Team:TU Darmstadt/Protocols

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<li><a href="/Team:TU_Darmstadt/Project" title="Project">Project</a><ul>
<li><a href="/Team:TU_Darmstadt/Project" title="Project">Project</a><ul>
        <li><a href="/Team:TU_Darmstadt/Project" title="Team:Overview">Overview</a></li>
        <li><a href="/Team:TU_Darmstadt/Project" title="Team:Overview">Overview</a></li>
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        <li><a href="/Team:TU_Darmstadt/Degradation" title="Degradation">1. Degradation</a></li>
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        <li><a href="/Team:TU_Darmstadt/Project/Degradation" title="Degradation">1. Degradation</a></li>
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        <li><a href="/Team:TU_Darmstadt/Transport" title="Transport">2. Transport</a></li>
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        <li><a href="/Team:TU_Darmstadt/Project/Transport" title="Transport">2. Transport</a></li>
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        <li><a href="/Team:TU_Darmstadt/Metabolism" title="Metabolism">3. Metabolism</a></li>
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        <li><a href="/Team:TU_Darmstadt/Project/Metabolism" title="Metabolism">3. Metabolism</a></li>
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        <li><a href="/Team:TU_Darmstadt/Material_Science" title="Material Science">4. Material Science</a></li>
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        <li><a href="/Team:TU_Darmstadt/Simulation" title="Simulation">5. Simulation</a></li>
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        <li><a href="/Team:TU_Darmstadt/Project/Simulation" title="Simulation">5. Simulation</a></li>
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        <li><a href="/Team:TU_Darmstadt/Ecology" title="Ecology">Ecology</a></li>
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        <li><a href="/Team:TU_Darmstadt/Project/Ecology" title="Ecology">Ecology</a></li>
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        <li><a href="/Team:TU_Darmstadt/Philosophy" title="Philosophy">Philosophy</a></li></ul></li>
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        <li><a href="/Team:TU_Darmstadt/Project/Philosophy" title="Philosophy">Philosophy</a></li></ul></li>
<li><a href="/Team:TU_Darmstadt/Team" title="Team:TU_Darmstadt/Team">Team</a><ul>
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        <li><a href="/Team:TU_Darmstadt/Team" title="Team:TU_Darmstadt/Team">Members</a></li>
        <li><a href="/Team:TU_Darmstadt/Team" title="Team:TU_Darmstadt/Team">Members</a></li>
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    <li><a href="/Team:TU_Darmstadt/Labjournal" title="Labjournal">Labjournal</a></li>
    <li><a href="/Team:TU_Darmstadt/Labjournal" title="Labjournal">Labjournal</a></li>
    <li><a href="/Team:TU_Darmstadt/Protocols" title="Protocols">Protocols</a></li>
    <li><a href="/Team:TU_Darmstadt/Protocols" title="Protocols">Protocols</a></li>
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<li><a href="/Team:TU_Darmstadt/Materials" title="Materials">Materials</a></li>
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<li><a href="/Team:TU_Darmstadt/Modeling" title="Modeling">Modeling</a></li>
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    <li><a href="/Team:TU_Darmstadt/Downloads" title="Downloads">Downloads</a></li></ul></li>
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<li><a href="/Team:TU_Darmstadt/Human_Practice" title="Human Practice">Human Practice</a><ul>
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    <li><a href="/Team:TU_Darmstadt/Panel_Discussion " title="Panel Discussion">Panel Discussion</a></li>
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<li><a href="/Team:TU_Darmstadt/Sponsors" title="Sponsors">Sponsors</a><ul>
<li><a href="/Team:TU_Darmstadt/Sponsors" title="Sponsors">Sponsors</a><ul>
    <li><a href="/Team:TU_Darmstadt/Sponsors" title="Sponsors">Overview</a></li>
    <li><a href="/Team:TU_Darmstadt/Sponsors" title="Sponsors">Overview</a></li>
    <li><a href="/Team:TU_Darmstadt/Contact" title="Contact">Benefits</a></li></ul></li> 
    <li><a href="/Team:TU_Darmstadt/Contact" title="Contact">Benefits</a></li></ul></li> 
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= Protocols =
 
