Team:Hong Kong HKUST/notebook/mod3
From 2013.igem.org
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#menubar | #menubar | ||
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+ | } | ||
+ | #hkust_Logo{ | ||
+ | width:60px; | ||
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+ | top:60px; | ||
+ | z-index:+15; | ||
+ | } | ||
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</head> | </head> | ||
<body> | <body> | ||
+ | <a href="https://2013.igem.org/Main_Page"><img id="iGEM_Logo" src="https://static.igem.org/mediawiki/2013/4/46/Igem_qgem_logo.png"></a> | ||
+ | |||
+ | |||
+ | <a href="http://www.ust.hk/eng/index.htm"><img id="hkust_Logo" src="https://static.igem.org/mediawiki/2013/5/55/Hkust_logo.gif"></a> | ||
+ | |||
<ol class="pos_fixed"> | <ol class="pos_fixed"> | ||
+ | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/notebook">Notebook</a></li> | ||
<li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/notebook/mod1">Module 1</a></li> | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/notebook/mod1">Module 1</a></li> | ||
<li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/notebook/mod2">Module 2</a></li> | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/notebook/mod2">Module 2</a></li> | ||
+ | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/notebook/mod3">Module 3</a></li> | ||
<li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/notebook/mod4">Module 4</a></il> | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/notebook/mod4">Module 4</a></il> | ||
</ol> | </ol> | ||
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<li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/advisors">Advisors</a></li> | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/advisors">Advisors</a></li> | ||
<li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/instructors">Instructors</a></li> | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/instructors">Instructors</a></li> | ||
+ | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/attribution">Attribution</a></li> | ||
+ | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/acknowledge">Acknowledgement</a></li> | ||
</ul> | </ul> | ||
</li> | </li> | ||
- | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/ | + | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/Project">Project</a> |
<ul> | <ul> | ||
<li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/abstract">Abstract</a></li> | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/abstract">Abstract</a></li> | ||
- | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/ | + | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/modules">Modules Description</a></li> |
- | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/ | + | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/data">Data Page</a></li> |
<li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/Parts">Parts</a></li> | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/Parts">Parts</a></li> | ||
- | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/ | + | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/characterization">Characterization</a></li> |
- | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/results"> | + | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/results">Result</a></li> |
+ | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/future">Future Work</a></li> | ||
</ul> | </ul> | ||
</li> | </li> | ||
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<li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/Wetlab">Wetlab</a> | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/Wetlab">Wetlab</a> | ||
<ul> | <ul> | ||
- | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/notebook"> | + | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/notebook">Notebook</a></li> |
- | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/protocols"> | + | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/protocols">Protocols</a></li> |
- | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/safety"> | + | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/safety">Safety</a></li> |
+ | |||
</ul> | </ul> | ||
</li> | </li> | ||
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<li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/hp">Human Practice</a> | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/hp">Human Practice</a> | ||
<ul> | <ul> | ||
- | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/hp/ | + | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/hp/cp">Country Profile</a></li> |
- | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/hp/ | + | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/hp/blog">Blog</a></li> |
- | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/hp/ | + | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/hp/interview">Interviews</a></li> |
- | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/hp/ | + | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/hp/article/genet">Article</a></li> |
+ | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/hp/video">Videos</a></li> | ||
+ | <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/hp/presentation">Presentations</a></li> | ||
</ul> | </ul> | ||
</li> | </li> | ||
</ul> | </ul> | ||
+ | |||
</div> | </div> | ||
<br><br><br><br><br><br><br><br> | <br><br><br><br><br><br><br><br> | ||
- | <div id="title"><h3>Protein Trafficking Module's Notebook</h3></div> | + | <div id="title"><center><h3>Protein Trafficking Module's Notebook</h3></center></div> |
<div id="flight"> | <div id="flight"> | ||
<div id="satu" align="center"> <h1>June 2013</h1> | <div id="satu" align="center"> <h1>June 2013</h1> | ||
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<p> </p> | <p> </p> | ||
<p><strong>24-6-2013</strong> <br /> | <p><strong>24-6-2013</strong> <br /> | ||
- | Inoculation of | + | Inoculation of pCMV/myc/mito </p> |
<p> </p> | <p> </p> | ||
<p><strong>25-6-2013</strong> <br /> | <p><strong>25-6-2013</strong> <br /> | ||
- | Plasmid extraction for | + | Plasmid extraction for pCMV/myc/mito <br /> |
- | Digestion of | + | Digestion of pCMV plasmid extraction product with PstI-HF and NotI-HF <br /> |
- | Gel electrophoresis of | + | Gel electrophoresis of pCMV digested product <br /> |
- | Gel check for | + | Gel check for pCMV digestion product </p> |
<p> </p> | <p> </p> | ||
<p><strong>26-6-2013</strong> <br /> | <p><strong>26-6-2013</strong> <br /> | ||
- | Gel purification of | + | Gel purification of pCMV gel product <br /> |
- | Gel check of | + | Gel check of pCMV gel purified product <br /> |
- | PCR clone MLS from | + | PCR clone MLS from pCMV/myc/mito <br /> |
Transformation of pEGFP-N1 with SURE </p> | Transformation of pEGFP-N1 with SURE </p> | ||
<p> </p> | <p> </p> | ||
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<p><strong>08-07-2013</strong> <br /> | <p><strong>08-07-2013</strong> <br /> | ||
Result of MLS Sanger sequencing showed that DNA is not enough, the sequencing failed <br /> | Result of MLS Sanger sequencing showed that DNA is not enough, the sequencing failed <br /> | ||
- | Inoculation of MLS. | + | Inoculation of MLS.pSB1C3 <br /> |
Plasmid extraction of pEGFP-N1 <br /> | Plasmid extraction of pEGFP-N1 <br /> | ||
Digestion of pEGFP-N1 with NotI-HF & PstI-HF <br /> | Digestion of pEGFP-N1 with NotI-HF & PstI-HF <br /> | ||
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<p> </p> | <p> </p> | ||
<p><strong>10-07-2013</strong> <br /> | <p><strong>10-07-2013</strong> <br /> | ||
- | + | pCMV/myc/mito & pEGFP-N1 ligation, and transform into SURE on AMP plate <br /> | |
MLS biobrick Sanger sequencing result showed there is no pellet, repeat Sanger sequencing <br /> | MLS biobrick Sanger sequencing result showed there is no pellet, repeat Sanger sequencing <br /> | ||
- | Run gel for digestion check of MLS. | + | Run gel for digestion check of MLS.pSB1C3 with EcoRI & PstI </p> |
<p> </p> | <p> </p> | ||
<p><strong>11-07-2013</strong> <br /> | <p><strong>11-07-2013</strong> <br /> | ||
- | Inoculation of | + | Inoculation of pCMV/myc/mito.EGFP <br /> |
MLS biobrick Sanger sequencing (Cont.) </p> | MLS biobrick Sanger sequencing (Cont.) </p> | ||
<p> </p> | <p> </p> | ||
<p><strong>12-07-2013</strong> <br /> | <p><strong>12-07-2013</strong> <br /> | ||
- | Plasmid extraction of | + | Plasmid extraction of pCMV/myc/mito.EGFP <br /> |
- | + | pCMV/myc/mito.EGFP transformation check by digesting with PstI & NotI</p> | |
<p>Spread plate for confirmed colony </p> | <p>Spread plate for confirmed colony </p> | ||
<p> </p> | <p> </p> | ||
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<p> </p> | <p> </p> | ||
<p><strong>15/7/2013</strong><br /> | <p><strong>15/7/2013</strong><br /> | ||
- | + | pCMV/myc/mito.GFP inoculation</p> | |
<p> </p> | <p> </p> | ||
<p><strong>16/7/2013</strong><br /> | <p><strong>16/7/2013</strong><br /> | ||
- | Plasmid Extraction of | + | Plasmid Extraction of pCMV/myc/mito.GFP<br /> |
Nanodrop: concentration is not high enough, will repeat inoculation</p> | Nanodrop: concentration is not high enough, will repeat inoculation</p> | ||
