Difference between revisions of "Davidson Missouri W/Davidson Protocols"

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'''General Lab Information'''
 
# [http://www.bio.davidson.edu/courses/molbio/labnotebook.html How to Keep a Lab Notebook]
 
# [http://www.bio.davidson.edu/courses/molbio/labnotebook.html How to Keep a Lab Notebook]
 
# [http://www.bio.davidson.edu/courses/Molbio/Protocols/reagents.html Common molecular reagents]
 
# [http://www.bio.davidson.edu/courses/Molbio/Protocols/reagents.html Common molecular reagents]
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# [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/pdf/am002240.pdf Using degradation tags on proteins such as GFP]
 
 
# [http://parts.mit.edu/registry/index.php/Assembly:Standard_assembly Standard Assembly]
 
# [http://parts.mit.edu/registry/index.php/Assembly:Standard_assembly Standard Assembly]
 
# [http://partsregistry.org/Help:BioBrick_Prefix_and_Suffix BioBrick Ends]
 
# [http://partsregistry.org/Help:BioBrick_Prefix_and_Suffix BioBrick Ends]
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#[http://www.bio.davidson.edu/courses/Molbio/Protocols/ORIs.html '''Compatibility of Plasmids''']
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# [http://www.bio.davidson.edu/courses/Molbio/Protocols/ORIs.html '''Compatibility of Plasmids''']
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# [http://www.bio.davidson.edu/courses/Molbio/Protocols/anneal_oligos.html Building dsDNA with Oligos]
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# [http://www.bio.davidson.edu/courses/Molbio/Protocols/clean_short.html Ethanol Precipitate DNA (short protocol)]
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# [http://www.bio.davidson.edu/courses/Molbio/Protocols/pcr.html Setting up PCR mixtures]
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# [[glycerolstocks How to Make Glycerol Stocks of Bacteria]]
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# [http://www.bio.davidson.edu/courses/Molbio/Protocols/magnesium.html PCR and Mg<sup>2+</sup> concentration]
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#[http://www.bio.davidson.edu/courses/Molbio/Protocols/Clean_Concentrate.html Clean and Concentrate DNA (after PCR, before digestion)]
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'''Gel Electrophoresis and Purification'''
 
# [http://www.bio.davidson.edu/courses/Molbio/Protocols/pourgel.html Pouring an agarose gel]
 
# [http://www.bio.davidson.edu/courses/Molbio/Protocols/pourgel.html Pouring an agarose gel]
 
# [http://www.bio.davidson.edu/courses/Molbio/Protocols/molwt.html Calculate MWs]
 
# [http://www.bio.davidson.edu/courses/Molbio/Protocols/molwt.html Calculate MWs]
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# [http://www.bio.davidson.edu/courses/Molbio/Protocols/digestion.html Digest DNA with restriction enzymes]
 
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# [[Davidson Missouri W/Double Digest Guide| Double Digest Guide]]
 
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# [http://www.bio.davidson.edu/courses/Molbio/Protocols/clean_short.html Ethanol Precipitate DNA (short protocol)]
 
 
# [http://www.bio.davidson.edu/courses/Molbio/Protocols/gels2002/1kbladder.pdf 1kb MW markers]
 
# [http://www.bio.davidson.edu/courses/Molbio/Protocols/gels2002/1kbladder.pdf 1kb MW markers]
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# [http://www.bio.davidson.edu/courses/Molbio/Protocols/SAP.html Shrimp Alkaline Phosphatase]
 
 
# [http://www.bio.davidson.edu/courses/Molbio/Protocols/Qiagen_gelpure.html Qiagen QIAquick Gel Purification]
 
# [http://www.bio.davidson.edu/courses/Molbio/Protocols/Qiagen_gelpure.html Qiagen QIAquick Gel Purification]
 
# [http://www.bio.davidson.edu/courses/Molbio/Protocols/QIAQuick_recycle.html Qiagen QIAquick Column Regeneration Protocol]
 
# [http://www.bio.davidson.edu/courses/Molbio/Protocols/QIAQuick_recycle.html Qiagen QIAquick Column Regeneration Protocol]
 
# [http://www.bio.davidson.edu/courses/Molbio/Protocols/gelpure.html ElectroElute Gel Purification]
 
# [http://www.bio.davidson.edu/courses/Molbio/Protocols/gelpure.html ElectroElute Gel Purification]
 
# [http://www.bio.davidson.edu/courses/Molbio/Protocols/ligation.html Ligation Protocol]
 
# [http://www.bio.davidson.edu/courses/Molbio/Protocols/ligation.html Ligation Protocol]
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'''Digestion, Ligation, Transformation'''
 +
# [http://www.bio.davidson.edu/courses/Molbio/Protocols/digestion.html Digest DNA with restriction enzymes]
 +
# [[Davidson Missouri W/Double Digest Guide| Double Digest Guide]]
 +
# [http://www.bio.davidson.edu/courses/Molbio/Protocols/SAP.html Shrimp Alkaline Phosphatase]
 +
# [http://www.bio.davidson.edu/courses/Molbio/Protocols/Tranformation_list.html Choices for Transformation: Heat Shock vs. Zyppy]
 
