NYMU Taipei/Protocols2

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<h3>Wet-Lab Protocols</h3>
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<ul>
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    <li><font size="2"><a href="http://www.protocol-online.org/">Protocol online</a></font></li>
 +
    <li><font size="2">PCR (7/20) </font>
 +
    <ul>
 +
        <li><font size="2">[[RT-PCR]] </font></li>
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        <li><font size="2">Q-PCR</font></li>
 +
    </ul>
 +
    </li>
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    <li><font size="2">Quantitation of&nbsp; Nucleic acid concentration</font>
 +
    <ul>
 +
        <li><font size="2"><a href="http://en.wikipedia.org/wiki/Quantification_of_nucleic_acids">Wikipedia</a></font></li>
 +
        <li><font size="2"><a href="http://www.piercenet.com/Objects/View.cfm?type=Page&amp;ID=0A0A7BB1-7582-4611-A116-6F583EC01666">Pierce</a></font></li>
 +
        <li><font size="2"><a href="http://mcbl.iisc.ernet.in/Welcome%20to%20MCBL/Faculty/Parag/microarray%20workshop%20details/quantitation.html">India</a></font></li>
 +
        <li><font size="2"><a href="http://www.kreatech.com/pages/Focus-Areas/*-Hybridization-___-Labeling-protocols/Small-RNA-Labeling-protocol/">Kreatech Biotechnology</a>&nbsp;</font></li>
 +
    </ul>
 +
    </li>
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    <li><font face="Arial" size="2"><span lang="EN-US" style="font-size: 9.5pt; font-family: Arial"><a href="http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/setting_up_reaction.asp">Setting Up a Restriction Endonuclease Reaction</a></span></font><font size="2"> </font></li>
 +
    <li><font size="2">DNA Analysis through Gel Electrophoresis</font></li>
 +
    <li><font size="2">Ligate blunt or cohesive ends in 5 minutes at room temperature</font>
 +
    <ul>
 +
        <li><font size="2"><a href="http://www.neb.com/nebecomm/products/productM2200.asp">Quick Ligation Kit&nbsp;(NEB)</a></font></li>
 +
        <li><font size="2"><a href="http://www.ubi.ca/cart/index.php/cPath/27_163_165">Fast Ligation Kit (UBI)</a></font></li>
 +
        <li><font size="2"><a href="http://www.epibio.com/item.asp?ID=296">Fast-Link DNA Ligation Kit (EPICENTRE Biotechnologies)</a></font></li>
 +
        <li><font size="2"><a href="http://www.fermentas.com/catalog/kits/kitrapidligation.htm">Rapid Ligation Kit (Fermentas)</a></font></li>
 +
        <li><font size="2">All of these are just normal ligase buffers with PEG8000 at a 10-12% concentration. The NEB catalogue gives the original reference.&nbsp;<br />
 +
        Use of crowding agents like PEG allow 5-minute sticky end ligations.</font></li>
 +
    </ul>
 +
    </li>
 +
    <li><font size="2">Vector construction </font>
 +
    <ul>
 +
        <li><font size="2">Vector sequences </font>
 +
        <ul>
 +
            <li><a href="http://seq.yeastgenome.org/vectordb/"><font size="2">VectorDB - Molecular Biology Vector Sequence Database</font></a><font size="2"> </font></li>
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            <li><a href="http://www.shigen.nig.ac.jp/cvector/cvector.html"><font size="2">The cloning vector collection</font></a><font size="2"> </font></li>
 +
            <li><a href="http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/dna_sequences_maps.asp"><font size="2">New England Biolabs (NEB) DNA Sequences and Maps</font></a><font size="2"> </font></li>
 +
            <li><a href="http://www.promega.com/vectors/cloning_vectors.htm"><font size="2">Promega Cloning Vectors</font></a><font size="2"> </font></li>
 +
            <li><a href="http://www.emdbiosciences.com/Products/BrowseProductsByCategory.asp?catid=1628"><font size="2">Novagen Vector Maps</font></a><font size="2"> </font></li>
 +
        </ul>
 +
        </li>
 +
        <li><a href="http://wishart.biology.ualberta.ca/PlasMapper/"><font size="2">PlasMapper Version 2.0 - automatically generates and annotates plasmid maps</font></a><font size="2"> </font></li>
 +
    </ul>
 +
    </li>
 +
    <li><font size="2">[[Transformation]] </font></li>
 +
    <li><font size="2">[[Production of heterologous proteins in Escherichia coli]] </font></li>
 +
    <li><a href="http://openwetware.org/wiki/Endy:Preparing_Antibiotic_Stocks"><font size="2">Antibiotics</font></a><font size="2"> </font></li>
 +
