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| <!------------------------------------------------------------------------------->
| | |
| <!------------------------Protocol News/Updates---------------------------------->
| | ==Contributing protocols== |
| <!------------------------------------------------------------------------------->
| | ===Add new protocols=== |
| ==Updates== | | *[[Protocols/Create|'''Add a new lab- or person-specific protocol''']] |
| • <font face="courier new" size=1>00/00/00 </font>ABC Improved <BR>
| | *[[Protocols/Consensus template|'''Add a consensus protocol''']] ([[Help:Consensus protocol|?]]) |
| • <font face="courier new" size=1>00/00/00 </font>ABC Added <BR>
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| | |
| | ===Improve protocols in development=== |
| | '''''Please Contribute!''''' |
| | <!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Needs attention]]--> |
| | {{#dpl:category=Needs attention|category=Protocol}} |
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| <div style="clear: right; text-align: left; float: left; padding: 0em .5em 0em">
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| <!------------------------------------------------------------------------------->
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| <!-----------------------------------In vivo------------------------------------->
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| <!------------------------------------------------------------------------------->
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| ==''In vivo''== | | ==''In vivo''== |
| <showhide>
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| {{size|2|'''''Escherichia coli'''''}}__HIDER__
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| <hide>
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| • [[Bacterial cell culture|<font style="color:#000000">Bacterial Cell culture</font>]] <BR>
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| • [[Bacterial Transformation |<font style="color:#000000">Bacterial Transformation</font>]] <BR>
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| • [[Preparing chemically competent cells|<font style="color:#ffffff" size=1>Preparing chemically competent cells (TSS)</font>]] <BR>
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| • [[Transforming chemically competent cells|<font style="color:#ffffff" size=1>Transforming chemically competent cells (TSS)</font>]] <BR>
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| • [[Electrocompetent cells|<font style="color:#ffffff" size=1>Preparing electrocompetent cells</font>]] <BR>
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| • [[Electroporation|<font style="color:#ffffff" size=1>Transforming electrocompetent cells</font>]] <BR>
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| • [[beta-Galactosidase Assay (better Miller)|<font style="color:#000000">β-Galactosidase Assay</font>]] <font size=1>(A better Miller)</font> <BR>
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| • [[Colony PCR|<font style="color:#000000">Colony PCR</font>]] <BR>
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| • [[Making a long term stock of bacteria|<font style="color:#000000">Making long-term stock bacteria</font>]] <BR>
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| • [[Miniprep|<font style="color:#000000">Miniprep</font>]] <BR>
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| • [[P1vir phage transduction|<font style="color:#000000">P1vir phage transduction</font>]] <BR>
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| • [[Pour plates|<font style="color:#000000">Pour LB plates</font>]] <BR>
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| • [http://www.cf.ac.uk/biosi/staff/ehrmann/tools/factors.htm <font style="color:#000000">Protein expression resource</font>] <BR>
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| • [[S_N Chemostat Protocol|<font style="color:#000000">S N Chemostat Protocol</font>]] <BR>
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| </hide>
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| </showhide>
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| <showhide> | | {{protocols group|''Acetobacter xylinum''|2= |
| {{size|2|'''''Mesoplasma florum'''''}}__HIDER__ | | <!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Acetobacter xylinum]]--> |
| <hide> | | {{#dpl:category=Acetobacter xylinum|category=Protocol|}} |
| • [[Mesoplama florum:Culture media|<font style="color:#000000">Preparing culture media</font>]] <BR>
| | }} |
| </hide>
