Team:UGent/Labjournal
From 2013.igem.org
(Difference between revisions)
(30 intermediate revisions not shown) | |||
Line 3: | Line 3: | ||
<html> | <html> | ||
<h1> Journal</h1> | <h1> Journal</h1> | ||
+ | |||
<h2> July </h2> | <h2> July </h2> | ||
</html>{{:Team:UGent/Templates/ToggleBoxStart}}Week 4: july 22 - 28 {{:Team:UGent/Templates/ToggleBoxStart1}}{{:Team:UGent/Templates/ToggleBoxStart2}}<html> | </html>{{:Team:UGent/Templates/ToggleBoxStart}}Week 4: july 22 - 28 {{:Team:UGent/Templates/ToggleBoxStart1}}{{:Team:UGent/Templates/ToggleBoxStart2}}<html> | ||
Line 15: | Line 16: | ||
</ul> | </ul> | ||
</html>{{:Team:UGent/Templates/ToggleBoxEnd}}<html> | </html>{{:Team:UGent/Templates/ToggleBoxEnd}}<html> | ||
- | |||
<h2> August </h2> | <h2> August </h2> | ||
</html>{{:Team:UGent/Templates/ToggleBoxStart}}Week 1: july 29 - august 4 {{:Team:UGent/Templates/ToggleBoxStart1}}{{:Team:UGent/Templates/ToggleBoxStart2}}{{:Team:UGent/Templates/ToggleBoxEnd}}{{:Team:UGent/Templates/ToggleBoxStart}}Week 2: august 5 - 11 {{:Team:UGent/Templates/ToggleBoxStart1}}{{:Team:UGent/Templates/ToggleBoxStart2}}<html> | </html>{{:Team:UGent/Templates/ToggleBoxStart}}Week 1: july 29 - august 4 {{:Team:UGent/Templates/ToggleBoxStart1}}{{:Team:UGent/Templates/ToggleBoxStart2}}{{:Team:UGent/Templates/ToggleBoxEnd}}{{:Team:UGent/Templates/ToggleBoxStart}}Week 2: august 5 - 11 {{:Team:UGent/Templates/ToggleBoxStart1}}{{:Team:UGent/Templates/ToggleBoxStart2}}<html> | ||
<ul> | <ul> | ||
+ | |||
<li> Experiment 1 </li> | <li> Experiment 1 </li> | ||
<ul class="a"> | <ul class="a"> | ||
Line 33: | Line 34: | ||
<li> <b>Control plasmid pTGD-<i>ccdA</i>-PMbAFGP-CmFRT: RD with AclI.</b> Expected fragments: 758 bp, 1730 bp and 3956 bp. Analytical gel: <b> negative </b> --> <u> Problem with plasmid pTGD-<i>ccdA</i>-PMbAFGP-CmFRT </u></li> | <li> <b>Control plasmid pTGD-<i>ccdA</i>-PMbAFGP-CmFRT: RD with AclI.</b> Expected fragments: 758 bp, 1730 bp and 3956 bp. Analytical gel: <b> negative </b> --> <u> Problem with plasmid pTGD-<i>ccdA</i>-PMbAFGP-CmFRT </u></li> | ||
- | <li> <b> Transformation</b>: Knock in with <u> | + | <li> <b> Transformation</b>: Knock in with <u>linear back-up</u> DNA by electroporation. Incubation of the transformed cells and transfer the culture on a Cm plate. </li> |
<li> Colony PCR on 48 colonies using crimson taq polymerase with two primer pairs: MDM0141/MDM0010 and MDM0046/MDM123. Expected fragments: 550bp & 2450 bp. Analytic gel: <b> 4 positives </b> | <li> Colony PCR on 48 colonies using crimson taq polymerase with two primer pairs: MDM0141/MDM0010 and MDM0046/MDM123. Expected fragments: 550bp & 2450 bp. Analytic gel: <b> 4 positives </b> | ||
<img src="https://static.igem.org/mediawiki/2013/0/02/UGent_2013_CPCR_KI.jpg" width="300"/></a></li> | <img src="https://static.igem.org/mediawiki/2013/0/02/UGent_2013_CPCR_KI.jpg" width="300"/></a></li> | ||
Line 45: | Line 46: | ||
<li> Experiment 2 </li> | <li> Experiment 2 </li> | ||
<ul class="a"> | <ul class="a"> | ||
- | <li> Inoculate <i>E. coli</i> DH5a + p5SpFRT-T7<i>ccdB</i> <BR> Inoculate <i>E. coli</i> DH5a + p10SpFRT-T7<i>ccdB</i> <BR> Inoculate <i>E. coli</i> DH5a + p20SpFRT-T7<i>ccdB</i> </li> | + | <li> Inoculate <i>E. coli</i> DH5a; + p5SpFRT-T7<i>ccdB</i> <BR> Inoculate <i>E. coli</i> DH5a; + p10SpFRT-T7<i>ccdB</i> <BR> Inoculate <i>E. coli</i> DH5a; + p20SpFRT-T7<i>ccdB</i> </li> |
<li> Purify plasmids using Qiagen spin mini kit: nanodrop <BR> p5SpFRT-T7<i>ccdB</i>: 119.6 ng/µl <BR> p10SpFRT-T7<i>ccdB</i>: 156.3 ng/µl <BR> p20SpFRT-T7<i>ccdB</i>: 392.9 ng/µl </li> | <li> Purify plasmids using Qiagen spin mini kit: nanodrop <BR> p5SpFRT-T7<i>ccdB</i>: 119.6 ng/µl <BR> p10SpFRT-T7<i>ccdB</i>: 156.3 ng/µl <BR> p20SpFRT-T7<i>ccdB</i>: 392.9 ng/µl </li> | ||
