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


== ''Escherichia coli'' ==
<div id="mainpage">
 
{|width="712px"
[[Bacterial cell culture]]
 
[[Chemically competent cells]]
 
[[Electrocompetent cells]]
 
[[Electroporation]]
 
[[Miniprep]]
 
[[Colony PCR]]
 
[[Pulse-chase protein production]]
 
== Yeast ==
 
[[High Efficiency Transformation]]
 
[[Yeast Colony PCR]]
 
[[Yeast DNA Prep]]
 
[[Cell Cycle Arrest]]
 
[[Fixing cells]]
 
[[B-galactosidase assay]]
 
[[Silver: Time-Lapse Microscopy|Time-Lapse Microscopy]]
 
[[Silver: Lysate for Western|Simple Yeast Lysate]] (for Western etc.)
 
[[Assaying mating]]
 
== T7 ==
[[Studier Lysate Prep|Simple lysate protocol from plaque or lysate]]
 
[[Cesium Chloride Purification of T7]]
 
== Mesoplasma florum ==
 
===Culture Media===
 
====ATCC 1161 Medium====
 
Mix a base broth in a 1 liter 45mm cap bottle the following chemicals:
 
{|
|-
| Heart Infusion Broth (Difco 0038)
|    17.5 g
|-
| Sucrose
|    40 g
|-
| Agar Noble (Difco 0142) if necessary
|    12 g
|-
| DI Water
|    710 ml
|-
|}
 
Autoclave at 121C for 20 minutes and cool to room temperture (broth) or 55C (Agar) on a 55C water bath.
 
Centrifuge 2 x 45 ml of Gibco 18180-059 liquid yeast extract at high speed to remove sediment. Pour only 45 ml into centrifuge bottles, eliminating as much as possible of the sediment in the bottom of the Gibco stock.
 
Thaw Sigma H-1138 heat inactivated horse serum.  For agar, bring both horse serum and centrifuged yeast extract to 37C.  Horse serum at 55C will sediment protein.
 
Assemble 150ml bottle top 0.22&mu; filter on the 1 liter bottle.  For agar, it is helpful to put the bottle on a foam insulating pad to delay cooling.  Add by vacuum filtration:
 
{|
|-
| Horse serum (Sigma H1138)
| 200 ml
|-
| Yeast extract
| 90 ml
|-
| Penicillin G 500,000 U/ml
| 400 &m;l
|-
|-
| 2% phenol red
|rowspan="2" width="221px" class="green1"|
| 2 ml
|}


Adjust pH to 7.4 with 100 mM HCl.  Measured pH of as-made broth is 7.46, probably close enough.
==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|?]])


Phenol red 2% solution must be neutralized with sufficient NaOH to convert it to the sodium salt.  The phenol red amount can be adjusted to control the depth of color to taste.


=''In vitro''=
===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}}


==Nucleic acids==
|width="267px" class="green3"|


[[Quantification of nucleic acids]]
==''In vivo''==


[[Phenol/chloroform extraction]]
{{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|}}
}}


[[Nucleic acid precipitation]]
{{protocols group|''Arabidopsis thaliana''|2=
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Arabidopsis thaliana]]-->
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}}


[[Denaturing acrylamide gel purification of nucleic acids]]
{{protocols group|''[[Escherichia coli]]''|2=
=== DNA ===
<!--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=%:%}}


[[Agarose gel]]
}}


[[Annealing Primers]]
{{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|}}


[[Designing primers]]
}}


[[DNA Ligation]]
{{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|}}


[[Library Generation]]
}}


[[PCR]]
{{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}}
}}


[[Phosphatase treatment of linearized vector]]
{{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}}
}}


[[PNK Treatment of DNA Ends]]
{{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}}
}}


[[Purification of DNA]]
{{protocols group|''[[Streptomyces:Information|Streptomyces]]''|2=
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Streptomyces]]-->
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}}


[[Reconstituting primers]]
{{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}}
}}


[[Restriction digest]]


