Difference between revisions of "Team:Bielefeld-CeBiTec/Notebook/Methods"

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</div>
 
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<div class="contentbox">
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<div class="contentbox">
 
<div class="content">
 
<div class="content">
 
<h3> Protocols </h3>
 
<h3> Protocols </h3>
 +
<div class="article">
 +
This page lists all regular methods used during our project. Special methods, which are not listed here, are described or linked on the corresponding result pages.
 +
</div>
 
<div class="contentline">
 
<div class="contentline">
 
<div class="half left">
 
<div class="half left">
 
<ul style="list-style-type: none">
 
<ul style="list-style-type: none">
 
<li><a href="https://static.igem.org/mediawiki/2017/8/85/T--Bielefeld-CeBiTec--protocol_50xTAE.pdf" target="blank">50xTAE Stock Solution</a></li>
 
<li><a href="https://static.igem.org/mediawiki/2017/8/85/T--Bielefeld-CeBiTec--protocol_50xTAE.pdf" target="blank">50xTAE Stock Solution</a></li>
−
<li><a href="https://static.igem.org/mediawiki/2017/1/15/T--Bielefeld-CeBiTec--protocol_acetone.pdf" target="blank">Acetone Precipitation</a></li>
+
<li><a href="https://static.igem.org/mediawiki/2017/6/61/T--Bielefeld-CeBiTec--CMZ-Acetone.pdf" target="blank">Acetone Precipitation</a></li>
−
<li><a href="https://static.igem.org/mediawiki/2017/f/fe/T--Bielefeld-CeBiTec--protocol_biotynilation.pdf" target="blank">Biotynilation of glass slides</a></li>
+
<li><a href="https://static.igem.org/mediawiki/2017/a/ae/T--Bielefeld-CeBiTec--CMZ-Biotin.pdf" target="blank">Biotinylation of glass slides</a></li>
 
<li><a href="https://static.igem.org/mediawiki/2017/3/3a/T--Bielefeld-CeBiTec--protocol_blunt-end-ligation.pdf" target="blank">Blunt end ligation</a></li>
 
<li><a href="https://static.igem.org/mediawiki/2017/3/3a/T--Bielefeld-CeBiTec--protocol_blunt-end-ligation.pdf" target="blank">Blunt end ligation</a></li>
 +
<li><a href="https://static.igem.org/mediawiki/2017/6/6f/T--Bielefeld-CeBiTec--RotiNanoquant.pdf">Roti_Nanoquant (for protein concentration estimation)</a></li>
 +
<li><a href="https://static.igem.org/mediawiki/2017/9/97/T--Bielefeld-CeBiTec--protocol_cloning_strategy_re.pdf" target="blank">Cloning Strategy with Restriction Enzymes</a></li>
 
<li><a href="https://static.igem.org/mediawiki/2017/c/cc/T--Bielefeld-CeBiTec--protocol_colonyPCR_GoTaq_G2.pdf" target="blank">Colony PCR GoTaq® G2 DNA Polymerase</a></li>
 
<li><a href="https://static.igem.org/mediawiki/2017/c/cc/T--Bielefeld-CeBiTec--protocol_colonyPCR_GoTaq_G2.pdf" target="blank">Colony PCR GoTaq® G2 DNA Polymerase</a></li>
−
<li><a href="https://static.igem.org/mediawiki/2017/a/ab/T--Bielefeld-CeBiTec--protocol_electrotrafo.pdf" target="blank">Transformation via electroporation</a></li>
+
<li><a href="https://static.igem.org/mediawiki/2017/2/25/T--Bielefeld-CeBiTec--CMZ-FastcellSDS.pdf" target="blank">Fast cell lysis sample buffer</a></li>
−
<li><a href="https://static.igem.org/mediawiki/2017/4/42/T--Bielefeld-CeBiTec--protocol_fast_cell_lysis_buffer.pdf" target="blank">Fast cell lysis sample buffer</a></li>
+
 
<li><a href="https://static.igem.org/mediawiki/2017/e/e0/T--Bielefeld-CeBiTec--protocol_fast_cell_lysis_SDS-Page.pdf" target="blank">Fast cell lysis for SDS-PAGE</a></li>
 