<li> <b>CcdB operon</b>: | <li> <b>CcdB operon</b>: | ||
Line 66: | Line 67: | ||
and grow overnight at 37°C | and grow overnight at 37°C | ||
<BR> -> Plates with transformants: pSB6A1 lots of colonies, pSB3T5 sufficient colonies and pSB4A5 no colonies | <BR> -> Plates with transformants: pSB6A1 lots of colonies, pSB3T5 sufficient colonies and pSB4A5 no colonies | ||
- | |||
</li> | </li> | ||
Line 83: | Line 83: | ||
</li> | </li> | ||
<li> Inoculate pSB3T5 and pSB6A1 again and in warm chamber (37°C). </li> | <li> Inoculate pSB3T5 and pSB6A1 again and in warm chamber (37°C). </li> | ||
- | <li> Inoculation colonies of pSB4A5 (plate 2, well 2J) and pSB6A1 (plate 2, well 2L) (2 times: one for further work and one for cryovials) | + | <li> Inoculation colonies of pSB4A5 (plate 2, well 2J) and pSB6A1 (plate 2, well 2L) (2 times: one for further work and one for cryovials) |
<li> Purification of plasmids pSB3T5, pSB6A1 and pSB4A5 </li> | <li> Purification of plasmids pSB3T5, pSB6A1 and pSB4A5 </li> | ||
<li> Generation of <b>restriction</b> digest fragments of T7-<i>ccdB</i> insert (from p5SpFRT-T7<i>ccdB</i> and p20SpFRT-T7<i>ccdB</i>) and vector (pSB3T5 (2x), pSB4A5 (from plate 2, well 2J) and pSB6A1 (1x from plate 5, well 1K and 1x from plate 2, well 2L) with XbaI and PstI-HF (gel purify RD-fragments using Qiagen Qiaquick gel extraction kit (expected fragment of 2157 bp for T7-<i>ccdB</i>, 3229 bp for pSB3T5, 3372 bp for pSB4A5 and 3999 bp for pSB6A1): Nanodrop | <li> Generation of <b>restriction</b> digest fragments of T7-<i>ccdB</i> insert (from p5SpFRT-T7<i>ccdB</i> and p20SpFRT-T7<i>ccdB</i>) and vector (pSB3T5 (2x), pSB4A5 (from plate 2, well 2J) and pSB6A1 (1x from plate 5, well 1K and 1x from plate 2, well 2L) with XbaI and PstI-HF (gel purify RD-fragments using Qiagen Qiaquick gel extraction kit (expected fragment of 2157 bp for T7-<i>ccdB</i>, 3229 bp for pSB3T5, 3372 bp for pSB4A5 and 3999 bp for pSB6A1): Nanodrop | ||
<br>p5: 43.7 ng/µl | <br>p5: 43.7 ng/µl | ||
<br>p20: 24.2 ng/µl | <br>p20: 24.2 ng/µl | ||
- | <br> | + | <br>pSB3T5 (inoculation 1): 23.5 ng/µl |
- | <br> | + | <br>pSB3T5 (inoculation 2): 23 ng/µl |
- | <br> | + | <br>pSB4A5: 40.5 ng/µl |
- | <br> | + | <br>pSB6A1 (plate 2, 2L): 40.1 ng/µl |
- | <br> | + | <br>pSB6A1 (plate 5, 1K): 30.4 ng/µl </li> |
<li> <b>Ligation</b> of T7-<i>ccdB</i> from p5SpFRT-T7<i>ccdB</i> and pSB6A1 (1x from plate 5, well 1K and 1x from plate 2, well 2L), p20SpFRT-T7<i>ccdB</i> and pSB3T5, p20SpFRT-T7<i>ccdB</i> and pSB4A5 (from plate 2, well 2J) (3(insert)/1(plasmid) ratio) </li> | <li> <b>Ligation</b> of T7-<i>ccdB</i> from p5SpFRT-T7<i>ccdB</i> and pSB6A1 (1x from plate 5, well 1K and 1x from plate 2, well 2L), p20SpFRT-T7<i>ccdB</i> and pSB3T5, p20SpFRT-T7<i>ccdB</i> and pSB4A5 (from plate 2, well 2J) (3(insert)/1(plasmid) ratio) </li> | ||
- | <li> <b>Transformation</b> in <i>E.coli</i> Top10 (heat shock)</li> | + | <li> <b>Transformation</b> in <i>E. coli</i> Top10 (heat shock)</li> |
<li> Plate transformation on ampicillin (pSB4A5 and pSB6A1) and tetracycline plate (pSB3T5) and grow overnight at 37°C (2 plates: 10<sup>-2</sup>, 10<sup>-1</sup>) | <li> Plate transformation on ampicillin (pSB4A5 and pSB6A1) and tetracycline plate (pSB3T5) and grow overnight at 37°C (2 plates: 10<sup>-2</sup>, 10<sup>-1</sup>) | ||
<br> -> Plates with transformants: no colonies</li> | <br> -> Plates with transformants: no colonies</li> | ||
- | <li> New <b>transformation</b> in <i>E.coli</i> Top10 from pSB4A5 and pSB6A1 using heat shock | + | <li> New <b>transformation</b> in <i>E. coli</i> Top10 from pSB4A5 and pSB6A1 using heat shock |