<p> </p> | <p> </p> | ||
<p><strong>17-7-2013</strong><br /> | <p><strong>17-7-2013</strong><br /> | ||
- | Inoculate 4 tubes of | + | Inoculate 4 tubes of pCMV/myc/mito.GFP</p> |
<p> </p> | <p> </p> | ||
<p><strong>18-7-2013</strong><br /> | <p><strong>18-7-2013</strong><br /> | ||
- | + | pCMV/myc/mito.GFP plasmid extraction<br /> | |
PCR clone MLS (RFC25)</p> | PCR clone MLS (RFC25)</p> | ||
<p> </p> | <p> </p> | ||
<p><strong>19-7-2013</strong><br /> | <p><strong>19-7-2013</strong><br /> | ||
- | Run gel for MLS( | + | Run gel for MLS(RFC25) PCR product, PCR clean up<br /> |
Digestion of the MLS PCR product using EcoRI and PstI, gel check<br /> | Digestion of the MLS PCR product using EcoRI and PstI, gel check<br /> | ||
Digestion of pSB1C3 with EcoRI & PstI, run gel</p> | Digestion of pSB1C3 with EcoRI & PstI, run gel</p> | ||
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Gel check of pSB1C3: band is too pale, repeat inoculation<br /> | Gel check of pSB1C3: band is too pale, repeat inoculation<br /> | ||
Inoculation of pSB1C3.J04450<br /> | Inoculation of pSB1C3.J04450<br /> | ||
- | Repeat PCR of MLS( | + | Repeat PCR of MLS(RFC25)<br /> |
Gel check of PCR product and PCR clean up<br /> | Gel check of PCR product and PCR clean up<br /> | ||
- | Digestion of MLS( | + | Digestion of MLS(RFC25) with EcoRI & SpeI, run gel</p> |
<p> </p> | <p> </p> | ||
<p><strong>23-7-2013<br /> | <p><strong>23-7-2013<br /> | ||
- | </strong>MLS( | + | </strong>MLS(RFC25) Gel purification (Cont), and gel check<br /> |
pSB1C3 plasmid extraction<br /> | pSB1C3 plasmid extraction<br /> | ||
Digestion of pSB1C3 with EcoRI & SpeI</p> | Digestion of pSB1C3 with EcoRI & SpeI</p> | ||
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<p><strong>24-7-2013</strong><br /> | <p><strong>24-7-2013</strong><br /> | ||
pSB1C3 Gel purification (Cont.)<br /> | pSB1C3 Gel purification (Cont.)<br /> | ||
- | MLS( | + | MLS(RFC25) & pSB1C3 ligation, and transform to CAM plate</p> |
<p> </p> | <p> </p> | ||
<p><strong>25-7-2013</strong><br /> | <p><strong>25-7-2013</strong><br /> | ||
- | Colony PCR of MLS. | + | Colony PCR of MLS.pSB1C3(RFC25)<br /> |
- | Inoculation of MLS. | + | Inoculation of MLS.pSB1C3(RFC25)</p> |
<p> </p> | <p> </p> | ||
<p><strong>26-7-2013</strong><br /> | <p><strong>26-7-2013</strong><br /> | ||
- | Plasmid extraction of MLS. | + | Plasmid extraction of MLS.pSB1C3(RFC25)<br /> |
Digestion of ligated MLS-pSB1C3 with EcoRI & SpeI, gel check<br /> | Digestion of ligated MLS-pSB1C3 with EcoRI & SpeI, gel check<br /> | ||
- | Gel check for MLS. | + | Gel check for MLS.pSB1C3(RFC25) colony PCR product<br /> |
Spread the remaining re-suspend of correct colony on CAM plate</p> | Spread the remaining re-suspend of correct colony on CAM plate</p> | ||
<p> </p> | <p> </p> | ||
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<p> </p> | <p> </p> | ||
<p><strong>29-7-2013</strong><br /> | <p><strong>29-7-2013</strong><br /> | ||
- | Repeat digestion of pSB1C3.MLS( | + | Repeat digestion of pSB1C3.MLS(RFC25) with EcoRI and SpeI, gel check and Sanger sequence<br /> |
- | Spread plate of GFP( | + | Spread plate of GFP(RFC25) transformed colonies</p> |
<p> </p> | <p> </p> | ||
<p><strong>30-7-2013</strong><br /> | <p><strong>30-7-2013</strong><br /> | ||
- | pSB1C3.MLS ( | + | pSB1C3.MLS (RFC25) digestion with EcoRI and SpeI<br /> |
Gel electrophoresis of digested pSB1C3.MLS product<br /> | Gel electrophoresis of digested pSB1C3.MLS product<br /> | ||
Streak plate for pSB1C3.MLS colony 1,2, and 3<br /> | Streak plate for pSB1C3.MLS colony 1,2, and 3<br /> | ||
Sanger sequencing of pSB1C3.MLS<br /> | Sanger sequencing of pSB1C3.MLS<br /> | ||
- | Streak plate of EGFP( | + | Streak plate of EGFP(RFC25) colonies</p> |
<p> </p> | <p> </p> | ||
<p><strong>31-7-2013</strong><br /> | <p><strong>31-7-2013</strong><br /> | ||
- | pSB1C3.MLS ( | + | pSB1C3.MLS (RFC25) Sanger sequence(Cont.)<br /> |
- | GFP ( | + | GFP (RFC25) inoculation</p> |
<p> </p> | <p> </p> | ||
<p><strong>01-08-2013</strong><br /> | <p><strong>01-08-2013</strong><br /> | ||
- | GFP( | + | GFP(RFC25) plasmid extraction<br /> |
Prepare the glycerol stock and stored it<br /> | Prepare the glycerol stock and stored it<br /> | ||
- | Digestion of GFP( | + | Digestion of GFP(RFC25) with EcoRI and SpeI, gel electrophoresis</p> |
<p> </p> | <p> </p> | ||
<p><strong>02-08-2013</strong><br /> | <p><strong>02-08-2013</strong><br /> | ||
- | GFP ( | + | GFP (RFC25) plasmid extraction<br /> |
