   <h3>Miniprep</h3>
<p>DNA was purified using <i>High Pure Plasmid Isolation Kit</i> of Roche.</p>
<p>DNA was purified using <i>High Pure Plasmid Isolation Kit</i> of Roche.</p>
<p>Yield: ~ 220 ng/µl</p>
<p>Yield: ~ 220 ng/µl</p>
-
   <h5>Test digest</h5>
+
   <h3>Test digest</h3>
<div class="floatleft">
<div class="floatleft">
<table class="tabelle">
<table class="tabelle">
Line 588: Line 2,074:
</div>
</div>
-
   <h5>Gel run</h5>
+
   <h3>Gel run</h3>
<div id="floathleft">
<div id="floathleft">
<table class="gelpic">
<table class="gelpic">
<tr>  
<tr>  
-
<td> <img class="gelpic" src="https://wiki.uni-freiburg.de/freigemintern/lib/exe/fetch.php?t=1376594355&w=500&h=376&media=15.08.13_test_digest_of_pig700x.jpg"> </td>
+
<td> <img class="gelpic" src="https://static.igem.org/mediawiki/2013/7/70/7_multiple_targeting_laabbook_freiburg_13.Jpg"> </td>
</tr>
</tr>
<tr>
<tr>
Line 601: Line 2,087:
</div>
</div>
-
<h3>16.08.13</h3>
+
<h2>16.08.13</h2>
-
   <h5>Midiprep</h5>
+
   <h3>Midiprep</h3>
<p>Though the sequencing did not have a result, plasmids were amplified and midiprepped by <i>Pure Yield Plasmid Midiprep System</i> from Promega because of the results of the test digest.</p>
<p>Though the sequencing did not have a result, plasmids were amplified and midiprepped by <i>Pure Yield Plasmid Midiprep System</i> from Promega because of the results of the test digest.</p>
-
   <h5>Seeding of cells for microscopy</h5>
+
   <h3>Seeding of cells for microscopy</h3>
<p>A 24 well plate with cover slips was filled with 50,000 cells per well.</p>
<p>A 24 well plate with cover slips was filled with 50,000 cells per well.</p>
-
<h3>17.08.13</h3>
+
<h2>17.08.13</h2>
-
   <h5>Transfection</h5>
+
   <h3>Transfection</h3>
<div class="floatleft">
<div class="floatleft">
Protocol:
Protocol:
Line 620: Line 2,106:
Transfection scheme:
Transfection scheme:
<div id="floathleft">
<div id="floathleft">
-
<img class="gelpic" src="https://wiki.uni-freiburg.de/freigemintern/lib/exe/fetch.php?t=1376814433&w=500&h=283&media=wiki:laborbuecher:michael:transfection_multiple_targets_i.png">
+
<img class="gelpic" src="https://static.igem.org/mediawiki/2013/d/d8/8_multiple_targeting_laabbook_freiburg_13.png">
</div>  
</div>  
-
<h3>18.08.13</h3>
+
<h2>18.08.13</h2>
-
   <h5>Fixation</h5>  
+
   <h3>Fixation</h3>  
<p>Cells were washed with 500 µl PBS per well and fixated with 200 µl PFA per well (incubation on ice for 45 min).</p>
<p>Cells were washed with 500 µl PBS per well and fixated with 200 µl PFA per well (incubation on ice for 45 min).</p>
<p>Cover slips were washed in dH<sub>2</sub>O and mounted on a drop of Mowiol with DABCO on a object slide.</p>
<p>Cover slips were washed in dH<sub>2</sub>O and mounted on a drop of Mowiol with DABCO on a object slide.</p>
-
<h3>19.08.13</h3>
+
<h2>19.08.13</h2>
-
   <h5>Flourescence microscopy</h5>
+
   <h3>Flourescence microscopy</h3>
<p>GFP and mCherry were expressed in all cells, only in the cells with TetR-VP16 there was a stronger signal. BFP was not detectable because of the microscope.</p>
<p>GFP and mCherry were expressed in all cells, only in the cells with TetR-VP16 there was a stronger signal. BFP was not detectable because of the microscope.</p>
-
<h3>21.08.13</h3>
+
<h2>21.08.13</h2>
-
   <h5>Seeding of cells for microscopy</h5>
+
   <h3>Seeding of cells for microscopy</h3>
<p>A 24 well plate with cover slips was filled with 50,000 CHO cells per well.</p>
<p>A 24 well plate with cover slips was filled with 50,000 CHO cells per well.</p>
-
<h3>22.08.13</h3>
+
<h2>22.08.13</h2>
-
   <h5>Transfection</h5>
+
   <h3>Transfection</h3>
<div class="floatleft">
<div class="floatleft">
Protocol:
Protocol:
Line 647: Line 2,133:
<li>Solution was spread drop-wise to the cells in the dish</li>
<li>Solution was spread drop-wise to the cells in the dish</li>
</div>
</div>
-
   <h5>Medium change</h5>
+
   <h3>Medium change</h3>
Medium was changed after 3 h.
Medium was changed after 3 h.
-
<h3>23.08.13</h3>
+
<h2>23.08.13</h2>
-
   <h5>Fixation</h5>
+
   <h3>Fixation</h3>
<p>Cells were washed with 500 µl PBS per well and fixated with 200 µl PFA per well (incubation on ice for 45 min).</p>
<p>Cells were washed with 500 µl PBS per well and fixated with 200 µl PFA per well (incubation on ice for 45 min).</p>
<p>Cover slips were washed in dH<sub>2</sub>O and mounted on a drop of Mowiol with DABCO on a object slide.</p>
<p>Cover slips were washed in dH<sub>2</sub>O and mounted on a drop of Mowiol with DABCO on a object slide.</p>
-
<h3>25.08.13</h3>
+
<h2>25.08.13</h2>
-
   <h5>Flourescence microscopy</h5>
+
   <h3>Flourescence microscopy</h3>
<p>GFP and mCherry were detectable, but no differences in fluorescence intensity.</p>
<p>GFP and mCherry were detectable, but no differences in fluorescence intensity.</p>
-
<h3>31.08.13</h3>
+
<h2>31.08.13</h2>
-
   <h5>Seeding of cells for flow cytometry</h5>
+
   <h3>Seeding of cells for flow cytometry</h3>
<p>A 24 well plate  was filled with 50,000 HEK cells per well.</p>
<p>A 24 well plate  was filled with 50,000 HEK cells per well.</p>
-
<h3>01.09.13</h3>
+
<div id="september">
-
   <h5>Transfection</h5>
+
<p id="h2">
 +
September
 +
</p>
 +
</div>
 +
 