<br> -> Plates with transformants: pSB6A1 2 colonies, pSB4A5 few colonies </li> | <br> -> Plates with transformants: pSB6A1 2 colonies, pSB4A5 few colonies </li> | ||
<li> New <b>ligation</b> with RD-fragments created before (vectors pSB3T5, pSB4A5, pSB6A1 (plate 5, well 1K) and insert T7-<i>ccdB</i> created in experiment 6), at 22.5°C o/n) </li> | <li> New <b>ligation</b> with RD-fragments created before (vectors pSB3T5, pSB4A5, pSB6A1 (plate 5, well 1K) and insert T7-<i>ccdB</i> created in experiment 6), at 22.5°C o/n) </li> | ||
Line 146: | Line 146: | ||
<br>p20: 21.1 ng/µl</li> | <br>p20: 21.1 ng/µl</li> | ||
<li><b>cPCR</b> with Taq polymerase of colonies pSB6A1 (primers: MDM0096 and CLG0019) and pSB4A5 (primers: MDM0095 and CLG0019): <b>negative</b> | <li><b>cPCR</b> with Taq polymerase of colonies pSB6A1 (primers: MDM0096 and CLG0019) and pSB4A5 (primers: MDM0095 and CLG0019): <b>negative</b> | ||
- | <li> New <b>transformation</b> with pSB3T5, pSB4A5 and pSB6A1 using heat shock in <i>E.coli</i> <b>DH5a</b> | + | <li> New <b>transformation</b> with pSB3T5, pSB4A5 and pSB6A1 using heat shock in <i>E. coli</i> <b>DH5a</b> |
<br> -> Plate on normal plates and glucose plates (100 ml 2% glucose, to avoid leaky expressing of <i>ccdB</i>) | <br> -> Plate on normal plates and glucose plates (100 ml 2% glucose, to avoid leaky expressing of <i>ccdB</i>) | ||
<br> -> Plates with transformants: pSB6A1 some colonies, pSB4A5 some colonies and pSB3T5 no colonies </li> | <br> -> Plates with transformants: pSB6A1 some colonies, pSB4A5 some colonies and pSB3T5 no colonies </li> | ||
Line 158: | Line 158: | ||
<li>New <b>ligation</b> with rest of RD-fragments of plasmids pSB3T5 (2 times) and pSB4A5 and CcdB from experiment 6 and <b>transformation</b> in DH5a using heat shock</li> | <li>New <b>ligation</b> with rest of RD-fragments of plasmids pSB3T5 (2 times) and pSB4A5 and CcdB from experiment 6 and <b>transformation</b> in DH5a using heat shock</li> | ||
<li>Due to lack of success: <b>start from the beginning</b>.</li> | <li>Due to lack of success: <b>start from the beginning</b>.</li> | ||
- | <li><b>Inoculation</b> of pSB3T5, pSB4A5, p5SpFRT-T7<i>ccdB</i>, p10SpFRT-T7<i>ccdB</i> and p10SpFRT-T7<i>ccdB</i> from cryovials. </li> <li>Also resuspend pSB3T5 (plate 5, well 7C) from iGEM kit, <b>transform</b> in <i>E. coli</i> DH5a using heat shock, plate on tetracycline plates and incubate overnight at 37°C | + | <li><b>Inoculation</b> of pSB3T5, pSB4A5, p5SpFRT-T7<i>ccdB</i>, p10SpFRT-T7<i>ccdB</i> and p10SpFRT-T7<i>ccdB</i> from cryovials. |
+ | <br> <img src="https://static.igem.org/mediawiki/2013/e/ee/UGent_2013_plasmids_for_purification.png" width="200"/></a></li> | ||
+ | <li>Also resuspend pSB3T5 (plate 5, well 7C) from iGEM kit, <b>transform</b> in <i>E. coli</i> DH5a using heat shock, plate on tetracycline plates and incubate overnight at 37°C | ||
<br> -> no colonies | <br> -> no colonies | ||
<br> -> transform again in DH5a using heat shock | <br> -> transform again in DH5a using heat shock | ||
Line 181: | Line 183: | ||
<ul class="a"> | <ul class="a"> | ||
<li> Inoculation KI-strain 5 & 8 from experiment 1 </li> | <li> Inoculation KI-strain 5 & 8 from experiment 1 </li> | ||
- | <li> <b> Transformation of pSB6A1 - T7-<i>ccdB</i> </b> in KI-strains | + | <li> <b> Transformation of pSB6A1 - T7-<i>ccdB</i> </b> in KI-strains 5 and 8 </li> |
<li> <b> Colony PCR </b>on kolonies from transformed strains using emerald polymerase with out primers to check KI: MDM0046/MDM0010. Expected fragment: ca. 5500 bp. Analytic gel: <b> positive </b> </li> | <li> <b> Colony PCR </b>on kolonies from transformed strains using emerald polymerase with out primers to check KI: MDM0046/MDM0010. Expected fragment: ca. 5500 bp. Analytic gel: <b> positive </b> </li> | ||
