Team:Michigan/Protocols

For additional information/questions, refer to [http://www.neb.com/nebecomm/tech_reference/modifying_enzymes/ligation_tips.asp NEB Ligation Tips]
Ligation
- Ginko Bioworks Protocol
- Jeremy Minty Protocol

Group-Specific Protocols

Oil Sands

Revised biofilm assay protocol

Biofilm assay protocol

Alex's biofilm assay protocol

General primer design

Detailed primer design

Colony PCR protocol

NanR cloning

Updated Colony PCR Protocol

NA Extraction Protocol

Pili

FimB Ligation

FimB PCR

Flocculation Protocol

Quorum Sensing

Logic Table

Lsr Circuit Test Protocols

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 {{Michigan Header}}
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-==General Outline for Biobrick Manipulations==
-[[Image:Igem_order_of_procedures.jpg|900px]]
 ==Protocols==
 '''Using Lab Equipment'''
+[[Media:Protocol_for_Obtaining_Deionized_Water_in_the_ERB.pdf|Obtaining Deionized Water in the ERB]]
+[[Media:ERB_Spectrophotometer_Usage_Protocol.pdf|ERB Spectrophotometer]]
 [[Media:7-6-2010_ERB_Autoclave_Liquid_Sterilization_Protocol.pdf|Enigeering Research Building Autoclave]]
+[[Media:Epifluorescence_Microscope_Usage_-_Dow.pdf|Epifluorescence Microscope Usage - H.H. Dow]]
 '''Cell Culture'''
-[[Media:6-28-2010_Protocol_for_making_cultures_from_a_-80C_freezer_stock.pdf|Making cultures from a -80C freezer stock]]
+[[Media:6-28-2010_Protocol_for_making_cultures_from_a_-80C_freezer_stock.pdf|Making cultures from a -80°C freezer stock]]
 [[Media:6-29-2010_Making_Frozen_Stoks.pdf|Making frozen stocks]]
 [[Media:6-27-2010_P._putida_antibiotic_resistance_protocol.pdf|''P. putida'' KT2440 antibotic resistance tolerance]]
+[[Media:Protocol_for_Culturing_Strains_from_CGSC.pdf‎|Culturing CGSC Strains]]
+[[Media:OD600 Cell Dilution Protocol.pdf‎|OD600 Cell Dilution Protocol]]
+[[Media:Quick Transformation of E. coli Competant Cell Preperation.pdf| Competent Cell Preparation for Quick Transformation of E. coli]]
 '''DNA Manipulation'''
-[[Media:Protocol_Heat_Shock_Transformation_2.pdf|Transformation-heat shock]]
+[[Media:Direct Plating Transformation Protocol.pdf|Direct Plating Transformation Protocol]]
+*Very simple protocol
+*Twice as efficient as standard heat shock
+[[Media:Protocol_Heat_Shock_Transformation_2.pdf|Transformation - heat shock]]
-''This is the procedure we can perform in the ERB''
 *Getting parts from the 360 well registry plates
 *Competent cell preparation
 *Heat shock
-[[Media:General_Transformation_Protocol.pdf|Transformation-electroporation]]
+[[Media:General_Transformation_Protocol.pdf|Transformation - electroporation]]
 *Getting parts from the 360 well registry plates
 *Competent cell preparation
 *Electroporation
-[[Media:General_Miniprep_Protocol.pdf|Miniprep]]
+[[Media:Electroporation Protocol 2.pdf|Electroporation Protocol 2]]
+*Adopted from Jeremy Minty's protocol
+*General protocol with specific instructions for ERB/Lin lab equipment
+[[Media:PCR Screening Protocol.pdf|PCR Screening Protocol]]
+*Efficient protocol for screening transformants after a ligation
+[[Media:MODIFIED_Miniprep_Protocol.pdf|MODIFIED Miniprep]]
+*[[Media:General_Miniprep_Protocol.pdf|Miniprep]]
+[[Media:Nanodrop_Protocol.pdf|Nanodrop]]
 [[Media:General_DNA_Digest_Protocol.pdf|DNA Digest]]
-[[Media:Protocol_for_Running_a_Gel.pdf|Running a Gel]]
+[[Media:_Digest_reagents_calculator.xls|Digest Reagents Calculator]]
+[[Media:Protocol_for_Running_a_Gel.pdf|Gel Electrophoresis]]
 [[Media:Protocol_for_DNA_Purification.pdf|DNA Purification]]
-[[Media:Ligation_Protocol.pdf|Ligation]]
+[[Media:Quick_Ligation_Protocol.pdf|Quick Ligation Protocol]]
-*Ginko Bioworks Protocol
-*Jeremy Minty Protocol
+[[Media:8-8-2010_Protocol_for_gel_extraction.pdf|Gel extraction]]
+[[Media:8-10-2010_Ligation_Calculations_updated.pdf|Updated T4 DNA Ligase Protocol (Not quick ligase)]]
+*For additional information/questions, refer to [http://www.neb.com/nebecomm/tech_reference/modifying_enzymes/ligation_tips.asp NEB Ligation Tips]
+*[[Media:Ligation_Protocol.pdf|Ligation]]
+**Ginko Bioworks Protocol
+**Jeremy Minty Protocol
+===Group-Specific Protocols===
+====Oil Sands====
+[[Media:8-6-2010_Biofilm_Formation_Experiment.pdf|Revised biofilm assay protocol]]
+*[[Media:7-28-2010_Biofilm_Formation_Experiment.pdf|Biofilm assay protocol]]
+[[Media:Static+biofilm+quantification.pdf|Alex's biofilm assay protocol]]
+[[Media:7-31-2010_Flu_operon_primers.pdf|General primer design]]
+[[Media:7-31-2010_Ag43_flu_gene_WITH_MODIFIED_PRIMER_SITES.pdf|Detailed primer design]]
+[[Media:8-4-2010_Colony_PCR_flu.pdf|Colony PCR protocol]]
+[[Media:NanR_Cloning.pdf|NanR cloning]]
+*Updated Colony PCR Protocol
+[[Media:NA Extraction.pdf|NA Extraction Protocol]]
+====Pili====
+[[Media:FimB_Ligation_Protocol.pdf|FimB Ligation]]
+[[Media:FimB_PCR.pdf|FimB PCR]]
+[[Media:Flocculation_protocol.pdf|Flocculation Protocol]]
+====Quorum Sensing====
+[[Media:Quorum+Sensing+Tables-1-.pdf|Logic Table]]
+[[Media:QS_Procedures-1-.pdf|Lsr Circuit Test Protocols]]
+==General Outline for Biobrick Manipulations==
+[[Image:Igem_order_of_procedures.jpg|900px]]