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Updates:
 
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==Contributing protocols==
</div>
===Add new protocols===
|}
*[[Protocols/Create|'''Add a new lab- or person-specific protocol''']]
{| cellspacing="1"
*[[Protocols/Consensus template|'''Add a consensus protocol''']] ([[Help:Consensus protocol|?]])
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===Improve protocols in development===
<!------------------------------------------------------------------------------->
'''''Please Contribute!'''''
<!-----------------------------------IN DEVELOPMENT------------------------------>
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Needs attention]]-->
<!------------------------------------------------------------------------------->
{{#dpl:category=Needs attention|category=Protocol}}
{{size|2|'''Protocols in Development'''}}<BR>
'''''Please Contribute!'''''<BR>
&bull; [[Pulse-chase protein production|<font style="color:#000000">Pulse-chase protein production</font>]] <BR>
&bull; [[Fixing cells|<font style="color:#000000">Fixing cells</font>]] <BR>
&bull; [[B-galactosidase assay|<font style="color:#000000">&beta;-galactosidase assay</font>]] <BR>
&bull; [[RNA Half-life|<font style="color:#000000">RNA Half-life</font>]] <BR>
&bull; [[Denaturing acrylamide gel purification of nucleic acids|<font style="color:#000000">Denaturing acrylamide gel purification NA</font>]] <BR>
&bull; [[Quantification of nucleic acids|<font style="color:#000000">Quantification of nucleic acids</font>]] <BR>
</div>


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<!------------------------------------------------------------------------------->
<!-----------------------------------In vivo------------------------------------->
<!------------------------------------------------------------------------------->


==''In vivo''==
==''In vivo''==
<showhide>
{{size|2|'''''Escherichia coli'''''}}__HIDER__
<hide>
&bull; [[Bacterial cell culture|<font style="color:#000000">Bacterial Cell culture</font>]] <BR>
&bull; [[Bacterial Transformation |<font style="color:#000000">Bacterial Transformation</font>]] <BR>
&bull; [[Preparing chemically competent cells|<font style="color:#ffffff" size=1>Preparing chemically competent cells (TSS)</font>]] <BR>
&bull; [[Transforming chemically competent cells|<font style="color:#ffffff" size=1>Transforming chemically competent cells (TSS)</font>]] <BR>
&bull; [[Electrocompetent cells|<font style="color:#ffffff" size=1>Preparing electrocompetent cells</font>]] <BR>
&bull; [[Electroporation|<font style="color:#ffffff" size=1>Transforming electrocompetent cells</font>]] <BR>
&bull; [[beta-Galactosidase Assay (better Miller)|<font style="color:#000000">&beta;-Galactosidase Assay</font>]] <font size=1>(A better Miller)</font> <BR>
&bull; [[Colony PCR|<font style="color:#000000">Colony PCR</font>]] <BR>
&bull; [[Making a long term stock of bacteria|<font style="color:#000000">Making long-term stock bacteria</font>]] <BR>
&bull; [[Miniprep|<font style="color:#000000">Miniprep</font>]] <BR>
&bull; [[P1vir phage transduction|<font style="color:#000000">P1vir phage transduction</font>]] <BR>
&bull; [[Pour plates|<font style="color:#000000">Pour LB plates</font>]] <BR>
&bull; [http://www.cf.ac.uk/biosi/staff/ehrmann/tools/factors.htm <font style="color:#000000">Protein expression resource</font>] <BR>
&bull; [[S_N Chemostat Protocol|<font style="color:#000000">S N Chemostat Protocol</font>]] <BR>
</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|}}
&bull; [[Mesoplama florum:Culture media|<font style="color:#000000">Preparing culture media</font>]] <BR>
}}
</hide>
</showhide>


<showhide>
{{protocols group|''Arabidopsis thaliana''|2=
{{size|2|'''T7'''}}__HIDER__
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Arabidopsis thaliana]]-->
<hide>
{{#dpl:category=Arabidopsis thaliana|category=Protocol|}}
&bull; [[Cesium Chloride Purification of T7|<font style="color:#000000">Purification T7: Cesium Chloride</font>]] <BR>
}}
&bull; [[Studier Lysate Prep|<font style="color:#000000">Simple lysate protocol from plaque/lysate</font>]] <BR>
</hide>
</showhide>


