Team:TU Eindhoven/Protocols

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Latest revision as of 00:06, 18 October 2014

iGEM Team TU Eindhoven 2014

Protocols

For this year's iGEM competition numerous protocols were devoloped to guide our experiments and keep our documentation neat and tidy. Because these protocols can also be useful to other projects, we decided to publish them on our wiki. You can find information and download links on this page down below.

Genetic Engineering Protocols

The following protocols are used in the Biolab during the modification of bacteria.

Antibody Labelling	Double Transformation	Plasmid Purification
Antibody Titration with FACS	FACS DBCO-PEG(10kDa)	Preparative Steps
Bacteria Cultering for Microfluidics	FACS for sorting with DBCO-TAMRA	Protein Expression
Casting and Running 15% PAGE Gel	Fluorescent labelling antibodies	Rolling Circle Amplification on membrane
Cell Viability Assay	Overhang PCR	Site Directed Mutagenesis
Colony PCR	PCR Purification of DNA Fragments	Vector Ligation
Creating Circular RCA Template	Plasmid Gene Digestion	Vector Transformation

Chemistry Protocols

The following protocols are used in the chemical synthesis processes.

SPAAC reaction monitoring with UV-Visible Spectroscopy

Labelling Amine-Modified DNA with DBCO-PEG₄-NHS Ester

Microfluidics Protocols

The following protocols are used in the Microfabrication lab for the production and running of microfluidic devices.

Droplet Device Testing	Oil and Water Phase (Polyacrylamide Beads)
Droplet Separation	Photolithography
Oil and Water Phase (Encapsulation)	Soft Lithography

