Team:Cambridge/Labwork/Protocols
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{{Template:Team:Cambridge/CAM_2011_TEMPLATE_HEAD}} | {{Template:Team:Cambridge/CAM_2011_TEMPLATE_HEAD}} | ||
- | + | =Protocols= | |
- | A list of all protocols developed during the project. | + | A list of all protocols developed during the project. We used this page as a reference throughout the competition. |
- | + | '''Amplification of DNA''' | |
- | + | ||
- | + | ||
- | + | *[[Team:Cambridge/Protocols/PCR | Polymerase Chain Reaction]] : A method for amplifying a section of DNA. | |
- | + | *[[Team:Cambridge/Protocols/Colony PCR | Colony PCR]] : PCR with cells as a template. Useful for checking the length of an insert in an introduced plasmid. | |
- | + | '''Analysis of DNA''' | |
- | + | ||
- | + | ||
- | + | ||
- | + | ||
- | + | ||
- | + | ||
- | + | ||
- | + | ||
- | + | *[[Team:Cambridge/Protocols/Gel_Electrophoresis |Gel Electrophoresis]] : A method used to separate DNA fragments of different sizes. | |
- | + | *[[Team:Cambridge/Protocols/Gel Extraction of DNA |Gel Extraction of DNA]] : A technique used to isolate a desired fragment of intact DNA from an agarose gel following agarose gel electrophoresis. | |
- | + | *[[Team:Cambridge/Protocols/DNA Precipitation |Rescue Precipitation of DNA]] : Creating a clean DNA solution after dissolving agarose gel. | |
- | + | *[[Team:Cambridge/Protocols/Restriction_Enzyme_Digestion | Restriction Enzyme Digestion]] : A method for creating a restriction map of a plasmid. | |
- | + | ||
- | + | ||
+ | '''Preparation of DNA Constructs''' | ||
- | + | *[[Team:Cambridge/Protocols/Primer_design |Primer Design]] : Some general guidelines on how to design successful primers. | |
- | + | *[[Team:Cambridge/Protocols/Gibson_Assembly |Gibson Assembly]] : An extremely powerful technique for joining multiple, arbitrary DNA sequences in one step, compatible with standard assembly. | |
- | + | ||
- | + | ||
- | + | '''Transformation of Bacterial Cells''' | |
- | + | ||
- | + | ||
- | + | *[[Team:Cambridge/Protocols/Making Competent Cells | Making Electro-Competent Bacterial Cells]] : The methods required to make various cells competent. | |
+ | *[[Team:Cambridge/Protocols/Transformation_of_E.Coli |Transformation of E.coli]] : A simple method of transforming competent E.coli with your DNA of choice. | ||
+ | *[[Team:Cambridge/Protocols/Transformation_of_B._subtilis | Tranformation of B.subtilis]] : A technique used to introduce foreign DNA into Bacillus cells. | ||
+ | *[[Team:Cambridge/Protocols/Transformation of E.coli by Electroporation| Transformation of E.coli by Electroporation]]: A technique for rapidly inserting DNA into cells, typically plasmid DNA, providing the cells are made competent in the correct manner. | ||
- | + | '''Bacterial Cultures''' | |
- | + | ||
- | + | *[[Team:Cambridge/Protocols/Overnight_Culture |E.coli Cell Culture]] : A method for growing a cell culture in liquid medium. | |
- | </ | + | *[[Team:Cambridge/Protocols/Glycerol Stocks | Glycerol Stocks]]: A method of storing E.coli cells preserving their viability. |
+ | |||
+ | '''Extraction of DNA''' | ||
+ | |||
+ | *[[Team:Cambridge/Protocols/Mini_Prep |MiniPrep]] : Extracting DNA from bacterial cells. | ||
+ | *[[Team:Cambridge/Protocols/Extraction_of_genomic_DNA_from_squid | Extraction of Genomic DNA from Squid]] : Two methods to extract genomic DNA from squid tissue. | ||
+ | *[[Team:Cambridge/Protocols/Filter_Paper | Extraction of DNA from Filter Paper ]] : Extraction of DNA from filter paper which is a safe way of shipping DNA. | ||
+ | <!--*[[Team:Cambridge/Protocols/Extraction_of_cleaner_genomic_DNA_from_squid | Extraction of cleaner genomic DNA from squid]] : A method to extract genomic DNA from squid tissue--> | ||
+ | |||
+ | '''Microscopy''' | ||
+ | *[[Team:Cambridge/Protocols/Confocal Microscopy of Loligo Eye and Mantle Dermis Samples | Confocal Microscopy]] : A method to visualise reflectins from squid samples. | ||
+ | *[[Team:Cambridge/Protocols/Preparing_Slides_With_Agarose_Supplement_To_Form_Microcolonies | Slide Preparation for Confocal Microscopy]] : A method of growing a monolayer of bacterial cells on a slide to aid their microscopic viewing. | ||
+ | *[[Team:Cambridge/Protocols/Trypsin | Trypsinisation]] : A method of dispersing cells from tissue, for microscopy. | ||
+ | |||
+ | '''Protein Purification''' | ||
+ | *[[Team:Cambridge/Protocols/Buffers | Buffer Preparation]] : Methods to prepare the various buffers used to purify his-tagged reflectin from inclusion bodies in E. coli. | ||
+ | *[[Team:Cambridge/Protocols/Inclusion_Body_Prep | Inclusion Body Prep]] : Isolation of insoluble inclusion bodies of recombinant proteins. | ||
+ | *[[Team:Cambridge/Protocols/Protein_Purification | His-Trap Protein Purification]] : A method to purify reflectin from E. coli lysate using an affinity column. | ||
+ | *[[Team:Cambridge/Protocols/Acetone_Precipitation_of_Proteins | Acetone Precipitation of Proteins]] : A method to concentrate solutions of protein. | ||
+ | *[[Team:Cambridge/Protocols/Ethanol Precipitation_of_Proteins| Ethanol Precipitation of Proteins]] : A method to concentrate solutions of protein. | ||