 +
<h2>01.09.13</h2>
 +
   <h3>Transfection</h3>
<div class="floatleft">
<div class="floatleft">
Protocol:
Protocol:
Line 677: Line 2,169:
</div>
</div>
-
<h3>03.09.13</h3>
+
<h2>03.09.13</h2>
-
   <h5>Preparation for flow cytometry</h5>
+
   <h3>Preparation for flow cytometry</h3>
<ul>
<ul>
<li>Removal of medium.</li>
<li>Removal of medium.</li>
Line 687: Line 2,179:
</ul>
</ul>
-
   <h5>Flow cytometry</h5>
+
   <h3>Flow cytometry</h3>
<p>Intensities of all flourescent protein were measured.</p>
<p>Intensities of all flourescent protein were measured.</p>

Latest revision as of 05:12, 28 October 2013

crRNA - Multiple targeting

May

28.05.13

PCR 1

for Gibson Assembly

Fragment 1 pACGFP1-Golgi oIG7001-F oIG7001-R 2209 bp
Fragment 2 pACGFP1-Golgi oIG7002-F oIG7002-R 2126 bp
Fragment 3 pKM006 oIG7003-F oIG7003-R 1100 bp
Stuff Volume
Template(Plasmid) 0,5µl
Primer(10 µM) each 1µl
Q5 Polymerase 0,5µl
dNTPs(2,5mM) 2µl
Q5 Buffer(5x) 4µl
Water 11µl
total 20µl

Program

98°C 5min Denaturation
98°C 30s Denaturation
60°C 30s Annealing
72°C 35s/kb Elongation
72°C 10min final Elongation
4°C hold

14 cycles

15µl of each product from PCR 1 were load on gel:

Products PCR 1
left to right:
1: ladder (1kb)
2: Fragment 1 (2209bp)
3:Fragment 2 (2126bp)
4:Fragment 3 (1100bp)

PCR 2

for Gibson Assembly
template: products from PCR 1

Stuff Volume
Template(PCR product) 2µl
Primer(10 µM) each 1µl
Q5 Polymerase 1µl
dNTPs(2,5mM) 5µl
Q5 Buffer(5x) 10µl
Water 30µl
total 50µl

Program

98°C 5min Denaturation
98°C 30s Denaturation
60°C 30s Annealing
72°C 35s/kb Elongation
72°C 10min final Elongation
4°C hold