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The following page(s) gives an overview of the protocols and possible modifications that where used and proven working during the iGEM PET.erminators project 2012.
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<span style="font-size:200%;"><span style="color:#00689D;">Protocols</span></span>
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The following page(s) gives an overview of the protocols and possible modifications that where used and proven working during the [https://2012.igem.org iGEM] PET.erminators [https://2012.igem.org/Team:TU_Darmstadt/Project project 2012]. The corresponding [https://2012.igem.org/Team:TU_Darmstadt/Materials materials] can be found in the [https://2012.igem.org/Team:TU_Darmstadt/Materials materials section].
== In vivo ==
== In vivo ==
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=== [[Escherichia coli]] ===
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=== [http://en.wikipedia.org/wiki/E._coli Escherichia coli] ===
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* [[Bacterial cell culture]]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Bacterial_cell_culture Bacterial cell culture]
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* [[Bacterial transformation]] aka TRAFO
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Bacterial_transformation Bacterial transformation] aka TRAFO
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* [[Cell counting/plating]]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Cell_counting/plating Cell counting/plating]
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* [[Chemically competent cells]]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Chemically_competent_cells Chemically competent cells]
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* [[Colony PCR]]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Colony_PCR Colony PCR]
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* [[Electrocompetent cells]]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electrocompetent_cells Electrocompetent cells]
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* [[Electroporation]]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Electroporation]
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* [[Engineering BioBrick vectors from BioBrick parts/Colony PCR]]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Glycerine_stock Glycerine Stocks]
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* [[In-fusion BioBrick assembly]]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Heat_Shock_Transformation Heat Shock Transformation]
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* [[Miniprep / Qiagen kit]]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep#Fermentas_kit Miniprep / Fermentas kit]
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* [[Transformation of chemically competent cells]]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep#Promega_kit Miniprep / Promega kit]
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* [[Western Blot]]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep#Qiagen_kit Miniprep / Qiagen kit]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Protein_Expression#Protein_Expression_Est13 Protein Expression Est13]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Protein_Expression#Protein_Expression_FsC Protein Expression FsC]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Western_Blot Western blot]
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=== [[Comamonas testosteroni]] ===
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=== [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Comamonas_testosteroni Comamonas testosteroni] ===
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* [[Reviving a freez dried cell culture]]
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* [http://www.dsmz.de/fileadmin/Bereiche/Microbiology/Dateien/Kultivierungshinweise/engl_Opening.pdf Reviving a freez dried cell culture]
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*
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== In vitro ==
== In vitro ==
===Nucleic acids ===
===Nucleic acids ===
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* [[Agarose gel electrophoresis]]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
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* [[PCR techniques]]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR_techniques PCR techniques]
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* [[SOE-PCR]]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR#SOE_PCR SOE-PCR]
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=== [[DNA]] ===
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* [[Agarose gel electrohporesis]]
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* [[Annealing and primer extension]]
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* [[Annealing primers]]
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* [[Assembly PCR]]
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* [[Cloning]]
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* [[DNA Ligation]]
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* [[DNA Quantification / NanoDrop]]
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* [[DNA Synthesis from Oligos]]
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* [[Engineering BioBrick vectors from BioBrick parts/Colony PCR]]
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* [[Miniprep]]
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* [[PCR]]
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* [[Polyacrylamide gel electrophoresis]]
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* [[Primer Design]]
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* [[Purification of DNA]]
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* [[Restriction digest]]
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* [[Resuspension of primers]]
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* [[Salting Out]]
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* [[Sequencing DNA]]
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=== [[RNA]] ===
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=== [[Protein]] ===
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== In silico ==