<li> <b> Colony PCR </b>on kolonies from transformed strains using emerald polymerase with MDM0096 & CLG0019 to check if plasmid is present. Expected fragment: 437 bp. Analytic gel: <b> positive </b><br> | <li> <b> Colony PCR </b>on kolonies from transformed strains using emerald polymerase with MDM0096 & CLG0019 to check if plasmid is present. Expected fragment: 437 bp. Analytic gel: <b> positive </b><br> | ||
Line 192: | Line 194: | ||
<br> -> Plate on chloramphenicol plate and grow overnight at 37°C: <b>negative</b> | <br> -> Plate on chloramphenicol plate and grow overnight at 37°C: <b>negative</b> | ||
<li> <b>CcdB operon</b>: HiFi PCR of plasmids p20SpFRT-T7<i>ccdB</i> with MDM0586/MDM0587 to amplify CcdB operon</li> | <li> <b>CcdB operon</b>: HiFi PCR of plasmids p20SpFRT-T7<i>ccdB</i> with MDM0586/MDM0587 to amplify CcdB operon</li> | ||
- | <li> New <b>restriction</b> of CcdB operon and pSB1C3 with | + | <li> New <b>restriction</b> of CcdB operon and pSB1C3 with Xba |
+ | I and PstI | ||
<br> -> Gel purify fragments using Qiagen Qiaquick gel extraction kit: nanodrop: | <br> -> Gel purify fragments using Qiagen Qiaquick gel extraction kit: nanodrop: | ||
<br> Restriction Digest of T7-<i>ccdB</i>: 16.6 ng/µl | <br> Restriction Digest of T7-<i>ccdB</i>: 16.6 ng/µl | ||
Line 238: | Line 241: | ||
<li> <b> Colony PCR with higher annealing temperature to minimize false priming</b> on kolonies from transformed strains using emerald polymerase with out primers to check KI: MDM0046/MDM0010. Expected fragment: ca. 5500 bp. Analytic gel: <b> positive </b> </li> | <li> <b> Colony PCR with higher annealing temperature to minimize false priming</b> on kolonies from transformed strains using emerald polymerase with out primers to check KI: MDM0046/MDM0010. Expected fragment: ca. 5500 bp. Analytic gel: <b> positive </b> </li> | ||
<li> <b> HiFi PCR using Q5 polymerase with two primer pairs generating overlapping fragments of the ccdA.gfp.cat construct </b>: MDM0046 (out) & MDM0123: 2130 bp and MEMO1237 & MDM0010 (out): 3400 bp. Analytic gel: <b>negative</b> </li> | <li> <b> HiFi PCR using Q5 polymerase with two primer pairs generating overlapping fragments of the ccdA.gfp.cat construct </b>: MDM0046 (out) & MDM0123: 2130 bp and MEMO1237 & MDM0010 (out): 3400 bp. Analytic gel: <b>negative</b> </li> | ||
- | |||
</ul> | </ul> | ||
<br> | <br> | ||
Line 249: | Line 251: | ||
-> Add phage lysate (10,20,40 & 80 µL)<br> | -> Add phage lysate (10,20,40 & 80 µL)<br> | ||
-> Wait untill lysis visible </li> | -> Wait untill lysis visible </li> | ||
- | <li> <b> Perform CIChE with 8 | + | <li> <b> Perform CIChE with 8 + pSB6A1 & 5 + pSB6A1 </b> (we will do 2 strains parallel): 0,0mM - 0,05mM IPTG </li> |
<li> <b> Transduction</b> of CIChe strains: no positive colonies after UV-test </li> | <li> <b> Transduction</b> of CIChe strains: no positive colonies after UV-test </li> | ||
</ul> | </ul> | ||
Line 315: | Line 317: | ||
<li> Experiment 3 </li> | <li> Experiment 3 </li> | ||
<ul class="a"> | <ul class="a"> | ||
- | + | <li> <b> Transformation </b> of plasmids:p5SpFRT-T7<i>ccdB</i>, p10SpFRT-T7<i>ccdB</i>, p20SpFRT-T7<i>ccdB</i> in KI-strain (8) and back-up strain 5 </u> </li> | |
- | <li> <b> Transformation </b> of plasmids:p5SpFRT-T7<i>ccdB</i>, p10SpFRT-T7<i>ccdB</i>, p20SpFRT-T7<i>ccdB</i> in KI-strain (8) and back-up strain | + | <li><b>Colony PCR</b> on 5 + pSB6A1/p5/p10/p20 using emerald polymerase with primerpairs MDM0046/MDM010 to check KI. Expected fragment: 5500bp. Analytic gel: <b> positive </b> <br><img src="https://static.igem.org/mediawiki/2013/8/88/UGent_2013_CPCR_MDMcm.jpg" width="150"></li> |