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| </showhide>
| | {{protocols group|''Arabidopsis thaliana''|2= |
| | <!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Arabidopsis thaliana]]--> |
| | {{#dpl:category=Arabidopsis thaliana|category=Protocol|}} |
| | }} |
| | |
| | {{protocols group|''[[Escherichia coli]]''|2= |
| | <!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Escherichia coli]]--> |
| | {{#dpl:category=Escherichia coli|category=Protocol|nottitlematch=%:%}} |
| | {{#dpl:category=Escherichia coli|category=Protocol|titlematch=%:%}} |
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| | }} |
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| <showhide>
| | {{protocols group|''Lactic Acid Bacteria''|2= |
| {{size|2|'''T7'''}}__HIDER__ | | <!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Lactobacillus]]--> |
| <hide> | | {{#dpl:category=Lactobacillus|category=Protocol|}} |
| • [[Cesium Chloride Purification of T7|<font style="color:#000000">Purification T7: Cesium Chloride</font>]] <BR>
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| • [[Studier Lysate Prep|<font style="color:#000000">Simple lysate protocol from plaque/lysate</font>]] <BR>
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| </hide>
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| </showhide>
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| <showhide>
| | }} |
| {{size|2|'''Yeast'''}}__HIDER__
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| <hide>
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| • [[Assaying mating|<font style="color:#000000">Assaying mating</font>]] <BR>
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| • [[Cell Cycle Arrest|<font style="color:#000000">Cell Cycle Arrest</font>]] <BR>
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| • [[Dropout plates for yeast|<font style="color:#000000">Dropout plates</font>]] <BR>
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| • [[High Efficiency Transformation|<font style="color:#000000">High Efficiency Transformation</font>]] <BR>
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| • [[Layered plates|<font style="color:#000000">Layering plates</font>]] <BR>
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| • [[Pour YPD plates|<font style="color:#000000">Pour YPD plates</font>]] <BR>
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| • [[Silver: Lysate for Western|<font style="color:#000000">Simple Yeast Lysate</font>]] <font size=1>(for Western etc.)</font> <BR>
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| • [[Silver: Time-Lapse Microscopy|<font style="color:#000000">Time-Lapse Microscopy</font>]] <BR>
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| • [[Yeast Colony PCR|<font style="color:#000000">Yeast Colony PCR</font>]] <BR>
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| • [[Yeast DNA Prep|<font style="color:#000000">Yeast DNA Prep</font>]] <BR>
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| </hide> | | {{protocols group|''[[Mesoplasma florum]]''|2= |
| </showhide> | | <!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Mesoplasma florum]]--> |
| | {{#dpl:category=Mesoplasma florum|category=Protocol|}} |
| | |
| | }} |
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| | {{protocols group|Mouse|2= |
| | <!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Mouse]]--> |
| | {{#dpl:category=Mouse|category=Protocol}} |
| | }} |
| | |
| | {{protocols group|''Mycobacterium smegmatis''|2= |
| | <!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Mycobacterium smegmatis]]--> |
| | {{#dpl:category=Mycobacterium smegmatis|category=Protocol}} |
| | }} |
| | |
| | {{protocols group|''[[Plasmodium falciparum]]''|2= |
| | <!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Plasmodium falciparum]]--> |
| | {{#dpl:category=Plasmodium falciparum|category=Protocol}} |
| | }} |
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| | {{protocols group|''[[Streptomyces:Information|Streptomyces]]''|2= |
| | <!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Streptomyces]]--> |
| | {{#dpl:category=Streptomyces|category=Protocol}} |
| | }} |
| | |
| | {{protocols group|T7|2= |
| | <!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:T7]]--> |
| | {{#dpl:category=T7|category=Protocol}} |
| | }} |
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| | |
| | {{protocols group|[[Yeast]]|2= |
| | <!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Yeast]]--> |
| | {{#dpl:category=Yeast|category=Protocol}} |
| | }} |
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| | |width="270px" class="green2"| |
