Latest revision as of 03:54, 27 October 2012

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Protocols

Here is a list of all the procedures we used this summer. Each contains a description and list of materials required.

General Protocols

Agarose Gel Electrophresis
Bacterial Genomic DNA Purification
Bacterial Transformation
Construction Techniques
GC-MS Analysis
Gel Extraction
Gibson Assembly
LB Agar Plates
M9 Minimal Media Preparation
Organic Extraction
Overnight Cultures
PCR Purification
PicoGreen Assay
Plasmid Purification (from E. coli)
Preparing Chemically Competent Cells (E. coli)
Preparing Glycerol Stocks (E. coli)
Rehydration of Registry DNA
Reviving Freeze-dried Bacterial Cultures from DSMZ
Site-Directed Mutagenesis
Splice Overlap Extension PCR (SOE PCR)

Electrochemistry Protocols

Cyclic Voltammetry
Potentiostatic Standard Curve Generation
Reporter Expression Detection

Desulfurization Protocols

Decarboxylation Protocols

PetroBrick Validation Assay
oleT Validation Assay

Denitrogenation Protocols

AmdA Characterization Assay
Carbazole Degradation Assay

Decatecholization Protocols

Decatecholization Assay

Transposon Mutant Library for Toxin Detection

Transposon-Mediated Mutant Library Generation

Kill Switch Protocols

Characterization of mgtA regulation with GFP
Characterization of mgtA regulation with S7 killgene
Characterization of P_rha with GFP
Kill Assay for rhamnose system
Glycine Auxotrophic Assays (Glycine Media Test, and Petrobrick Test)
Nuclease assay

Bioreactor Assays Protocols

Bacterial Growth Experiments

Belt Selection Tests:

Modeling Protocols

Modelling validation experiments

@@ Line 8: / Line 8: @@
 <h2>General Protocols</h2>
 <li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/agarosegel">Agarose Gel Electrophresis</a></li>
-<li><a href="">Bacterial Genomic DNA Purification</a></li>
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/gemomicprep">Bacterial Genomic DNA Purification</a></li>
 <li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/transformation">Bacterial Transformation</a></li>
 <li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/construction">Construction Techniques</a></li>
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/Carbazole GC-MS Analysis">GC-MS Analysis</a></li>
 <li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/gelextraction">Gel Extraction</a></li>
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/Gibson Assembly">Gibson Assembly</a></li>
 <li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/lbagar">LB Agar Plates</a></li>
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/m9media">M9 Minimal Media Preparation</a></li>
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/oextraction">Organic Extraction</a></li>
 <li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/onculture">Overnight Cultures</a></li>
 <li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/pcrpurification">PCR Purification</a></li>
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/picogreen">PicoGreen Assay</a></li>
 <li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/plasmidminiprep">Plasmid Purification (from <i>E. coli</i>)</a></li>
 <li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/compcells">Preparing Chemically Competent Cells (<i>E. coli</i>)</a></li>
 <li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/glycerolstock">Preparing Glycerol Stocks (<i>E. coli</i>)
 <li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/dnarehydration">Rehydration of Registry DNA</a></li>
-<li><a href="">Site-Directed Mutagenesis</a></li>
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/dmszfreezedry">Reviving Freeze-dried Bacterial Cultures from DSMZ</a></li>
-<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/taqpcr">Taq PCR Protocol</a></li>
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/mutagenesis">Site-Directed Mutagenesis</a></li>
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/soe">Splice Overlap Extension PCR (SOE PCR)</a></li>
 <h2>Electrochemistry Protocols</h2>
-<li><a href="l">Electorchemistry protocols (include agarose bead making) </a></li>
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/cvs">Cyclic Voltammetry</a></li>
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/potstd">Potentiostatic Standard Curve Generation</a></li>
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/potentiostatic">Reporter Expression Detection</a></li>
-<h2>Desulfurization</h2>
+<h2>Desulfurization Protocols</h2>
-<li><a href="">Desulphuirzation assay protocol</a></li>
 <li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/catalase">Catalase assay</a></li>
-<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/hpac">HPAC assay</a></li>
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/desulfur">Desulfurization Assay</a></li>
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/hpac">HpaC assay</a></li>
+<h2>Decarboxylation Protocols</h2>
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/PetroBrick Validation Assay">PetroBrick Validation Assay </a></li>
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/oleT in  Validation Assay">oleT Validation Assay </a></li>
+<h2>Denitrogenation Protocols</h2>
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/AmidaseAssay"><i>AmdA</i> Characterization Assay</a></li>
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/carbazole">Carbazole Degradation Assay</a></li>
+<h2>Decatecholization Protocols</h2>
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/decatecholization">Decatecholization Assay</a></li>
+<h2>Transposon Mutant Library for Toxin Detection</h2>
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/tnscreen">Transposon-Mediated Mutant Library Generation</a></li>
+<h2>Kill Switch Protocols</h2>
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/mgcircuit">Characterization of mgtA regulation with GFP </a></li>
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/mgtacircuit">Characterization of mgtA regulation with S7 killgene </a></li>
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/Prha Characterization">Characterization of <i>P<sub>rha</sub></i> with GFP</a></li>
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/escapersassay">Kill Assay for rhamnose system</a></li>
+</a></li>
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/GlycineAssays">Glycine Auxotrophic Assays (Glycine Media Test, and Petrobrick Test)
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/nucleaseassay">Nuclease assay</a></li>
+</a></li>
+<h2>Bioreactor Assays Protocols</h2>
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/bacgrowth">Bacterial Growth Experiments</a></li>
+<p>Belt Selection Tests:</p>
+<ul>
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/bactest">Bacteria Test</a></li>
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/hcseptest">Hydrocarbon Separation Test</a></li><li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/hctest">Hydrocarbon Test</a></li>
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/hdbeltskim">NA and Hexadecane Belt Skim Test</a></li>
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/tailingtest">Tailings Test</a></li>
+</ul>
-<h2>Decarboxylation</h2>
-<li><a href="">Petrobrick/oleT assay protocols/ GC MS</a></li>
-<h2>Denitrogenation</h2>
-<h2>Decatecholization</h2>
-<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/decatecholization">Decatecholization (xylE and incubation with the Petrobrick)</a></li>
-<h2>Transposon</h2>
-<h2>Kill Switch</h2>
-<li><a href="">Rhamnose, magnesium and manganese, kill gene assay (nuclease)</a></li>
-<h2>Bioreactor</h2>
-<li><a href="">Bioreactor assays</a></li>
-<h2>Modeling</h2>
+<h2>Modeling Protocols</h2>
-<li><a href="">Modelling validation experiments</a></li>
+<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/Modelvalidation">Modelling validation experiments</a></li>