Difference between revisions of "Template:Team:TU Eindhoven/Timeline HTML"
| Line 92: | Line 92: | ||
<span class="activiteit"> Gibson Assembly:</span> | <span class="activiteit"> Gibson Assembly:</span> | ||
<ul class="activiteitlijst"> | <ul class="activiteitlijst"> | ||
| − | <li><span class="activiteit">Linearizing pET-Duet-1 for Gibson Assembly </span></li> | + | <li><span class="activiteit">Linearizing MCS-1 of pET-Duet-1 for Gibson Assembly </span></li> |
| + | <li><span class="activiteit">Digestion of the template using DpnI </span></li> | ||
| + | <li><span class="activiteit">Running a gel to check whether the linearization was successful </span></li> | ||
<li><span class="activiteit">Our first Gibson Assembly!</span></li> | <li><span class="activiteit">Our first Gibson Assembly!</span></li> | ||
| + | <li><span class="activiteit">Plasmid amplification into NEB 5-alpha </span></li> | ||
</ul> | </ul> | ||
<br \> | <br \> | ||
| Line 110: | Line 113: | ||
<span class="activiteit"> Gibson Assembly:</span> | <span class="activiteit"> Gibson Assembly:</span> | ||
<ul class="activiteitlijst"> | <ul class="activiteitlijst"> | ||
| − | <li><span class="activiteit">Linearizing pET-Duet-1 for Gibson Assembly and debugging: sequencing results came back disastrous. It seemed as if pETDuet-1 had turned on us. In the end, however, it turned out that we had used the wrong primers. Always use the right primers, folks! </span></li> | + | <li><span class="activiteit">Linearizing MCS-1 of pET-Duet-1 for Gibson Assembly and debugging: sequencing results came back disastrous. It seemed as if pETDuet-1 had turned on us. In the end, however, it turned out that we had used the wrong primers. Always use the right primers, folks! </span></li> |
<li><span class="activiteit">Digestion of the template using DpnI </span></li> | <li><span class="activiteit">Digestion of the template using DpnI </span></li> | ||
<li><span class="activiteit">Running a gel to check whether the linearization was successful </span></li> | <li><span class="activiteit">Running a gel to check whether the linearization was successful </span></li> | ||
| − | <li><span class="activiteit">Gibson Assembly for | + | <li><span class="activiteit">Gibson Assembly for MCS-1 </span></li> |
| − | <li><span class="activiteit"> | + | <li><span class="activiteit">Plasmid amplification into NEB 5-alpha </span></li> |
</ul> | </ul> | ||
<br \> | <br \> | ||
| Line 138: | Line 141: | ||
<span class="activiteit"> Gibson Assembly:</span> | <span class="activiteit"> Gibson Assembly:</span> | ||
<ul class="activiteitlijst"> | <ul class="activiteitlijst"> | ||
| − | <li><span class="activiteit">Plasmid isolation, followed by sequencing of the insert on | + | <li><span class="activiteit">Plasmid isolation, followed by sequencing of the insert on MCS-1 </span></li> |
| − | <li><span class="activiteit">Linearization of the vector on | + | <li><span class="activiteit">Linearization of the vector on MCS-2 </span></li> |
| − | <li><span class="activiteit">Gibson Assembly of | + | <li><span class="activiteit">Gibson Assembly of MCS-2 </span></li> |
| − | <li><span class="activiteit">Colony PCR of | + | <li><span class="activiteit">Plasmid amplification into NEB 5-alpha </span></li> |
| + | <li><span class="activiteit">Colony PCR of MCS-2, showing promising results! </span></li> | ||
<li><span class="activiteit">Culturing and preparing for protein expression </span></li> | <li><span class="activiteit">Culturing and preparing for protein expression </span></li> | ||
</ul> | </ul> | ||
Revision as of 01:45, 19 September 2015
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Timeline
Somewhere in the beginning of July, we started our wetwork. We started the summer off working in smaller teams: we had a team working on Gibson Assembly, a team responsible for Traditional Cloning and a team working on Interlab. In this way, we could fit tons of wetwork within the few weeks of the summer holidays. Below, we hope to give a short overview of how we started off and which experiments we carried out in which weeks.
See the black timeline below for a global impression of the major experiments carried out by the teams working with Gibson Assembly and Traditional cloning. These experiments brougth us were we are today and results can be seen here.
Week 26
- Preparing for take-off
- Inventory of the lab supplies
- Pouring LB Agar plates
- Amplification of the pET-Duet-1 vector
- Assessment of the safety requirements
- Preparing stocks for antibiotics, glycerol, LB & MilliQ
Week 27
- The Clone Wars
Gibson Assembly:
Traditional cloning:
- Linearizing MCS-1 of pET-Duet-1 for Gibson Assembly
- Digestion of the template using DpnI
- Running a gel to check whether the linearization was successful
- Our first Gibson Assembly!
- Plasmid amplification into NEB 5-alpha
Traditional cloning:
- Amplification of the pET-Duet-1 vector
- Nde1 & Kpn1 digestion of the pET-Duet-1 vector (MCS-2) for traditional cloning
Week 28
- Et tu, pET-Duet?