<li><a href="https://static.igem.org/mediawiki/2017/e/e0/T--Bielefeld-CeBiTec--protocol_fast_cell_lysis_SDS-Page.pdf" target="blank">Fast cell lysis for SDS-PAGE</a></li>
 
<li><a href="https://static.igem.org/mediawiki/2017/3/39/T--Bielefeld-CeBiTec--protocol_GeneJET_DNA_Purification_Thermo.pdf.pdf" target="blank">GeneJET Genomic DNA Purification Kit (Thermo Fisher Scientific)</a></li>
 
<li><a href="https://static.igem.org/mediawiki/2017/3/39/T--Bielefeld-CeBiTec--protocol_GeneJET_DNA_Purification_Thermo.pdf.pdf" target="blank">GeneJET Genomic DNA Purification Kit (Thermo Fisher Scientific)</a></li>
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<li><a href="https://static.igem.org/mediawiki/2017/4/42/T--Bielefeld-CeBiTec--protocol_generating_chemocompetent_cells.pdf" target="blank">Generating chemocompetent cells</a></li>
 
<li><a href="https://static.igem.org/mediawiki/2017/4/42/T--Bielefeld-CeBiTec--protocol_generating_chemocompetent_cells.pdf" target="blank">Generating chemocompetent cells</a></li>
 
<li><a href="https://static.igem.org/mediawiki/2017/6/6c/T--Bielefeld-CeBiTec--protocol_generating_electrocompetent_cells.pdf" target="blank">Generating electrocompetent cells</a></li>
 
<li><a href="https://static.igem.org/mediawiki/2017/6/6c/T--Bielefeld-CeBiTec--protocol_generating_electrocompetent_cells.pdf" target="blank">Generating electrocompetent cells</a></li>
 +
<li><a href="https://static.igem.org/mediawiki/2017/3/37/T--Bielefeld-CeBiTec--protocol_genome_editing_codA.pdf">Genome editing via the CRISP-Cas9 system</a></li>
 
<li><a href="https://static.igem.org/mediawiki/2017/5/55/T--Bielefeld-CeBiTec--protocol_gibson_assembly.pdf" target="blank">Gibson Assembly</a></li>
 
<li><a href="https://static.igem.org/mediawiki/2017/5/55/T--Bielefeld-CeBiTec--protocol_gibson_assembly.pdf" target="blank">Gibson Assembly</a></li>
−
<li><a href="https://static.igem.org/mediawiki/2017/a/a0/T--Bielefeld-CeBiTec--protocol_heatshock.pdf" target="blank">Transformation via heat shock</a></li>
+
 
 +
<li><a href="https://static.igem.org/mediawiki/2017/3/3f/T--Bielefeld-CeBiTec--CMZ-Membrane.pdf" target="blank">Isolation of the Inner Membrane Fraction</a></li>
 +
 
 +
 
 
<li><a href="https://static.igem.org/mediawiki/2017/7/75/T--Bielefeld-CeBiTec--protocol_innuPREP_Gel_analytikJena.pdf" target="blank">innuPREP Gel Extraktion Kit (Analytik Jena)</a></li>
 
<li><a href="https://static.igem.org/mediawiki/2017/7/75/T--Bielefeld-CeBiTec--protocol_innuPREP_Gel_analytikJena.pdf" target="blank">innuPREP Gel Extraktion Kit (Analytik Jena)</a></li>
 +
<li><a href="https://static.igem.org/mediawiki/2017/8/8c/T--Bielefeld-CeBiTec--YKE_lycopene_protocol.pdf" target="blank">Lycopene extraction</a></li>
 
<li><a href="https://static.igem.org/mediawiki/2017/a/a7/T--Bielefeld-CeBiTec--protocol_LB.pdf" target="blank">Lysogeny Broth (LB)</a></li>
 
<li><a href="https://static.igem.org/mediawiki/2017/a/a7/T--Bielefeld-CeBiTec--protocol_LB.pdf" target="blank">Lysogeny Broth (LB)</a></li>
−
<li><a href="https://static.igem.org/mediawiki/2017/9/97/T--Bielefeld-CeBiTec--protocol_cloning_strategy_re.pdf" target="blank">Cloning Strategy with Restriction Enzymes</a></li>
+
 