18 cycles

Concentration of PCR-Products:
1: 990 ng/µl 2: 900 ng/µl 3: 870 ng/µl

4µl of each product from PCR 2 were load on gel:

Products PCR 2
left to right:
2: ladder (1kb)
3: Fragment 1 (2209bp))
4: Fragment 2 (2126bp)
5: Fragment 3 (1100bp)

Gibson Assembly

Calculation of DNA mix for Gibson Assembly:
concentration [ng/µl] * size [kbp] * 0.00023 [1/(ng*kb)]
1h in 1 aliquot of Gibson mix (according to protocol)
→ pIG7001a , heat shock transfection in E. coli (according to protocol)

29.05.13

6 colonys pIG7001a were picked and plated

Colony PCR

from 6 colonies with pIG7001a (Gibson Assembly 28-05)

Product pKM006 oIG7003-F oIG7003-R 1100bp
Volume Stuff
Template (Bacteria from colonie)
1µl Taq Standart buffer (10x)
0,5µl Primer1
0,5µl Primer2
2.5µl dNTPs
0.5µl Taq polymerase
7µl H2O
10µl total

Program

98°C 7min Denaturation
98°C 30s Denaturation
67°C 30s Annealing
72°C 50s Elongation
72°C 10min final Elongation
4°C hold

30 cycles

10µl of each PCR product were load on a gel:

Products Colony-PCR
left to right:
1: ladder (1kb)
2-7: colonie 1-6 from pIG7001a (gibson assembly 05-28)
8: negativ control
9: positive control (template is pKM006)
PCR did not work

30.05.13

6 minipreps of pIG7001a:
cancentrations: 196 ng/µl, 175 ng/µl, 195 ng/µl, 133 ng/µl, 203 ng/µl, 197 ng/µl

Double-Digest of pIG7001a

used: minipreps of colonies 1-6, NgoMIV, PstI HF

µl type
5 DNA
1 NEB-Buffer 4
0.5 Pst1 HF
0.5 NgoMIV
Add to 10 µl H2O
  • Temp.: 37°C
  • Incubation time: 1h

the whole mix was load on a gel:

expected bands
Products double digest:
pIG7001a (Prep 1-6) with Pst1 and NgoMIV

PCR 1

colonie 1 was used (oIG7001a)
for Gibson Assembly 2:

Fragment 1 pIG7001a oIG7004-F oIG7004-R 2274 bp
Fragment 2 pIG7001a oIG7005-F oIG7005-R 2248 bp
Fragment 3 GW1-Peredox_mCherry-NLS oIG7006-F oIG7006-R 741 bp
for Gibson Assembly 3:
Fragment 1 pIG7001a oIG7004-F oIG7004-R 2274 bp
Fragment 2 pIG7001a oIG7005-F oIG7005-R 2248 bp
Fragment 3 pFucci-G1-Orange oIG7007-F oIG7007-R 659 bp
for Gibson Assembly 4:
Fragment 1 pIG7001a oIG7004-F oIG7004-R 2274 bp
Fragment 2 pIG7001a oIG7005-F oIG7005-R 2248 bp
Fragment 3 pDS47-BFP-dGEM-trunc oIG7008-F oIG7008-R 679 bp
µl type
4 Q5-HF Reaction Buffer
0,5 Template
1 each Primer
5 dNTPs
0.5 Q5-HF Polymerase
Add to 20 H2O
  • Gibson 1 program was used

5µl of each product were load on a gel

Products of PCR 1

Product 3 from Gibson 2 is missing → 0,2 µl extra plasmid template was added for PCR 2

PCR 2

for gibson assembly 2, 3, and 4
template: products from 1. PCR

µl type
4 Q5-HF Reaction Buffer
2 Template
1 each Primer
5 dNTPs
0.5 Q5-HF Polymerase
Add to 20 H2O
  • Gibson 2 program was used

concetration of PCR products:
Gibson 2: 1415 ng/µl, 1417 ng/µl, 1315 ng/µl
Gibson 3: 2874 ng/µl, 1436 ng/µl, 337 ng/µl
Gibson 4: 324 ng/µl, 325 ng/µl, 2047 ng/µl

5µl of each PCR product were load on a gel

Products of PCR 2

Gibson Assembly

volumes were calculated with excel sheet with concentration and length:
used volumes:
Gibson 2: 0,3 µl, 0,3 µl, 0,1 µl
Gibson 3: 0,15 µl, 0,3 µl, 0,4 µl
Gibson 4: 1,4 µl, 1,4 µl, 0,1 µl
1h in 1 aliquot of Gibson mix (according to protocol)
→ pIG7002a, heat shock transfection in E. coli (according to protocol)
→ pIG7003a, heat shock transfection in E. coli (according to protocol)
→ pIG7004a, heat shock transfection in E. coli (according to protocol)

