Team:Southampton/Notebook/Labbook
From 2009.igem.org
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<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Project">Project Description</a></li> | <li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Project">Project Description</a></li> | ||
<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Projection">Project Projection</a></li> | <li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Projection">Project Projection</a></li> | ||
+ | <li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Refer">References and Links</a></li> | ||
<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Protocols"><span>Protocols</span><![if gt IE 6]></a><![endif]><!--[if lte IE 6]><table><tr><td><![endif]--> | <li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Protocols"><span>Protocols</span><![if gt IE 6]></a><![endif]><!--[if lte IE 6]><table><tr><td><![endif]--> | ||
<ul class=" cssMenum"> | <ul class=" cssMenum"> | ||
<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Protocols">Protocol Overview</a></li> | <li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Protocols">Protocol Overview</a></li> | ||
+ | <li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Protocols/Theory1">Protocol Theory</a></li> | ||
<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Protocols/Transformation">Biobrick Transformation</a></li> | <li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Protocols/Transformation">Biobrick Transformation</a></li> | ||
<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Protocols/ColonyPCR">Colony PCR</a></li> | <li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Protocols/ColonyPCR">Colony PCR</a></li> | ||
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</ul> | </ul> | ||
<!--[if lte IE 6]></td></tr></table></a><![endif]--></li> | <!--[if lte IE 6]></td></tr></table></a><![endif]--></li> | ||
- | <li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Parts">Biobrick Parts</a></li> | + | <li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Parts">Biobrick Parts<![if gt IE 6]></a><![endif]><!--[if lte IE 6]><table><tr><td><![endif]--> |
+ | <ul class=" cssMenum"> | ||
+ | <li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Parts/GoL">Game of Life</a></li> | ||
+ | <li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Parts/RPS">Rock Paper Scissors</a></li> | ||
+ | </ul></li> | ||
<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Team"><span>Team</span><![if gt IE 6]></a><![endif]><!--[if lte IE 6]><table><tr><td><![endif]--> | <li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Team"><span>Team</span><![if gt IE 6]></a><![endif]><!--[if lte IE 6]><table><tr><td><![endif]--> | ||
<ul class=" cssMenum"> | <ul class=" cssMenum"> | ||
<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Team">Team Profiles</a></li> | <li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Team">Team Profiles</a></li> | ||
- | <li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Team/Advisors">Advisor Profiles</a></li> | + | <li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Team/Advisors">Advisor Profiles</a></li> |
+ | <li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Team/Southampton">Southampton Profile</a></li> | ||
+ | <li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Team/University">University Profile</a></li> | ||
<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Team/Gallery">Gallery</a></li> | <li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Team/Gallery">Gallery</a></li> | ||
</ul> | </ul> | ||
<!--[if lte IE 6]></td></tr></table></a><![endif]--></li> | <!--[if lte IE 6]></td></tr></table></a><![endif]--></li> | ||
- | <li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Modeling">Modelling</a></li> | + | |
- | + | <li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Modeling"><span>Modelling</span><![if gt IE 6]></a><![endif]><!--[if lte IE 6]><table><tr><td><![endif]--> | |
+ | <ul class=" cssMenum"> | ||
+ | <li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Modeling/GoL">Game Of Life</a></li> | ||
+ | <li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Modeling/RPS">Rock Paper Scissors</a></li> | ||
+ | <li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Modeling/Open">Open Access</a></li> | ||
+ | </ul> | ||
+ | <!--[if lte IE 6]></td></tr></table></a><![endif]--></li> | ||
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<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/HP"><span>Human Practices</span><![if gt IE 6]></a><![endif]><!--[if lte IE 6]><table><tr><td><![endif]--> | <li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/HP"><span>Human Practices</span><![if gt IE 6]></a><![endif]><!--[if lte IE 6]><table><tr><td><![endif]--> | ||
<ul class=" cssMenum"> | <ul class=" cssMenum"> | ||
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<ul class=" cssMenum"> | <ul class=" cssMenum"> | ||
<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Sponsors">Sponsors</a></li> | <li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Sponsors">Sponsors</a></li> | ||
- | <li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Southampton">Southampton</a></li> | + | <li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Southampton">Team Southampton</a></li> |
</ul> | </ul> | ||
<!--[if lte IE 6]></td></tr></table></a><![endif]--></li> | <!--[if lte IE 6]></td></tr></table></a><![endif]--></li> |
Revision as of 15:44, 10 October 2009
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Lab Notebook
Week Beginning: 20th July 2009 |
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Experiments |
Conclusion |
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Monday |
No experiments were undertaken |
The aim of the week was to become acquainted with the protocols. |
Tuesday |
No experiments were undertaken |
|
Wednesday |
Pure Yield Plasmid Prep: practice session |
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Thursday |
No experiments were undertaken |
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Friday |
DNA Gel Electrophoresis: practice session |
Week Beginning: 27th July 2009 |
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Experiments |
Conclusion |
|
Monday |
Bio brick elution and transformation |
Experiments were carried out to become acquainted with the protocols. |
Tuesday |
Double digestion protocol |
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Wednesday |
Gel extraction and purification |
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Thursday |
High fidelity PCR |
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Friday |
No experiments were undertaken |
Week Beginning: 3rd Aug 2009 |
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|
Experiments |
