Protocols: Difference between revisions

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==Contributing protocols==
==Contributing protocols==
===Add new protocols===
===Add new protocols===
*[[Protocols/Template|'''Add a new lab- or person-specific protocol''']]
*[[Protocols/Create|'''Add a new lab- or person-specific protocol''']]
*[[Protocols/Consensus template|'''Add a consensus protocol''']] ([[Help:Consensus protocol|?]])
*[[Protocols/Consensus template|'''Add a consensus protocol''']] ([[Help:Consensus protocol|?]])


*[[OpenWetWare:Nature Methods article|'''Nature Methods article on OWW protocols''']]


===Improve protocols in development===
===Improve protocols in development===
'''''Please Contribute!'''''
'''''Please Contribute!'''''
* [[Pulse-chase protein production]]
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Needs attention]]-->
* [[Fixing cells]]
{{#dpl:category=Needs attention|category=Protocol}}
* [[Q-PCR]]
 
* [[B-galactosidase assay|&beta;-galactosidase assay]] 
* [[Denaturing acrylamide gel purification of nucleic acids]]
* [[Quantitating nucleic acids]]
* [[Bacterial species identification]]
* [[Yeast artificial chromosomes]]
* [[One step 'miniprep' method for the isolation of plasmid DNA]]
* [[Cleaning Glass Coverslips]]
* [["Core Sample" PCR: Amplifying DNA from agarose gels]]
* [[Broncho-alveolar Lavage]]
* [[Artificial transcriptional terminators]]
* [[Codon usage optimization]]
* [[Making construction plasmid]]
* [[Isolation of murine splenocytes]]
* [[Intracellular cytokine staining for flow cytometry (mouse)]]
* [[Streptavidin purification of DNA fragments]]
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==''In vivo''==
==''In vivo''==


{{protocols group|''Acetobacter xylinum''|2=
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Acetobacter xylinum]]-->
{{#dpl:category=Acetobacter xylinum|category=Protocol|}}
}}
{{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=
{{protocols group|''[[Escherichia coli]]''|2=
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Escherichia coli]]-->
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Escherichia coli]]-->
{{#dpl:category=Escherichia coli|category=Protocol}}
{{#dpl:category=Escherichia coli|category=Protocol|nottitlematch=%:%}}
{{#dpl:category=Escherichia coli|category=Protocol|titlematch=%:%}}
 
}}
 
{{protocols group|''Lactic Acid Bacteria''|2=
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Lactobacillus]]-->
{{#dpl:category=Lactobacillus|category=Protocol|}}
 
}}
}}


{{protocols group|''Mesoplasma florum''|2=
{{protocols group|''[[Mesoplasma florum]]''|2=
* [[Mesoplama florum:Culture media|Culture media]]  
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Mesoplasma florum]]-->
* [[Mesoplasma florum:Microarray design]]
{{#dpl:category=Mesoplasma florum|category=Protocol|}}
* [[Mesoplasma florum:Codon usage]]
 
* [[Mesoplasma florum:Physiology]]
* [[Mesoplasma florum:Genome]]
}}
}}


{{protocols group|Mouse|2=
{{protocols group|Mouse|2=
* [[Mouse keratinocyte cultures]]
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Mouse]]-->
* [[Mouse tissue lysis for genotyping]]
{{#dpl:category=Mouse|category=Protocol}}
}}
}}


{{protocols group|''Mycobacterium smegmatis''|2=
{{protocols group|''Mycobacterium smegmatis''|2=
* [[Transformation by electroporation]]
<!--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}}
}}
 
{{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=
{{protocols group|T7|2=
* [[Cesium Chloride Purification of T7]]  
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:T7]]-->
* [[Studier Lysate Prep]]  
{{#dpl:category=T7|category=Protocol}}
}}
}}


{{protocols group|Yeast|2=
{{protocols group|[[Yeast]]|2=
* [[Yeast culture media]]
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Yeast]]-->
* [[Preserving yeast cultures]]
{{#dpl:category=Yeast|category=Protocol}}
* [[Assaying mating]]
* [[Cell Cycle Arrest]]
* [[Dropout plates for yeast]]
* [[High Efficiency Transformation]]
* [[Spheroplast Transformation]]
* [[Layered plates]]
* [[Silver: Lysate for Western]] <font size=1>(for Western etc.)</font>  
* [[Silver: Time-Lapse Microscopy]]
* [[Yeast Colony PCR]]
* [[Yeast DNA Prep]]
}}
}}


