NYMU Taipei/Protocols2

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<h3>Wet-Lab Protocols</h3>
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[https://2007.igem.org/NYMU_Taipei/Welcome Back]
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<ul>
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    <li><font size="2">[http://www.protocol-online.org/ Protocol online]</font></li>
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    <li><font size="2">PCR (7/20) </font>
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    <ul>
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        <li><font size="2">RT-PCR </font></li>
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        <li><font size="2">Q-PCR</font></li>
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    </ul>
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    </li>
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    <li><font size="2">Quantitation of&nbsp; Nucleic acid concentration</font>
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    <ul>
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        <li><font size="2">[http://en.wikipedia.org/wiki/Quantification_of_nucleic_acids Wikipedia]</font></li>
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        <li><font size="2">[http://www.piercenet.com/Objects/View.cfm?type=Page&amp;ID=0A0A7BB1-7582-4611-A116-6F583EC01666 Pierce]</font></li>
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        <li><font size="2">[http://mcbl.iisc.ernet.in/Welcome%20to%20MCBL/Faculty/Parag/microarray%20workshop%20details/quantitation.html India]</font></li>
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        <li><font size="2">[http://www.kreatech.com/pages/Focus-Areas/*-Hybridization-___-Labeling-protocols/Small-RNA-Labeling-protocol/ Kreatech Biotechnology]&nbsp;</font></li>
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    </ul>
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    </li>
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    <li>[http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/setting_up_reaction.asp Setting Up a Restriction Endonuclease Reaction]</li>
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    <li><font size="2">DNA Analysis through Gel Electrophoresis</font></li>
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    <li><font size="2">Ligate blunt or cohesive ends in 5 minutes at room temperature</font>
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    <ul>
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        <li><font size="2">[http://www.neb.com/nebecomm/products/productM2200.asp Quick Ligation Kit&nbsp;(NEB)]</font></li>
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        <li><font size="2">[http://www.ubi.ca/cart/index.php/cPath/27_163_165 Fast Ligation Kit (UBI)]</font></li>
 +
        <li><font size="2">[http://www.epibio.com/item.asp?ID=296 Fast-Link DNA Ligation Kit (EPICENTRE Biotechnologies)]</font></li>
 +
        <li><font size="2">[http://www.fermentas.com/catalog/kits/kitrapidligation.htm Rapid Ligation Kit (Fermentas)]</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>
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    <li><font size="2">Vector construction </font>
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    <ul>
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        <li><font size="2">Vector sequences </font>
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        <ul>
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            <li>[http://seq.yeastgenome.org/vectordb/ <font size="2">VectorDB - Molecular Biology Vector Sequence Database</font>]<font size="2"> </font></li>
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            <li>[http://www.shigen.nig.ac.jp/cvector/cvector.html <font size="2">The cloning vector collection</font>]<font size="2"> </font></li>
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            <li>[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>]<font size="2"> </font></li>
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            <li>[http://www.promega.com/vectors/cloning_vectors.htm <font size="2">Promega Cloning Vectors</font>]<font size="2"> </font></li>
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            <li>[http://www.emdbiosciences.com/Products/BrowseProductsByCategory.asp?catid=1628 <font size="2">Novagen Vector Maps</font>]<font size="2"> </font></li>
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        </ul>
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        </li>
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        <li>[http://wishart.biology.ualberta.ca/PlasMapper/ <font size="2">PlasMapper Version 2.0 - automatically generates and annotates plasmid maps</font>]<font size="2"> </font></li>
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    </ul>
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    </li>
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    <li><font size="2">[Transformation] </font></li>
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    <li><font size="2">[https://2007.igem.org/NYMU_Taipei/Protocols2/Production_of_heterologous_proteins_in_Escherichia_coli Production of heterologous proteins in Escherichia coli] </font></li>
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    <li>[http://openwetware.org/wiki/Endy:Preparing_Antibiotic_Stocks <font size="2">Antibiotics</font>]<font size="2"> </font></li>
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    <li>[http://openwetware.org/wiki/Synthetic_Biology:BioBricks/Part_fabrication <font face="Arial" size="2">Part fabrication</font>]<font size="2"> (</font>[http://openwetware.org/wiki/Enzyme_selection_for_BioBricks_digest <font size="2">Enzyme selection for BioBricks digest</font>]<font size="2">!!) </font></li>
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    <li>[http://openwetware.org/wiki/BioBricks_construction_tutorial <font size="2">BioBricks construction tutorial</font>]<font size="2"> </font></li>
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    <li>[http://openwetware.org/wiki/Silver:_BB_Strategy <font size="2">Fusion protein</font>]<font size="2"> </font></li>