- | <li><b>Colony PCR</b> on | + | <li><b>Colony PCR</b> on 5 + pSB6A1/p5/p10/p20 using emerald polymerase with primerpairs MDM0096/CGL0019 for pSB6A1 and MDM0039/MDM0060 for p5/p10/p20. Expected fragment: 437bp & 910 bp. Analytic gel: <b> positive for p5/p10/p20</b> </li> |
- | <li><b>Colony PCR</b> on | + | <li><b> New transformation </b> 5 +pSB6A1 and check KI + plasmid as described above. Analytic gel: <b> positive </b>.</li> |
- | <li><b> New transformation </b> | + | |
</ul> | </ul> | ||
<br> | <br> | ||
Line 325: | Line 326: | ||
<li> Experiment 4 </li> | <li> Experiment 4 </li> | ||
<ul class="a"> | <ul class="a"> | ||
- | <li> <b> Abort CIChe with 8 | + | <li> <b> Abort CIChe with 8+pSB6A1 & 5+pSB6A1 </b> because of mutation in pSB6A1 </li> |
<li> Lysate preparation </li> | <li> Lysate preparation </li> | ||
- | + | <li> <b> Transduction: </b> on CIChE strains described above </li> | |
- | <li> <b> Transduction: </b> on CIChE strains described above | + | <li> Test lysate by performing transduction on strain 5 with different concentrations of lysate: <b>negative</b> </li> |
- | + | ||
- | <li> Test lysate by performing transduction on | + | |
- | + | ||
</ul> | </ul> | ||
<br> | <br> | ||
Line 413: | Line 411: | ||
<br> -> Wild type | <br> -> Wild type | ||
<br> -> DH5a + pTGD-ccd-Pmb1GFP-CmFRT | <br> -> DH5a + pTGD-ccd-Pmb1GFP-CmFRT | ||
- | <br> -> Strains with GFP: 8/ | + | <br> -> Strains with GFP: 8 / 5 + pSB6A1/p5/p10/p20 -- 0mM & 0.01 mM IPTG </li> |
<li> Test evaluation GFP with EZrich-medium: | <li> Test evaluation GFP with EZrich-medium: | ||
<br> -> Wild type | <br> -> Wild type | ||
<br> -> DH5a + pTGD-ccd-Pmb1GFP-CmFRT | <br> -> DH5a + pTGD-ccd-Pmb1GFP-CmFRT | ||
- | <br> -> Strains with GFP: 8/ | + | <br> -> Strains with GFP: 8 / 5 + pSB6A1/p5/p10/p20 -- 0mM/0.01mM/0.05mM & 0.2mMM IPTG </li> |
</ul> | </ul> | ||
<br> | <br> | ||
Line 498: | Line 496: | ||
<br>-> Plate on ampicillin plate and grow overnight at 37°C: <b>positive</b> </li> | <br>-> Plate on ampicillin plate and grow overnight at 37°C: <b>positive</b> </li> | ||
<li> <b>Colony PCR</b> (Crimson): there is only 1 colony. We tested this colony (using primers MDM0606 and MDM0607) and it show the right fragment (2486 bp) on gel | <li> <b>Colony PCR</b> (Crimson): there is only 1 colony. We tested this colony (using primers MDM0606 and MDM0607) and it show the right fragment (2486 bp) on gel | ||
+ | <br><img src="https://static.igem.org/mediawiki/2013/3/31/UGent_2013_Ene_colonie_4A5.jpg" width="50"/> | ||
<br>-> Inoculate these colonies</li> | <br>-> Inoculate these colonies</li> | ||
<li> Plasmid purification of the colonies, using Qiagen Qiaprep Spin minikit</li> | <li> Plasmid purification of the colonies, using Qiagen Qiaprep Spin minikit</li> | ||
Line 518: | Line 517: | ||
<li> We made our own competent cells which have the <i>ccdA</i> gene in the genome, so they will be more tolerant to CcdB. We hope on no mutations this time. | <li> We made our own competent cells which have the <i>ccdA</i> gene in the genome, so they will be more tolerant to CcdB. We hope on no mutations this time. | ||
<br>-> <b>Q5 PCR</b>: Control of Knock-In | <br>-> <b>Q5 PCR</b>: Control of Knock-In | ||
- | <br> -> Control on gel: <b>positive</b></li> | + | <br> -> Control on gel: <b>positive</b> |
- | <li> Second <b>transformation</b> in | + | <br> <img src="https://static.igem.org/mediawiki/2013/0/08/UGent_2013_Control_ccda_competente_cellen.jpg" width="50"/> |
+ | <br> -> Further on we will call these cells competent strain 8 | ||
+ | </li> | ||
+ | <li> Second <b>transformation</b> in competent strain 8, using electroporation (Time Constant: 1.6) | ||