iGEM Team TU Eindhoven 2014

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-     <td><a target="_blank" href="https://static.igem.org/mediawiki/2014/0/08/TU_Eindhoven_Antibody_labeling.pdf">Antibody Labeling</a></td>
+     <td><a target="_blank" href="https://static.igem.org/mediawiki/2014/e/eb/TU_Eindhoven_Antibody_labelling.pdf">Antibody Labelling</a></td>
-     <td><a target="_blank" href="https://static.igem.org/mediawiki/2014/8/81/Protocol_-_Overhang_PCR.pdf">Overhang PCR</a></td>
+     <td> <a target="_blank" href="https://static.igem.org/mediawiki/2014/9/94/TU_Eindhoven_Protocol_Double_Transformation.pdf">Double Transformation</a> </td>
-     <td><a target="_blank" href="https://static.igem.org/mediawiki/2014/f/f8/Protocol_-_Protein_Expression_Curve.pdf">Protein Expression Curve</a></td>
+     <td>  <a target="_blank" href="https://static.igem.org/mediawiki/2014/2/2b/TU_Eindhoven_Protocol_Plasmid_purification.pdf">Plasmid Purification</a> </td>
    </tr>
    <tr>
-     <td><a target="_blank" href="https://static.igem.org/mediawiki/2014/b/b1/Protocol_-_FACS_%28Antibody_Titration%29.pdf">Antibody Titration with FACS</a></td>
+     <td><a target="_blank" href="https://static.igem.org/mediawiki/2014/1/16/TU_Eindhoven_Protocol_FACS_%28Antibody_Titration%29.pdf">Antibody Titration with FACS</a></td>
-    <td><a target="_blank"  href="https://static.igem.org/mediawiki/2014/0/0a/Protocol_-_PCR_Purification_of_Insert_Fragment.pdf">PCR Purification of DNA Fragments</a></td>
+<td>  <a target="_blank" href="https://static.igem.org/mediawiki/2014/d/de/TU_Eindhoven_FACS_%28DBCO-PEG_10_kDa%29.pdf">FACS DBCO-PEG(10kDa)</a> </td>
-     <td><a target="_blank" href="https://static.igem.org/mediawiki/2014/6/62/Protocol_-_Site_Directed_Mutagenesis.pdf">Site Directed Mutagenesis</a></td>
+     <td>  <a target="_blank" href="https://static.igem.org/mediawiki/2014/3/35/TU_Eindhoven_Protocol_Preparative_steps.pdf">Preparative Steps</a> </td>
    </tr>
    <tr>
-     <td><a target="_blank" href="https://static.igem.org/mediawiki/2014/3/35/TU_Eindhoven_Antifouling.pdf">Antifouling</a></td>
+     <td><a href="https://static.igem.org/mediawiki/2014/8/80/TU_Eindhoven_Protocol_bacteria_culturing_for_microfluidics.pdf" target="_blank">Bacteria Cultering for Microfluidics</a></td>
-     <td><a target="_blank" href="https://static.igem.org/mediawiki/2014/2/22/Protocol_-_Plasmid_Amplification.pdf">Plasmid Amplification</a></td>
+     <td>  <a target="_blank"  href="https://static.igem.org/mediawiki/2014/0/07/TU_Eindhoven_Protocol_FACS_%28DBCO-56-TAMRA%29l.pdf">FACS for sorting with DBCO-TAMRA</a> </td>
-     <td><a target="_blank" href="https://static.igem.org/mediawiki/2014/a/ae/Protocol_-_Insert_%2B_Vector_Ligation.pdf">Vector Ligation</a></td>
+     <td>  <a target="_blank" href="https://static.igem.org/mediawiki/2014/6/6f/TU_Eindhoven_Protocol_Protein_expression.pdf">Protein Expression</a> </td>
    </tr>
    <tr>
-     <td><a target="_blank" href="https://static.igem.org/mediawiki/2014/0/00/TU_Eindhoven_Casting_and_running_PAGE_gel.pdf">Casting and Running 15% PAGE Gel</a></td>
+     <td> <a target="_blank" href="https://static.igem.org/mediawiki/2014/0/00/TU_Eindhoven_Casting_and_running_PAGE_gel.pdf">Casting and Running 15% PAGE Gel</a> </td>
-     <td><a target="_blank" href="https://static.igem.org/mediawiki/2014/0/07/Protocol_-_Plasmid_and_gene_digestion.pdf">Plasmid Gene Digestion</a></td>
+     <td>  <a target="_blank" href="https://static.igem.org/mediawiki/2014/c/cc/TU_Eindhoven_Protocol_Labelling_antibodies_with_56-TAMRA-NHS.pdf">Fluorescent labelling antibodies</a> </td>
-     <td><a target="_blank" href="https://static.igem.org/mediawiki/2014/b/b5/Protocol_-_Transformation.pdf">Vector Transformation</a></td>
+     <td>  <a target="_blank" href="https://static.igem.org/mediawiki/2014/8/8f/TU_Eindhoven_Protocol_Rolling_Circle_Amplification_on_cell_membrane.pdf">Rolling Circle Amplification on membrane</a> </td>
    </tr>
    <tr>
-     <td><a target="_blank" href="https://static.igem.org/mediawiki/2014/5/50/TU_Eindhoven_Creating_circular_RCA_template.pdf">Creating Circular RCA Template</a></td>
+     <td> <a target="_blank" href="https://static.igem.org/mediawiki/2014/6/6c/TU_Eindhoven_Protocol_Cell_viability.pdf">Cell Viability Assay</a> </td>
-     <td><a target="_blank" href="https://static.igem.org/mediawiki/2014/2/29/Protocol_-_Plasmid_purification.pdf">Plasmid Purification</a></td>
+     <td><a target="_blank" href="https://static.igem.org/mediawiki/2014/1/1e/TU_Eindhoven_Protocol_Overhang_PCR.pdf">Overhang PCR</a><a target="_blank" href="https://static.igem.org/mediawiki/2014/9/94/TU_Eindhoven_Protocol_Double_Transformation.pdf"></a></td>
-     <td></td>
+     <td>  <a target="_blank" href="https://static.igem.org/mediawiki/2014/7/74/TU_Eindhoven_Protocol_Site_Directed_Mutagenesis.pdf">Site Directed Mutagenesis</a> </td>
    </tr>
    <tr>