# [http://www.bio.davidson.edu/courses/Molbio/Protocols/Promegacompcells.pdf Heat Shock Transformation] OR [http://www.bio.davidson.edu/courses/Molbio/Protocols/transformation.html Short version of Heat Shock]
 
# [http://www.bio.davidson.edu/courses/Molbio/Protocols/Promegacompcells.pdf Heat Shock Transformation] OR [http://www.bio.davidson.edu/courses/Molbio/Protocols/transformation.html Short version of Heat Shock]
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#[http://www.bio.davidson.edu/courses/Molbio/Protocols/Zippy_Transformation.html Zippy Transformation]
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# [http://www.bio.davidson.edu/courses/Molbio/Protocols/Zippy_Transformation.html Zippy Transformation]
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#[[TSS Competent Cells|TSS Competent Cell Transformation]]
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# [[TSS Competent Cells|TSS Competent Cell Transformation]]
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#[http://www.bio.davidson.edu/courses/Molbio/Protocols/ColonyPCR_Screening.html Colony PCR to Screen for Successful Ligations]
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'''Minipreps'''
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# [http://www.bio.davidson.edu/courses/Molbio/Protocols/MiniPrep_list.html Choices for Mini-Preps: Promega vs. Zyppy]
 
# [http://www.bio.davidson.edu/courses/Molbio/Protocols/miniprepPrmega.html Promega miniprep]
 
# [http://www.bio.davidson.edu/courses/Molbio/Protocols/miniprepPrmega.html Promega miniprep]
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#[http://www.bio.davidson.edu/courses/Molbio/Protocols/Tranformation_list.html Choices for Transformation: Heat Shock vs. Zyppy]
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−
#[http://www.bio.davidson.edu/courses/Molbio/Protocols/MiniPrep_list.html Choices for Mini-Preps: Promega vs. Zyppy]
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'''Making New Parts and PCR'''
 +
# [http://www.bio.davidson.edu/courses/Molbio/Protocols/anneal_oligos.html Building dsDNA with Oligos]
 +
# [http://www.bio.davidson.edu/courses/Molbio/Protocols/pcr.html Setting up PCR mixtures]
 +
# [http://www.bio.davidson.edu/courses/Molbio/Protocols/magnesium.html PCR and Mg<sup>2+</sup> concentration]
 
# [[Davidson Missouri W/Primer_dimer| Making dsDNA Using Primer Dimers]]
 
# [[Davidson Missouri W/Primer_dimer| Making dsDNA Using Primer Dimers]]
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#[[Genomic Insertion Protocol|Genomic Insertion Protocol]]
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# [http://www.bio.davidson.edu/courses/Molbio/Protocols/Clean_Concentrate.html Clean and Concentrate DNA (after PCR, before digestion)]
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# [[glycerolstocks How to Make Glycerol Stocks of Bacteria]]
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# [http://www.bio.davidson.edu/courses/Molbio/Protocols/ColonyPCR_Screening.html Colony PCR to Screen for Successful Ligations]
 +
 
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'''Expression of Phenotypes'''
 +
# [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106306/pdf/am002240.pdf Using degradation tags on proteins such as GFP]
 +
# [[Genomic Insertion Protocol|Genomic Insertion Protocol]]
 
# When inducing with IPTG, use '''3 µL of stock''' (0.2 g/mL = 20% w/v) '''to every 1 mL''' of LB or other liquid.  
 
# When inducing with IPTG, use '''3 µL of stock''' (0.2 g/mL = 20% w/v) '''to every 1 mL''' of LB or other liquid.  
 
# When inducing with Arabinose, use "2 µL of stock" (10% w/v L-Arabinose) "to every 1 mL" of LB or other liquid.
 
# When inducing with Arabinose, use "2 µL of stock" (10% w/v L-Arabinose) "to every 1 mL" of LB or other liquid.
  
 
'''Computer Tools We Use'''
 