- | Digestion of GFP( | + | Digestion of GFP(RFC25) with EcoRI and SpeI, gel electrophoresis<br /> |
- | Inoculate BBa_J176171 using Amp LB, and BBa_K404108 using CAM LB</p> | + | Inoculate <a href="http://parts.igem.org/Part:BBa_J176171">BBa_J176171</a> using Amp LB, and <a href="http://parts.igem.org/Part:BBa_K404108">BBa_K404108</a> using CAM LB</p> |
<p> </p> | <p> </p> | ||
</div> | </div> | ||
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<p> </p> | <p> </p> | ||
<p><strong>5-8-2013</strong><br /> | <p><strong>5-8-2013</strong><br /> | ||
- | GFP ( | + | GFP (RFC25) PCR Check with VR VF2, gel check (over ran)<br /> |
BBa_J176171 digestion using SpeI and PstI-HF to extract the backbone<br /> | BBa_J176171 digestion using SpeI and PstI-HF to extract the backbone<br /> | ||
PolyA / BBa_K404108 digestion using XbaI and PstI-HF<br /> | PolyA / BBa_K404108 digestion using XbaI and PstI-HF<br /> | ||
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<p> </p> | <p> </p> | ||
<p><strong>6-8-2013</strong><br /> | <p><strong>6-8-2013</strong><br /> | ||
- | Repeat PCR check of GFP ( | + | Repeat PCR check of GFP (RFC25)<br /> |
pSB1C3 plasmid extraction<br /> | pSB1C3 plasmid extraction<br /> | ||
PolyA / BBa_K404108 gel purification and gel check<br /> | PolyA / BBa_K404108 gel purification and gel check<br /> | ||
BBa_J176171 PCR clean up<br /> | BBa_J176171 PCR clean up<br /> | ||
- | BBa_K929000 & BBa_J52034 transformation using CAM plate<br /> | + | <a href="http://parts.igem.org/Part:BBa_K929000">BBa_K929000</a> & <a href="http://parts.igem.org/Part:BBa_J52034">BBa_J52034</a> transformation using CAM plate<br /> |
- | PCR amplify MLS in RFC 10 and | + | PCR amplify MLS in RFC 10 and RFC25 format</p> |
<p> </p> | <p> </p> | ||
<p><strong>7-8-2013</strong><br /> | <p><strong>7-8-2013</strong><br /> | ||
- | MLS (RFC 10 & | + | MLS (RFC 10 & RFC25) PCR clean up<br /> |
Nanodrop and gel check for the PCR clean up product<br /> | Nanodrop and gel check for the PCR clean up product<br /> | ||
Digestion using EcoRI and PstI<br /> | Digestion using EcoRI and PstI<br /> | ||
PolyA / BBa_K404108 gel check<br /> | PolyA / BBa_K404108 gel check<br /> | ||
pSB1C3 digestion with EcoRI & PstI<br /> | pSB1C3 digestion with EcoRI & PstI<br /> | ||
- | GFP( | + | GFP(RFC25) digestion with EcoRI & SpeI</p> |
<p> </p> | <p> </p> | ||
<p><strong>8/8/2013</strong><br /> | <p><strong>8/8/2013</strong><br /> | ||
- | Gel purification of<strong> </strong> | + | Gel purification of<strong> </strong>GFP(RFC25) & pSB1C3, then nanodrop and gel check <br /> |
polyA digestion with EcoRI and XbaI, and PCR clean up<br /> | polyA digestion with EcoRI and XbaI, and PCR clean up<br /> | ||
Inoculation of BBa_K929000 & BBa_J52034</p> | Inoculation of BBa_K929000 & BBa_J52034</p> | ||
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<p> </p> | <p> </p> | ||
<p><strong>13/08/2013</strong><br /> | <p><strong>13/08/2013</strong><br /> | ||
- | + | MLS(RFC10).pSB1C3 & gpf.polyA plasmid extraction<br /> | |
- | Digestion of | + | Digestion of MLS(RFC10).pSB1C3 & gpf.polyA with EcoRI-HF and PstI-HF <br /> |
K929000 gel check<br /> | K929000 gel check<br /> | ||
pSB1C3 digestion with EcoRI & PstI<br /> | pSB1C3 digestion with EcoRI & PstI<br /> | ||
- | + | MLS(RFC25).pSB1C3<br /> | |
- | Streak plate with transformed | + | Streak plate with transformed MLS(RFC25).pSB1C3 to purify colony</p> |
<p> </p> | <p> </p> | ||
<p><strong>14/08/2013</strong><br /> | <p><strong>14/08/2013</strong><br /> | ||
- | Inoculation of | + | Inoculation of MLS(RFC25).pSB1C3 & GFP.PolyA</p> |
<p> </p> | <p> </p> | ||
<p><strong>15/08/2013</strong><br /> | <p><strong>15/08/2013</strong><br /> | ||
pSB1C3 gel purification<br /> | pSB1C3 gel purification<br /> | ||
- | + | MLS(RFC10).pSB1C3 Sanger sequencing (did not submit as the colony turn out to be not single)<br /> | |
- | Plasmid extraction of | + | Plasmid extraction of MLS(RFC25).pSB1C3 & GFP<br /> |
- | Digestion check of | + | Digestion check of MLS(RFC25) with EcoRI & PstI; GFP.polya with ApaLI & AgeI HF</p> |
<p> </p> | <p> </p> | ||
<p><strong>16/08/2013</strong><br /> | <p><strong>16/08/2013</strong><br /> | ||
- | pCMV(Amplify by PCR from pEGFP-N1) PCR clean up<br /> | + | pCMV (Amplify by PCR from pEGFP-N1) PCR clean up<br /> |
pSB1C3 dephosphorylation<br /> | pSB1C3 dephosphorylation<br /> | ||
- | Run gel of | + | Run gel of MLS(RFC25).pSB1C3 & gpf.polya<br /> |
- | + | MLS(RFC25).pSB1C3 PCR check<br /> | |
- | Streak plate with transformed | + | Streak plate with transformed MLS(RFC10).pSB1C3 to get single colony <br /> |