<br>-> Plate on ampicillin plate and grow overnight at 37°C: <b> negative</b> </li> | <br>-> Plate on ampicillin plate and grow overnight at 37°C: <b> negative</b> </li> | ||
<li> <b>Gibson Assembly</b> | <li> <b>Gibson Assembly</b> | ||
<br> -> melting oligos first: 5 minutes at 95°C + infinite at 50°C | <br> -> melting oligos first: 5 minutes at 95°C + infinite at 50°C | ||
<br> -> 6192bp-fragment and oligos at 50°C (1 h)</li> | <br> -> 6192bp-fragment and oligos at 50°C (1 h)</li> | ||
- | <li> <b>Transformation</b> in | + | <li> <b>Transformation</b> in competent strain 8, using electroporation (Time Constant: 1.7) |
<br>-> Plate on ampicillin plate and grow overnight at 37°C: <b> negative</b> </li> | <br>-> Plate on ampicillin plate and grow overnight at 37°C: <b> negative</b> </li> | ||
</ul> | </ul> | ||
Line 537: | Line 539: | ||
<br> -> STEP: 0mM - 0.1mM IPTG | <br> -> STEP: 0mM - 0.1mM IPTG | ||
<br> -> JUMP: 0mM - 0.5mM IPTG </li> | <br> -> JUMP: 0mM - 0.5mM IPTG </li> | ||
- | <li> CIChE with strains | + | <li> CIChE with strains 5 + p5/p10/p20: |
<br> -> STEP + JUMP: 0 - 0.01mM </li> | <br> -> STEP + JUMP: 0 - 0.01mM </li> | ||
+ | |||
</ul> | </ul> | ||
<br> | <br> | ||
<li> Experiment 5 </li> | <li> Experiment 5 </li> | ||
<ul class="a"> | <ul class="a"> | ||
- | <li> Evaluation GFP 4 colonies/strain - 3 repeats | + | <li> <b> MTP experiment: version 1 (using precultures) </b> |
+ | <br> (Evaluation GFP 4 colonies/strain - 3 repeats) | ||
<br> -> 8+pSB6A1 - sequential: 0mM - 0.5mM IPTG | <br> -> 8+pSB6A1 - sequential: 0mM - 0.5mM IPTG | ||
<br> -> 8+pSB6A1 - strains grown without antibiotics: 0mM - 0.5mM IPTG | <br> -> 8+pSB6A1 - strains grown without antibiotics: 0mM - 0.5mM IPTG | ||
<br> -> 8+p10 - sequential: 0mM - 0.05mM IPTG </li> | <br> -> 8+p10 - sequential: 0mM - 0.05mM IPTG </li> | ||
+ | <li> Measure the OD and the GFP (using FLUOstar)</li> | ||
</ul> | </ul> | ||
Line 573: | Line 578: | ||
<br>(Time Constant for colony 1: 4.0, for colony 2: 4.1) | <br>(Time Constant for colony 1: 4.0, for colony 2: 4.1) | ||
<br>-> Plate on chloramphenicol plate and grow overnight at 37°C: <b> positive</b> </li> | <br>-> Plate on chloramphenicol plate and grow overnight at 37°C: <b> positive</b> </li> | ||
- | <li> We made our own competent cells which have the <i>ccdA</i> gene in the genome, so they will be more tolerant to CcdB. | + | <li> We made our own competent cells which have the <i>ccdA</i> gene in the genome = strain 8, so they will be more tolerant to CcdB. |
<br> We hope on no mutations this time | <br> We hope on no mutations this time | ||
<br>-> <b>Q5 PCR</b>: Control of Knock-In | <br>-> <b>Q5 PCR</b>: Control of Knock-In | ||
- | <br> -> Control on gel: <b>positive</b></li> | + | <br> -> Control on gel: <b>positive</b> |
- | <li> Second <b>transformation</b> in | + | <br> <img src="https://static.igem.org/mediawiki/2013/0/08/UGent_2013_Control_ccda_competente_cellen.jpg" width="50"/> |
+ | </li> | ||
+ | <li> Second <b>transformation</b> in competent strain 8, using electroporation | ||
<br>(Time Constant for colony 1: 1.5, for colony 2: 1.4) | <br>(Time Constant for colony 1: 1.5, for colony 2: 1.4) | ||
<br>-> Plate on chloramphenicol plate and grow overnight at 37°C: <b> positive</b> </li> | <br>-> Plate on chloramphenicol plate and grow overnight at 37°C: <b> positive</b> </li> | ||
Line 583: | Line 590: | ||
<br> -> melting oligos first: 5 minutes at 95°C + infinite at 50°C | <br> -> melting oligos first: 5 minutes at 95°C + infinite at 50°C | ||
<br> -> 4233bp-fragment and oligos at 50°C (1 h)</li> | <br> -> 4233bp-fragment and oligos at 50°C (1 h)</li> | ||
