Protocols: Difference between revisions

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==Contributing protocols==
===Add new protocols===
*[[Protocols/Create|'''Add a new lab- or person-specific protocol''']]
*[[Protocols/Consensus template|'''Add a consensus protocol''']] ([[Help:Consensus protocol|?]])
 
 
===Improve protocols in development===
'''''Please Contribute!'''''
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Needs attention]]-->
{{#dpl:category=Needs attention|category=Protocol}}
 
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==''In vivo''==
==''In vivo''==
===''Escherichia coli''===
*[[beta-Galactosidase Assay (A better Miller)]]
*[[Bacterial cell culture]]
*[[Preparing chemically competent cells]]
*[[Transforming chemically competent cells]]
*[[Electrocompetent cells]]
*[[Electroporation]]
*[[Miniprep]]
*[[Colony PCR]]
*[[Pulse-chase protein production]]
*[[Pour plates|Pour LB plates]]
*[[S_N Chemostat Protocol]]
*[[Sauer:P1vir phage transduction|P1vir phage transduction]]
*[http://www.cf.ac.uk/biosi/staff/ehrmann/tools/factors.htm Protein expression resource]


===''Mesoplasma florum''===
{{protocols group|''Acetobacter xylinum''|2=
*[[Mesoplama florum:Culture media|Preparing culture media]]
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Acetobacter xylinum]]-->
===T7===
{{#dpl:category=Acetobacter xylinum|category=Protocol|}}
*[[Studier Lysate Prep|Simple lysate protocol from plaque or lysate]]
}}
*[[Cesium Chloride Purification of T7]]
 
===Yeast===
{{protocols group|''Arabidopsis thaliana''|2=
*[[High Efficiency Transformation]]
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Arabidopsis thaliana]]-->
*[[Yeast Colony PCR]]
{{#dpl:category=Arabidopsis thaliana|category=Protocol|}}
*[[Yeast DNA Prep]]
}}
*[[Cell Cycle Arrest]]
 
*[[Fixing cells]]
{{protocols group|''[[Escherichia coli]]''|2=
*[[B-galactosidase assay]]
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Escherichia coli]]-->
*[[Silver: Time-Lapse Microscopy|Time-Lapse Microscopy]]
{{#dpl:category=Escherichia coli|category=Protocol|nottitlematch=%:%}}
*[[Silver: Lysate for Western|Simple Yeast Lysate]] (for Western etc.)
{{#dpl:category=Escherichia coli|category=Protocol|titlematch=%:%}}
*[[Assaying mating]]
 
*[[Pour YPD plates]]
}}
*[[Dropout plates for yeast]]
 
*[[Layered plates]]
{{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|}}


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{{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}}
}}
 
 
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<!------------------------------------------------------------------------------->
<!-----------------------------------In vitro----------------------------------->
<!------------------------------------------------------------------------------->


==''In vitro''==
==''In vitro''==
===Nucleic acids===
*[[Quantification of nucleic acids]]
*[[Phenol/chloroform extraction]]
*[[Nucleic acid precipitation]]
*[[Denaturing acrylamide gel purification of nucleic acids]]
====DNA====
*[[Agarose gel electrophoresis]]
*[[Annealing Primers]]
*[[Designing primers]]
*[[DNA Ligation]]
*[[Library Generation]]
*[[Miniprep]]
*[[PCR]]
*[[Phosphatase treatment of linearized vector]]
*[[PNK Treatment of DNA Ends]]
*[[Purification of DNA]]
*[[Reconstituting primers]]
*[[Restriction digest]]
*[['Round-the-horn site-directed mutagenesis]]
*[[Sequencing DNA]]
*[[Site-directed mutagenesis]]
*[[Templiphi]]
*[http://arep.med.harvard.edu/polony/polony_protocols Church/Mitra Lab Polony Protocols]


====RNA====
{{protocols group|Nucleic acids|2=
*[[RNA Extraction]]
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In vitro]] and [[Category:DNA]] and [[Category:RNA-->
*[[Northern Blot, 32P End-Labeled Probes |Northern Blot, <sup>32</sup>P End-Labeled Probes]]
{{#dpl:category=DNA|category=RNA|category=In vitro|category=Protocol|nottitlematch=%:%}}
*[[Probe Prep, 32P End-Labeled Probes|Probe Prep, <sup>32</sup>P End-Labeled Probes]]
{{#dpl:category=DNA|category=RNA|category=In vitro|category=Protocol|titlematch=%:%}}
*[[RNase Protection Assay]]
}}
*[[In vitro transcription with T7 RNA polymerase]]
 
*[[RNA Half-life]]
{{protocols group|[[DNA]]|2=
===Protein===
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In vitro]] and [[Category:DNA]]-->
*[[Acrylamide Gels|Acrylamide gels and SDS-PAGE]]
{{#dpl:category=DNA|category=In vitro|category=Protocol|nottitlematch=%:%}}
*[[Silver: Coomassie Stain|Coomassie Stain]]
{{#dpl:category=DNA|category=In vitro|category=Protocol|titlematch=%:%}}
*[[Silver: Destain|Coomassie Destain]]
}}
*[[Sauer:Silver staining|Silver staining]]
 
*[[Western Blot]]
{{protocols group|[[RNA]]|2=
*[[Keating:Experimental Protocols:HPLC|HPLC]]
<!--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|[[Protein]]|2=
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In vitro]] and [[Category:Protein]]-->
{{#dpl:category=Protein|category=In vitro|category=Protocol|nottitlematch=%:%}}
{{#dpl:category=Protein|category=In vitro|category=Protocol|titlematch=%:%}}
}}
 
{{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''==
 
{{protocols group|[[Cloning]]|2=
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In silico]] and [[Category:Cloning]]-->
{{#dpl:category=Cloning|category=In silico|category=Protocol|titlematch=%:%}}
}}
 
{{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=%:%}}
}}


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{{protocols group|[[Structure analysis]]|2=
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{{#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==
==Other==
===Flow Cytometry===
*[[Flow Calibration]]
===Microfluidics===
*[[Design a Microfluidic Chip]]
*[[Order a Microfluidic Chip from the Foundry]]
*[[Operate Microfluidic Chemostat]]
===Microscopy===
*[[Agarose Pads for Microscopy]]
*[[Quantitative Microscopy]]
*[[Silver: Time-Lapse Microscopy|Time-Lapse Microscopy]]
===Plate reader===
*[[Endy:Victor3 plate reader| Perkin Elmer Victor<sup>3</sup> plate reader usage protocols]]


===General resources===
{{protocols group|General resources|2=
*[http://protocol-online.org Protocol-online]- Contains a lot of useful protocols and a popular discussion section.
*[http://www.currentprotocols.com/WileyCDA/ Current Protocols] Most comprehensive source of protocols ranging from molecular biology to neuroscience.
*[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=
<!--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]]
}}
{{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]]
}}
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Revision as of 14:35, 30 July 2015

Labs & Groups
From around the world 		Courses
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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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