- | Inoculation of pEGFP-N1, | + | Inoculation of pEGFP-N1, pCMV/my/mito.GFP, pCMV/myc/mito<br /> |
Streak plate with transformed pEGFP-N1</p> | Streak plate with transformed pEGFP-N1</p> | ||
<p> </p> | <p> </p> | ||
Line 621: | Line 651: | ||
Ligation of CMV and pSB1C3 (1st try)<br /> | Ligation of CMV and pSB1C3 (1st try)<br /> | ||
Transformation of CMV and pSB1C3 into DH5alpha<br /> | Transformation of CMV and pSB1C3 into DH5alpha<br /> | ||
- | Streak | + | Streak pCMV/myc/mito.GFP and pCMV/myc/mito.EGFP to AMP plate<br /> |
- | + | MLS(RFC25).pSB1C3 & GFP.polya digestion with AgeI & ApaLI, and transformation of the correct colony<br /> | |
- | + | MLS(RFC25).pSB1C3 Sanger Sequencing</p> | |
<p> </p> | <p> </p> | ||
<p><strong>20/8/2013</strong><br /> | <p><strong>20/8/2013</strong><br /> | ||
- | + | MLS(RFC25).pSB1C3 Sanger Sequencing(Cont.)<br /> | |
- | Plasmid extraction of pEGFP-N1, | + | Plasmid extraction of pEGFP-N1, pCMV/myc/mito.GFP and pCMV/myc/mito.EGFP<br /> |
- | + | MLS(RFC25).pSB1C3 digestion with AgeI-HF & PstI-HF<br /> | |
- | GFP.polya. | + | GFP.polya.pSB1C3(1st try) digestion with NgoMIV & PstI-HF<br /> |
Repeat PCR for CMV(2nd try), digestion with EcoRI-HF & PstI-HF, PCR clean up</p> | Repeat PCR for CMV(2nd try), digestion with EcoRI-HF & PstI-HF, PCR clean up</p> | ||
<p> </p> | <p> </p> | ||
Line 635: | Line 665: | ||
Gel purification of GFP/polyA digested with NgoMIV & PstI-HF : too low concentration<br /> | Gel purification of GFP/polyA digested with NgoMIV & PstI-HF : too low concentration<br /> | ||
EtOH precipitation of GFP/polyA digested with NgoMIV & PstI-HF<br /> | EtOH precipitation of GFP/polyA digested with NgoMIV & PstI-HF<br /> | ||
- | + | P<i>cmv</i>.pSB1C3(2nd) ligation, and transformation to DH5alpha<br /> | |
- | + | MLS(RFC10) bacteria inoculation</p> | |
<p> </p> | <p> </p> | ||
<p><strong>22/08/2013</strong><br /> | <p><strong>22/08/2013</strong><br /> | ||
- | + | MLS(RFC10).pSB1C3 plasmid extraction, PCR check with VR VF2<br /> | |
Repeat digestion of GFP.polyA with NgoMIV & PstI-HF (2nd) with NgoMIV & PstI-HF<br /> | Repeat digestion of GFP.polyA with NgoMIV & PstI-HF (2nd) with NgoMIV & PstI-HF<br /> | ||
- | + | P<i>cmv</i>.pSB1C3 (3rd) ligation and transformation<br /> | |
- | Inoculation of | + | Inoculation of P<i>cmv</i>.pSB1C3 (2nd)<br /> |
GFP.polyA with NgoMIV & PstI-HF (1st) gel check<br /> | GFP.polyA with NgoMIV & PstI-HF (1st) gel check<br /> | ||
</p> | </p> | ||
<p><br /> | <p><br /> | ||
<strong>23/08/2013</strong><br /> | <strong>23/08/2013</strong><br /> | ||
- | Sanger Sequencing for | + | Sanger Sequencing for MLS(RFC10).pSB1C3 and MLS(RFC25).pSB1C3<br /> |
- | + | P<i>cmv</i>.pSB1C3 (2nd) plasmid extraction, and digestion check with EcoRI & NdeI<br /> | |
- | Streak the right colony of | + | Streak the right colony of P<i>cmv</i>.pSB1C3 (2nd) into plate <br /> |
GFP.polyA with NgoMIV & PstI-HF (2nd) gel purification</p> | GFP.polyA with NgoMIV & PstI-HF (2nd) gel purification</p> | ||
<p> </p> | <p> </p> | ||
Line 659: | Line 689: | ||
<p> </p> | <p> </p> | ||
<p><strong>26/8/2013</strong><br /> | <p><strong>26/8/2013</strong><br /> | ||
- | Sanger sequencing for | + | Sanger sequencing for P<i>cmv</i>.pSB1C3 (#1), MLS(RFC10).pSB1C3 (#4.3), and MLS(RFC25).pSB1C3 #1.1)<br /> |
Gel check for GFP.polyA (NgoMIV & PstI-HF) for 1st & 2nd<br /> | Gel check for GFP.polyA (NgoMIV & PstI-HF) for 1st & 2nd<br /> | ||
GFP.polyA digestion with XbaI & PstI-HF, run gel and gel purification<br /> | GFP.polyA digestion with XbaI & PstI-HF, run gel and gel purification<br /> | ||
- | + | P<i>cmv</i> digestion with SpeI & PstI-HF, dephosphorylated<br /> | |
- | + | MLS(RFC25).pSB1C3 digestion with AgeI & PstI-HF, dephosphorylated<br /> | |
- | Repeat Sequencing for | + | Repeat Sequencing for MLS(RFC25).pSB1C3</p> |
<p> </p> | <p> </p> | ||
<p><strong>27/8/2013</strong><br /> | <p><strong>27/8/2013</strong><br /> | ||
- | + | MLS(RFC25).pSB1C3 Sequencing (Cont.)<br /> | |
- | Repeat Sequencing for | + | Repeat Sequencing for P<i>cmv</i>.pSB1C3<br /> |
- | + | MLS(RFC10).pSB1C3 Sequencing (Cont.), transformed new plate with correct colony (#4.3)<br /> | |
GFP.polyA(XbaI & PstI-HF) gel Purification(Cont.), and gel check<br /> | GFP.polyA(XbaI & PstI-HF) gel Purification(Cont.), and gel check<br /> | ||
- | Gel check for | + | Gel check for P<i>cmv</i> (SpeI & PstI-HF) & MLS(RFC25).pSB1C3(AgeI & PstI-HF) <br /> |
- | + | GFP(RFC25) digestion with EcoRI-HF & PstI-HF, transformed new plate for correct colony (#2)</p> | |