    <li><a href="http://openwetware.org/wiki/Synthetic_Biology:BioBricks/Part_fabrication"><font face="Arial" size="2">Part fabrication</font></a><font size="2"> (</font><a href="http://openwetware.org/wiki/Enzyme_selection_for_BioBricks_digest"><font size="2">Enzyme selection for BioBricks digest</font></a><font size="2">!!) </font></li>
 +
    <li><a href="http://openwetware.org/wiki/BioBricks_construction_tutorial"><font size="2">BioBricks construction tutorial</font></a><font size="2"> </font></li>
 +
    <li><a href="http://openwetware.org/wiki/Silver:_BB_Strategy"><font size="2">Fusion protein</font></a><font size="2"> </font></li>
 +
    <li><font size="2">Glucose assay </font>
 +
    <ul>
 +
        <li><font color="#000000" size="2"><a href="http://en.wikipedia.org/wiki/Blood_sugar">Blood sugar (from Wikipedia)</a></font><font size="2"> </font></li>
 +
        <li><a href="http://www.genengnews.com/articles/chtitem.aspx?tid=1624&amp;chid=3"><font size="2">Glucose Measurement for Cell Culture</font></a><font size="2"> </font></li>
 +
        <li><a href="http://www.sigmaaldrich.com/Area_of_Interest/Life_Science/Metabolomics/Product_Highlights/Enzymatic_Kits.html"><font size="2">Glucose Assay Kits from SigmaAldrich</font></a><font size="2"> </font></li>
 +
        <li><a href="http://www.bioassaysys.com/Order.html"><font size="2">Glucose Assay Kit from QuantiChrom</font></a><font size="2"> </font></li>
 +
        <li><a href="http://www.rpbiotech.com/Biochem_diag_kits/Glucose_Diagnostic_Kit.htm"><font size="2">Biochemical glucose kit from rpbiotech</font></a><font size="2"> </font></li>
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        <li><a href="http://www.anilinepharma.com/products.php?catg=ds&amp;id=1"><font size="2">Glucose Meter from AnilinePharma</font></a><font size="2"> </font></li>
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    </ul>
 +
    </li>
 +
    <li><font size="2">Mammalian Gene Collection (MGC) Full-length cDNA clones </font>
 +
    <ul>
 +
        <li><a href="http://mgc.nci.nih.gov/"><font size="2">at National Cancer Institute of NIH</font></a><font size="2"> </font></li>
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        <li><a href="http://genome.ym.edu.tw/libres/MGC_clones/index.htm"><font size="2">at Genome Research Center of NYMU</font></a><font size="2"> </font></li>
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        <li><a href="http://www.ncbi.nlm.nih.gov/FLC/getmgc.cgi"><font size="2">NCBI MGC retrieval</font></a><font size="2"> </font></li>
 +
    </ul>
 +
    </li>
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</ul>
 +
<h3><hr />
 +
</h3>
 +
<h3>Dry-Lab Protocols</h3>
 +
<ul>
 +
    <li><a href="http://serialbasics.free.fr/Serial_Cloner.html">serial cloner</a></li>
 +
    <li>Protein Fusion Design
 +
    <ul>
 +
        <li>rcsC-envZ cimaera design</li>
 +
    </ul>
 +
    <ul>
 +
        <li>[[Literature review]]</li>
 +
    </ul>
 +
    <ul>
 +
        <li>[[Computational analysis]]</li>
 +
    </ul>
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    </li>
 +
    <li>Twin-Arginine Translocation Pathway Signal Peptide
 +
    <ul>
 +
        <li>Lee et al., 2006. The Bacterial Twin-Arginine Translocation Pathway. Annu. Rev. Microbiol., 60, p373-395
 +
        <ul>
 +
            <li>[[Properties of TAT Signal Peptides]]</li>
 +
            <li><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></li>
 +
            <li>[[29 putative signal peptides]]&nbsp;</li>
 +
            <li>[[Selected TAT signal peptides]]</li>
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            <li>[[Signal peptides and insulin A, B chain]]</li>
 +
            <li>[[Signal peptides and IDE coding sequence]]</li>
 +
        </ul>
 +
        </li>
 +
    </ul>
 +
    </li>
 +
</ul>
 +
<hr />
 +
<h3>General references</h3>
 +
<ul>
 +
    <li><a href="http://www.neb.com/nebecomm/tech_reference/default.asp">New England Biolab (NEB) technical references</a></li>
 +
</ul>
[https://2007.igem.org/NYMU_Taipei/Welcome Back]
[https://2007.igem.org/NYMU_Taipei/Welcome Back]

Revision as of 13:37, 18 October 2007

Wet-Lab Protocols

  • <a href="http://www.protocol-online.org/">Protocol online</a>
  • PCR (7/20)
  • 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>

Dry-Lab Protocols

General references

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

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