| <!-------------------------------------------------------------------------------> | | <!-------------------------------------------------------------------------------> |
| <!-----------------------------------Empty Col-----------------------------------> | | <!-----------------------------------In vitro-----------------------------------> |
| <!-------------------------------------------------------------------------------> | | <!-------------------------------------------------------------------------------> |
| |rowspan="2" width="20px" style="border: 0px solid #000000; color: #000; background-color: #5A87B6" valign="top"|
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| </div>
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| |width="265px" style="border: 0px solid #000000; color: #000; background-color: #517AA3" valign="top"| | | ==''In vitro''== |
| <div style="clear: right; text-align: left; float: left; padding: 0em .5em 0em"> | | |
| | {{protocols group|Nucleic acids|2= |
| | <!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In vitro]] and [[Category:DNA]] and [[Category:RNA--> |
| | {{#dpl:category=DNA|category=RNA|category=In vitro|category=Protocol|nottitlematch=%:%}} |
| | {{#dpl:category=DNA|category=RNA|category=In vitro|category=Protocol|titlematch=%:%}} |
| | }} |
| | |
| | {{protocols group|[[DNA]]|2= |
| | <!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In vitro]] and [[Category:DNA]]--> |
| | {{#dpl:category=DNA|category=In vitro|category=Protocol|nottitlematch=%:%}} |
| | {{#dpl:category=DNA|category=In vitro|category=Protocol|titlematch=%:%}} |
| | }} |
| | |
| | {{protocols group|[[RNA]]|2= |
| | <!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In vitro]] and [[Category:RNA]]--> |
| | {{#dpl:category=RNA|category=In vitro|category=Protocol|nottitlematch=%:%}} |
| | {{#dpl:category=RNA|category=In vitro|category=Protocol|titlematch=%:%}} |
| | }} |
| | |
| | {{protocols group|[[Protein]]|2= |
| | <!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In vitro]] and [[Category:Protein]]--> |
| | {{#dpl:category=Protein|category=In vitro|category=Protocol|nottitlematch=%:%}} |
| | {{#dpl:category=Protein|category=In vitro|category=Protocol|titlematch=%:%}} |
| | }} |
| | |
| | {{protocols group|[[Lipid]]|2= |
| | <!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In vitro]] and [[Category:Lipid]]--> |
| | {{#dpl:category=Lipid|category=In vitro|category=Protocol|nottitlematch=%:%}} |
| | {{#dpl:category=Lipid|category=In vitro|category=Protocol|titlematch=%:%}} |
| | }} |
| | |
| | {{protocols group|Mammalian cell culture|2= |
| | <!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In vitro]] and [[Category:Mammalian cell culture]]--> |
| | {{#dpl:category=Mammalian cell culture|category=In vitro|category=Protocol}} |
| | }} |
| | |
| | {{protocols group|Plant specific protocols|2= |
| | <!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In vitro]] and [[Category:Plant]]--> |
| | {{#dpl:category=Plant|category=In vitro|category=Protocol}} |
| | }} |
| | |- |
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| | |width="265px" class="green2"| |
| <!-------------------------------------------------------------------------------> | | <!-------------------------------------------------------------------------------> |
| <!-----------------------------------In silico-----------------------------------> | | <!-----------------------------------In silico------------------------------------> |
| <!-------------------------------------------------------------------------------> | | <!-------------------------------------------------------------------------------> |
| | |
| ==''In silico''== | | ==''In silico''== |
| <showhide>
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| {{size|2|'''Sequence Analysis'''}}__HIDER__
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| <hide>
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| • [[BLAST|<font style="color:#000000">BLAST</font>]] <BR>
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| • [[CLUSTALW|<font style="color:#000000">CLUSTALW</font>]] <BR>
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| </hide>
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| </showhide>
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| <showhide> | | {{protocols group|[[Cloning]]|2= |
| {{size|2|'''Structure'''}}__HIDER__ | | <!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In silico]] and [[Category:Cloning]]--> |
| <hide>
| | {{#dpl:category=Cloning|category=In silico|category=Protocol|titlematch=%:%}} |
