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

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

@@ Line 23: / Line 23: @@
 							<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/2017/1/15/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/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/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/2017/6/6f/T--Bielefeld-CeBiTec--RotiNanoquant.pdf">Bradford estimation using RotiNanoquant</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/2017/4/42/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/2017/2/25/T--Bielefeld-CeBiTec--CMZ-FastcellSDS.pdf" target="blank">Fast cell lysis sample buffer</a></li>
 								<li><a href="https://static.igem.org/mediawiki/2017/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>
@@ Line 37: / Line 37: @@
 								<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/2017/3/3f/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/2017/8/8c/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/a4/T--Bielefeld-CeBiTec--CMZ-Maldi.pdf" target="blank">Malditof sample preparation</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>
@@ Line 48: / Line 55: @@
 							<ul style="list-style-type: none">
 								<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/2017/2/2b/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/2017/8/88/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/2017/1/16/T--Bielefeld-CeBiTec--CMZ-PCRQ5.pdf" target="blank">PCR with Q5 High-Fidelity Polymerase</a></li>
-								<li><a href="https://static.igem.org/mediawiki/2017/3/33/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/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/2017/0/0e/T--Bielefeld-CeBiTec--ImpactProtocol.pdf">Protein Purification Impact Protocol</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/2017/0/0d/T--Bielefeld-CeBiTec--protocol_SDS-PAGE.pdf" target="blank">SDS-PAGE</a></li>
-								<li><a href="https://static.igem.org/mediawiki/2017/1/15/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/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/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/2017/1/15/T--Bielefeld-CeBiTec--protocol_CBT-asparagine.pdf" target="blank">Synthesis of CBT-asparagine</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/2017/1/15/T--Bielefeld-CeBiTec--protocol_TLC.pdf" target="blank">TLC analysis</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/2017/2/2e/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/2017/8/88/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>
 							</ul>
@@ Line 168: / Line 180: @@
 						</thead>
 						<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>
 								<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>
 							</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>
@@ Line 179: / Line 208: @@
 								<td>Thermo Fisher Scientific</td>
 							</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.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.neb.com/products/m0491-q5-high-fidelity-dna-polymerase">Q5 High-Fidelity DNA polymerase </a></td>
@@ Line 194: / Line 224: @@
 </tr>
-<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="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>
-		<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>
-		<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>