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]] 
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* [[Denaturing acrylamide gel purification of nucleic acids]]  
 
* [[Quantification of nucleic acids]]  
==''In vivo''==
* [[Bacterial species identification]]
 
* [[Yeast artificial chromosomes]]
{{protocols group|''Acetobacter xylinum''|2=
* [[One step 'miniprep' method for the isolation of plasmid DNA]]
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Acetobacter xylinum]]-->
* [[Cleaning Glass Coverslips]]
{{#dpl:category=Acetobacter xylinum|category=Protocol|}}
* [["Core Sample" PCR: Amplifying DNA from agarose gels]]
}}
* [["Broncho-alveolar Lavage]]
 
* [[Artificial transcriptional terminators]]
{{protocols group|''Arabidopsis thaliana''|2=
* [[Codon usage optimization]]
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Arabidopsis thaliana]]-->
* [[Electrophoretic mobility shift assay | Gel shift assay]]
{{#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=%:%}}
 
}}
 
{{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=
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Mesoplasma florum]]-->
{{#dpl:category=Mesoplasma florum|category=Protocol|}}


}}


[[Protocols/Template|'''Adding new protocols''']]
{{protocols group|Mouse|2=
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<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Mouse]]-->
{{#dpl:category=Mouse|category=Protocol}}
}}


==''In vivo''==
{{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}}
}}


<showhide>
{{protocols group|''[[Plasmodium falciparum]]''|2=
{{size|2|'''''Drosophila'''''}}__HIDER__
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Plasmodium falciparum]]-->
<hide>
{{#dpl:category=Plasmodium falciparum|category=Protocol}}
* [[Drosophila CHiP on chip|Drosophila CHiP on Chip]]  
}}
</hide>
</showhide>


<showhide>
{{protocols group|''[[Streptomyces:Information|Streptomyces]]''|2=
{{size|2|'''''Escherichia coli'''''}}__HIDER__
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Streptomyces]]-->
<hide>
{{#dpl:category=Streptomyces|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]]
* [[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|T7|2=
{{size|2|'''''Mesoplasma florum'''''}}__HIDER__
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:T7]]-->
<hide>
{{#dpl:category=T7|category=Protocol}}
* [[Mesoplama florum:Culture media|Culture media]]  
}}
</hide>
</showhide>


<showhide>
{{size|2|'''Mouse'''}}__HIDER__
<hide>
* [[Mouse keratinocyte cultures]]
</hide>
</showhide>


<showhide>
{{protocols group|[[Yeast]]|2=
{{size|2|'''T7'''}}__HIDER__
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Yeast]]-->
<hide>
{{#dpl:category=Yeast|category=Protocol}}
* [[Cesium Chloride Purification of T7]]  
}}
* [[Studier Lysate Prep]]  
</hide>
</showhide>


<showhide>
{{size|2|'''Yeast'''}}__HIDER__
<hide>
* [[Assaying mating]]
* [[Cell Cycle Arrest]]
* [[Dropout plates for yeast]]
* [[High Efficiency Transformation]]
* [[Layered plates]]
* [[Pour YPD 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]]
</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=
* [[DNA Synthesis from Oligos]]
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In vitro]] and [[Category:DNA]]-->
* [[Double stranding oligo libraries]]
{{#dpl:category=DNA|category=In vitro|category=Protocol|nottitlematch=%:%}}
* [[Library Generation]]
{{#dpl:category=DNA|category=In vitro|category=Protocol|titlematch=%:%}}
* [[Miniprep]]  
}}
* [[PCR]]  
* [[PCR Overlap Extension]]
* [[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=%:%}}
* [[Keating:Experimental Protocols:HPLC]]  
}}
* [[Silver staining]]  
* Protein Preps: Yeast
** [[Endy: Denaturing Protein Extraction Yeast| Denaturing Protein Extraction]]  
** [[Endy: Native Protein Extraction Yeast| Native Protein Extraction]]
* Western Blots
** [[Endy:Tris-Tricine Acrylamide Gels| Pouring Tris-Tricine Acrylamide Gels]]
** [[Western Blot| E. coli Western Blot]]
** [[Endy: General Western Blot| General Western Blot]]
* [[Purification of His-tagged proteins]]
* [[Free Sulfhydryl Determination]]
*[[Sauer:Expression/purification of 35S-Met proteins|Expression and purification of <sup>35</sup>S-labeled proteins]]
</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]]
</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>
{{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=%:%}}
}}
 
{{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=%:%}}
}}


<showhide>
[[Tregwiki:Main_Page|Transcriptional Regulation]]
{{size|2|'''Pathway Modelling'''}}__HIDER__
<hide>
* [[FBA]]
* [[MoMA]]  
</hide>
</showhide>


<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]]-->
</hide>
{{#dpl:category=Microscopy|category=Protocol}}
</showhide>
}}
|}
 
{{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}}
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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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