−
<li><a href="https://static.igem.org/mediawiki/2017/e/e8/T--Bielefeld-CeBiTec--protocol_biotinylierung_of_glass_slides.pdf" target="blank">Biotinylation of glass slides</a></li>
+
<li><a href="https://static.igem.org/mediawiki/2017/a/a4/T--Bielefeld-CeBiTec--CMZ-Maldi.pdf" target="blank">Malditof sample preparation</a></li>
−
<li><a href="https://static.igem.org/mediawiki/2017/3/33/T--Bielefeld-CeBiTec--protocol_golden_gate.pdf" target="blank">Plasmid Assembly Protocol with Golden Gate Assembly</a></li>
+
 
 +
<li><a href="https://static.igem.org/mediawiki/2017/8/8a/T--Bielefeld-CeBiTec--protocol_Monarch_Miniprep_kit_NEB.pdf" target="blank">Monarch® Plasmid Miniprep Kit (NEB)</a></li>
 +
<li><a href="https://static.igem.org/mediawiki/2017/0/0e/T--Bielefeld-CeBiTec--protocol_Monarch_PCR_and_DNA_clean_up_kit_NEB.pdf" target="blank">Monarch® PCR & DNA Cleanup Kit (NEB)</a></li>
 +
<li><a href="https://static.igem.org/mediawiki/2017/7/7d/T--Bielefeld-CeBiTec--protocol_MOPS.pdf" target="blank">MOPS Minimal Medium</a></li>
 
</ul>
 
</ul>
 
</div>
 
</div>
 
<div class="half right">
 
<div class="half right">
 
<ul style="list-style-type: none">
 
<ul style="list-style-type: none">
−
<li><a href="https://static.igem.org/mediawiki/2017/8/8a/T--Bielefeld-CeBiTec--protocol_Monarch_Miniprep_kit_NEB.pdf" target="blank">Monarch® Plasmid Miniprep Kit (NEB)</a></li>
 
−
<li><a href="https://static.igem.org/mediawiki/2017/0/0e/T--Bielefeld-CeBiTec--protocol_Monarch_PCR_and_DNA_clean_up_kit_NEB.pdf" target="blank">Monarch® PCR & DNA Cleanup Kit (NEB)</a></li>
 
−
<li><a href="https://static.igem.org/mediawiki/2017/7/7d/T--Bielefeld-CeBiTec--protocol_MOPS.pdf" target="blank">MOPS Minimal Medium</a></li>
 
 
<li><a href="https://static.igem.org/mediawiki/2017/e/e6/T--Bielefeld-CeBiTec--protocol_native_PAGE.pdf" target="blank">Native DNA PAGE</a></li>
 
<li><a href="https://static.igem.org/mediawiki/2017/e/e6/T--Bielefeld-CeBiTec--protocol_native_PAGE.pdf" target="blank">Native DNA PAGE</a></li>
−
<li><a href="https://static.igem.org/mediawiki/2017/6/63/T--Bielefeld-CeBiTec--protocol_PBJR_buffer.pdf" target="blank">PBJR buffer</a></li>
+
<li><a href="https://static.igem.org/mediawiki/2017/6/62/T--Bielefeld-CeBiTec--CMZ-PBJRbuffer.pdf" target="blank">PBJR buffer</a></li>
−
<li><a href="https://static.igem.org/mediawiki/2017/8/88/T--Bielefeld-CeBiTec--protocol_PCR_Q5_HF_Polymerase.pdf" target="blank">PCR with Q5 High-Fidelity Polymerase</a></li>
+
<li><a href="https://static.igem.org/mediawiki/2017/2/2b/T--Bielefeld-CeBiTec--ProtocolPhusion.pdf" target="blank">PCR with Phusion High Fidelity Master Mix with HC enhancer</a></li>
−
<li><a href="https://static.igem.org/mediawiki/2017/2/2b/T--Bielefeld-CeBiTec--ProtocolPhusion.pdf" target="blank">PCR with Phusion High Fidelity Master Mix with HC enhancer</a></li>
+
<li><a href="https://static.igem.org/mediawiki/2017/1/16/T--Bielefeld-CeBiTec--CMZ-PCRQ5.pdf" target="blank">PCR with Q5 High-Fidelity Polymerase</a></li>
−
<li><a href="https://static.igem.org/mediawiki/2017/2/2e/T--Bielefeld-CeBiTec--protocol_PCR_Gel_Cleanup_wizzard.pdf" target="blank">Wizard® SV Gel and PCR Clean-Up System (Promega)</a></li>
+
<li><a href="https://static.igem.org/mediawiki/2017/e/ec/T--Bielefeld-CeBiTec--CMZ-GoldenGate.pdf" target="blank">Plasmid Assembly Protocol with Golden Gate Assembly</a></li>
 +
 
