Protocols: Difference between revisions

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==Contributing protocols==
[[Image:OWWProtocols.png]]
===Add new protocols===
<hr class=divider>
*[[Protocols/Create|'''Add a new lab- or person-specific protocol''']]
*[[Protocols/Consensus template|'''Add a consensus protocol''']] ([[Help:Consensus protocol|?]])


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==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}}
* [[Real-time RT-PCR]]
* [[B-galactosidase assay|&beta;-galactosidase assay]] 
* [[Denaturing acrylamide gel purification of nucleic acids]]
* [[Quantification of nucleic acids]]
* [[Bacterial species identification]]
 


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==''In vivo''==
==''In vivo''==
<showhide>
{{size|2|'''''Escherichia coli'''''}}__HIDER__
<hide>
* [[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)]]
* [[beta-Galactosidase Assay (A better Miller)]]
* [[Colony PCR]]
* [[Making a long term stock of bacteria]]
* [[Miniprep]]
* [[P1vir phage transduction]]
* [[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|''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|Culture media]]  
}}
</hide>
 
</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=%:%}}


<showhide>
}}
{{size|2|'''T7'''}}__HIDER__
<hide>
* [[Cesium Chloride Purification of T7]]
* [[Studier Lysate Prep]]
</hide>
</showhide>


<showhide>
{{protocols group|''Lactic Acid Bacteria''|2=
{{size|2|'''Yeast'''}}__HIDER__
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Lactobacillus]]-->
<hide>
{{#dpl:category=Lactobacillus|category=Protocol|}}
* [[Assaying mating]]  
 
* [[Cell Cycle Arrest]]  
}}
* [[Dropout plates for yeast]]  
 
* [[High Efficiency Transformation]]  
{{protocols group|''[[Mesoplasma florum]]''|2=
* [[Layered plates]]  
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Mesoplasma florum]]-->
* [[Pour YPD plates]]  
{{#dpl:category=Mesoplasma florum|category=Protocol|}}
* [[Silver: Lysate for Western]] <font size=1>(for Western etc.)</font>
 
* [[Silver: Time-Lapse Microscopy]]  
}}
* [[Yeast Colony PCR]]  
 
* [[Yeast DNA Prep]]  
{{protocols group|Mouse|2=
</hide>
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Mouse]]-->
</showhide>
{{#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|'''Mouse'''}}__HIDER__
<hide>
* [[Mouse keratinocyte cultures]]
</hide>
</showhide>


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==''In vitro''==
==''In vitro''==
<showhide>
{{size|2|'''Nucleic acids'''}}__HIDER__
<hide>
* [[Nucleic acid precipitation]]
* [[Phenol/chloroform extraction]]
</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]]  
}}
* [[Designing primers]]
 
* [[DNA Ligation]]  
{{protocols group|[[DNA]]|2=
* [[Double stranding oligo libraries]]
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In vitro]] and [[Category:DNA]]-->
* [[Library Generation]]
{{#dpl:category=DNA|category=In vitro|category=Protocol|nottitlematch=%:%}}
* [[Miniprep]]
{{#dpl:category=DNA|category=In vitro|category=Protocol|titlematch=%:%}}
* [[PCR]]
}}
* [[Phosphatase treatment of linearized vector]]
* [http://arep.med.harvard.edu/polony/polony_protocols Polony Protocols]
* [[PNK Treatment of DNA Ends]]  
* [[Purification of DNA]]  
* [[Reconstituting primers]]  
* [[Restriction digest]]  
* [['Round-the-horn site-directed mutagenesis]]
* [[Sequencing DNA]]
* [[Site-directed mutagenesis]]
* [[Templiphi]]
</hide>
</showhide>


<showhide>
{{protocols group|[[RNA]]|2=
{{size|2|'''RNA'''}}__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=%:%}}
* [[In vitro transcription with T7 RNA polymerase]]  
{{#dpl:category=RNA|category=In vitro|category=Protocol|titlematch=%:%}}
* [[Northern Blot, 32P End-Labeled Probes ]]  
}}
* [[Probe Prep, 32P End-Labeled Probes]]  
* [[RNA Extraction]]  
* [[RNase Protection Assay]]
* [[RNA Half-life]]
</hide>
</showhide>


<showhide>
{{protocols group|[[Protein]]|2=
{{size|2|'''Protein'''}}__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=%:%}}
* [[Acrylamide Gels]]  
{{#dpl:category=Protein|category=In vitro|category=Protocol|titlematch=%:%}}
* [[Silver: Destain]]  
}}
* [[Silver: Coomassie Stain]]  
* [[Keating:Experimental Protocols:HPLC]]  
* [[Silver staining]]
* [[Western Blot]]
* [[Purification of His-tagged proteins]]
* [[Free Sulfhydryl Determination]]
</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 silicio''==
==''In silico''==
<showhide>
 
{{size|2|'''Sequence Analysis'''}}__HIDER__
{{protocols group|[[Cloning]]|2=
<hide>
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In silico]] and [[Category:Cloning]]-->
* [[BLAST]]  
{{#dpl:category=Cloning|category=In silico|category=Protocol|titlematch=%:%}}
* [[CLUSTALW]]  
}}
</hide>
 
</showhide>
{{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|[[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=%:%}}
}}


<showhide>
{{protocols group|[[Structure analysis]]|2=
{{size|2|'''Structure'''}}__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=%:%}}
* [[THREADER]]
{{#dpl:category=Structure|category=In silico|category=Protocol|titlematch=%:%}}
* [[Homology Modelling]]  
}}
</hide>
 
</showhide>
[[Tregwiki:Main_Page|Transcriptional Regulation]]


<showhide>
{{size|2|'''Pathway Modelling'''}}__HIDER__
<hide>
* [[FBA]]
* [[MoMA]]
</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>


{{size|2|'''General resources'''}}
{{protocols group|Microfluidics|2=
* [http://protocol-online.org Protocol-online] <font size=1>Contains a lot of useful protocols and a popular discussion section.</font>  
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Microfluidics]]-->
{{#dpl:category=Microfluidics|category=Protocol}}
}}


|}
{{protocols group|[[Microscopy]]|2=
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Microscopy]]-->
{{#dpl:category=Microscopy|category=Protocol}}
}}
 
{{protocols group|Plate reader|2=
*[[Endy:Victor3 plate reader|Plate reader usage protocols]]
}}


<showhide>
{{protocols group|Miscellaneous|2=
__SHOWALL__ __HIDEALL__
<!--To list a protocol here, "tag" the protocol page with only [[Category:Protocol]]-->
</showhide>
{{#dpl:categoriesminmax=,1|category=Protocol}}
}}


{{protocols group|Need help with protocols?|2=
*[[Questions and Answers|Questions and Answers on OWW]]
}}
|}
{{show hide all}}
<sitesearch>
title=Search Protocols
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__NOTOC__
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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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