<p> </p> | <p> </p> | ||
<p><strong>28/8/2013</strong><br /> | <p><strong>28/8/2013</strong><br /> | ||
- | Ligation of | + | Ligation of P<i>cmv</i> (S&P) and GFP (X&P), transformed<br /> |
Ligation of MLS (A&P) and GFP (N&P), transformed<br /> | Ligation of MLS (A&P) and GFP (N&P), transformed<br /> | ||
- | + | P<i>cmv</i>.pSB1C3 and MLS(RFC25) sequence confirmed<br /> | |
- | + | GFP(RFC25) gel purification, EtOH precipitation<br /> | |
- | + | GFP(RFC25) nanodrop: concentration is too low, abandone</p> | |
<p> </p> | <p> </p> | ||
<p><strong>29/8/2013</strong><br /> | <p><strong>29/8/2013</strong><br /> | ||
Line 706: | Line 736: | ||
Digestion check of CMV.GFP.polyA with EcoRV-HF & AgeI-HF<br /> | Digestion check of CMV.GFP.polyA with EcoRV-HF & AgeI-HF<br /> | ||
Run gel and gel purification of MLS.GFP.polyA (X & P)<br /> | Run gel and gel purification of MLS.GFP.polyA (X & P)<br /> | ||
- | + | P<i>cmv</i> digestion with SpeI and PstI-HF, dephosphorylated and PCR clean up<br /> | |
BBa_J176171 digestion with SpeI & PstI-HF, dephosphorylation and PCR clean up</p> | BBa_J176171 digestion with SpeI & PstI-HF, dephosphorylation and PCR clean up</p> | ||
<p> </p> | <p> </p> | ||
Line 717: | Line 747: | ||
<p> </p> | <p> </p> | ||
<p><strong>6/9/2013</strong><br /> | <p><strong>6/9/2013</strong><br /> | ||
- | Digestion of CMV. | + | Digestion of CMV.pSB1C3 (1) & GFP.polyA(4) by EcoRI-HF & PstI-HF<br /> |
Gel check: decided that cmv is defect, will order new primer</p> | Gel check: decided that cmv is defect, will order new primer</p> | ||
<p> </p> | <p> </p> | ||
Line 731: | Line 761: | ||
<p> </p> | <p> </p> | ||
<p><strong>10/9/2013</strong><br /> | <p><strong>10/9/2013</strong><br /> | ||
- | Gel purification of | + | Gel purification of pSB1C3<br /> |
Plasmid extraction of pEGFP-N1</p> | Plasmid extraction of pEGFP-N1</p> | ||
<p> </p> | <p> </p> |
Latest revision as of 23:14, 27 September 2013
Protein Trafficking Module's Notebook
June 2013
24-6-2013
Inoculation of pCMV/myc/mito
25-6-2013
Plasmid extraction for pCMV/myc/mito
Digestion of pCMV plasmid extraction product with PstI-HF and NotI-HF
Gel electrophoresis of pCMV digested product
Gel check for pCMV digestion product
26-6-2013
Gel purification of pCMV gel product
Gel check of pCMV gel purified product
PCR clone MLS from pCMV/myc/mito
Transformation of pEGFP-N1 with SURE
27-6-2013
Gel check for the MLS PCR product and PCR Clean Up
Digestion of MLS clean up product with EcoRI & PstI-HF
Inoculation of pEGFP-N1
28-6-2013
PCR Clean up of digested MLS
Plasmid Extraction of pEGFP-N1
Digestion of pEGFP-N1 with PstI-HF & NotI-HF
July 2013
02-07-2013
Gel Check of pEGFP-N1 plasmid extraction product to confirm presence of DNA
Digestion of pEGFP-N1 (with NotI-HF and PstI-HF) 2nd EGFP product:repeat digestion
Inoculation of pEGFP-N1 3rd EGFP: repeat Inoculation
Get pSB1C3.J04450 plasmid extraction product from Bida
Digestion of pSB1C3 with EcoRI and PstI-HF
03-07-2013
Gel electrophoresis of digested EGFP (2nd)
Plasmid extraction of pEGFP-N1 (3rd)
Digetion of pEGFP-N1 (3rd) using NotI-HF and PstI-HF
Ligation of MLS with pSB1C3
Transformation of ligated pSB1C3-MLS
04-07-2013
Gel purification of pEGFP-N1 (2nd) (cont.)
Gel analysis and gel electrophoresis of pEGFP-N1 (3rd)
Run gel for remaining 3rd EGFP (digested)
Ethanol precipitation of pEGFP-N1 (4th) (using remaining 3rd EGFP plasmid)
Digestion of pEGFP-N1 (4th) and gel electrophoresis
Transformation of pEGFP-N1 into DH10B
Colony PCR of MLS biobrick and gel electrophoresis
Inoculation of MLS colony no.2 & spread the remaining re-suspend colony 2 on CAM plate
05-07-2013
pEGFP-N1 troubleshoot
Digestion by PstI-HF, NotI-HF, PstI-HF +NotI-HF and gel check
Inoculate EGFP from transformed new competent cell
Plasmid extraction of MLS Biobrick
Sanger sequencing of MLS
08-07-2013
Result of MLS Sanger sequencing showed that DNA is not enough, the sequencing failed
Inoculation of MLS.pSB1C3
Plasmid extraction of pEGFP-N1
Digestion of pEGFP-N1 with NotI-HF & PstI-HF
Run gel, and it turned out that NotI-HF did not work
09-07-2013
Plasmid extraction of MLS biobrick
Digestion check on MLS.pSB1C3 product with EcoRI & PstI
Sanger sequencing of MLS biobrick
pEGFP-N1 digestion with PstI & NotI
10-07-2013
pCMV/myc/mito & pEGFP-N1 ligation, and transform into SURE on AMP plate
MLS biobrick Sanger sequencing result showed there is no pellet, repeat Sanger sequencing
Run gel for digestion check of MLS.pSB1C3 with EcoRI & PstI
11-07-2013
Inoculation of pCMV/myc/mito.EGFP
MLS biobrick Sanger sequencing (Cont.)