 +
<li><a href="https://static.igem.org/mediawiki/2017/d/d7/T--Bielefeld-CeBiTec--CMZ-Mikroskopie.pdf" target="blank">Protocol for GFP immunofluorescence (whole Bacteria)</a></li>
 +
<li><a href="https://static.igem.org/mediawiki/2017/0/0e/T--Bielefeld-CeBiTec--ImpactProtocol.pdf">Protein Purification Impact-CN Protocol</a></li>
 
<li><a href="https://static.igem.org/mediawiki/2017/9/96/T--Bielefeld-CeBiTec--protocol_PCR_PureYield_PlasmidMiniprep_Promega.pdf" target="blank">PureYield<sup>TM</sup> Plasmid Miniprep System (Promega)</a></li>
 
<li><a href="https://static.igem.org/mediawiki/2017/9/96/T--Bielefeld-CeBiTec--protocol_PCR_PureYield_PlasmidMiniprep_Promega.pdf" target="blank">PureYield<sup>TM</sup> Plasmid Miniprep System (Promega)</a></li>
−
<li><a href="https://static.igem.org/mediawiki/2017/2/23/T--Bielefeld-CeBiTec--protocol_Restriction_Digest.pdf" target="blank">"Typical" Restriction Digest</a></li>
+
<li><a href="https://static.igem.org/mediawiki/2017/0/0d/T--Bielefeld-CeBiTec--protocol_SDS-PAGE.pdf" target="blank">SDS-PAGE</a></li>
 
<li><a href="https://static.igem.org/mediawiki/2017/a/a2/T--Bielefeld-CeBiTec--protocol_SDS-PAGE_running_buffer.pdf" target="blank">SDS-PAGE running buffer</a></li>
 
<li><a href="https://static.igem.org/mediawiki/2017/a/a2/T--Bielefeld-CeBiTec--protocol_SDS-PAGE_running_buffer.pdf" target="blank">SDS-PAGE running buffer</a></li>
 +
<li><a href="https://static.igem.org/mediawiki/2017/1/19/T--Bielefeld-CeBiTec--protocol_SiO2_column.pdf" target="blank">SiO2 Column Chromatography with Gradient</a></li>
 
<li><a href="https://static.igem.org/mediawiki/2017/f/fe/T--Bielefeld-CeBiTec--protocol_SOC.pdf" target="blank">SOC-medium</a></li>
 
<li><a href="https://static.igem.org/mediawiki/2017/f/fe/T--Bielefeld-CeBiTec--protocol_SOC.pdf" target="blank">SOC-medium</a></li>
 
<li><a href="https://static.igem.org/mediawiki/2017/d/d1/T--Bielefeld-CeBiTec--protocol_ssDNA_annealing.pdf" target="blank">ssDNA Annealing</a></li>
 
<li><a href="https://static.igem.org/mediawiki/2017/d/d1/T--Bielefeld-CeBiTec--protocol_ssDNA_annealing.pdf" target="blank">ssDNA Annealing</a></li>
 
<li><a href="https://static.igem.org/mediawiki/2017/8/84/T--Bielefeld-CeBiTec--protocol_Standard_Biobrick.pdf" target="blank">Standard BioBrick Assembly</a></li>
 
<li><a href="https://static.igem.org/mediawiki/2017/8/84/T--Bielefeld-CeBiTec--protocol_Standard_Biobrick.pdf" target="blank">Standard BioBrick Assembly</a></li>
 +
<li><a href="https://static.igem.org/mediawiki/2017/a/a6/T--Bielefeld-CeBiTec--protocol_CBT-asparagine.pdf" target="blank">Synthesis of CBT-asparagine</a></li>
 
