Difference between revisions of "Team:TUDelft/Wetlab/Interlab"
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<div class="spcmkr" id="introinterlab"></div> | <div class="spcmkr" id="introinterlab"></div> | ||
<h1 class="adpbl">1. Introduction</h1> | <h1 class="adpbl">1. Introduction</h1> | ||
| − | <p> | + | <p>The InterLab studies have been contributing in developing a robust measurement procedure for green fluorescent protein (GFP) over several years now. The goal of this year’s InterLab to identify and correct the sources of systematic variability in synthetic biology measurements of GFP. In order to answer the following research question formulated by the iGEM Measurement Committee: Can we reduce lab-to-lab variability in fluorescence measurements by normalizing to absolute cell count or colony-forming units (CFU) instead of OD? The following two approaches were used to obtain results for this study: |
| + | <br><br> | ||
| + |    1. Converting between absorbance of cells to absorbance of a known <br>   concentration of beads. | ||
| + | <br><br>   2. Counting colony-forming units (CFUs) from the sample. | ||
| + | |||
| + | <br> <br> The results of these two approaches were compared to determine how much the results were in accordance with each other to see whether using one (or both) of the methods can help to reduce the lab-to-lab variability in measurements. | ||
| + | |||
| + | To get the best comparable results between all the teams performing the InterLab studies the InterLab Study Protocol was followed explicitly. The first step performed was the transformation of 8 strains with plasmids from the iGEM 2018 Distribution Kit. The different strains contained a Negative control, Positive control and 6 test strains which expressed different levels of GFP. The strains and their corresponding plasmids (parts) used from the Distribution Kit for transformation are shown in table 1. For transformation the iGEM protocol was used. | ||
| + | |||
<!-- TABEL WITH STRAIN OVERVIEW --> | <!-- TABEL WITH STRAIN OVERVIEW --> | ||
| − | <table> | + | <br><table> |
<tr class="tableheaderadpbl"> | <tr class="tableheaderadpbl"> | ||
<th class="tableheaderadpbl">Strain</th> | <th class="tableheaderadpbl">Strain</th> | ||
| − | <th class="tableheaderadpbl"> | + | <th class="tableheaderadpbl">Part Number</th> |
| − | <th class="tableheaderadpbl"> | + | <th class="tableheaderadpbl">Plate</th> |
| − | <th class="tableheaderadpbl"> | + | <th class="tableheaderadpbl">Location</th> |
| − | + | ||
</tr> | </tr> | ||
<tr class="tableunevenadpbl"> | <tr class="tableunevenadpbl"> | ||
| − | <td> | + | <td>Negative control</td> |
| − | <td> | + | <td>BBa_R0040</td> |
| − | <td> | + | <td>Kit plate 7</td> |
| − | <td> | + | <td>Well 2D</td> |
| − | + | ||
</tr> | </tr> | ||
<tr class="tableevenadpbl"> | <tr class="tableevenadpbl"> | ||
| − | <td> | + | <td>Positive control</td> |
| − | <td> | + | <td>BBa_I20270</td> |
| − | <td> | + | <td>Kit plate 7</td> |
| − | <td> | + | <td>Well 2B</td> |
| − | + | ||
</tr> | </tr> | ||
<tr class="tableunevenadpbl"> | <tr class="tableunevenadpbl"> | ||
| − | <td> | + | <td>Test Device 1</td> |
| − | <td> | + | <td>BBa_J364000</td> |
| − | <td> | + | <td>Kit plate 7</td> |
| − | <td> | + | <td>Well 2F</td> |
| − | + | ||
</tr> | </tr> | ||
<tr class="tableevenadpbl"> | <tr class="tableevenadpbl"> | ||
| − | <td> | + | <td>Test Device 2</td> |
| − | <td> | + | <td>BBa_J364001</td> |
| − | <td> | + | <td>Kit plate 7</td> |
| − | <td> | + | <td>Well 2H</td> |
| − | + | ||
</tr> | </tr> | ||
<tr class="tableunevenadpbl"> | <tr class="tableunevenadpbl"> | ||