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    <li><font size="2">Glucose assay </font>
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    <ul>
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        <li><font color="#000000" size="2">[http://en.wikipedia.org/wiki/Blood_sugar Blood sugar (from Wikipedia)]</font><font size="2"> </font></li>
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        <li>[http://www.genengnews.com/articles/chtitem.aspx?tid=1624&amp;chid=3 <font size="2">Glucose Measurement for Cell Culture</font>]<font size="2"> </font></li>
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        <li>[http://www.sigmaaldrich.com/Area_of_Interest/Life_Science/Metabolomics/Product_Highlights/Enzymatic_Kits.html <font size="2">Glucose Assay Kits from SigmaAldrich</font>]<font size="2"> </font></li>
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        <li>[http://www.bioassaysys.com/Order.html <font size="2">Glucose Assay Kit from QuantiChrom</font>]<font size="2"> </font></li>
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        <li>[http://www.rpbiotech.com/Biochem_diag_kits/Glucose_Diagnostic_Kit.htm <font size="2">Biochemical glucose kit from rpbiotech</font>]<font size="2"> </font></li>
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        <li>[http://www.anilinepharma.com/products.php?catg=ds&amp;id=1 <font size="2">Glucose Meter from AnilinePharma</font>]<font size="2"> </font></li>
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    </ul>
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    </li>
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    <li><font size="2">Mammalian Gene Collection (MGC) Full-length cDNA clones </font>
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    <ul>
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        <li>[http://mgc.nci.nih.gov/ <font size="2">at National Cancer Institute of NIH</font>]<font size="2"> </font></li>
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        <li>[http://genome.ym.edu.tw/libres/MGC_clones/index.htm <font size="2">at Genome Research Center of NYMU</font>]<font size="2"> </font></li>
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        <li>[http://www.ncbi.nlm.nih.gov/FLC/getmgc.cgi <font size="2">NCBI MGC retrieval</font>]<font size="2"> </font></li>
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    </ul>
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    </li>
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</ul>
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<h3><hr />
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</h3>
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<h3>Dry-Lab Protocols</h3>
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<ul>
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    <li>[http://serialbasics.free.fr/Serial_Cloner.html serial cloner]</li>
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    <li>Protein Fusion Design
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    <ul>
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        <li>rcsC-envZ cimaera design</li>
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    </ul>
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    <ul>
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        <li>[https://2007.igem.org/NYMU_Taipei/Protocols2/Literature_reiew Literature review]</li>
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    </ul>
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    <ul>
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        <li>[https://2007.igem.org/NYMU_Taipei/Protocols2/Computational_analysis Computational analysis]</li>
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    </ul>
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    </li>
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    <li>Twin-Arginine Translocation Pathway Signal Peptide
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    <ul>
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        <li>Lee et al., 2006. The Bacterial Twin-Arginine Translocation Pathway. Annu. Rev. Microbiol., 60, p373-395
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        <ul>
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            <li>[https://2007.igem.org/NYMU_Taipei/Protocols2/Properties_of_TAT_Signal_Peptides Properties of TAT Signal Peptides]</li>
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            <li>[http://www.jic.bbsrc.ac.uk/staff/tracy-palmer/signals.htm A link to a list of Tat signal sequences provided by Tracy Palmer]</li>
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            <li>[https://2007.igem.org/NYMU_Taipei/Protocols2/29_putative_signal_peptides 29 putative signal peptides]&nbsp;</li>
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            <li>[https://2007.igem.org/NYMU_Taipei/Protocols2/Selected_TAT_signal_peptides Selected TAT signal peptides]</li>
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            <li>[https://2007.igem.org/NYMU_Taipei/Protocols2/Signal_peptides_and_insulin_A,_B_chain Signal peptides and insulin A, B chain]</li>
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            <li>[https://2007.igem.org/NYMU_Taipei/Protocols2/Signal_peptides_and_IDE_coding_sequence Signal peptides and IDE coding sequence]</li>
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        </ul>
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        </li>
 +
    </ul>
 +
    </li>
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</ul>
 +
<hr />
 +
<h3>General references</h3>
 +
<ul>
 +
    <li>[http://www.neb.com/nebecomm/tech_reference/default.asp New England Biolab (NEB) technical references]</li>
 +
</ul>
 +
[https://2007.igem.org/Taipei Back]

Latest revision as of 05:02, 27 October 2007

Wet-Lab Protocols

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

Dry-Lab Protocols

General references

  • [http://www.neb.com/nebecomm/tech_reference/default.asp New England Biolab (NEB) technical references]

Back

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