12-07-2013
Plasmid extraction of pCMV/myc/mito.EGFP
pCMV/myc/mito.EGFP transformation check by digesting with PstI & NotI
Spread plate for confirmed colony
15/7/2013
pCMV/myc/mito.GFP inoculation
16/7/2013
Plasmid Extraction of pCMV/myc/mito.GFP
Nanodrop: concentration is not high enough, will repeat inoculation
17-7-2013
Inoculate 4 tubes of pCMV/myc/mito.GFP
18-7-2013
pCMV/myc/mito.GFP plasmid extraction
PCR clone MLS (RFC25)
19-7-2013
Run gel for MLS(RFC25) PCR product, PCR clean up
Digestion of the MLS PCR product using EcoRI and PstI, gel check
Digestion of pSB1C3 with EcoRI & PstI, run gel
22-7-2013
Gel purification of pSB1C3
Gel check of pSB1C3: band is too pale, repeat inoculation
Inoculation of pSB1C3.J04450
Repeat PCR of MLS(RFC25)
Gel check of PCR product and PCR clean up
Digestion of MLS(RFC25) with EcoRI & SpeI, run gel
23-7-2013
MLS(RFC25) Gel purification (Cont), and gel check
pSB1C3 plasmid extraction
Digestion of pSB1C3 with EcoRI & SpeI
24-7-2013
pSB1C3 Gel purification (Cont.)
MLS(RFC25) & pSB1C3 ligation, and transform to CAM plate
25-7-2013
Colony PCR of MLS.pSB1C3(RFC25)
Inoculation of MLS.pSB1C3(RFC25)
26-7-2013
Plasmid extraction of MLS.pSB1C3(RFC25)
Digestion of ligated MLS-pSB1C3 with EcoRI & SpeI, gel check
Gel check for MLS.pSB1C3(RFC25) colony PCR product
Spread the remaining re-suspend of correct colony on CAM plate
29-7-2013
Repeat digestion of pSB1C3.MLS(RFC25) with EcoRI and SpeI, gel check and Sanger sequence
Spread plate of GFP(RFC25) transformed colonies
30-7-2013
pSB1C3.MLS (RFC25) digestion with EcoRI and SpeI
Gel electrophoresis of digested pSB1C3.MLS product
Streak plate for pSB1C3.MLS colony 1,2, and 3
Sanger sequencing of pSB1C3.MLS
Streak plate of EGFP(RFC25) colonies
31-7-2013
pSB1C3.MLS (RFC25) Sanger sequence(Cont.)
GFP (RFC25) inoculation
01-08-2013
GFP(RFC25) plasmid extraction
Prepare the glycerol stock and stored it
Digestion of GFP(RFC25) with EcoRI and SpeI, gel electrophoresis
02-08-2013
GFP (RFC25) plasmid extraction
Digestion of GFP(RFC25) with EcoRI and SpeI, gel electrophoresis
Inoculate BBa_J176171 using Amp LB, and BBa_K404108 using CAM LB
August 2013
5-8-2013
GFP (RFC25) PCR Check with VR VF2, gel check (over ran)
BBa_J176171 digestion using SpeI and PstI-HF to extract the backbone
PolyA / BBa_K404108 digestion using XbaI and PstI-HF
Inoculation of pSB1C3
6-8-2013
Repeat PCR check of GFP (RFC25)
pSB1C3 plasmid extraction
PolyA / BBa_K404108 gel purification and gel check
BBa_J176171 PCR clean up
BBa_K929000 & BBa_J52034 transformation using CAM plate
PCR amplify MLS in RFC 10 and RFC25 format
7-8-2013
MLS (RFC 10 & RFC25) PCR clean up
Nanodrop and gel check for the PCR clean up product
Digestion using EcoRI and PstI
PolyA / BBa_K404108 gel check
pSB1C3 digestion with EcoRI & PstI
GFP(RFC25) digestion with EcoRI & SpeI
8/8/2013
Gel purification of GFP(RFC25) & pSB1C3, then nanodrop and gel check
polyA digestion with EcoRI and XbaI, and PCR clean up
Inoculation of BBa_K929000 & BBa_J52034
9/8/2013
BBa_K929000 & BBa_J52034 plasmid extraction: J52034 is not transformed
MLS.pSB1C3 & GFP.PolyA ligation, and transform to SURE on CAM plate
12/8/2013
Digestion check of K929000 with ApaLI & NdeI
MLS.pSB1C3 & GFP.PolyA inoculation
Transformation of J52034
13/08/2013
MLS(RFC10).pSB1C3 & gpf.polyA plasmid extraction
Digestion of MLS(RFC10).pSB1C3 & gpf.polyA with EcoRI-HF and PstI-HF
K929000 gel check
pSB1C3 digestion with EcoRI & PstI
MLS(RFC25).pSB1C3
Streak plate with transformed MLS(RFC25).pSB1C3 to purify colony
14/08/2013
Inoculation of MLS(RFC25).pSB1C3 & GFP.PolyA
15/08/2013
pSB1C3 gel purification
MLS(RFC10).pSB1C3 Sanger sequencing (did not submit as the colony turn out to be not single)
Plasmid extraction of MLS(RFC25).pSB1C3 & GFP
Digestion check of MLS(RFC25) with EcoRI & PstI; GFP.polya with ApaLI & AgeI HF
16/08/2013
pCMV (Amplify by PCR from pEGFP-N1) PCR clean up
pSB1C3 dephosphorylation
Run gel of MLS(RFC25).pSB1C3 & gpf.polya
MLS(RFC25).pSB1C3 PCR check
Streak plate with transformed MLS(RFC10).pSB1C3 to get single colony
Inoculation of pEGFP-N1, pCMV/my/mito.GFP, pCMV/myc/mito
Streak plate with transformed pEGFP-N1
19/08/2013
Ligation of CMV and pSB1C3 (1st try)
Transformation of CMV and pSB1C3 into DH5alpha
Streak pCMV/myc/mito.GFP and pCMV/myc/mito.EGFP to AMP plate
MLS(RFC25).pSB1C3 & GFP.polya digestion with AgeI & ApaLI, and transformation of the correct colony
MLS(RFC25).pSB1C3 Sanger Sequencing
20/8/2013
MLS(RFC25).pSB1C3 Sanger Sequencing(Cont.)