<showhide>
{{protocols group|''[[Escherichia coli]]''|2=
{{size|2|'''Yeast'''}}__HIDER__
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Escherichia coli]]-->
<hide>
{{#dpl:category=Escherichia coli|category=Protocol|nottitlematch=%:%}}
&bull; [[Assaying mating|<font style="color:#000000">Assaying mating</font>]] <BR>
{{#dpl:category=Escherichia coli|category=Protocol|titlematch=%:%}}
&bull; [[Cell Cycle Arrest|<font style="color:#000000">Cell Cycle Arrest</font>]] <BR>
 
&bull; [[Dropout plates for yeast|<font style="color:#000000">Dropout plates</font>]] <BR>
}}
&bull; [[High Efficiency Transformation|<font style="color:#000000">High Efficiency Transformation</font>]] <BR>
 
&bull; [[Layered plates|<font style="color:#000000">Layering plates</font>]] <BR>
{{protocols group|''Lactic Acid Bacteria''|2=
&bull; [[Pour YPD plates|<font style="color:#000000">Pour YPD plates</font>]] <BR>
<!--To list a protocol here, "tag" the protocol page with the [[Category:Protocol]] and [[Category:Lactobacillus]]-->
&bull; [[Silver: Lysate for Western|<font style="color:#000000">Simple Yeast Lysate</font>]] <font size=1>(for Western etc.)</font> <BR>
{{#dpl:category=Lactobacillus|category=Protocol|}}
&bull; [[Silver: Time-Lapse Microscopy|<font style="color:#000000">Time-Lapse Microscopy</font>]] <BR>
 
&bull; [[Yeast Colony PCR|<font style="color:#000000">Yeast Colony PCR</font>]] <BR>
}}
&bull; [[Yeast DNA Prep|<font style="color:#000000">Yeast DNA Prep</font>]] <BR>
 
{{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 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}}
}}


</hide>
</showhide>
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<!------------------------------------------------------------------------------->
<!------------------------------------------------------------------------------->
<!-----------------------------------Blank temp---------------------------------->
<!-----------------------------------In vitro----------------------------------->
<!------------------------------------------------------------------------------->
<!------------------------------------------------------------------------------->
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==''In vitro''==
<div style="clear: right; text-align: left; float: left; padding: 0em .5em 0em">
 
{{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=%:%}}
}}
 
{{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=%:%}}
}}
 
{{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=%:%}}
}}
 
{{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------------------------------------>
<!------------------------------------------------------------------------------->
<!------------------------------------------------------------------------------->
==''In silico''==
==''In silico''==
<showhide>
{{size|2|'''Sequence Analysis'''}}__HIDER__
<hide>
&bull; [[BLAST|<font style="color:#000000">BLAST</font>]] <BR>
&bull; [[CLUSTALW|<font style="color:#000000">CLUSTALW</font>]] <BR>
</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=%:%}}
&bull; [[THREADER|<font style="color:#000000">THREADER</font>]] <BR>
}}
&bull; [[Homology Modelling|<font style="color:#000000">Homology Modeling</font>]] <BR>
</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=%:%}}
&bull; [[FBA|<font style="color:#000000">Flux Balance Analysis</font>]] <BR>
{{#dpl:category=Data analysis|category=In silico|category=Protocol|titlematch=%:%}}
&bull; [[MoMA|<font style="color:#000000">Minimisation of Metabolic Adjustment</font>]] <BR>
}}
</hide>
 
</showhide>
{{protocols group|[[Databases]]|2=
</div>
<!--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=%:%}}
}}


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{{protocols group|[[Sequence analysis]]|2=
<div style="clear: right; text-align: left; float: left; padding: 0em .5em 0em">
<!--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=%:%}}
<!-----------------------------------In vitro------------------------------------>
{{#dpl:category=Sequence analysis|category=In silico|category=Protocol|titlematch=%:%}}
<!------------------------------------------------------------------------------->
}}
==''In vitro''==
<showhide>
{{size|2|'''Nucleic acids'''}}__HIDER__
<hide>
&bull; [[Nucleic acid precipitation|<font style="color:#000000">Nucleic acid precipitation</font>]] <BR>
&bull; [[Phenol/chloroform extraction|<font style="color:#000000">Phenol/chloroform extraction</font>]] <BR>
</hide>
</showhide>