<li><a href="https://static.igem.org/mediawiki/2017/d/d4/T--Bielefeld-CeBiTec--protocol_TAE_buffer.pdf" target="blank">TAE buffer</a></li>
 
<li><a href="https://static.igem.org/mediawiki/2017/d/d4/T--Bielefeld-CeBiTec--protocol_TAE_buffer.pdf" target="blank">TAE buffer</a></li>
 +
<li><a href="https://static.igem.org/mediawiki/2017/a/a2/T--Bielefeld-CeBiTec--protocol_TLC.pdf" target="blank">TLC analysis</a></li>
 +
<li><a href="https://static.igem.org/mediawiki/2017/a/ab/T--Bielefeld-CeBiTec--protocol_electrotrafo.pdf" target="blank">Transformation via electroporation</a></li>
 +
<li><a href="https://static.igem.org/mediawiki/2017/a/a0/T--Bielefeld-CeBiTec--protocol_heatshock.pdf" target="blank">Transformation via heat shock</a></li>
 +
<li><a href="https://static.igem.org/mediawiki/2017/2/23/T--Bielefeld-CeBiTec--protocol_Restriction_Digest.pdf" target="blank">"Typical" Restriction Digest</a></li>
 +
 +
<li><a href="https://static.igem.org/mediawiki/2017/8/88/T--Bielefeld-CeBiTec--CMZ-Westernblot.pdf" target="blank">Western Blot</a></li>
 +
 +
<li><a href="https://static.igem.org/mediawiki/2017/2/2e/T--Bielefeld-CeBiTec--protocol_PCR_Gel_Cleanup_wizzard.pdf" target="blank">Wizard® SV Gel and PCR Clean-Up System (Promega)</a></li>
 
<li><a href="https://static.igem.org/mediawiki/2017/1/13/T--Bielefeld-CeBiTec--protocol_ZymoPURETM_PlasmidMiniprep_Kit.pdf" target="blank">ZymoPURE<sup>TM</sup> Plasmid Miniprep Kit (Zymo Research)</a></li>
 
<li><a href="https://static.igem.org/mediawiki/2017/1/13/T--Bielefeld-CeBiTec--protocol_ZymoPURETM_PlasmidMiniprep_Kit.pdf" target="blank">ZymoPURE<sup>TM</sup> Plasmid Miniprep Kit (Zymo Research)</a></li>
−
<li><a href="https://static.igem.org/mediawiki/2017/0/0d/T--Bielefeld-CeBiTec--protocol_SDS-PAGE.pdf" target="blank">SDS-PAGE</a></li>
 
−
<li><a href="https://static.igem.org/mediawiki/2017/3/37/T--Bielefeld-CeBiTec--protocol_genome_editing_codA.pdf">Genome editing via the CRISP-Cas9 system</a></li>
 
 
</ul>
 
</ul>
 
</div>
 
</div>
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<tr>
 
<tr>
 
<td><a href="https://www.thermofisher.com/order/catalog/product/ER0301"><i>Eco</i>RV</a></td>
 
<td><a href="https://www.thermofisher.com/order/catalog/product/ER0301"><i>Eco</i>RV</a></td>
−
<td>Fermentas</td>
+
<td>Thermo Fisher Scientific</td>
 
</tr>
 
</tr>
 
 
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</thead>
 
</thead>
 
<tbody>
 
<tbody>
−
+
<tr>
−
+
<td><a target="_blank"href="https://www.highqu.com/allintmhifi-dna-polymerase-2-u-l.html">Allin HiFi DNA polymerase</a></td>
 +
<td>highQu</td>
 +
</tr>
 +
 
 +
<tr>
 +
<td><a target="_blank"href=" http://biolabmix.ru/en/products/klassicheskaja_pcr/biomaster_hs-taq_pcr-color__2_/"> BioMaster-HS Taq </a></td>
 +
<td>Biolabmix</td>
 +
</tr>
 +
 +
<tr>
 +
<td><a target="_blank"href=" https://www.sbd.ee/EN/products/pcr/firepol "> FirePol DNA polymerase </a></td>
 +
<td>Solis Biodyne</td>
 +
</tr>
 