Conclusion |
Monday |
No experiments undertaken |
The aim of the week was to start transforming the necessary biobricks needed for the project. |
Tuesday |
Biobrick DNA Elution and Transformation:E0040 K145270 C0012 I719005 R0071 K084009 C0161 K091100 |
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Wednesday |
Plasmid Prep (using transformed biobricks prepared yesterday – except C0161)DNA Elution and Transformation |
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Thursday |
Plasmid Prep (using biobricks transformed yesterday) |
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Friday |
Repeat Biobrick transformations: |
Week Beginning: 10th August 2009 |
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|
Experiments |
Conclusion |
Monday |
Culture overnight of transformed partsB0015-Failed B0034 –Failed J23119-Failed C0161-Failed R0062 C0170 C0171 R0079 |
The main aim of this week was to grow up any bio-bricks that may be required. Several parts failed and so had to be repeated. There are many reasons for the failure, one being the use of the wrong cells and transformations failing. |
Tuesday |
Plasmid Maxiprep of the overnight cultures |
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Wednesday |
Culture overnight of transformed partsC0161 B0034 B0015 J23119 R0010 R0011 |
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Thursday |
Plasmid maxiprep of the overnight cultures |
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Friday |
Digestion of parts for Quality control |
Week Beginning: 17th Aug 2009 |
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Experiments |
Conclusion |
Monday |
No experiments were undertaken |
The aim of the week was to start ligating biobrick parts together. The aim for next week is to check that the ligations have been successful. |
Tuesday |
Digestion of parts for quality control.Polymerase Chain Reaction:C0012 C0170 C0171 C0179 C0161 C0178 |
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Wednesday |
Polymerase Chain Reaction: the reaction from yesterday failed hence the PCR was repeatedStarter Culture and Maxi Prep:
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|
Thursday |
Double Digestion of PCR samples:
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Friday |
Ligation of Biobrick parts- all the following parts were ligated with B0034:C0171 C0179 C0012 C0178 C0170 C0062 C0161 |
Week Beginning: 24th August 2009 |
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|
Experiments |
Conclusion |
Monday |
Ligation of B0034 with C0178, C0062, E0040, C0171, C0179, C0170, C0012, C0161, E0040
|
The main aim of this week was to get our first ligations to work, however this wasn’t the case and so after the ligations were repeated and failed again, troubleshooting began. |
Tuesday |
Transformation of B0034 |
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Wednesday |
Colony PCR of ligated parts
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|
Thursday |
Repeat of Colony PCR, which had previously failed. |
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Friday |
PCR of biobrick insertsC0178, C0062, E0040, C0171, C0179, C0170, C0012, C0161, E0040 |
Week Beginning: 31st Aug 2009 |
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|
Experiments |
Conclusion |
Monday |
No experiments were done today |
The aim of this week was to continue trying to get our first ligations to work, this wasn’t successful the digestion was found not to be complete and so this is thought to be one of the reasons behind the failed ligations. The next set of Digestions will be done overnight instead of the usual 2 hours. |
Tuesday |
Repeat of Colony PCR of: pTac – B0034DNA Double Digestion: (pTac – B0034)Ligation: (pTac – B0034) |
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Wednesday |
Colony PCR Control:
|
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Thursday |
Mini Prep |
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Friday |
Second Single Digestion:C0171 C0170 C0012 C0179 E0040 0034 |
Week Beginning: 7th Sept 2009 |
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|
Experiments |
Conclusion |
Monday |
PCR of Pmal to produce Ptac |
TSAP (thermo sensitive alkaline phosphatase) was used on the plasmid to dephosphorylate the plasmid so it cannot religate. Digestions with PstI were done for 8 hours and every other digestion was run for 3 hours. Ligations are now ran overnight at 4C. |
Tuesday |
Digestion of Ptac with EcoRI and XbaI and RBS with XbaL and Spel RBS was treated with SAP |
|
Wednesday |
A maxiprep was performed on the parts, which were previously cultured overnight. Digestion of the parts with Pstl to check that the parts were correct. |
|
Thursday |
PCR of C0161, C0178, C0062 which didn’t work |
|
Friday |
PCR of Gfp-LVA, which didn’t work. |
Week Beginning: 14th Sept 2009 |
||
|
Experiments |
Conclusion |
Monday |
Transformation of C0170, C0012 and pTac to RBS |
The ligations of Ptac didn’t work with the 3-hour digestion and TA cloning was inconclusive, due to a lack of resources. Parts, which were shown to be dodgy, were re-grown and checked for quality control. |
Tuesday |
Colony PCR of the ligated parts |
|
Wednesday |
Digestion of Biobricks pLux, STOP and LacI.followed by an overnight ligation of the parts |
|
Thursday |
Transformation of the ligated parts |
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Friday |
Colony PCR of the ligated parts |
Week Beginning: 21st Sept 2009 |
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|
Experiments |
Conclusion |
Monday |
Diluted colony PCR of the C0012-B0015, R0062-C0012. |
TA cloning was performed on Gfp-LVA to check the prefix and the suffix was digested properly. Ptac also had a successful TA cloned vector. This means that the work to check for complete digestion can begin. The main focus of this week was to finish any wiki work as this is the last week for the iGEM students. |
Tuesday |
PCR of Ptac from Pmal |
|
Wednesday |
Digestion of C0012 and C0179 |
|
Thursday |
Repeat of the previous day’s experiment followed by ligation overnight.Culture of the Gfp which was TA cloned |
|
Friday |
Maxiprep of the cultured Gfp. This failed as the DNA was sheared.
|
Week Beginning: 28th Sept 2009 |
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|
Experiments |
Conclusion |
Monday |
Culture of the TA cloned Ptac |
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Tuesday |
The Ptac and Gfp-LVA which was TA cloned was digested overnight. |
|
Wednesday |
A gel was run on the Ptac and was shown to have digested improperly. Gel purification was performed on Gfp-LVA |
|
Thursday |
Digestion of Ptac overnight and further purification of GFP-LVA. |
|
Friday |
Ligations of Ptac and Gfp-LVA with PSB1A3. |