Team:BostonU/Workflow

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Latest revision as of 02:44, 18 October 2014

Workflow

For a detailed example of our Chimera Characterization Workflow, please check out the Chimera Example page. Below, we present a brief outline of the major steps involved in each stage (Design, Build, Test) of the Chimera workflow, along with a few high level examples. We also define what we consider Phase I, II, and III to be for our workflow. Phase I - Build and test basic parts. Key software tools: TASBE Tools, Eugene (optional), Raven (optional)
General Chimera Workflow	Case Study: BU Priority Encoder
	• Add parts to MoClo library. The following parts were found to be necessary for our priority encoder: • 3 MoClo level 1 and 3 MoClo level 2 backbones, each with a different origin of replication: • ColE1 • p15A • pSC101 • 4 MoClo level 0 fusion proteins: • tetR_GFP • tetR_YFP • araC_YFP • araC_GFP • X MoClo level 0 tandem promoters: • pTet_pBad • pBad_pTet These parts were cloned into a E. coli Bioline strain using our MoClo and transformation protocols. They were purified and sequenced. Additionally, we built testing devices for each of the new parts. Details can be found on the fusion proteins , tandem promoters , and origin of replication project pages. We tested these using our FACS Workflow and our BD LSRFortessa flow cytometer.The TASBE Tools were then employed to characterize their expression.
Phase II - Build and characterize TU behavior. Key software tools: TASBE Tools, Eugene, Raven
General Chimera Workflow	Case Study: BU Priority Encoder
	• Run one-pot Multiplexing MoClo reaction. We initially multiplexed RBSs. • Eugene was employed to visualize all possible part substitutions. • Raven was employed to optimize the assembly of these combinations. • Clone multiplexed reactions into Pro strain of E. coli using Pro Transformation protocol. • Pick 20 colonies per plate, purify, and sequence. • Test using flow cytometry workflow and analyze data using the TASBE Tools.
Phase III - Test regulatory arcs and assemble final device. Key software tools: TASBE Tools, Eugene, Raven
General Chimera Workflow	Case Study: BU Priority Encoder
	• Test individual TU regulatory arcs • Use Eugene to plan final device topology. • Use Raven to guide MoClo assembly of encoder. • Clone multiplexed reactions into Pro strain of E. coli using Pro Transformation protocol. • Pick colonies, purify, and sequence. • Test using flow cytometry workflow and analyze data using the TASBE Tools.