| • [[THREADER|<font style="color:#000000">THREADER</font>]] <BR>
| | }} |
| • [[Homology Modelling|<font style="color:#000000">Homology Modeling</font>]] <BR>
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| </hide>
| | {{protocols group|[[Data analysis]]|2= |
| </showhide>
| | <!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In silico]] and [[Category:Data analysis]]--> |
| | {{#dpl:category=Data analysis|category=In silico|category=Protocol|nottitlematch=%:%}} |
| | {{#dpl:category=Data analysis|category=In silico|category=Protocol|titlematch=%:%}} |
| | }} |
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| <showhide>
| | {{protocols group|[[Databases]]|2= |
| {{size|2|'''Pathway Modelling'''}}__HIDER__ | | <!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In silico]] and [[Category:Databases]]--> |
| <hide> | | {{#dpl:category=Databases|category=In silico|category=Protocol|titlematch=%:%}} |
| • [[FBA|<font style="color:#000000">Flux Balance Analysis</font>]] <BR>
| | }} |
| • [[MoMA|<font style="color:#000000">Minimisation of Metabolic Adjustment</font>]] <BR>
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| </hide>
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| </showhide>
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| </div>
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| |- | | {{protocols group|[[Modelling]]|2= |
| | <!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In silico]] and [[Category:Modelling]]--> |
| | {{#dpl:category=Modelling|category=In silico|category=Protocol|nottitlematch=%:%}} |
| | {{#dpl:category=Modelling|category=In silico|category=Protocol|titlematch=%:%}} |
| | }} |
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| |width="280px" style="border: 0px solid #000000; color: #000; background-color: #517AA3" valign="top"| | | {{protocols group|[[Sequence analysis]]|2= |
| <div style="clear: right; text-align: left; float: left; padding: 0em .5em 0em">
| | <!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In silico]] and [[Category:Sequence analysis]]--> |
| <!-------------------------------------------------------------------------------> | | {{#dpl:category=Sequence analysis|category=In silico|category=Protocol|nottitlematch=%:%}} |
| <!-----------------------------------In vitro------------------------------------>
| | {{#dpl:category=Sequence analysis|category=In silico|category=Protocol|titlematch=%:%}} |
| <!------------------------------------------------------------------------------->
| | }} |
| ==''In vitro''== | |
| <showhide>
| |
| {{size|2|'''Nucleic acids'''}}__HIDER__ | |
| <hide>
| |
| • [[Nucleic acid precipitation|<font style="color:#000000">Nucleic acid precipitation</font>]] <BR>
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| • [[Phenol/chloroform extraction|<font style="color:#000000">Phenol/chloroform extraction</font>]] <BR>
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| </hide>
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| </showhide>
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| <showhide>
| | {{protocols group|[[Structure analysis]]|2= |
| {{size|2|'''DNA'''}}__HIDER__ | | <!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In silico]] and [[Category:Sequence analysis]]--> |
| <hide>
| | {{#dpl:category=Structure|category=In silico|category=Protocol|nottitlematch=%:%}} |
| • [[Agarose gel electrophoresis|<font style="color:#000000">Agarose gel electrophoresis</font>]] <BR>
| | {{#dpl:category=Structure|category=In silico|category=Protocol|titlematch=%:%}} |
| • [[Annealing Primers|<font style="color:#000000">Annealing Primers</font>]] <BR>
| | }} |
| • [[Designing primers|<font style="color:#000000">Designing Primers</font>]] <BR>
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| • [[DNA Ligation|<font style="color:#000000">DNA Ligation</font>]] <BR>
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| • [[Library Generation|<font style="color:#000000">Library Generating</font>]] <BR>
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| • [[Miniprep|<font style="color:#000000">Miniprep</font>]] <BR>
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| • [[PCR|<font style="color:#000000">PCR</font>]] <BR>
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| • [[Phosphatase treatment of linearized vector|<font style="color:#000000">Phosphate treatment linearized vector</font>]] <BR>
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| • [http://arep.med.harvard.edu/polony/polony_protocols <font style="color:#000000">Polony Protocols</font>]<font size=1>(Church/Mitra Lab)</font> <BR>
