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!'''''
* [[Turner:Quick_Transformant_Screen|Cloning - quick transformant screen]]
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Needs attention]]-->
* [[Pulse-chase protein production]]
{{#dpl:category=Needs attention|category=Protocol}}
* [[Fixing cells]]  
* [[Real-time RT-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)]]


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==''In vivo''==
==''In vivo''==


<showhide>
{{protocols group|''Acetobacter xylinum''|2=
{{size|2|'''''Escherichia coli'''''}}__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|}}
* [[Bacterial cell culture]]
}}
* [[Bacterial Transformation ]]
** [[Preparing chemically competent cells]]
** [[Transforming chemically competent cells]]
** [[Electrocompetent cells]]
** [[Electroporation]]
** [[Preparing chemically competent cells (Inoue)]]
** [[Transforming chemically competent cells (Inoue)]]
** [[TOP10 chemically competent cells]]
* [[beta-Galactosidase Assay (A better Miller)]]
* [[Colony PCR]]
* [[Making a long term stock of bacteria]]
* [[Maxiprep]]
* [[Miniprep]]
* [[P1vir phage transduction]]
* [[Recombineering]]
* [[Endy:Pouring plates]]  
* [http://www.cf.ac.uk/biosi/staff/ehrmann/tools/factors.htm Protein expression resource]
* [[S_N Chemostat Protocol]]
</hide>
</showhide>


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


<showhide>
{{protocols group|''[[Escherichia coli]]''|2=
{{size|2|'''Mouse'''}}__HIDER__
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Escherichia coli]]-->
<hide>
{{#dpl:category=Escherichia coli|category=Protocol|nottitlematch=%:%}}
* [[Mouse keratinocyte cultures]]
{{#dpl:category=Escherichia coli|category=Protocol|titlematch=%:%}}
</hide>
</showhide>


<showhide>
}}
{{size|s|'''''Mycobacterium smegmatis'''''}}__HIDER__
<hide>
* [[Transformation by electroporation]]
</hide>
</showhide>


<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]]  
 
* [[Studier Lysate Prep]]  
}}
</hide>
 
</showhide>
{{protocols group|''[[Mesoplasma florum]]''|2=
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Mesoplasma florum]]-->
{{#dpl:category=Mesoplasma florum|category=Protocol|}}
 
}}
 
{{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}}
}}
 
{{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}}
}}
 
 
{{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}}
}}


<showhide>
{{size|2|'''Yeast'''}}__HIDER__
<hide>
* [[Yeast culture media]]
* [[Preserving yeast cultures]]
* [[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]]
</hide>
</showhide>


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==''In vitro''==
==''In vitro''==
<showhide>
{{size|2|'''Nucleic acids'''}}__HIDER__
<hide>
* [[Nucleic acid precipitation]]
* [[Phenol/chloroform extraction]]
* [[Quantitating nucleic acids]]
</hide>
</showhide>


<showhide>
{{protocols group|Nucleic acids|2=
{{size|2|'''DNA'''}}__HIDER__
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In vitro]] and [[Category:DNA]] and [[Category:RNA-->
<hide>
{{#dpl:category=DNA|category=RNA|category=In vitro|category=Protocol|nottitlematch=%:%}}
* [[Agarose gel electrophoresis]]  
{{#dpl:category=DNA|category=RNA|category=In vitro|category=Protocol|titlematch=%:%}}
* [[Annealing Primers]]
}}
* [[Centrifugal filtration/Nucleic acids]]
* [[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]]
* [[TempliPhi]]
* [[Affymetrix DNA labelling for gene expression arrays|Affymetrix DNA Labeling]]
</hide>
</showhide>


<showhide>
{{protocols group|[[DNA]]|2=
{{size|2|'''RNA'''}}__HIDER__
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In vitro]] and [[Category:DNA]]-->
<hide>
{{#dpl:category=DNA|category=In vitro|category=Protocol|nottitlematch=%:%}}
* [[RNA Quality Control]]
{{#dpl:category=DNA|category=In vitro|category=Protocol|titlematch=%:%}}
* [[In vitro transcription with T7 RNA polymerase]]
}}
* [[Northern Blot, 32P End-Labeled Probes ]]
* [[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]]
</hide>
</showhide>


<showhide>
{{protocols group|[[RNA]]|2=
{{size|2|'''Protein'''}}__HIDER__
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In vitro]] and [[Category:RNA]]-->
<hide>
{{#dpl:category=RNA|category=In vitro|category=Protocol|nottitlematch=%:%}}
* [[Acrylamide gels]]
{{#dpl:category=RNA|category=In vitro|category=Protocol|titlematch=%:%}}
* [[Chromatin Immunoprecipitation]]
}}
* [[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]]
</hide>
</showhide>