[['Round-the-horn site-directed mutagenesis]]
{{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}}
}}


[[Sequencing DNA]]


[[Site-directed mutagenesis]]
|width="270px" class="green2"|
<!------------------------------------------------------------------------------->
<!-----------------------------------In vitro----------------------------------->
<!------------------------------------------------------------------------------->


[[Templiphi]]
==''In vitro''==


=== RNA ===
{{protocols group|Nucleic acids|2=
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In vitro]] and [[Category:DNA]] and [[Category:RNA-->
{{#dpl:category=DNA|category=RNA|category=In vitro|category=Protocol|nottitlematch=%:%}}
{{#dpl:category=DNA|category=RNA|category=In vitro|category=Protocol|titlematch=%:%}}
}}


[[RNA Extraction]]
{{protocols group|[[DNA]]|2=
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In vitro]] and [[Category:DNA]]-->
{{#dpl:category=DNA|category=In vitro|category=Protocol|nottitlematch=%:%}}
{{#dpl:category=DNA|category=In vitro|category=Protocol|titlematch=%:%}}
}}


[[Northern Blot, 32P End-Labeled Probes |Northern Blot, <sup>32</sup>P End-Labeled Probes]]
{{protocols group|[[RNA]]|2=
<!--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=%:%}}
}}


[[Probe Prep, 32P End-Labeled Probes|Probe Prep, <sup>32</sup>P End-Labeled Probes]]
{{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=%:%}}
}}


[[RNase Protection Assay]]
{{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=%:%}}
}}


[[In vitro transcription with T7 RNA polymerase]]
{{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}}
}}


[[RNA Half-life]]
{{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}}
}}
|-


== Protein ==
|width="265px" class="green2"|
<!------------------------------------------------------------------------------->
<!-----------------------------------In silico------------------------------------>
<!------------------------------------------------------------------------------->


[[Acrylamide Gels|Acrylamide gels and SDS-PAGE]]
==''In silico''==


[[Silver: Coomassie Stain|Coomassie Stain]]
{{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=%:%}}
}}


[[Silver: Destain|Coomassie Destain]]
{{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]]-->
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}}


[[Sauer:Silver staining|Silver staining]]
{{protocols group|[[Databases]]|2=
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:In silico]] and [[Category:Databases]]-->
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}}


[[Western Blot]]
{{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=%:%}}
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}}


= Microfluidics =
{{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=%:%}}
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}}


[[Design a Microfluidic Chip]]
{{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=%:%}}
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}}


[[Order a Microfluidic Chip from the Foundry]]
[[Tregwiki:Main_Page|Transcriptional Regulation]]


[[Operate Microfluidic Chemostat]]


= Microscopy =
|width="260px" class="green3"|
<!------------------------------------------------------------------------------->
<!-----------------------------------OTHER--------------------------------------->
<!------------------------------------------------------------------------------->


[[Agarose Pads for Microscopy]]
==Other==


[[Quantitative Microscopy]]
{{protocols group|General resources|2=
*[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]  
}}


= Flow Cytometry =
{{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}}
}}


[[Flow Calibration]]
{{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}}
}}


= Miscellaneous =
{{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}}
}}


[[Endy:Victor3 counteracting evaporation in long time courses|Counteracting evaporation from wells in a Victor3 plate reader]]
{{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}}
}}


[[Pour plates|Pour LB plates]]
{{protocols group|Plate reader|2=
*[[Endy:Victor3 plate reader|Plate reader usage protocols]]
}}


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


[[Layered plates]]
{{protocols group|Need help with protocols?|2=
 
*[[Questions and Answers|Questions and Answers on OWW]]
[[S_N Chemostat Protocol]]
}}
 
|}
[[beta-Galactosidase Assay (A better Miller)]]
{{show hide all}}
 
<sitesearch>
[[Silver: 10x PBS|10x PBS]]
title=Search Protocols
 
qualifier=protocol
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__NOTOC__

Revision as of 14:35, 30 July 2015

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Contributing protocols

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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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