31.05.13

Digest of pIG7001a

used: colonie 1 (pIG7001a), NcoI, PstI HF, XbaI

µl type
5 DNA
1 NEB-Buffer 4
0,5 XbaI
0,1 BSA
Add to 10µl H2O
µl type
5 DNA
1 NEB-Buffer 4
0,5 NcoI HF
Add to 10µl H2O
µl type
5 DNA
1 NEB-Buffer 4
0,5 PstI HF
Add to 10µl H2O
  • Temp.: 37°C
  • Incubation time: 1h
expected bands
pIG7001a digest
left to right:
1: ladder (1kb)
2: XbaI
3: NcoI
4: PstI
5: negative control

XbaI did only cut once instead of twice, NcoI and PstI cut as expected

Sequencing of pIG7001a(1)

GATC-Watch-box: 706894
→ Sequence of pIG7001a ok

June

01.06.13

Repetition of gibson assembly 2,3,4 with old PCR products new 2. PCR only for fragment 3 of gibson 3 –> contamination with plasmid template

PCR 2 (fragment 3 / gibson 3)

same protocol was used 5µl of PCR product were load on gel

Products of PCR 2
Fragment 3, Gibson 3

Gibson Assembly

volumes were calculated with excel sheet only by length:
used volumes:
Gibson 2: 1,5 µl, 1,5 µl, 0,5 µl
Gibson 3: 1,5 µl, 1,5 µl, 0,5 µl
Gibson 4: 1,5 µl, 1,5 µl, 1,0 µl

→ pIG7002a, heat shock transfection in E. coli (according to protocol)
→ pIG7003a, heat shock transfection in E. coli (according to protocol)
→ pIG7004a, heat shock transfection in E. coli (according to protocol)

02.06.13

6 colonys each (pIG7002a,pIG7003a, pIG7004a) were picked and plated
2 colonys control were picked and plated

03.06.13

Doubledigest of pIG7002a, pIG7003a, pIG7004a

PstI and HindIII

Expected bands
Digest of pIG7002a, pIG7003a, pIG7004a with PstI and HindIII
  • For pIG7002a only the plasmid form colony 4 shows expected bands.
  • No colony from pIG7003a is positive.
  • Only the plasmid from colony 4 of pIG7004a shows the expected bands.

Sequencing of pIG7002a (4) and pIG7004a (4)

GATC-Watch-box: 707852
→ Sequence of pIG7002a ok
→ Frameshift in pIG7004a ok

04.06.13

6 Minipreps of 6 new colonys with pIG7003a: (7)-(12)

Doubledigest of pIG7003a

PstI and HindIII

Digest of pIG7003a (7)-(12)

05.06.13

Sequencing of pIG7003a (12)

→ Sequence of pIG7003a (12) not ok: mito-sequence missing

06.06.13

6 colonys od pIG7004a were picked and plated

07.06.13

6 Minipreps of 6 new colonies of pIG7004a (7)-(12)

Doubledigest of pIG7004a

PstI and HindIII

Sequencing of pIG7004a (7)

→ Sequence of pIG7004a (7) ok

11.06.13

12 colonys od pIG7003a were picked and plated

12.06.13

12 Minipreps of 12 new colonys with pIG7003a(13) - (24)

Doubledigest of pIG7003a

BamHI and AflII

Digest of pIG7003a (13)-(24) with BamHI and AflII

Sequencing results of pIG7001(1), pIG7002(4), pIG7004(7)

→ tetO13 sequence is not complete in pIG7001(1), pIG7002(4) and pIG7004(7)

Sequencing of pIG7003a(13) and (14)

→Sequence of pIG7003a (13) not ok: promotor and mito sequences missing, tetO13 not complete
→Sequence of pIG7003a (14) not ok: mko missing, tetO 13 not complete

13.06.13

Repetition of Gibson assembly 3 with new pcr products

PCR 1

Fragment 1 pIG7001a oIG7004-F oIG7004-R 2274 bp
Fragment 2 pIG7001a oIG7005-F oIG7005-R 2248 bp
Fragment 3 pFucci-G1-Orange oIG7007-F oIG7007-R 659 bp

PCR program

98°C 5min Denaturation
98°C 30s Denaturation
60°C 30s Annealing
72°C 40s/kb Elongation
72°C 10min final Elongation
4°C hold