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{{protocols group|Nucleic acids|2=
{{protocols group|Nucleic acids|2=
* [[Nucleic acid precipitation]]  
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In vitro]] and [[Category:DNA]] and [[Category:RNA-->
* [[Phenol/chloroform extraction]]  
{{#dpl:category=DNA|category=RNA|category=In vitro|category=Protocol|nottitlematch=%:%}}
* [[Quantitating nucleic acids]]
{{#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|DNA|2=
{{protocols group|[[Protein]]|2=
* [[Agarose gel electrophoresis]]  
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In vitro]] and [[Category:Protein]]-->
* [[Annealing Primers]]
{{#dpl:category=Protein|category=In vitro|category=Protocol|nottitlematch=%:%}}
* [[Centrifugal filtration/Nucleic acids]]
{{#dpl:category=Protein|category=In vitro|category=Protocol|titlematch=%:%}}
* [[DNA Ligation]]
* [[DNA Synthesis from Oligos]]
* [[Designing primers]]  
* [[Double stranding oligo libraries]]
* [[Library Generation]]
* [[Miniprep]]
* [[PCR]]
* [[PCR Overlap Extension]]
* [[PNK Treatment of DNA Ends]]
* [[Phosphatase treatment of linearized vector]]
* [http://arep.med.harvard.edu/polony/polony_protocols Polony Protocols]
* [[Purification of DNA]]
* [[Reconstituting primers]]
* [[Restriction digest]]  
* [['Round-the-horn site-directed mutagenesis]]
* [[Sequencing DNA]]
* [[Site-directed mutagenesis]]
* [[Sauer:Stitching Genes by PCR]]
* [[TempliPhi]]
* [[Affymetrix DNA labelling for gene expression arrays|Affymetrix DNA Labeling]]
}}
}}


{{protocols group|RNA|2=
{{protocols group|[[Lipid]]|2=
* [[RNA Quality Control]]
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In vitro]] and [[Category:Lipid]]-->
* [[In vitro transcription with T7 RNA polymerase]]
{{#dpl:category=Lipid|category=In vitro|category=Protocol|nottitlematch=%:%}}
* [[Northern Blot, 32P End-Labeled Probes ]]
{{#dpl:category=Lipid|category=In vitro|category=Protocol|titlematch=%:%}}
* [[Probe Prep, 32P End-Labeled Probes]]
* [[RNA Extraction|RNA extraction]]
* [[Sauer:RNA Purification from E. coli]]
* [[RNA electrophoresis]]
* [[RNA Half-life|RNA half-life]]
* [[RNase Protection Assay]]
* [[Affymetrix One Cycle Eukaryotic Gene Expression Sample Processing|Affymetrix One cycle labeling]]
* [[Affymetrix Two Cycle Eukaryotic Gene Expression Sample Processing|Affymetrix Small sample labeling]]
* [[Affymetrix Prokaryotic Gene Expression Sample Processing|Affymetrix Prokaryotic Labeling]]
}}
}}


{{protocols group|Protein|2=
{{protocols group|Mammalian cell culture|2=
* [[Acrylamide gels]]
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In vitro]] and [[Category:Mammalian cell culture]]-->
* [[Chromatin Immunoprecipitation]]
{{#dpl:category=Mammalian cell culture|category=In vitro|category=Protocol}}
* [[Electrophoretic mobility shift assay]]
* [[Keating:Experimental Protocols:HPLC]]  
* Protein Preps: Yeast
** [[Endy: Denaturing Protein Extraction Yeast| Denaturing Protein Extraction]]  
** [[Endy: Native Protein Extraction Yeast| Native Protein Extraction]]  
* [[Purification of His-tagged proteins]]
* [[Free Sulfhydryl Determination]]
* [[Sauer:Lysing E. coli with Lysozymes]]
* [[Sauer:Expression/purification of 35S-Met proteins|Expression and purification of <sup>35</sup>S-labeled proteins]]
* [[Silver staining]]
* [[Western blot]]
* [[Dot Blot]]
}}
}}


{{protocols group|Plant specific protocols|2=
{{protocols group|Plant specific protocols|2=
* [[Hop DNA Isolation]]
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In vitro]] and [[Category:Plant]]-->
* [[Transformation Protocol for Tobacco]]
{{#dpl:category=Plant|category=In vitro|category=Protocol}}
* [[Transformation Protocol for Arabidopsis]]
}}
}}
|-
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==''In silico''==
==''In silico''==


{{protocols group|Sequence Analysis|2=
{{protocols group|[[Cloning]]|2=
* [[BLAST]]  
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In silico]] and [[Category:Cloning]]-->
* [[CLUSTALW]]  
{{#dpl:category=Cloning|category=In silico|category=Protocol|titlematch=%:%}}
* [[Protein motifs]]
}}
* [[Plasmapper]]
 
{{protocols group|[[Data analysis]]|2=
<!--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=%:%}}
}}
 
{{protocols group|[[Databases]]|2=
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In silico]] and [[Category:Databases]]-->
{{#dpl:category=Databases|category=In silico|category=Protocol|titlematch=%:%}}
}}
}}


{{protocols group|Structure|2=
{{protocols group|[[Modelling]]|2=
* [[THREADER]]  
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In silico]] and [[Category:Modelling]]-->
* [[Homology Modelling]]  
{{#dpl:category=Modelling|category=In silico|category=Protocol|nottitlematch=%:%}}
{{#dpl:category=Modelling|category=In silico|category=Protocol|titlematch=%:%}}
}}
}}


