Team:Cambridge/Labwork/Protocols

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==Protocols==
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=Protocols=
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A list of all protocols developed during the project. To add one, press edit and follow the instructions in the comments
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A list of all protocols developed during the project. We used this page as a reference throughout the competition.
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#[[Team:Cambridge/Protocols/PCR | Polymerase Chain Reaction]] : A method for amplifying a section of DNA
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'''Amplification of DNA'''   
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#[[Team:Cambridge/Protocols/Gibson_Assembly |Gibson Assembly]] : A relatively new technique of joining multiple DNA strands reliably
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#[[Team:Cambridge/Protocols/Gel_Electrophoresis |Gel electrophoresis]] : A method used to separate DNA fragments of different sizes
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==Adding new Protocol==
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*[[Team:Cambridge/Protocols/PCR | Polymerase Chain Reaction]] : A method for amplifying a section of DNA.
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To add a new protocol, enter the name in the box below and click new to create the new page. You must return to this page in order to add in a link to the page by copying the code below.
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*[[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.
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<html>
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'''Analysis of DNA'''
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  <form name="new_prot" method="GET" action="https://2011.igem.org/wiki/index.php" onsubmit="setTitle();">
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    <p>
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      <input type="text" name="title" id="prot_name" value="New Protocol Name"\>
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      <input type="hidden" name="action" value="edit"/>
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      <input type="hidden" name="preload" value="Template:Team:Cambridge/PROTOCOL"/>
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      <input type="Submit" value="New"/>
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    </p>
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  </form>
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  <script type="text/javascript">
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*[[Team:Cambridge/Protocols/Gel_Electrophoresis |Gel Electrophoresis]] : A method used to separate DNA fragments of different sizes.
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    function setTitle()
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*[[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.
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    {
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*[[Team:Cambridge/Protocols/DNA Precipitation |Rescue Precipitation of DNA]] : Creating a clean DNA solution after dissolving agarose gel.
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      var x = document.getElementById('prot_name');
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*[[Team:Cambridge/Protocols/Restriction_Enzyme_Digestion | Restriction Enzyme Digestion]] : A method for creating a restriction map of a plasmid.
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      x.value = 'Team:Cambridge/Protocols/' + x.value.split(' ').join('_');
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    }
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'''Preparation of DNA Constructs'''
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    function reset()
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*[[Team:Cambridge/Protocols/Primer_design |Primer Design]] : Some general guidelines on how to design successful primers.
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    {
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*[[Team:Cambridge/Protocols/Gibson_Assembly |Gibson Assembly]] : An extremely powerful technique for joining multiple, arbitrary DNA sequences in one step, compatible with standard assembly.
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      document.getElementById('prot_name').value = "New Protocol Name";
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    }
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  //reset the name if the user goes and uses the back button
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'''Transformation of Bacterial Cells'''
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  window.onload = reset()
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</script>
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</html>
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*[[Team:Cambridge/Protocols/Making Competent Cells | Making Electro-Competent Bacterial Cells]] : The methods required to make various cells competent.
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*[[Team:Cambridge/Protocols/Transformation_of_E.Coli |Transformation of E.coli]] : A simple method of transforming competent E.coli with your DNA of choice.
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*[[Team:Cambridge/Protocols/Transformation_of_B._subtilis | Tranformation of B.subtilis]] : A technique used to introduce foreign DNA into Bacillus cells.
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*[[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.
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Add a new link on this page with
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'''Bacterial Cultures'''
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<pre>
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#[[Team:Cambridge/Protocols/PROTOCOL_NAME_HERE |PROTOCOL NAME HERE]] : Insert description here
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*[[Team:Cambridge/Protocols/Overnight_Culture |E.coli Cell Culture]] : A method for growing a cell culture in liquid medium.
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</pre>
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*[[Team:Cambridge/Protocols/Glycerol Stocks | Glycerol Stocks]]: A method of storing E.coli cells preserving their viability.
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'''Extraction of DNA'''
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*[[Team:Cambridge/Protocols/Mini_Prep |MiniPrep]] : Extracting DNA from bacterial cells.
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*[[Team:Cambridge/Protocols/Extraction_of_genomic_DNA_from_squid | Extraction of Genomic DNA from Squid]] : Two methods to extract genomic DNA from squid tissue.
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*[[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.
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<!--*[[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-->
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'''Microscopy'''
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*[[Team:Cambridge/Protocols/Confocal Microscopy of Loligo Eye and Mantle Dermis Samples | Confocal Microscopy]] : A method to visualise reflectins from squid samples.
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*[[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.
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*[[Team:Cambridge/Protocols/Trypsin | Trypsinisation]] : A method of dispersing cells from tissue, for microscopy.
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'''Protein Purification'''
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*[[Team:Cambridge/Protocols/Buffers | Buffer Preparation]] : Methods to prepare the various buffers used to purify his-tagged reflectin from inclusion bodies in E. coli.
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*[[Team:Cambridge/Protocols/Inclusion_Body_Prep | Inclusion Body Prep]] : Isolation of insoluble inclusion bodies of recombinant proteins.
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*[[Team:Cambridge/Protocols/Protein_Purification | His-Trap Protein Purification]] : A method to purify reflectin from E. coli lysate using an affinity column.
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*[[Team:Cambridge/Protocols/Acetone_Precipitation_of_Proteins | Acetone Precipitation of Proteins]] : A method to concentrate solutions of protein.
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*[[Team:Cambridge/Protocols/Ethanol Precipitation_of_Proteins| Ethanol Precipitation of Proteins]] : A method to concentrate solutions of protein.
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*[[Team:Cambridge/Protocols/Chloroform Precipitation_of_Proteins| Chloroform/Methanol Precipitation of Proteins]] : A method to concentrate solutions of protein whilst removing salts and detergents.
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*[[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.
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*[[Team:Cambridge/protocols/Norgen | Norgen Proteospin Inclusion Body Prep]] : A proprietary kit.
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'''Thin Film Preparation'''
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*[[Team:Cambridge/Protocols/Substrate_Preparation_for_Flow_Coating_and_Spin_Coating | Substrate Preparation]]:How to prepare a substrate for flow coating and spin coating.
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*[[Team:Cambridge/Protocols/Spin Coating |Spin Coating to Make a Thin Film]]: Our Spin Coating Protocol.
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*[[Team:Cambridge/Protocols/Flow_coating | Flow Coating]]:  How to flow coat a thin film.
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*[[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
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'''Gel Electrophoresis by SDS PAGE'''
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*[[Team:Cambridge/Protocols/Gel_Electrophoresis_of_Protein | Protein Identification by SDS PAGE]]: A method used to separate polypeptides of different lengths.
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Latest revision as of 19:52, 21 September 2011

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OVERVIEW
home

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

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

Bacterial Cultures

Extraction of DNA

Microscopy

Protein Purification

Thin Film Preparation

Gel Electrophoresis by SDS PAGE


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