<tr>
 
<tr>
 
<td><a href="https://www.promega.de/products/pcr/endpoint-pcr/gotaq-dna-polymerase/?catNum=M3001">Go Taq DNA polymerase</a></td>
 
<td><a href="https://www.promega.de/products/pcr/endpoint-pcr/gotaq-dna-polymerase/?catNum=M3001">Go Taq DNA polymerase</a></td>
 
<td>Promega</td>
 
<td>Promega</td>
 
</tr>
 
</tr>
 +
<tr>
 +
<td><a target="_blank"href="https://www.analytik-jena.de/fileadmin/content/import/imported_dam/br_Product_Guide_Reagents_Plastic_WEB_geschuetzt.pdf">innuDRY DNA polymerase </a></td>
 +
<td>Analytik Jena</td>
 +
</tr>
 +
 
 
 
<tr>
 
<tr>
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<td>Thermo Fisher Scientific</td>
 
<td>Thermo Fisher Scientific</td>
 
</tr>
 
</tr>
 +
<tr>
 +
<td><a href="https://www.neb.com/products/m0530-phusion-high-fidelity-dna-polymerase#Product%20Information">Phusion High-Fidelity DNA polymerase </a></td>
 +
<td>NEB</td>
 +
</tr>
 +
 
 
−
<tr>
+
−
<td><a href="https://www.promega.de/products/pcr/endpoint-pcr/gotaq-dna-polymerase/?catNum=M3001">Phusion High-Fidelity DNA polymerase </a></td>
+
−
<td>NEB</td>
+
−
</tr>
+
−
+
 
<tr>
 
<tr>
 
<td><a href="https://www.neb.com/products/m0491-q5-high-fidelity-dna-polymerase">Q5 High-Fidelity DNA polymerase </a></td>
 
<td><a href="https://www.neb.com/products/m0491-q5-high-fidelity-dna-polymerase">Q5 High-Fidelity DNA polymerase </a></td>
 
<td>NEB</td>
 
<td>NEB</td>
 
</tr>
 
</tr>
 +
<tr>
 +
<td><a target="_blank"href="http://www.clontech.com/DE/Products/PCR/High_Yield_PCR/Titanium_Taq_DNA_Polymerase?sitex=10024:22372:US">Titanium Taq</a></td></td>
 +
<td>Clonetech</td>
 +
</tr>
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
<tr>
 +
 +
 
 
−
<tr>
 
−
<td><a href="https://www.jenabioscience.com/molecular-biology/standard-pcr/ready-to-use-mixes/pcr-108-red-load-taq-master">Taq Polymerase </a></td>
 
−
<td>Jena Bioscience</td>
 
−
</tr>
 
 
</tbody>
 
</tbody>
 
</table>
 
</table>

Latest revision as of 03:29, 2 November 2017

Methods

Protocols

This page lists all regular methods used during our project. Special methods, which are not listed here, are described or linked on the corresponding result pages.

Enzymes

Digestion enzymes

Enzyme Producer
AgeI-HF NEB
BsaI NEB
DpnI NEB
DpnI Jena Bioscience
EciI NEB
EcoRV Thermo Fisher Scientific
MnlI NEB
NotI Jena Bioscience
PstI NEB
PstI Thermo Fisher Scientific
PstI-HF NEB
SapI NEB
SpeI NEB
XbaI NEB
XbaI Jena Bioscience

Polymerases

Enzyme Producer
Allin HiFi DNA polymerase highQu
BioMaster-HS Taq Biolabmix
FirePol DNA polymerase Solis Biodyne
Go Taq DNA polymerase Promega
innuDRY DNA polymerase Analytik Jena
Klenow Fragment Thermo Fisher Scientific
Phusion High-Fidelity DNA polymerase NEB
Q5 High-Fidelity DNA polymerase NEB
Titanium Taq Clonetech

Other Enzymes

Enzyme Producer
Shrimp Alkaline Phosphatase Jena Bioscience
T4 DNA Ligase NEB
T4 DNA Ligase Thermo Fisher Scientific
T4 Polynucleotide Kinase NEB