15 cycles

no products visible --> PCR did not work

14.06.13

Repetition of Gibson assembly 3 with new pcr products

PCR 1

Fragment 1 pIG7001a oIG7004-F oIG7004-R 2274 bp
Fragment 2 pIG7001a oIG7005-F oIG7005-R 2248 bp
Fragment 3 pFucci-G1-Orange oIG7007-F oIG7007-R 659 bp

PCR program

98°C 5min Denaturation
98°C 30s Denaturation
60°C 30s Annealing
72°C 35s/kb Elongation
72°C 10min final Elongation
4°C hold

20 cycles

PCR 2

template: products of PCR 1

PCR program

98°C 5min Denaturation
98°C 30s Denaturation
60°C 30s Annealing
72°C 35s/kb Elongation
72°C 10min final Elongation
4°C hold

20 cycles

all products visible

Gibson Assembly

volumes were calculated with excel sheet with concentration and length:
used volumes:
Gibson: 0,88µl, 0,88µl, 0,2µl 1h in 1 aliquot of Gibson mix (according to protocol)
→ pIG7003a, heat shock transfection in E. coli (according to protocol)

15.06.13

3 colonys of pIG7003a were picked and plated

17.06.13

3 Minipreps of 3 colonys (pIG7003a(25)-(27))

Doubledigest of pIG7003a

BamHI and AflII

Digest of pIG7003a (25)-(27) with BamHI and AflII

Restrictiondigest of pIG7001a, pIG7002a, pIG7004a, pKM006

EcoRV and NruI

Restrictiondigest with EcoRV and NruI
left to right:
1:pIG7001a
2:pIG7002a
3:pIG7004a
4:pKM006
  • Bands are to weak for quadruple ligation with pKM006

Gibson Assembly

Repetition of the Gibson Assembly from 14.06.2013
used volumes (products from PCR2):
Gibson: 0,88µl, 0,88µl, 0,2µl 1h in 1 aliquot of Gibson mix (according to protocol)
→ pIG7003a, heat shock transfection in E. coli (according to protocol)

18.06.13

Gibson Assembly

no colonies on Gibson plate from 17.06.2013 → Repetition of the Gibson Assembly from 14.06.2013
used volumes (products from PCR2):
Gibson: 0,9µl, 0,9µl, 0,4µl 1h in 1 aliquot of Gibson mix (according to protocol)
→ pIG7003a, heat shock transfection in E. coli (according to protocol)

Restrictiondigest of pIG7001a, pIG7002a, pIG7004a, pKM006

Repetition of the restrictiondigest from 17.06.2013
EcoRV and NruI

Restrictiondigest with EcoRV and NruI
left to right:
1:pIG7001a
2:pIG7002a
3:pIG7004a
4:pKM006
  • Bands for the backbones (big fragments) are cut out of pIG7001a, pIG7002a and pIG7004a lane
    and tet013 (small fragment) is cut out of the pKM006 lanes
  • → Gelextraction of gel slices (according to protocoll)
    concentrations:
    pIG7001a= 13 ng/µl
    pIG7002a= 10 ng/µl
    pIG7004a= 14 ng/µl
    pKM006= 1,3-1,5 ng/µl

Ligation of pIG7001a, pIG7002a and pIG7004a

Insert pKM006 11µl
Backbone pIG7001a; pIG7002a; pIG7004a 11µl
10x Puffer 2,5µl
T4 DNA Ligase 1µl
  • Incubation for 15 minutes (RT)

→ pIG7001b, pIG7002b, pIG7004b, heat shock transfection in E. coli (according to protocol)
used: 5µl Ligationmix for 50µl TOP10 cells

19.06.13

5 colonies picked and plated for pIG7003a (Gibson)
6 colonies each picked and plated for pIG7001b, pIG7002b, pIG7004b(Ligation)

Seeding of HELAs

for transfection

  • count: 22*10^4 cells/ml
  • used volume (24 well plate): 0,5 ml/well
  • used concentration (24 well plate): 8*10^4 cells/well → 8*10^4[cells/ml] / 0,5[ml] =16*10^4 [cells/ml]
  • 12 wells needed → 6ml total needed

calculation:
c1*v1=c2*v2
v1=(c2*v2)/c1
v1=(16*10^4 [cells/ml] * 6 [ml])/ 22*10^4 [cells/ml]
v1=4,3 ml
→ 4,3 ml cells + 1,7 ml medium