+ | *[[Team:Cambridge/Protocols/Chloroform Precipitation_of_Proteins| Chloroform/Methanol Precipitation of Proteins]] : A method to concentrate solutions of protein whilst removing salts and detergents. | ||
+ | *[[Team:Cambridge/Protocols/Dialysis_of_Proteins| Dialysis of Proteins]] : A method for removing salts, urea and contaminants by the use of a semi-permeable membrane and a concentration gradient. | ||
+ | *[[Team:Cambridge/protocols/Norgen | Norgen Proteospin Inclusion Body Prep]] : A proprietary kit. | ||
+ | |||
+ | '''Thin Film Preparation''' | ||
+ | *[[Team:Cambridge/Protocols/Substrate_Preparation_for_Flow_Coating_and_Spin_Coating | Substrate Preparation]]:How to prepare a substrate for flow coating and spin coating. | ||
+ | *[[Team:Cambridge/Protocols/Spin Coating |Spin Coating to Make a Thin Film]]: Our Spin Coating Protocol. | ||
+ | *[[Team:Cambridge/Protocols/Flow_coating | Flow Coating]]: How to flow coat a thin film. | ||
+ | *[[Team:Cambridge/Protocols/Surface_chemistry | Altering Substrate Surface Chemistry]]: Various methods to alter the surface chemistry of silicon and PDMS to achieve better wetting and thin film production | ||
+ | |||
+ | '''Gel Electrophoresis by SDS PAGE''' | ||
+ | *[[Team:Cambridge/Protocols/Gel_Electrophoresis_of_Protein | Protein Identification by SDS PAGE]]: A method used to separate polypeptides of different lengths. | ||
{{Template:Team:Cambridge/CAM_2011_TEMPLATE_FOOT}} | {{Template:Team:Cambridge/CAM_2011_TEMPLATE_FOOT}} |
Latest revision as of 19:52, 21 September 2011
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Protocols
A list of all protocols developed during the project. We used this page as a reference throughout the competition.
Amplification of DNA
- Polymerase Chain Reaction : A method for amplifying a section of DNA.
- Colony PCR : PCR with cells as a template. Useful for checking the length of an insert in an introduced plasmid.
Analysis of DNA
- Gel Electrophoresis : A method used to separate DNA fragments of different sizes.
- Gel Extraction of DNA : A technique used to isolate a desired fragment of intact DNA from an agarose gel following agarose gel electrophoresis.
- Rescue Precipitation of DNA : Creating a clean DNA solution after dissolving agarose gel.
- Restriction Enzyme Digestion : A method for creating a restriction map of a plasmid.
Preparation of DNA Constructs
- Primer Design : Some general guidelines on how to design successful primers.
- Gibson Assembly : An extremely powerful technique for joining multiple, arbitrary DNA sequences in one step, compatible with standard assembly.
Transformation of Bacterial Cells
- Making Electro-Competent Bacterial Cells : The methods required to make various cells competent.
- Transformation of E.coli : A simple method of transforming competent E.coli with your DNA of choice.
- Tranformation of B.subtilis : A technique used to introduce foreign DNA into Bacillus cells.
- Transformation of E.coli by Electroporation: A technique for rapidly inserting DNA into cells, typically plasmid DNA, providing the cells are made competent in the correct manner.
Bacterial Cultures
- E.coli Cell Culture : A method for growing a cell culture in liquid medium.
- Glycerol Stocks: A method of storing E.coli cells preserving their viability.
Extraction of DNA
- MiniPrep : Extracting DNA from bacterial cells.
- Extraction of Genomic DNA from Squid : Two methods to extract genomic DNA from squid tissue.
- Extraction of DNA from Filter Paper : Extraction of DNA from filter paper which is a safe way of shipping DNA.
Microscopy
- Confocal Microscopy : A method to visualise reflectins from squid samples.
- Slide Preparation for Confocal Microscopy : A method of growing a monolayer of bacterial cells on a slide to aid their microscopic viewing.
- Trypsinisation : A method of dispersing cells from tissue, for microscopy.
Protein Purification
- Buffer Preparation : Methods to prepare the various buffers used to purify his-tagged reflectin from inclusion bodies in E. coli.
- Inclusion Body Prep : Isolation of insoluble inclusion bodies of recombinant proteins.
- His-Trap Protein Purification : A method to purify reflectin from E. coli lysate using an affinity column.
- Acetone Precipitation of Proteins : A method to concentrate solutions of protein.
- Ethanol Precipitation of Proteins : A method to concentrate solutions of protein.
- Chloroform/Methanol Precipitation of Proteins : A method to concentrate solutions of protein whilst removing salts and detergents.
- Dialysis of Proteins : A method for removing salts, urea and contaminants by the use of a semi-permeable membrane and a concentration gradient.
- Norgen Proteospin Inclusion Body Prep : A proprietary kit.
Thin Film Preparation
- Substrate Preparation:How to prepare a substrate for flow coating and spin coating.
- Spin Coating to Make a Thin Film: Our Spin Coating Protocol.
- Flow Coating: How to flow coat a thin film.
- Altering Substrate Surface Chemistry: Various methods to alter the surface chemistry of silicon and PDMS to achieve better wetting and thin film production
Gel Electrophoresis by SDS PAGE
- Protein Identification by SDS PAGE: A method used to separate polypeptides of different lengths.