-     <td><a target="_blank" href="https://static.igem.org/mediawiki/2014/f/f0/Protocol_-_FACS_%28DBCO-PEG_10_kDa%29.pdf">FACS for sorting with DBCO-PEG(10kDa)</a></td>
+     <td>  <a target="_blank" href="https://static.igem.org/mediawiki/2014/3/3d/TU_Eindhoven_Protocol_Colony_PCR.pdf">Colony PCR</a> </td>
-     <td><a target="_blank" href="https://static.igem.org/mediawiki/2014/1/13/Protocol_-_Preparative_steps.pdf">Preparative Steps</a></td>
+     <td>  <a target="_blank"  href="https://static.igem.org/mediawiki/2014/9/90/TU_Eindhoven_Protocol_PCR_Purification_of_Insert_Fragment.pdf">PCR Purification of DNA Fragments</a> </td>
-     <td></td>
+     <td> <a target="_blank" href="https://static.igem.org/mediawiki/2014/3/35/TU_Eindhoven_Protocol_Insert_%2B_Vector_Ligation.pdf">Vector Ligation</a> </td>
    </tr>
    <tr>
-     <td><a target="_blank"  href="https://static.igem.org/mediawiki/2014/7/7e/Protocol_-_FACS_%28DBCO-56-TAMRA%29.pdf">FACS for sorting with DBCO-TAMRA</a></td>
-     <td><a target="_blank" href="https://static.igem.org/mediawiki/2014/4/45/Protocol_-_Protein_expression.pdf">Protein Expression</a></td>
+     <td>  <a target="_blank" href="https://static.igem.org/mediawiki/2014/5/50/TU_Eindhoven_Creating_circular_RCA_template.pdf">Creating Circular RCA Template</a> </td>
-     <td></td>
+     <td>  <a target="_blank" href="https://static.igem.org/mediawiki/2014/7/7d/TU_Eindhoven_Protocol_Plasmid_and_gene_digestion.pdf">Plasmid Gene Digestion</a> </td>
+     <td><a target="_blank" href="https://static.igem.org/mediawiki/2014/8/8a/TU_Eindhoven_Protocol_Transformation.pdf">Vector Transformation</a><a target="_blank" href="https://static.igem.org/mediawiki/2014/6/6c/TU_Eindhoven_Protocol_Cell_viability.pdf"></a></td>
    </tr>
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@@ Line 175: / Line 176: @@
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    <tr>
-     <td><a href="https://static.igem.org/mediawiki/2014/3/3d/Protocol_-_Monitoring_SPAAC_with_UVVIS.pdf" target="_blank">SPAAC reaction monitoring with UV-Visible Spectroscopy</a></td>
+     <td><a href="https://static.igem.org/mediawiki/2014/1/1d/TU_Eindhoven_Protocol_Monitoring_SPAAC_with_UVVIS.pdf" target="_blank">SPAAC reaction monitoring with UV-Visible Spectroscopy</a></td>
 </tr>
 <tr>
-     <td><a target="_blank" href="https://static.igem.org/mediawiki/2014/2/2f/TU_Eindhoven_Labelling_amine-modified_DNA_with_DBCO-PEG4-NHS_ester.pdf">Labeling Amine-Modified DNA with DBCO-PEG4-NHS Ester</a></td>
+     <td><a target="_blank" href="https://static.igem.org/mediawiki/2014/2/2f/TU_Eindhoven_Labelling_amine-modified_DNA_with_DBCO-PEG4-NHS_ester.pdf">Labelling Amine-Modified DNA with DBCO-PEG<sub>4</sub>-NHS Ester</a></td>
    </tr>
 </table>
-                   <h3>Microfluidics Protocols</h3>
+                   <h3 id='Micro'>Microfluidics Protocols</h3>
 <p><em>The following protocols are used in the Microfabrication lab for the production and running of microfluidic devices.</em></p>
 <table border="0" style="width:1085px;background:none;">
    <tr>
-     <td><a href="https://static.igem.org/mediawiki/2014/a/a2/TU_Eindhoven_Microfluidic_Device_Testing_%28Droplets%29_-_finished.pdf" target="_blank"></a>Droplet Device Testing</a></td>
+     <td><a href="https://static.igem.org/mediawiki/2014/2/2e/TU_Eindhoven_Protocol_Microfluidic_Device_Testing_%28Droplets%29.pdf" target="_blank">Droplet Device Testing</a></td>
-    <td><a href="https://static.igem.org/mediawiki/2014/9/9a/TU_Eindhoven_Photolithography_-_finished.pdf" target="_blank"></a>Photolithography</a></td>
+<td><a target="_blank" href="https://static.igem.org/mediawiki/2014/d/d5/TU_Eindhoven_Protocol_oil_and_continuous_phase.pdf">Oil and Water Phase (Polyacrylamide Beads)</a></td>
-</tr>
+    </tr>
 <tr>
-    <td><a target="_blank" href="https://static.igem.org/mediawiki/2014/d/d2/TU_Eindhoven_Droplet_Separation_-_finished.pdf"></a>Droplet Separation</a></td>
+   <td><a target="_blank" href="https://static.igem.org/mediawiki/2014/0/09/TU_Eindhoven_Protocol_droplet_separation.pdf">Droplet Separation</a></td>
-        <td><a target="_blank" href="https://static.igem.org/mediawiki/2014/1/1c/TU_eindhoven_Soft_Lithography_-_finished.pdf"></a>Soft Lithography</a></td>
+    <td><a href="https://static.igem.org/mediawiki/2014/9/9f/TU_Eindhoven_Protocol_Photolithography.pdf" target="_blank">Photolithography</a></td>
    </tr>
 <tr>
-<td><a target="_blank" href="https://static.igem.org/mediawiki/2014/6/68/TU_Eindhoven_Oil_and_Water_Phase_-_finished.pdf"></a>Oil and Water Phase</a></td>
+    <td><a href="https://static.igem.org/mediawiki/2014/1/1e/TU_Eindhoven_Protocol_oil_and_water_phase_bead_and_bacterial_cell_encapsulation.pdf" target="_blank">Oil and Water Phase (Encapsulation)</a></td>
+        <td><a target="_blank" href="https://static.igem.org/mediawiki/2014/8/89/TU_Eindhoven_Protocol_Soft_Lithography.pdf">Soft Lithography</a></td>
    </tr>
 </table>