<showhide>
{{protocols group|[[Protein]]|2=
{{size|2|'''Plant specific protocols'''}}__HIDER__
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In vitro]] and [[Category:Protein]]-->
<hide>
{{#dpl:category=Protein|category=In vitro|category=Protocol|nottitlematch=%:%}}
* [[Banana DNA Isolation]]
{{#dpl:category=Protein|category=In vitro|category=Protocol|titlematch=%:%}}
</hide>
}}
</showhide>


{{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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==''In silico''==
==''In silico''==
<showhide>
{{size|2|'''Sequence Analysis'''}}__HIDER__
<hide>
* [[BLAST]]
* [[CLUSTALW]]
* [[Protein motifs]]
* [[Plasmapper]]
</hide>
</showhide>


<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]]  
}}
* [[Homology Modelling]]  
</hide>
</showhide>


<showhide>
{{protocols group|[[Data analysis]]|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:Data analysis]]-->
<hide>
{{#dpl:category=Data analysis|category=In silico|category=Protocol|nottitlematch=%:%}}
* [[FBA]]  
{{#dpl:category=Data analysis|category=In silico|category=Protocol|titlematch=%:%}}
* [[MoMA]]  
}}
</hide>
 
</showhide>
{{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|[[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=%:%}}
}}
 
{{protocols group|[[Sequence analysis]]|2=
<!--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=%:%}}
{{#dpl:category=Sequence analysis|category=In silico|category=Protocol|titlematch=%:%}}
}}
 
{{protocols group|[[Structure analysis]]|2=
<!--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]]


<showhide>
{{size|2|'''X-Ray Crystallography'''}}__HIDER__
<hide>
* [[Coot_and_WinCoot_for_X-ray_Crystallography_Model_Building | Coot for Model Building]]
</hide>
</showhide>


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==Other==
==Other==
<showhide>
{{size|2|'''Flow Cytometry'''}}__HIDER__
<hide>
* [[Flow Calibration]]
* [[Endy:FACS protocols]]
</hide>
</showhide>


<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]]  
*[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]]  
*[http://protocol-online.org Protocol-online] Useful protocols and a popular discussion section.
* [[Operate Microfluidic Chemostat]]  
*[http://www.springerprotocols.com Springer Protocols]
</hide>
}}
</showhide>


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


<showhide>
{{protocols group|[[Flow cytometry]]|2=
{{size|2|'''Plate reader'''}}__HIDER__
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Flow cytometry]]-->
<hide>
{{#dpl:category=Flow cytometry|category=Protocol}}
*[[Endy:Victor3 plate reader]]<font size=1>Plate reader usage protocols</font>  
}}
</hide>
</showhide>


<showhide>
{{protocols group|Microfluidics|2=
{{size|2|'''General resources'''}}__HIDER__
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Microfluidics]]-->
<hide>
{{#dpl:category=Microfluidics|category=Protocol}}
*[http://www.mrw.interscience.wiley.com/cp/cpmb/cpmb_contents_fs.html Current Protocols in Molecular Biology] <font size=1>Downloadable pdfs.</font>
}}
*[http://www.molecularcloning.com/members/toc.jsp Molecular Cloning]  
 
*[http://protocol-online.org Protocol-online] <font size=1>Useful protocols and a popular discussion section.</font>
{{protocols group|[[Microscopy]]|2=
*[http://www.invitrogen.com/iProtocol iProtocol] <font size=1>Abridged ''Current Protocols'' Invitrogen protocols.  Not amenable to printing.</font>
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Microscopy]]-->
*[http://www.myjove.com/ JoVE] is an online research journal for publishing visualized (video-based) biological experiments.
{{#dpl:category=Microscopy|category=Protocol}}
</hide>
}}
</showhide>
 
<showhide>
{{protocols group|Plate reader|2=
{{size|2|'''Need help with protocols?'''}}__HIDER__
*[[Endy:Victor3 plate reader|Plate reader usage protocols]]
<hide>
}}
 
{{protocols group|Miscellaneous|2=
<!--To list a protocol here, "tag" the protocol page with only [[Category:Protocol]]-->
{{#dpl:categoriesminmax=,1|category=Protocol}}
}}
 
{{protocols group|Need help with protocols?|2=
*[[Questions and Answers|Questions and Answers on OWW]]
*[[Questions and Answers|Questions and Answers on OWW]]
</hide>
}}
</showhide>
|}
|}
 
{{show hide all}}
<showhide>
<sitesearch>
__SHOWALL__ __HIDEALL__
title=Search Protocols
</showhide>
qualifier=protocol
 
target=
</sitesearch>
</div>
</div>
__NOTOC__
__NOTOC__

Revision as of 14:35, 30 July 2015

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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