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=== Data analysis ===
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* [[R Programming]]
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* [[Mathlab / Simulink]]
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=== Databases ===
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* [[PDB]]
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* [[CAS]]
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=== Modelling ===
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=== [http://en.wikipedia.org/wiki/DNA DNA] ===
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* [[SVEN!!!]]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Ammonium_sulfate_precipitation Ammonium acetate precipitation]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Cloning Cloning]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Dephosphorylation Dephosphorylation]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/DNA_Ligation DNA Ligation]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/ DNA Ligation à la group transport]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/DNA_Quantification_/_NanoDrop DNA Quantification / NanoDrop]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/mutagenic_PCR Mutagenic PCR]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Purification_of_DNA  Purification of DNA]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Salting_Out Salting Out]
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* [http://www.eurofinsdna.com/de/home.html?wmc=GA_DE-Corporate&gclid=CODAs8CZ1LICFQVf3god9AIAag Sequencing DNA]
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=== Sequence analysis ===
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=== [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Protein Protein] ===
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* [[BLAST]]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Activity_assay Activity assay]
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* [[SAGE]]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Affinity_chromatography Affinity chromatography]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/IMAC Immobilized metal ion affinity chromatography (IMAC)]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/pNP_Assay#Bacteria pNP-Assay Bacteria]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/pNP_Assay#Enzyme pNP-Assay Enzyme]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Proteinpurification Proteinpurification]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Purification_of_Periplasmatic_Proteins Purification of Periplasmatic Proteins]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/SDS-Page SDS-Page]
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=== Structure analysis ===
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== Material Science ==
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* [[PDB]]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Synthesis_of_paranitrophenylesters_with_acyl_chlorides_in_presence_of_triethylamine Synthesis of paranitrophenylesters with acyl chlorides in presence of triethylamine]
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* [[Protein structure prediction]]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Synthesis_of_polyethylene_terephthalate_in_presence_of_sulfuric_acid Synthesis of polyethylene terephthalate in presence of sulfuric acid]
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* [[RNA secondary structure prediction]]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Surface_analysis_of_polyethylene_terephthalate_with_atomic_force_microscopy Surface analysis of polyethylene terephthalate with atomic force microscopy]
== Miscellaneous ==
== Miscellaneous ==
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=== Cell culture ===
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=== Staining ===
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* [[Pouring LB plates]]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Antibody_staining Antibody staining]
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=== Microscopy ===
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=== Analytics ===
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* [[Determining an objects size]]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/TEM-EDX TEM-EDX Measurements]
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* [[Preparing slides]]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/GC-MS GC-MS Measurements]
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* [[Staining]]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/SamplePreparationEDX Preparation of Escherichia Coli for the energy dispersive X-ray spectroscopy (EDX)]
=== ILDs / Improvised Lab Devices ===
=== ILDs / Improvised Lab Devices ===
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* [[x bp Primer Designer]]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/x_bp_Primer_Designer x bp Primer Designer]
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* [[Enhancing a thermo cyclers cooling capabilites]]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Enhancing_a_thermo_cyclers_cooling_capabilites Enhancing a thermo cyclers cooling capabilites]
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* [[Gel pocket size reduction]]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Gel_pocket_size_reduction Gel pocket size reduction]
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* [[Growing iGEMlers]]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Growing_iGEMlers Growing iGEMlers]

Latest revision as of 21:45, 26 September 2012

Protocols

The following page(s) gives an overview of the protocols and possible modifications that where used and proven working during the iGEM PET.erminators project 2012. The corresponding materials can be found in the materials section.

Contents

In vivo

[http://en.wikipedia.org/wiki/E._coli Escherichia coli]

Comamonas testosteroni

  • [http://www.dsmz.de/fileadmin/Bereiche/Microbiology/Dateien/Kultivierungshinweise/engl_Opening.pdf Reviving a freez dried cell culture]

In vitro

Nucleic acids

[http://en.wikipedia.org/wiki/DNA DNA]

Protein

Material Science

Miscellaneous

Staining

Analytics

ILDs / Improvised Lab Devices

Retrieved from "http://2012.igem.org/Team:TU_Darmstadt/Protocols"