Inoculation of liquid cultures

for MIDIprep with pIG7001a, pIG7002a, pIG7004a
used: 100ml LB-medium,100µl kanamycin

20.06.13

Miniprep of 5 colonies with pIG7003a(28-32)
Miniprep of 6 colonies each with pIG7001b(1-6), pIG7002b(1-6), pIG7004b(1-6)
Midiprep of pIG7001a, pIG7002a, pIG7004a → no template

Doubledigest of pIG7003a

BamHI and AflII

Doubledigest with BamHI and AflII

Doubledigest of pIG7001b, pIG7002b, pIG7004b

EcoRV and PstI

Doubledigest with EcoRV and Pst

Sequencing of pIG7003a (29) and (30)

→ Sequence not ok, mito sequence missing

Transfection of HELAs

with pIG7001a, pIG7002a and pIG7004a + pSAM200 (according to protocol)
→ no fluorescence visable

21.06.13

Doubledigest of pIG7001b, pIG7002b, pIG7004b

EcoRI and PstI

Doubledigest with EcoRI and Pst

22.06.13

Repetition of Gibson Assembly for pIG7003a with new strategy

PCR

Fragment 1 pIG7001a oIG7004-F oIG7004-R 2274 bp
Fragment 2 pIG7001a oIG7005-F oIG7005-R 2248 bp
Fragment 3 pFucci-G1-Orange oIG7007-F oIG7007-R 659 bp

PCR program

98°C 5min Denaturation
98°C 30s Denaturation
60°C 30s Annealing
72°C 35s/kb Elongation
72°C 10min final Elongation
4°C hold

15 cycles

Gelextraction

23.06.13

4 colonies are picked and plated

24.06.13

Miniprep of pIG7003a(1-4)

Doubledigest of pIG7003a (1-4)

EcoRV and NruI

Restrictiondigest with EcoRV and NruI
left to right
1:Marker
2,3,4,5:pIG7003a(1-4)

Sequencing of pIG7003a(4)

→ Sequence not ok, mito Sequence missing

27.06.13

Gelextraction

Restrictiondigest with EcoRV and NruI
left to right
1:Marker
2,3:pIG7002a
4,5:pIG7004a

Bands for the backbones are cut out

Restrictiondigest with EcoRV and NruI
left to right
1:Marker
2,3:pKM006

Bands for tetO13 are cut out

July

13.07.13

Repetition of the restrictiondigest (pIG7001a, pIG7002a, pIG7004a and pKM006)
EcoRV and NruI
Bands for the backbones (big fragments) are cut out of pIG7001a, pIG7002a and pIG7004a lane and tet013 (small fragment) is cut out of the pKM006 lanes

15.07.13

Ligation of pIG7001b, pIG7002b and pIG7004b

Insert pKM006 11µl
Backbone pIG7001a; pIG7002a; pIG7004a 11µl
10xBuffer 2,5µl
T4 DNA Ligase 1µl
  • incubation for 15 minutes (RT)

→ pIG7001b, pIG7002b, pIG7004b, heat shock transfection in E. coli (according to protocol)
used: 5µl Ligationmix for 50µl TOP10 cells

16.07.13

-2 colonies picked and plated for pIG7001b, pIG7002b and pIG7004b in liquid culture
Miniprep of pIG7001b (1-2), pIG7002b (1-2), pIG7004b (1-2)

18.07.13

Doubledigest of pIG7001b(1-2), pIG7002b(1-2), pIG7004b(1-2)

EcoRV and NheI

Restrictiondigest with EcoRV and NheI
left to right
1:pIG7001b(1)
2:pIG7001b(2)
3:pIG7002b(1)
4:pIG7002b(2)
5:pIG7004b(1)
6:pIG7004b(2)

Sequencing of pIG7001b(2), pIG7002b(2), pIG7004b(2)

→ Sequence ok

19.07.13

Changing of the target cassett in two constructs (pIG7002b and pIG7004b)
→ every construct can be targeted seperately

PCR

amplifying the 400bp cassett out of the opposite construct (pIG7002 insert for pIG7004b backbone; pIG7004 insert for pIG7002b backbone)

Fragment 1 pIG7002b oIG7009-F oIG7009-R 400bp
Fragment 2 pIG7004b oIG7011-F oIG7011-R 400bp

PCR program

98°C 5min Denaturation
95°C 30s Denaturation
60°C 30s Annealing
72°C 30s/kb Elongation
72°C 10min final Elongation
4°C hold

15 cycles

→ PCR product 2 and 4

22.07.13

Restrictiondigest of pIG7002b, pIG7004b, PCR product 2 and PCR product 4

DNA Enzyme
pIG7002b NruI and NheI
pIG7004b PstI and NheI
PCR product 2 PstI and NheI
PCR product 4 NheI

Restricted DNA was load on gel:

Restrictiondigest with EcoRV and NheI
left to right
1:pIG7002b
2:PCR product 2
3:pIG7004b(1)
4:PCR product 4

→ no bands for both PCR products visible, pIG7002b and pIG7004b: restricted DNA band not differentiable from not restricted

23.07.13

- Repetition of PCR (19.07.) and Restriction (22.07.)

