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Revision as of 13:32, 19 October 2007

Wet-Lab Protocols

• Protocol online
• PCR (7/20)
  • RT-PCR
  • Q-PCR
• Quantitation of  Nucleic acid concentration
  • <a href="http://en.wikipedia.org/wiki/Quantification_of_nucleic_acids">Wikipedia</a>
  • <a href="http://www.piercenet.com/Objects/View.cfm?type=Page&ID=0A0A7BB1-7582-4611-A116-6F583EC01666">Pierce</a>
  • <a href="http://mcbl.iisc.ernet.in/Welcome%20to%20MCBL/Faculty/Parag/microarray%20workshop%20details/quantitation.html">India</a>
  • <a href="http://www.kreatech.com/pages/Focus-Areas/*-Hybridization-___-Labeling-protocols/Small-RNA-Labeling-protocol/">Kreatech Biotechnology</a> 
• <a href="http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/setting_up_reaction.asp">Setting Up a Restriction Endonuclease Reaction</a>
• DNA Analysis through Gel Electrophoresis
• Ligate blunt or cohesive ends in 5 minutes at room temperature
  • <a href="http://www.neb.com/nebecomm/products/productM2200.asp">Quick Ligation Kit (NEB)</a>
  • <a href="http://www.ubi.ca/cart/index.php/cPath/27_163_165">Fast Ligation Kit (UBI)</a>
  • <a href="http://www.epibio.com/item.asp?ID=296">Fast-Link DNA Ligation Kit (EPICENTRE Biotechnologies)</a>
  • <a href="http://www.fermentas.com/catalog/kits/kitrapidligation.htm">Rapid Ligation Kit (Fermentas)</a>
  • All of these are just normal ligase buffers with PEG8000 at a 10-12% concentration. The NEB catalogue gives the original reference. 
    Use of crowding agents like PEG allow 5-minute sticky end ligations.
• Vector construction
  • Vector sequences
    • <a href="http://seq.yeastgenome.org/vectordb/">VectorDB - Molecular Biology Vector Sequence Database</a>
    • <a href="http://www.shigen.nig.ac.jp/cvector/cvector.html">The cloning vector collection</a>
    • <a href="http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/dna_sequences_maps.asp">New England Biolabs (NEB) DNA Sequences and Maps</a>
    • <a href="http://www.promega.com/vectors/cloning_vectors.htm">Promega Cloning Vectors</a>
    • <a href="http://www.emdbiosciences.com/Products/BrowseProductsByCategory.asp?catid=1628">Novagen Vector Maps</a>
  • <a href="http://wishart.biology.ualberta.ca/PlasMapper/">PlasMapper Version 2.0 - automatically generates and annotates plasmid maps</a>
• Transformation
• Production of heterologous proteins in Escherichia coli
• <a href="http://openwetware.org/wiki/Endy:Preparing_Antibiotic_Stocks">Antibiotics</a>
• <a href="http://openwetware.org/wiki/Synthetic_Biology:BioBricks/Part_fabrication">Part fabrication</a> (<a href="http://openwetware.org/wiki/Enzyme_selection_for_BioBricks_digest">Enzyme selection for BioBricks digest</a>!!)
• <a href="http://openwetware.org/wiki/BioBricks_construction_tutorial">BioBricks construction tutorial</a>
• <a href="http://openwetware.org/wiki/Silver:_BB_Strategy">Fusion protein</a>
• Glucose assay
  • <a href="http://en.wikipedia.org/wiki/Blood_sugar">Blood sugar (from Wikipedia)</a>
  • <a href="http://www.genengnews.com/articles/chtitem.aspx?tid=1624&chid=3">Glucose Measurement for Cell Culture</a>
  • <a href="http://www.sigmaaldrich.com/Area_of_Interest/Life_Science/Metabolomics/Product_Highlights/Enzymatic_Kits.html">Glucose Assay Kits from SigmaAldrich</a>
  • <a href="http://www.bioassaysys.com/Order.html">Glucose Assay Kit from QuantiChrom</a>
  • <a href="http://www.rpbiotech.com/Biochem_diag_kits/Glucose_Diagnostic_Kit.htm">Biochemical glucose kit from rpbiotech</a>
  • <a href="http://www.anilinepharma.com/products.php?catg=ds&id=1">Glucose Meter from AnilinePharma</a>
• Mammalian Gene Collection (MGC) Full-length cDNA clones
  • <a href="http://mgc.nci.nih.gov/">at National Cancer Institute of NIH</a>
  • <a href="http://genome.ym.edu.tw/libres/MGC_clones/index.htm">at Genome Research Center of NYMU</a>
  • <a href="http://www.ncbi.nlm.nih.gov/FLC/getmgc.cgi">NCBI MGC retrieval</a>

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Dry-Lab Protocols

• <a href="http://serialbasics.free.fr/Serial_Cloner.html">serial cloner</a>
• Protein Fusion Design
  • rcsC-envZ cimaera design
  • Literature review
  • Computational analysis
• Twin-Arginine Translocation Pathway Signal Peptide
  • Lee et al., 2006. The Bacterial Twin-Arginine Translocation Pathway. Annu. Rev. Microbiol., 60, p373-395
    • Properties of TAT Signal Peptides
    • <a href="http://www.jic.bbsrc.ac.uk/staff/tracy-palmer/signals.htm">A link to a list of Tat signal sequences provided by Tracy Palmer</a>
    • 29 putative signal peptides 
    • Selected TAT signal peptides
    • Signal peptides and insulin A, B chain
    • Signal peptides and IDE coding sequence

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General references

• <a href="http://www.neb.com/nebecomm/tech_reference/default.asp">New England Biolab (NEB) technical references</a>

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