{{protocols group|Pathway Modelling|2=
{{protocols group|[[Sequence analysis]]|2=
* [[FBA]]  
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In silico]] and [[Category:Sequence analysis]]-->
* [[MoMA]]  
{{#dpl:category=Sequence analysis|category=In silico|category=Protocol|nottitlematch=%:%}}
{{#dpl:category=Sequence analysis|category=In silico|category=Protocol|titlematch=%:%}}
}}
}}


{{protocols group|X-Ray Crystallography|2=
{{protocols group|[[Structure analysis]]|2=
* [[Coot_and_WinCoot_for_X-ray_Crystallography_Model_Building | Coot for Model Building]]
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In silico]] and [[Category:Sequence analysis]]-->
{{#dpl:category=Structure|category=In silico|category=Protocol|nottitlematch=%:%}}
{{#dpl:category=Structure|category=In silico|category=Protocol|titlematch=%:%}}
}}
}}
[[Tregwiki:Main_Page|Transcriptional Regulation]]
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==Other==
==Other==


{{protocols group|Flow Cytometry|2=
{{protocols group|General resources|2=
* [[Flow Calibration]]  
*[http://www.currentprotocols.com/WileyCDA/ Current Protocols] Most comprehensive source of protocols ranging from molecular biology to neuroscience.
* [[Endy:FACS protocols]]  
*[http://mrw.interscience.wiley.com/emrw/9780471142720/home/ Current Protocols in Molecular Biology]
*[http://www.myjove.com/ JoVE] Journal of Visualized Experiments: An online research journal for publishing visualized (video-based) biological experiments.
*[http://protocol-online.org Protocol-online] Useful protocols and a popular discussion section.
*[http://www.springerprotocols.com Springer Protocols]
}}
 
{{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}}
}}
}}


{{protocols group|Microfluidics|2=
{{protocols group|Microfluidics|2=
* [[Design a Microfluidic Chip]]  
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Microfluidics]]-->
* [[Order a Microfluidic Chip from the Foundry]]  
{{#dpl:category=Microfluidics|category=Protocol}}
* [[Operate Microfluidic Chemostat]]
}}
}}


{{protocols group|Microscopy|2=
{{protocols group|[[Microscopy]]|2=
* [[Agarose Pads for Microscopy]]  
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Microscopy]]-->
* [[Quantitative Microscopy]]  
{{#dpl:category=Microscopy|category=Protocol}}
* [[Silver: Time-Lapse Microscopy]]
}}
}}


{{protocols group|Plate reader|2=
{{protocols group|Plate reader|2=
*[[Endy:Victor3 plate reader]]<font size=1>Plate reader usage protocols</font>
*[[Endy:Victor3 plate reader|Plate reader usage protocols]]
}}
}}


{{protocols group|General resources|2=
{{protocols group|Miscellaneous|2=
*[http://www.mrw.interscience.wiley.com/cp/cpmb/cpmb_contents_fs.html Current Protocols in Molecular Biology] <font size=1>Downloadable pdfs.</font>
<!--To list a protocol here, "tag" the protocol page with only [[Category:Protocol]]-->
*[http://www.molecularcloning.com/members/toc.jsp Molecular Cloning]  
{{#dpl:categoriesminmax=,1|category=Protocol}}
*[http://protocol-online.org Protocol-online] <font size=1>Useful protocols and a popular discussion section.</font>  
*[http://www.invitrogen.com/iProtocol iProtocol] <font size=1>Abridged ''Current Protocols'' Invitrogen protocols.  Not amenable to printing.</font>
*[http://www.myjove.com/ JoVE] is an online research journal for publishing visualized (video-based) biological experiments.
}}
}}


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}}
}}
|}
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{{show hide all}}
{{show hide all}}
<sitesearch>
title=Search Protocols
qualifier=protocol
target=
</sitesearch>
</div>
</div>
__NOTOC__
__NOTOC__

Revision as of 10:52, 18 September 2012

Labs & Groups
From around the world 		Courses
Host & view classes 		Protocols
Share techniques & more 		Blogs
Read OWW blogs

Contributing protocols

Add new protocols


Improve protocols in development

Please Contribute!

In vivo

Acetobacter xylinum

Arabidopsis thaliana

Escherichia coli

Lactic Acid Bacteria

Mesoplasma florum

Mouse

Mycobacterium smegmatis

Plasmodium falciparum

Streptomyces

T7

Yeast


In vitro

Nucleic acids

DNA

RNA

Protein

Lipid

Mammalian cell culture

Plant specific protocols

In silico

Cloning

Data analysis

Databases

Modelling

Sequence analysis

Structure analysis

Transcriptional Regulation


Other

General resources

Aseptic Technique

Flow cytometry

Microfluidics

Microscopy

Plate reader

Miscellaneous

Need help with protocols?

[show all] [hide all] <sitesearch> title=Search Protocols qualifier=protocol target= </sitesearch>

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