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| • [[PNK Treatment of DNA Ends|<font style="color:#000000">PNK Treatment of DNA ends</font>]] <BR>
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| • [[Purification of DNA|<font style="color:#000000">Purification of DNA</font>]] <BR>
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| • [[Reconstituting primers|<font style="color:#000000">Reconstituting Primers</font>]] <BR>
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| • [[Restriction digest|<font style="color:#000000">Restriction Digest</font>]] <BR>
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| • [['Round-the-horn site-directed mutagenesis|<font style="color:#000000">'Round-the-horn site-directed mutagenesis</font>]] <BR>
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| • [[Sequencing DNA|<font style="color:#000000">Sequencing DNA</font>]] <BR>
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| • [[Site-directed mutagenesis|<font style="color:#000000">Site-directed Mutagenesis</font>]] <BR>
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| • [[Templiphi|<font style="color:#000000">Templiphi</font>]] <BR>
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| </hide>
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| </showhide>
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| <showhide>
| | [[Tregwiki:Main_Page|Transcriptional Regulation]] |
| {{size|2|'''RNA'''}}__HIDER__
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| <hide>
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| • [[In vitro transcription with T7 RNA polymerase|<font style="color:#000000">In vitro transcription w/ T7 RNA polymerase</font>]] <BR>
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| • [[Northern Blot, 32P End-Labeled Probes |<font style="color:#000000">Northern Blot, <sup>32</sup>P End-Labeled Probes</font>]] <BR>
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| • [[Probe Prep, 32P End-Labeled Probes|<font style="color:#000000">Probe Prep, <sup>32</sup>P End-Labeled Probes</font>]] <BR>
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| • [[RNA Extraction|<font style="color:#000000">RNA Extraction</font>]] <BR>
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| • [[RNase Protection Assay|<font style="color:#000000">RNAse Protection Assay</font>]] <BR>
| |
| </hide>
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| </showhide>
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| <showhide>
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| {{size|2|'''Protein'''}}__HIDER__
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| <hide>
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| • [[Acrylamide Gels|<font style="color:#000000">Acrylamide gels and SDS-PAGE</font>]] <BR>
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| • [[Silver: Destain|<font style="color:#000000">Coomassie Destain</font>]] <BR>
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| • [[Silver: Coomassie Stain|<font style="color:#000000">Coomassie Stain</font>]] <BR>
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| • [[Keating:Experimental Protocols:HPLC|<font style="color:#000000">HPLC</font>]] <BR>
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| • [[Silver staining|<font style="color:#000000">Silver staining</font>]] <BR>
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| • [[Western Blot|<font style="color:#000000">Western Blot</font>]] <BR>
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| • [[Purification of His-tagged proteins|<font style="color:#000000">Purification His-tagged proteins</font>]] <BR>
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| </hide>
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| </showhide>
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| </div>
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| <div style="clear: right; text-align: left; float: left; padding: 0em .5em 0em">
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| <!-------------------------------------------------------------------------------> | | <!-------------------------------------------------------------------------------> |
| <!-----------------------------------OTHER---------------------------------------> | | <!-----------------------------------OTHER---------------------------------------> |
| <!-------------------------------------------------------------------------------> | | <!-------------------------------------------------------------------------------> |
| | |
| ==Other== | | ==Other== |