Fragment 1 pIG7002b oIG7009-F oIG7009-R 400bp
Fragment 2 pIG7004b oIG7011-F oIG7011-R 400bp

PCR program

95°C 30s Denaturation
95°C 30s Denaturation
60°C 30s Annealing
68°C 30s/kb Elongation
68°C 5min final Elongation
4°C hold

30 cycles

→ PCR product 2 and 4

24.07.13

Doubledigest of PCR product 2 and 4
- bands for both PCR products visible

Restrictiondigest of pIG7002b, pIG7004b, PCR product 2 and PCR product 4

DNA Enzyme
pIG7002b NruI and NheI
pIG7004b PstI and NheI
PCR product 2 PstI and NheI
PCR product 4 NheI

Restricted DNA was load on gel:

Restrictiondigest
left to right
1:Marker
2:PCR product 2
3:PCR product 4
Restrictiondigest
left to right
1:Marker
2:pIG7002b
3:pIG7004b

Bands are cut out
Gelextraction concentrations:
pIG7002b: 10,7 ng/µl
pIG7004b: 31 ng/µl
PCR product 2: 14,4 ng/µl
PCR product 4: 3,3 ng/µl

Ligation

for pIG7002c

Stuff Amount
restricted pIG7002b 5µl
restricted PCR product 4 4µl
T4 Ligase Buffer (10X) 2µl
T4 Ligase 1µl
water 8µl
total 20µl

for pIG7004c

Stuff Amount
restricted pIG7004b 1,8µl
restricted PCR product 2 1µl
T4 Ligase Buffer (10X) 2µl
T4 Ligase 1µl
water 14,2µl
total 20µl

incubation for 30 minutes (RT)

→ pIG7002c, pIG7004c, heat shock transfection in E. coli (according to protocol)
used: 1µl Ligationmix for 25µl TOP10 cells

25.07.13

6 colonies each are picked and plated

26.07.13

Miniprep of all 12 colonies
Sequencing of the first 3 colonies each

27.07.13

Sequences not ok
Sequencing of the last 3 colonies each

28.07.13

Sequences not ok
→ Ligation failed

August

12.08.13

Digest of reporter plasmids

µl type
3 µg DNA (pKM602, pKM608, pKM611)
5 NEB-Buffer 4
1 Nhe I HF
1 Ssp I HF
0,5 BSA
Add to 50µl H2O
  • Temp.: 37°C
  • Incubation time: 2h
µl type
3 µg DNA (pIG7001b, pIG7002b, pIG7004b)
5 Promega MC Buffer
1 Promega Nhe I
2 Promega Nru I
0.5 BSA
Add to 50µl H2O
  • Temp.: 37°C
  • Incubation time: o/n

13.08.13

Gel run

A) Digest of pIG700..

From left to right: Marker (1 kb Roth); pIG7001; pIG7002; pIG7004 (50 & 4 µl); pIG7004 undigested (4 µl)
From left to right: Marker (1 kb Roth); pIG7001; pIG7002; pIG7004 (50 & 4 µl); pIG7004 undigested (4 µl)

B) Digest of pKM60..

From left to right: Marker (2 log NEB); pKM602; pKM608; pKM611 (50 & 4 µl)
From left to right: Marker (2 log NEB); pKM602; pKM608; pKM611 (50 & 4 µl)

All bands are at the expected sizes.

Gel extraction

DNA were purified using High Pure Plasmid Isolation Kit of Roche.

Changes to the protocol:

  • incubation at 56 °C for 10 min for gel dissolving
  • elution with dH2O (incubation at 50 °C for 4 min before centrifugation)

Yield: 10 ng/µl (pIG700..); 2 ng/µl (pKM60..)

Recombination of cutted parts

ingredient amount
pIG7001/2 2.5 µl
pKM602/11 2 µl
T4-Ligase 1 µl
T4-Ligase buffer 2 µl
dH2O up to 20 µl
Incubation at 22 °C for 1 h.
ingredient amount
pIG7004 4.3 µl
pKM608 1.2 µl
T4-Ligase 1 µl
T4-Ligase buffer 2 µl
dH2O up to 20 µl
Incubation at 22 °C for 1 h.