- | <li> <b>Transformation</b> in | + | <li> <b>Transformation</b> in competent strain 8, using electroporation (Time Constant for colony 1: 1.5, for colony 2: 1.4) |
<br>-> Plate on chloramphenicol plate and grow overnight at 37°C: <b> positive</b> </li> | <br>-> Plate on chloramphenicol plate and grow overnight at 37°C: <b> positive</b> </li> | ||
Line 595: | Line 602: | ||
<li> Plasmid pSB3T5</li> | <li> Plasmid pSB3T5</li> | ||
<ul class="a"> | <ul class="a"> | ||
- | <li> <b>Transformation</b> in | + | <li> <b>Transformation</b> in competent strain 8, using electroporation (Time Constant: 1.4) |
<br>-> Plate on tetracyclin plate and grow overnight at 37°C: <b> negative</b></li> | <br>-> Plate on tetracyclin plate and grow overnight at 37°C: <b> negative</b></li> | ||
- | <li> <b>Transformation</b> in | + | <li> <b>Transformation</b> in competent strain 8, using electroporation |
<br> (Time Constant: pSB3T5+T7-<i>ccdB</i> of p10: 4.1, pSB3T5+T7-<i>ccdB</i> of p20: 2.2) | <br> (Time Constant: pSB3T5+T7-<i>ccdB</i> of p10: 4.1, pSB3T5+T7-<i>ccdB</i> of p20: 2.2) | ||
<br>-> Plate on tetracyclin plate and grow overnight at 37°C: <b> positive</b>, but also red colonies </li> | <br>-> Plate on tetracyclin plate and grow overnight at 37°C: <b> positive</b>, but also red colonies </li> | ||
Line 605: | Line 612: | ||
<li> Plasmid pSB4A5</li> | <li> Plasmid pSB4A5</li> | ||
<ul class="a"> | <ul class="a"> | ||
- | <li> <b>Transformation</b> in | + | <li> <b>Transformation</b> in competent strain 8, using electroporation (Time Constant: 1.5) |
<br>-> Plate on ampicillin plate and grow overnight at 37°C: <b> negative</b></li> | <br>-> Plate on ampicillin plate and grow overnight at 37°C: <b> negative</b></li> | ||
- | <li> <b>Transformation</b> in | + | <li> <b>Transformation</b> in competent strain 8, using electroporation |
<br> (Time Constant: pSB3T5+T7-<i>ccdB</i> of p10: 2.7, pSB3T5+T7-<i>ccdB</i> of p20: 2.6) | <br> (Time Constant: pSB3T5+T7-<i>ccdB</i> of p10: 2.7, pSB3T5+T7-<i>ccdB</i> of p20: 2.6) | ||
<br>-> Plate on ampicillin plate and grow overnight at 37°C: <b> positive</b>, but also red colonies </li> | <br>-> Plate on ampicillin plate and grow overnight at 37°C: <b> positive</b>, but also red colonies </li> | ||
Line 631: | Line 638: | ||
<br>-> send this 2 good strains to iGEM (<b>BioBrick</b>)</li> | <br>-> send this 2 good strains to iGEM (<b>BioBrick</b>)</li> | ||
</ul> | </ul> | ||
+ | </ul> | ||
+ | <br> | ||
+ | |||
+ | <li> Experiment 3 </li> | ||
+ | <ul class="a"> | ||
+ | <li>Transformation | ||
</ul> | </ul> | ||
<br> | <br> | ||
Line 639: | Line 652: | ||
<br> -> STEP: 0.1mM - 1.0mM IPTG | <br> -> STEP: 0.1mM - 1.0mM IPTG | ||
<br> -> JUMP: 0.5mM - 3mM IPTG </li> | <br> -> JUMP: 0.5mM - 3mM IPTG </li> | ||
- | <li> CIChE with strains | + | <li> CIChE with strains 5 + p5/p10/p20: |
<br> -> STEP: 0.01mM - 0.5mM IPTG | <br> -> STEP: 0.01mM - 0.5mM IPTG | ||
<br> -> JUMP: 0.5mM - 1.0mM IPTG </li> | <br> -> JUMP: 0.5mM - 1.0mM IPTG </li> | ||
- | <li> CIChE with strains 8 + pSB6A1 (New plasmids from colony 4 & 16 (exp 2): | + | <li> CIChE with strains 8 + pSB6A1 (New plasmids from colony 4 & 16 (exp 2)): |
<br> -> STEP: 0mM - 0.2mM IPTG | <br> -> STEP: 0mM - 0.2mM IPTG | ||
<br> -> JUMP: 0.5mM - 5.0mM IPTG </li> | <br> -> JUMP: 0.5mM - 5.0mM IPTG </li> | ||
Line 669: | Line 682: | ||
<li> Experiment 4 </li> | <li> Experiment 4 </li> | ||
<ul class="a"> | <ul class="a"> | ||
- | <li> CIChE with strains | + | <li> CIChE with strains 5 + p5/p10/P20: |
<br> -> STEP: 1.0mM - 4.0mM IPTG</li> | <br> -> STEP: 1.0mM - 4.0mM IPTG</li> | ||
<li> CIChE with strain 8 + pSB6A1: | <li> CIChE with strain 8 + pSB6A1: | ||
Line 678: | Line 691: | ||
<li> Experiment 5 </li> | <li> Experiment 5 </li> | ||