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@@ Line 13: / Line 13: @@
        <tr>
-         <th scope="col" colspan="2"><h2>Phase I - Build and test basic parts.</h2>
+         <td scope="col" colspan="2">
+<center><img src="https://static.igem.org/mediawiki/2014/1/1a/BU14_DBTcycle.png" width="40%"></center>
+<br>
+For a detailed example of our Chimera Characterization Workflow, please check out the <a href="https://2014.igem.org/Team:BostonU/ChimeraExample">Chimera Example</a> page. Below, we present a brief outline of the major steps involved in each stage (Design, Build, Test) of the Chimera workflow, along with a few high level examples. We also define what we consider Phase I, II, and III to be for our workflow.
+<br><br>
+<h2>Phase I - Build and test basic parts.</h2>
             Key software tools: TASBE Tools, Eugene (optional), Raven (optional)
-</th></tr>
+</td></tr>
 <tr>
-         <th scope="col" width="50%"><center><h3>General Chimera Workflow</center></h3></th>
+         <td scope="col" width="50%"><center><h3>General Chimera Workflow</center></h3></td>
-         <th scope="col" class="tableborderleft" style="padding-left: 15px"><center><h3>Case Study: BU Priority Encoder</h3></center>
+         <td scope="col" class="tableborderleft" style="padding-left: 15px"><center><h3>Case Study: BU Priority Encoder</h3></center>
        </tr>
 <tr>
-         <th scope="col" style="padding-left: 15px"> <p class="dtab">
+         <td scope="col" >
-•	Break down large device into TUs and further break down into individual genetic parts (promoters, RBS, CDS, terminator)<br><br>
+<center><img src="https://static.igem.org/mediawiki/2014/a/a2/Phase_I_Chimera.png" width="100%"></center>
-•	Decide which parts will be necessary that don't yet exist in your parts collection<br><br>
-•	If new to synbio/wetlab work, use Raven to design primers and generate steps for building<br><br>
-•	If unsure, read through literature for ideas of how to design part<br><br>
-•	If experienced, design primers while keeping in mind you'll have to combine new part with other genetic parts to test it<br><br>
-•	After building part: test for function<br><br>
-</p> </th>
-<th scope="col" class="tableborderleft" style="padding-left: 15px">
-•	Add parts to <a href="https://2014.igem.org/Team:BostonU/MoClo">MoClo library</a>. These parts were found to be necessary for our priority encoder:<br><br>
+</p> </td>
+<td scope="col" class="tableborderleft" style="padding-left: 15px">
+•	Add parts to <a href="https://2014.igem.org/Team:BostonU/MoClo">MoClo library</a>. The following parts were found to be necessary for our priority encoder:<br><br>
 <p class="tab">•	3 MoClo level 1 and 3 MoClo level 2 backbones, each with a different <a href="https://2014.igem.org/Team:BostonU/Backbones">origin of replication</a>:<br></p>
@@ Line 45: / Line 48: @@
 <p class="tab">•	4 MoClo level 0 <a href="https://2014.igem.org/Team:BostonU/FusionProteins">fusion proteins</a>:<br></p>
 <p class="dtab">
-•	TetR_GFP<br>
+•	<i>tetR</i>_GFP<br>
-•	TetR_YFP<br>
+•	<i>tetR</i>_YFP<br>
-•	AraC_YFP<br>
+•	<i>araC</i>_YFP<br>
-•	AraC_GFP<br>
+•	<i>araC</i>_GFP<br>
 <br><br>
 </p>
@@ Line 57: / Line 60: @@
 •	pBad_pTet<br>
 </p>
-These parts were cloned into a <i>E. coli</i> Bioline strain using our MoClo and transformation protocols. They were purified, sequenced, and tested using our FACS Workflow. These parts were then cloned into appropriate vectors and tested in our Fortessa flow cytometer. The TASBE Tools were then employed to characterize their expression.
+These parts were cloned into a <i>E. coli</i> Bioline strain using our MoClo and transformation protocols. They were purified and sequenced. Additionally, we built testing devices for each of the new parts. Details can be found on the <a href="https://2014.igem.org/Team:BostonU/FusionProteins">fusion proteins </a>, <a href="https://2014.igem.org/Team:BostonU/ProjectTandemPromoters">tandem promoters </a>, and <a href="https://2014.igem.org/Team:BostonU/Backbones">origin of replication</a> project pages. We tested these using our <a href="https://static.igem.org/mediawiki/2014/7/7c/Flow_Cytometer_WorkflowYABU.xls">FACS Workflow</a> and our BD LSRFortessa flow cytometer.The TASBE Tools were then employed to characterize their expression.
-</th>
+</td>
        </tr>
 <tr>
-         <th scope="col" colspan="2"><h2>Phase II - Build and characterize TU behavior.</h2>
+<br><br>
+         <td scope="col" colspan="2"><h2>Phase II - Build and characterize TU behavior.</h2>
             Key software tools: TASBE Tools, Eugene, Raven
-</th></tr>
+</td></tr>
 <tr>
-         <th scope="col" width="50%"><center><h3>General Chimera Workflow</center></h3></th>
+         <td scope="col" width="50%"><center><h3>General Chimera Workflow</center></h3></td>
-         <th scope="col" class="tableborderleft" style="padding-left: 15px"><center><h3>Case Study: BU Priority Encoder</h3></center>
+         <td scope="col" class="tableborderleft" style="padding-left: 15px"><center><h3>Case Study: BU Priority Encoder</h3></center>
        </tr>
 <tr>
-         <th scope="col" style="padding-left: 15px"> <p class="dtab">
+         <td scope="col">
-•	Use Eugene and Raven to generate all possible combinations of genetic parts and narrow down based on rules<br><br>
+<center><img src="https://static.igem.org/mediawiki/2014/f/fb/Phase_II_Chimera_updated.png" width="100%"></center>
-•	Create TUs and test using Flow Cytometry<br><br>
-•	Analyze transfer curves and choose combinations based on resulting transfer curves and desired function<br><br>
-</p> </th>
-<th scope="col" class="tableborderleft" style="padding-left: 15px">
+</p> </td>
-•	Run one-pot Multiplexing MoClo reaction. We initially multiplexed 5' UTIs and Terminators<br>
+<td scope="col" class="tableborderleft" style="padding-left: 15px">
+•	Run one-pot <a href="https://2014.igem.org/Team:BostonU/Multiplexing">Multiplexing MoClo reaction</a>. We initially multiplexed RBSs.
 <p class="tab">•	Eugene was employed to visualize all possible part substitutions.<br>
 •	Raven was employed to optimize the assembly of these combinations.</p><br><br>
@@ Line 90: / Line 93: @@
 <tr>
-         <th scope="col" colspan="2"><h2>Phase III - Test regulatory arcs and assemble final device.</h2>
+<br><br>
+         <td scope="col" colspan="2"><h2>Phase III - Test regulatory arcs and assemble final device.</h2>
             Key software tools: TASBE Tools, Eugene, Raven
-</th></tr>
+</td></tr>
 <tr>
-         <th scope="col" width="50%"><center><h3>General Chimera Workflow</center></h3></th>
+         <td scope="col" width="50%"><center><h3>General Chimera Workflow</center></h3></td>
-         <th scope="col" class="tableborderleft" style="padding-left: 15px"><center><h3>Case Study: BU Priority Encoder</h3></center>
+         <td scope="col" class="tableborderleft" style="padding-left: 15px"><center><h3>Case Study: BU Priority Encoder</h3></center>
        </tr>
 <tr>
-         <th scope="col">For phase III of our hybridized workflow, we will put together the new transcriptional units according to regulatory arcs and test them individually. To do that, using Raven and Eugene will be very beneficial as they can generate designs and assembly plans for very large devices. Testing several pairs of units with varying concentrations of small molecule induction is always a good idea so that a large range of data can be collected. This data will then be analyzed to gauge the efficacy of the device. </th>
+         <td scope="col">
+<center><img src="https://static.igem.org/mediawiki/2014/2/29/Phase_III_Chimera_updated.png" width="100%"></center>
+</td>
-<th scope="col" class="tableborderleft" style="padding-left: 15px">
+<td scope="col" class="tableborderleft" style="padding-left: 15px">
-•	Test individual TU regulatory arcs:<br>
+•	Test individual TU regulatory arcs<br>
-<p class="tab">•	...<br></p>
 •	Use Eugene to plan final device topology.<br><br>
 •	Use Raven to guide MoClo assembly of encoder.<br><br>