'''Computer Tools We Use'''
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#[http://gcat.davidson.edu/iGEM08/tools.html All Sites In One Place]
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# [http://gcat.davidson.edu/iGEM08/tools.html All Sites In One Place]
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#[http://gcat.davidson.edu/iGEM08/gelwebsite/gelwebsite.html Optimize your Gel]
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# [http://gcat.davidson.edu/iGEM08/gelwebsite/gelwebsite.html Optimize your Gel]
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#[http://gcat.davidson.edu/iGEM07/genesplitter.html Gene Splitting Web Site]
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# [http://gcat.davidson.edu/iGEM07/genesplitter.html Gene Splitting Web Site]
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#[http://gcat.davidson.edu/iGEM08/bbprimer.html PCR Primers w/ BioBricks]
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# [http://gcat.davidson.edu/iGEM08/bbprimer.html PCR Primers w/ BioBricks]
 
# [http://www.promega.com/biomath/calc11.htm Promega T<sub>m</sub> Calculator]
 
# [http://www.promega.com/biomath/calc11.htm Promega T<sub>m</sub> Calculator]
 
# [http://partsregistry.org/AHL List of auto-inducers and their catalog numbers]
 
# [http://partsregistry.org/AHL List of auto-inducers and their catalog numbers]
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#[[Sequencing at Agencourt| Sequencing at Agencourt Bioscience]]
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# [[Sequencing at Agencourt| Sequencing at Agencourt Bioscience]]
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#[[Davidson Missouri W/CUGI_Seuqencing| Sequencing at CUGI]]
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# [[Davidson Missouri W/CUGI_Seuqencing| Sequencing at CUGI]]
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#[http://gcat.davidson.edu/GcatWiki/images/3/3b/Ape_protocol.pdf Analyzing Sequences with aPe]
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# [http://gcat.davidson.edu/GcatWiki/images/3/3b/Ape_protocol.pdf Analyzing Sequences with aPe]
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#[http://gcat.davidson.edu/IGEM06/oligo.html Lance-olator Oligos for dsDNA assembly]
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# [http://gcat.davidson.edu/IGEM06/oligo.html Lance-olator Oligos for dsDNA assembly]
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#[http://gcat.davidson.edu/GCATalog Access the GCAT-alog of Davidson and MWSU DNA Freezer Stocks]
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# [http://gcat.davidson.edu/GCATalog Access the GCAT-alog of Davidson and MWSU DNA Freezer Stocks]
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#[[Using Apes (A Plasmid Editor)]]
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# [[Using Apes (A Plasmid Editor)]]

Revision as of 21:20, 13 March 2010

General Lab Information

  1. How to Keep a Lab Notebook
  2. Common molecular reagents
  3. Standard Assembly
  4. BioBrick Ends
  5. Compatibility of Plasmids
  6. Ethanol Precipitate DNA (short protocol)
  7. glycerolstocks How to Make Glycerol Stocks of Bacteria


Gel Electrophoresis and Purification

  1. Pouring an agarose gel
  2. Calculate MWs
  3. 1kb MW markers
  4. Qiagen QIAquick Gel Purification
  5. Qiagen QIAquick Column Regeneration Protocol
  6. ElectroElute Gel Purification
  7. Ligation Protocol

Digestion, Ligation, Transformation

  1. Digest DNA with restriction enzymes
  2. Double Digest Guide
  3. Shrimp Alkaline Phosphatase
  4. Choices for Transformation: Heat Shock vs. Zyppy
  5. Heat Shock Transformation OR Short version of Heat Shock
  6. Zippy Transformation
  7. TSS Competent Cell Transformation

Minipreps

  1. Choices for Mini-Preps: Promega vs. Zyppy
  2. Promega miniprep

Making New Parts and PCR

  1. Building dsDNA with Oligos
  2. Setting up PCR mixtures
  3. PCR and Mg2+ concentration
  4. Making dsDNA Using Primer Dimers
  5. Clean and Concentrate DNA (after PCR, before digestion)
  6. Colony PCR to Screen for Successful Ligations

Expression of Phenotypes

  1. Using degradation tags on proteins such as GFP
  2. Genomic Insertion Protocol
  3. When inducing with IPTG, use 3 µL of stock (0.2 g/mL = 20% w/v) to every 1 mL of LB or other liquid.
  4. When inducing with Arabinose, use "2 µL of stock" (10% w/v L-Arabinose) "to every 1 mL" of LB or other liquid.

Computer Tools We Use

  1. All Sites In One Place
  2. Optimize your Gel
  3. Gene Splitting Web Site
  4. PCR Primers w/ BioBricks
  5. Promega Tm Calculator
  6. List of auto-inducers and their catalog numbers
  7. Sequencing at Agencourt Bioscience
  8. Sequencing at CUGI
  9. Analyzing Sequences with aPe
  10. Lance-olator Oligos for dsDNA assembly
  11. Access the GCAT-alog of Davidson and MWSU DNA Freezer Stocks
  12. Using Apes (A Plasmid Editor)
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