<ul class="a"> | <ul class="a"> | ||
+ | <li> <b> MTP experiment: version 1 (using precultures) </b> | ||
+ | <br> -> Plate1: 8 + p5;STEP; 0mM Day1 - 0.5mM Day2 | ||
+ | <br> -> Plate2: 8 + p10;STEP; 0mM Day1 - 0.5mM Day2 | ||
+ | <br> -> Plate3: 8 + p20;STEP; 0mM Day1 - 0.5mM Day2 | ||
+ | <br> -> Plate4: 8 + pSB6A1-16;STEP; 0mM Day1 - 0.05mM Day2 | ||
+ | <br> -> Plate5: 8 + p5;JUMP; 0mM Day1 - 2mM Day2 | ||
+ | <br> -> Plate6: 8 + p10;JUMP; 0mM Day1 - 2mM Day2 | ||
+ | <br> -> Plate7: 8 + p20;JUMP; 0mM Day1 - 2mM Day2 | ||
+ | </li> | ||
+ | <li> Measure the OD and the GFP of all previous plates (using FLUOstar)</li> | ||
+ | <li> <b> MTP experiment: Test version 2 </b> | ||
+ | <br> (to know how long they have to grow until they reach a sufficient OD: 4 - 5 hours) | ||
+ | </li> | ||
<li> <b> MTP experiment: version 2 </b> | <li> <b> MTP experiment: version 2 </b> | ||
<br> -> Plate1: 8 + p5;STEP; 0mM Day1 - 0.5mM Day2 | <br> -> Plate1: 8 + p5;STEP; 0mM Day1 - 0.5mM Day2 | ||
Line 690: | Line 716: | ||
<br> -> Plate10: 8 + pSB6A1-4;STEP; 1.0mM Day1 - 2.0mM Day1 & JUMP; 0mM Day1 - 1.5mM Day1 | <br> -> Plate10: 8 + pSB6A1-4;STEP; 1.0mM Day1 - 2.0mM Day1 & JUMP; 0mM Day1 - 1.5mM Day1 | ||
<br> -> Plate11: 8 + pSB6A1-4;JUMP; 1.5mM Day2 - 30.0mM Day2 | <br> -> Plate11: 8 + pSB6A1-4;JUMP; 1.5mM Day2 - 30.0mM Day2 | ||
- | <br> -> Plate12: 8 + pSB6A1-4;JUMP; 60.0mM Day2 - 120.0mM Day1 | + | <br> -> Plate12: 8 + pSB6A1-4;JUMP; 60.0mM Day2 - 120.0mM Day1 <b>&</b> 5 + p5;STEP;0mM Day1 - 0.2mM Day1 |
- | <br> -> Plate13: | + | <br> -> Plate13: 5 + p5;STEP; 0.2mM Day2 - 3.0mM Day2 |
- | <br> -> Plate14: | + | <br> -> Plate14: 5 + p5;STEP; 3.5mM Day1 & JUMP;0mM Day1- 1mM Day1 |
- | <br> <b> | + | <br> <b> & </b> 5 + p10;STEP;0mM Day1 - 0,01mM Day1 |
- | <br> -> Plate15: | + | <br> -> Plate15: 5 + p10;STEP; 0.01mM Day2 - 1.0mM Day2 |
- | <br> -> Plate16: | + | <br> -> Plate16: 5 + p10;STEP; 2mM Day1 - 3.5mM Day1 & JUMP;0mM Day1 - 0.1mM Day1 |
- | <br> -> Plate17: | + | <br> -> Plate17: 5 + p10;JUMP; 0.1mM Day2 - 1.0mM Day1 <b> & </b> 5 + p20;STEP; 0mM Day1 - 0.1mM Day2 |
- | <br> -> Plate18: | + | <br> -> Plate18: 5 + p20;STEP; 0.2mM Day1 - 3.0mM Day1 |
- | <br> -> Plate19: | + | <br> -> Plate19: 5 + p20;STEP; 3.0mM Day1 - 3.5mM Day1 & JUMP;0mM Day1 - 1mM day1 |
</li> | </li> | ||
+ | <li> Measure the OD and the GFP of all plates (using FLUOstar)</li> | ||
</ul | </ul | ||
</ul> | </ul> | ||
Line 710: | Line 737: | ||
<li> Experiment 4 </li> | <li> Experiment 4 </li> | ||
<ul class="a"> | <ul class="a"> | ||
- | <li> CIChE with strains | + | <li> CIChE with strains 5 + p5/p10/P20: |
<br> -> STEP: 4.0mM - 5.0mM IPTG </li> | <br> -> STEP: 4.0mM - 5.0mM IPTG </li> | ||
<li> CIChE with strain 8 + pSB6A1: | <li> CIChE with strain 8 + pSB6A1: | ||
Line 717: | Line 744: | ||
</ul> | </ul> | ||
<br> | <br> | ||
+ | <li> Experiment 5 </li> | ||
+ | <ul class="a"> | ||
+ | <li> <b> MTP experiment: version 2 </b> | ||
+ | <br> -> Plate20: 8 + pSB6A1-4;STEP; 2.5mM Day2 - 3.0mM Day2 & JUMP; 120mM Day2 - 240mM Day2 | ||
+ | <br> -> Plate21: 5 + p5;STEP; 3.5mM Day2 - 5mM Day2 <b> & </b> 5 + p10;STEP; 3.5mM Day2 - 5mM Day2 | ||
+ | <br> -> Plate22: 5 + p20;STEP; 3.5mM Day2 - 5mM Day2 <b> & </b> 5 + p5;STEP; 1mM Day1 and 3mM Day1 | ||
+ | <br><b> & </b> 5 + p10;STEP; 1mM Day1 and 3mM Day1<b> & </b> 5 + p20;STEP; 1mM Day1 and 3mM Day1 | ||
+ | </li> | ||
+ | <li> Measure the OD and the GFP of the 3 plates (using FLUOstar)</li> | ||
</ul> | </ul> | ||
</ul> | </ul> |
Latest revision as of 01:35, 5 October 2013
JournalJuly
August
Close Week 5: august 26 - september 1
September
OctoberWeek 1: september 30 - october 4
|
![]() Tweets van @iGEM_UGent |
|
|