Protocols: Difference between revisions

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(→‎''In vitro'': removed some material pages from protocols section)
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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]]
* [[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]]


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==''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/Template|'''Adding new protocols''']]
{{protocols group|''Arabidopsis thaliana''|2=
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<!--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=%:%}}
 
}}
 
{{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|}}
 
}}


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


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


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


<showhide>
{{protocols group|T7|2=
{{size|2|'''Mouse'''}}__HIDER__
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:T7]]-->
<hide>
{{#dpl:category=T7|category=Protocol}}
* [[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]]
{{protocols group|[[RNA]]|2=
* [[Phosphatase treatment of linearized vector]]  
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In vitro]] and [[Category:RNA]]-->
* [http://arep.med.harvard.edu/polony/polony_protocols Polony Protocols]
{{#dpl:category=RNA|category=In vitro|category=Protocol|nottitlematch=%:%}}
* [[PNK Treatment of DNA Ends]]
{{#dpl:category=RNA|category=In vitro|category=Protocol|titlematch=%:%}}
* [[Purification of DNA]]
}}
* [[Reconstituting primers]]
* [[Restriction digest]]  
* [['Round-the-horn site-directed mutagenesis]]
* [[Sequencing DNA]]  
* [[Site-directed mutagenesis]]  
* [[Templiphi]]  
</hide>
</showhide>


<showhide>
{{protocols group|[[Protein]]|2=
{{size|2|'''RNA'''}}__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=%:%}}
* [[In vitro transcription with T7 RNA polymerase]]  
{{#dpl:category=Protein|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|[[Lipid]]|2=
{{size|2|'''Protein'''}}__HIDER__
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In vitro]] and [[Category:Lipid]]-->
<hide>
{{#dpl:category=Lipid|category=In vitro|category=Protocol|nottitlematch=%:%}}
* [[Acrylamide Gels]]
{{#dpl:category=Lipid|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|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>
</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>
 
{{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}}
}}


<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]]  
}}
* [[Quantitative Microscopy]]  
* [[Silver: Time-Lapse Microscopy]]
</hide>
</showhide>


<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 size=1>Plate reader usage protocols</font>  
}}
</hide>
</showhide>


<showhide>
{{protocols group|Plate reader|2=
{{size|2|'''General resources'''}}__HIDER__
*[[Endy:Victor3 plate reader|Plate reader usage protocols]]
<hide>
}}
* [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>
* [http://www.invitrogen.com/iProtocol iProtocol] <font size=1>Abridged ''Current Protocols'' Invitrogen protocols.  Not amenable to printing.</font>
</hide>
</showhide>
|}


<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 10:52, 18 September 2012

Labs & Groups
From around the world 		Courses
Host & view classes 		Protocols
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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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