Trafo

  1. 4 µl of plasmid were added to 25 µl of chemically competent E. coli cells
  2. incubation for 10 min on ice
  3. heatshock (42 °C for 45 s)
  4. incubation for 2 min on ice
  5. addition of 300 µl LB medium
  6. incubation for 1 h at 37 °C (shaking)
  7. distribution of 300 µl on LB plates with kanamycin
  8. incubation over night at 37 °C

14.08.13

Picking of clones

From each Ligation 7 clones were picked and spread on 1/4 plates.

15.08.13

Miniprep

DNA was purified using High Pure Plasmid Isolation Kit of Roche.

Yield: ~ 220 ng/µl

Test digest

ingredient volume
plasmids (220 ng/µl) 1.2 µl
EcoRV-HF 0.5 µl
NEB buffer 4 1 µl
dH2O up to 10 µl
Incabation at 37 °C for 2 h.

Gel run

From left to right: Marker (1 kb Roth); pIG7005 (3x); pIG7006 (3x); pIG7007 (3x)

pIG7005_2, all clones of pIG7006 and pIG7007_1 & 3 showed the expected bands. pIG7005_2, pIG7006_1 and pIG7007_3 were send in for sequencing.

16.08.13

Midiprep

Though the sequencing did not have a result, plasmids were amplified and midiprepped by Pure Yield Plasmid Midiprep System from Promega because of the results of the test digest.

Seeding of cells for microscopy

A 24 well plate with cover slips was filled with 50,000 cells per well.

17.08.13

Transfection

Protocol:
  1. 40 µl Opti-MEM + 1.5 µl PEI-solution were mixed in a 1.5 ml Eppi.
  2. 0.5 µg of the DNA of interest were prepaired in another Eppi .
  3. Addition of the DNA to former Eppi, vortexing for 10 s and incubation for 15 min at RT
  4. Solution was spread drop-wise to the cells in the dish
Transfection scheme:

18.08.13

Fixation

Cells were washed with 500 µl PBS per well and fixated with 200 µl PFA per well (incubation on ice for 45 min).

Cover slips were washed in dH2O and mounted on a drop of Mowiol with DABCO on a object slide.

19.08.13

Flourescence microscopy

GFP and mCherry were expressed in all cells, only in the cells with TetR-VP16 there was a stronger signal. BFP was not detectable because of the microscope.

21.08.13

Seeding of cells for microscopy

A 24 well plate with cover slips was filled with 50,000 CHO cells per well.

22.08.13

Transfection

Protocol:
  1. 40 µl Opti-MEM + 2.25 µl PEI-solution were mixed in a 1.5 ml Eppi.
  2. 0.75 µg of the DNA of interest were prepaired in another Eppi .
  3. Addition of the DNA to former Eppi, vortexing for 10 s and incubation for 15 min at RT
  4. Solution was spread drop-wise to the cells in the dish

Medium change

Medium was changed after 3 h.

23.08.13

Fixation

Cells were washed with 500 µl PBS per well and fixated with 200 µl PFA per well (incubation on ice for 45 min).

Cover slips were washed in dH2O and mounted on a drop of Mowiol with DABCO on a object slide.

25.08.13

Flourescence microscopy

GFP and mCherry were detectable, but no differences in fluorescence intensity.

31.08.13

Seeding of cells for flow cytometry

A 24 well plate was filled with 50,000 HEK cells per well.

September

01.09.13

Transfection

Protocol:
  1. 40 µl Opti-MEM + 2.25 µl PEI-solution were mixed in a 1.5 ml Eppi.
  2. 0.75 µg of the DNA of interest were prepaired in another Eppi .
  3. Addition of the DNA to former Eppi, vortexing for 10 s and incubation for 15 min at RT
  4. Solution was spread drop-wise to the cells in the dish

DNA amount of effectors was 6 times higher than DNA amount of fluorescence proteins.

03.09.13

Preparation for flow cytometry

  • Removal of medium.
  • Washing with PBS.
  • Detaching of the cells with 25 µl trypsin per well.
  • Addition of 250 µl FACS buffer (PBS with 1 % FCS).
  • Samples were filled in little FACS tubes.

Flow cytometry

Intensities of all flourescent protein were measured.

Retrieved from "http://2013.igem.org/Team:Freiburg/Notebook/lab_multiple_targeting"