Plasmid extraction of pEGFP-N1, pCMV/myc/mito.GFP and pCMV/myc/mito.EGFP
MLS(RFC25).pSB1C3 digestion with AgeI-HF & PstI-HF
GFP.polya.pSB1C3(1st try) digestion with NgoMIV & PstI-HF
Repeat PCR for CMV(2nd try), digestion with EcoRI-HF & PstI-HF, PCR clean up
21/08/2013
Gel purification of GFP/polyA digested with NgoMIV & PstI-HF : too low concentration
EtOH precipitation of GFP/polyA digested with NgoMIV & PstI-HF
Pcmv.pSB1C3(2nd) ligation, and transformation to DH5alpha
MLS(RFC10) bacteria inoculation
22/08/2013
MLS(RFC10).pSB1C3 plasmid extraction, PCR check with VR VF2
Repeat digestion of GFP.polyA with NgoMIV & PstI-HF (2nd) with NgoMIV & PstI-HF
Pcmv.pSB1C3 (3rd) ligation and transformation
Inoculation of Pcmv.pSB1C3 (2nd)
GFP.polyA with NgoMIV & PstI-HF (1st) gel check
23/08/2013
Sanger Sequencing for MLS(RFC10).pSB1C3 and MLS(RFC25).pSB1C3
Pcmv.pSB1C3 (2nd) plasmid extraction, and digestion check with EcoRI & NdeI
Streak the right colony of Pcmv.pSB1C3 (2nd) into plate
GFP.polyA with NgoMIV & PstI-HF (2nd) gel purification
26/8/2013
Sanger sequencing for Pcmv.pSB1C3 (#1), MLS(RFC10).pSB1C3 (#4.3), and MLS(RFC25).pSB1C3 #1.1)
Gel check for GFP.polyA (NgoMIV & PstI-HF) for 1st & 2nd
GFP.polyA digestion with XbaI & PstI-HF, run gel and gel purification
Pcmv digestion with SpeI & PstI-HF, dephosphorylated
MLS(RFC25).pSB1C3 digestion with AgeI & PstI-HF, dephosphorylated
Repeat Sequencing for MLS(RFC25).pSB1C3
27/8/2013
MLS(RFC25).pSB1C3 Sequencing (Cont.)
Repeat Sequencing for Pcmv.pSB1C3
MLS(RFC10).pSB1C3 Sequencing (Cont.), transformed new plate with correct colony (#4.3)
GFP.polyA(XbaI & PstI-HF) gel Purification(Cont.), and gel check
Gel check for Pcmv (SpeI & PstI-HF) & MLS(RFC25).pSB1C3(AgeI & PstI-HF)
GFP(RFC25) digestion with EcoRI-HF & PstI-HF, transformed new plate for correct colony (#2)
28/8/2013
Ligation of Pcmv (S&P) and GFP (X&P), transformed
Ligation of MLS (A&P) and GFP (N&P), transformed
Pcmv.pSB1C3 and MLS(RFC25) sequence confirmed
GFP(RFC25) gel purification, EtOH precipitation
GFP(RFC25) nanodrop: concentration is too low, abandone
29/8/2013
Inoculation of MLS.GFP.polyA and CMV.GFP.polyA
30/8/2013
Plasmid extraction of MLS.GFP.polyA & CMV.GFP.polyA
Digestion check of MLS.GFP.polyA with EcoRV-HF & NdeI, and CMV.GFP.polyA with EcoRV-HF & AgeI-HF
Transfection of CMV.GFP.polyA #1
September 2013
2/9/2013
Repeat Digestion check for MLS.GFP.polyA & CMV.GFP.polyA
Gel check of CMV.GFP.polyA: long gel, delayed since not enough time to run gel
Digestion of MLS.GFP.polyA with XbaI & PstI-HF
3/9/2013
Digestion check of CMV.GFP.polyA with EcoRV-HF & AgeI-HF
Run gel and gel purification of MLS.GFP.polyA (X & P)
Pcmv digestion with SpeI and PstI-HF, dephosphorylated and PCR clean up
BBa_J176171 digestion with SpeI & PstI-HF, dephosphorylation and PCR clean up
4/9/2013
GEl purification for MLS.GFP.polyA
5/9/2013
Gel check for CMV.GFP.polyA (E&P), CMV.pSB1C3 (E&P), and GFP.polyA.pSB1C3(E&P)
Run gel for MLS.GFP.polyA(XbaI&PstI-HF), CMV(SpeI&PstI-HF), BBa_J176171(SpeI&PstI-HF), and CMV.GFP.polyA (EcoRV-HF, AgeI-HF)
6/9/2013
Digestion of CMV.pSB1C3 (1) & GFP.polyA(4) by EcoRI-HF & PstI-HF
Gel check: decided that cmv is defect, will order new primer
9/9/2013
pSB1C3 digestion with EcoRI-HF & PstI-HF
Inoculation of pEGFP-n1 (from confirmed colony spread plate)
10/9/2013
Gel purification of pSB1C3
Plasmid extraction of pEGFP-N1
12/9/2013
Digestion of MLS.GFP.polyA and GFP.polyA with SpeI & PstI, dephosphorylated
Amplify CMV with PCR using new primer