Gibson Assembly:
Traditional cloning:
- Linearizing MCS-1 of pET-Duet-1 for Gibson Assembly and debugging: sequencing results came back disastrous. It seemed as if pETDuet-1 had turned on us. In the end, however, it turned out that we had used the wrong primers. Always use the right primers, folks!
- Digestion of the template using DpnI
- Running a gel to check whether the linearization was successful
- Gibson Assembly for MCS-1
- Plasmid amplification into NEB 5-alpha
Traditional cloning:
- Amplification of the inserts
- Xbal & Pstl digestion of the pET-Duet-1 vector (MCS-1)
- Xba1 & Pst1 digestion of the inserts (MCS-1)
- Nde1 & Kpn1 digestion of the inserts (MCS-2)
- Ligation
- Transformation in NB
- Colony PCR & gel electrophorese: The inserts are succesfully ligated
- Culturing of the colonies with the correct plasmid
- Making a glycerol stock & sending the DNA for sequencing
Week 29
- Hopeful results
Gibson Assembly:
Protein expression:
Traditional cloning:
The sequencing results are positive, everything is built in correctly.
- Plasmid isolation, followed by sequencing of the insert on MCS-1
- Linearization of the vector on MCS-2
- Gibson Assembly of MCS-2
- Plasmid amplification into NEB 5-alpha
- Colony PCR of MCS-2, showing promising results!
- Culturing and preparing for protein expression
Protein expression:
- Double transformation of pET-Duet-1 (MCS1) and pEVOL in BL21.
- Culturing & making a glycerol stock
Traditional cloning:
The sequencing results are positive, everything is built in correctly.
Week 30
- The moment of truth
Gibson Assembly:
Protein expression of the plasmids containing MCS-1:
Double transformation & protein expression of the plasmids containing MCS-1 & MCS-2:
Traditional cloning
- Plasmid Isolation, followed by sequencing of the insert on MCS2
Protein expression of the plasmids containing MCS-1:
- Culturing and protein expression of pET-Duet-1 (MCS-1)
- Labelling the bacteria with DBCO-PEG4-Tamra
- FACS results don't show the click reaction...
Double transformation & protein expression of the plasmids containing MCS-1 & MCS-2:
- Double transformation, culturing and protein expression of pET-Duet-1 (MCS-1 & MCS-2)
- The click reaction occured according to FACS results
Traditional cloning
- The vector which already contained MCS-1 is digested at MCS-2
- Ligation of vector & insert. This results in a plasmid containing MCS-1 (OmpX-NanoLuc) and MCS-2 (OmpX-neongreen)
Week 31
- busy times
FACS:
Traditional Cloning:
Gibson Assembly:
- Protein expression of bacteria containing MCS-1 and bacteria containing MCS-1 & MCS-2
- FACS (labelling bacteria with DBCO-PEG4-tamra) shows a click reaction with bacteria containing MCS-1 & MCS-2. No click reaction occurs with bacteria containing only MCS-1
Traditional Cloning:
- Transform of the newly created plasmid MCS-1 (OmpX-NanoLuc) and MCS-2 (OmpX-neongreen)
- Colony PCR
Gibson Assembly:
- Succesfull double transformation of 12.2 at 20 ng/uL (rather than 4)
- Gibson Assembly, Colony PCR and transformation of NeonGreen into MCS1
Week 32
- shine some light
FACS:
Traditional Cloning:
Gibson Assembly:
- Protein expression of bacteria containing a split luciferase in MCS-1 and bacteria containing mNeongreen in MCS1
Traditional Cloning:
- Protein expression of constructs with mNeongreen and Nanoluc
- Luminescence and fluorescence assays of expressed proteins: neongreen is present
- Verification of protein expression using a 10% SDS-PAGE gel
Gibson Assembly:
- Succesfull double transformation of pEvol plasmid & plasmid containing Neongreen in MCS1.
- Sequencing of the constructs
Week 33
- Oh when it all, it all falls down
Gibson:
FACS:
- Linearization of the pETDuet-1 vector containing the NeonGreen insert
- Gibson Assembly of the linearized vector with the NanoLuc insert
- Linearization of pETDuet-1 at MCS1
- Gibson Assembly of the linearized pETDuet-1 vector with NanoLuc
- Miniprepping and double transformation of the NL-vectors
FACS:
- Protein expression of constructs with mNeongreen and Nanoluc
- Luminescence and fluorescence assays of expressed proteins: neongreen is present
- Verification of protein expression using a 10% SDS-PAGE gel
- Setting up a crime scene
- Succesful double transformation of pEvol plasmid & plasmid containing Neongreen in MCS1.
- Sequencing of the constructs
Week 34
- Sherlocking our way to salvation
FACS:
- Protein expression of all NG+NL containing vectors
- Redoing some transformations
- Measuring bioluminescence & fluorescence
- FACS'ing all expressed constructs
- Salvation: a faulty transformation had caused trouble Gibson:
- Miniprepping and analyzing some constructs through PCR
- Replacing NanoLuc with mTurquoise to obtain a FRET-sensor as a back up plan
Week 35
- How did it get so late so soon?
Gibson:
Finalizing the backup construct with mTurquoise
Gibson Assembly of SmBiT in MCS2
Protein Expression:
Protein Expression:
- Obtaining all data about bioluminescense and fluorescense
- Testing the sensor with complementarty DNA
- Testing aptamers + thrombin