| − | <td> | + | <td>Test Device 3</td> |
| − | <td> | + | <td>BBa_J364002</td> |
| − | <td> | + | <td>Kit plate 7</td> |
| − | <td> | + | <td>Well 2J</td> |
| − | + | ||
</tr> | </tr> | ||
<tr class="tableevenadpbl"> | <tr class="tableevenadpbl"> | ||
| − | <td> | + | <td>Test Device 4</td> |
| − | <td> | + | <td>BBa_J364007</td> |
| − | <td> | + | <td>Kit plate 7</td> |
| − | <td> | + | <td>Well 2L</td> |
| − | <td> | + | |
| + | </tr> | ||
| + | <tr class="tableevenadpbl"> | ||
| + | <td>Test Device 5</td> | ||
| + | <td>BBa_J364008</td> | ||
| + | <td>Kit plate 7</td> | ||
| + | <td>Well 2N</td> | ||
| + | |||
| + | </tr> | ||
| + | <tr class="tableevenadpbl"> | ||
| + | <td>Test Device 6</td> | ||
| + | <td>BBa_J364009</td> | ||
| + | <td>Kit plate 7</td> | ||
| + | <td>Well 2P</td> | ||
| + | |||
</tr> | </tr> | ||
</table> | </table> | ||
| − | + | ||
| − | + | ||
| − | + | <br>Table 1: Test Devices. The 8 Test Devices created by transformation of Escherichia coli DH5⍺ with the 8 plasmids from the Distribution Kit. | |
| − | + | </p> | |
<div class="spcmkr" id="experimentalsetupinterlab"></div> | <div class="spcmkr" id="experimentalsetupinterlab"></div> | ||
Revision as of 16:10, 4 October 2018
1. Introduction
The InterLab studies have been contributing in developing a robust measurement procedure for green fluorescent protein (GFP) over several years now. The goal of this year’s InterLab to identify and correct the sources of systematic variability in synthetic biology measurements of GFP. In order to answer the following research question formulated by the iGEM Measurement Committee: Can we reduce lab-to-lab variability in fluorescence measurements by normalizing to absolute cell count or colony-forming units (CFU) instead of OD? The following two approaches were used to obtain results for this study:
1. Converting between absorbance of cells to absorbance of a known
concentration of beads.
2. Counting colony-forming units (CFUs) from the sample.
The results of these two approaches were compared to determine how much the results were in accordance with each other to see whether using one (or both) of the methods can help to reduce the lab-to-lab variability in measurements.
To get the best comparable results between all the teams performing the InterLab studies the InterLab Study Protocol was followed explicitly. The first step performed was the transformation of 8 strains with plasmids from the iGEM 2018 Distribution Kit. The different strains contained a Negative control, Positive control and 6 test strains which expressed different levels of GFP. The strains and their corresponding plasmids (parts) used from the Distribution Kit for transformation are shown in table 1. For transformation the iGEM protocol was used.
| Strain | Part Number | Plate | Location |
|---|---|---|---|
| Negative control | BBa_R0040 | Kit plate 7 | Well 2D |
| Positive control | BBa_I20270 | Kit plate 7 | Well 2B |
| Test Device 1 | BBa_J364000 | Kit plate 7 | Well 2F |
| Test Device 2 | BBa_J364001 | Kit plate 7 | Well 2H |
| Test Device 3 | BBa_J364002 | Kit plate 7 | Well 2J |
| Test Device 4 | BBa_J364007 | Kit plate 7 | Well 2L |
| Test Device 5 | BBa_J364008 | Kit plate 7 | Well 2N |
| Test Device 6 | BBa_J364009 | Kit plate 7 | Well 2P |
Table 1: Test Devices. The 8 Test Devices created by transformation of Escherichia coli DH5⍺ with the 8 plasmids from the Distribution Kit.
2. Experimental Setup
Text about the experimental setup :):):)
3. Results
Text about the Results:):):)
3.1 More results
3.2 Results even more
4. Conclusion
Text about the conclusion:):):)