| <showhide>
| |
| {{size|2|'''Flow Cytometry'''}}__HIDER__
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| <hide>
| |
| • [[Flow Calibration|<font style="color:#000000">Flow Calibration</font>]] <BR>
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| </hide>
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| </showhide>
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| <showhide>
| | {{protocols group|General resources|2= |
| {{size|2|'''Microfluidics'''}}__HIDER__ | | *[http://www.currentprotocols.com/WileyCDA/ Current Protocols] Most comprehensive source of protocols ranging from molecular biology to neuroscience. |
| <hide>
| | *[http://mrw.interscience.wiley.com/emrw/9780471142720/home/ Current Protocols in Molecular Biology] |
| • [[Design a Microfluidic Chip|<font style="color:#000000">Design Microfluidic Chip</font>]] <BR>
| | *[http://www.myjove.com/ JoVE] Journal of Visualized Experiments: An online research journal for publishing visualized (video-based) biological experiments. |
| • [[Order a Microfluidic Chip from the Foundry|<font style="color:#000000">Order Microfluidic Chip from Foundry</font>]] <BR>
| | *[http://protocol-online.org Protocol-online] Useful protocols and a popular discussion section. |
| • [[Operate Microfluidic Chemostat|<font style="color:#000000">Operate Microfluidic Chemostat</font>]] <BR>
| | *[http://www.springerprotocols.com Springer Protocols] |
| </hide>
| | }} |
| </showhide>
| | |
| | {{protocols group|[[Aseptic Technique]]|2= |
| | <!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Aseptic Technique]]--> |
| | {{#dpl:category=Aseptic Technique|category=Protocol}} |
| | }} |
| | |
| | {{protocols group|[[Flow cytometry]]|2= |
| | <!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Flow cytometry]]--> |
| | {{#dpl:category=Flow cytometry|category=Protocol}} |
| | }} |
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| <showhide>
| | {{protocols group|Microfluidics|2= |
| {{size|2|'''Microscopy'''}}__HIDER__ | | <!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Microfluidics]]--> |
| <hide> | | {{#dpl:category=Microfluidics|category=Protocol}} |
| • [[Agarose Pads for Microscopy|<font style="color:#000000">Agarose Pads</font>]] <BR>
| | }} |
| • [[Quantitative Microscopy|<font style="color:#000000">Quantitative Microscopy</font>]] <BR>
| |
| • [[Silver: Time-Lapse Microscopy|<font style="color:#000000">Time-Lapse Microscopy</font>]] <BR>
| |
| </hide>
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| </showhide>
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| <showhide>
| | {{protocols group|[[Microscopy]]|2= |
| {{size|2|'''Plate reader'''}}__HIDER__ | | <!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Microscopy]]--> |
| <hide> | | {{#dpl:category=Microscopy|category=Protocol}} |
| • [[Endy:Victor3 plate reader|<font style="color:#000000">Perkin Elmer Victor<sup>3</sup></font>]]<font size=1><BR>Plate reader usage protocols</font> <BR>
| | }} |
| </hide>
| |
| </showhide>
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| {{size|2|'''General resources'''}}<BR> | | {{protocols group|Plate reader|2= |
| • [http://protocol-online.org <font style="color:#000000">Protocol-online</font>] <font size=1><BR>Contains a lot of useful protocols and a popular discussion section.</font> <BR>
| | *[[Endy:Victor3 plate reader|Plate reader usage protocols]] |
| <!------------------------------------------------------------------------------->
| | }} |
| <!-----------------------------------IN DEVELOPMENT------------------------------>
| |
| <!------------------------------------------------------------------------------->
| |
| {{size|2|'''Protocols in Development'''}}
| |
| '''Please Contribute!'''<BR>
| |
| • [[Pulse-chase protein production|<font style="color:#000000">Pulse-chase protein production</font>]] <BR>
| |
| • [[Fixing cells|<font style="color:#000000">Fixing cells</font>]] <BR>
| |
| • [[B-galactosidase assay|<font style="color:#000000">β-galactosidase assay</font>]] <BR>
| |
| • [[RNA Half-life|<font style="color:#000000">RNA Half-life</font>]] <BR>
| |
| • [[Denaturing acrylamide gel purification of nucleic acids|<font style="color:#000000">Denaturing acrylamide gel purification NA</font>]] <BR>
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| • [[Quantification of nucleic acids|<font style="color:#000000">Quantification of nucleic acids</font>]] <BR>
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| </div>
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| |}
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