<showhide>
{{protocols group|[[Structure analysis]]|2=
{{size|2|'''DNA'''}}__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=%:%}}
&bull; [[Agarose gel electrophoresis|<font style="color:#000000">Agarose gel electrophoresis</font>]] <BR>
{{#dpl:category=Structure|category=In silico|category=Protocol|titlematch=%:%}}
&bull; [[Annealing Primers|<font style="color:#000000">Annealing Primers</font>]] <BR>
}}
&bull; [[Designing primers|<font style="color:#000000">Designing Primers</font>]] <BR>
&bull; [[DNA Ligation|<font style="color:#000000">DNA Ligation</font>]] <BR>
&bull; [[Library Generation|<font style="color:#000000">Library Generating</font>]] <BR>
&bull; [[Miniprep|<font style="color:#000000">Miniprep</font>]] <BR>
&bull; [[PCR|<font style="color:#000000">PCR</font>]] <BR>
&bull; [[Phosphatase treatment of linearized vector|<font style="color:#000000">Phosphate treatment linearized vector</font>]] <BR>
&bull; [http://arep.med.harvard.edu/polony/polony_protocols <font style="color:#000000">Polony Protocols</font>]<font size=1>(Church/Mitra Lab)</font> <BR>
&bull; [[PNK Treatment of DNA Ends|<font style="color:#000000">PNK Treatment of DNA ends</font>]] <BR>
&bull; [[Purification of DNA|<font style="color:#000000">Purification of DNA</font>]] <BR>
&bull; [[Reconstituting primers|<font style="color:#000000">Reconstituting Primers</font>]] <BR>
&bull; [[Restriction digest|<font style="color:#000000">Restriction Digest</font>]] <BR>
&bull; [['Round-the-horn site-directed mutagenesis|<font style="color:#000000">'Round-the-horn site-directed mutagenesis</font>]] <BR>
&bull; [[Sequencing DNA|<font style="color:#000000">Sequencing DNA</font>]] <BR>
&bull; [[Site-directed mutagenesis|<font style="color:#000000">Site-directed Mutagenesis</font>]] <BR>
&bull; [[Templiphi|<font style="color:#000000">Templiphi</font>]] <BR>
</hide>
</showhide>


<showhide>
[[Tregwiki:Main_Page|Transcriptional Regulation]]
{{size|2|'''RNA'''}}__HIDER__
<hide>
&bull; [[In vitro transcription with T7 RNA polymerase|<font style="color:#000000">In vitro transcription w/ T7 RNA polymerase</font>]] <BR>
&bull; [[Northern Blot, 32P End-Labeled Probes |<font style="color:#000000">Northern Blot, <sup>32</sup>P End-Labeled Probes</font>]] <BR>
&bull; [[Probe Prep, 32P End-Labeled Probes|<font style="color:#000000">Probe Prep, <sup>32</sup>P End-Labeled Probes</font>]] <BR>
&bull; [[RNA Extraction|<font style="color:#000000">RNA Extraction</font>]] <BR>
&bull; [[RNase Protection Assay|<font style="color:#000000">RNAse Protection Assay</font>]] <BR>
</hide>
</showhide>


<showhide>
{{size|2|'''Protein'''}}__HIDER__
<hide>
&bull; [[Acrylamide Gels|<font style="color:#000000">Acrylamide gels and SDS-PAGE</font>]] <BR>
&bull; [[Silver: Destain|<font style="color:#000000">Coomassie Destain</font>]] <BR>
&bull; [[Silver: Coomassie Stain|<font style="color:#000000">Coomassie Stain</font>]] <BR>
&bull; [[Keating:Experimental Protocols:HPLC|<font style="color:#000000">HPLC</font>]] <BR>
&bull; [[Silver staining|<font style="color:#000000">Silver staining</font>]] <BR>
&bull; [[Western Blot|<font style="color:#000000">Western Blot</font>]] <BR>
&bull; [[Purification of His-tagged proteins|<font style="color:#000000">Purification His-tagged proteins</font>]] <BR>
</hide>
</showhide>
</div>


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<!------------------------------------------------------------------------------->
<!------------------------------------------------------------------------------->
<!-----------------------------------OTHER--------------------------------------->
<!-----------------------------------OTHER--------------------------------------->
<!------------------------------------------------------------------------------->
<!------------------------------------------------------------------------------->
==Other==
==Other==
<showhide>
{{size|2|'''Flow Cytometry'''}}__HIDER__
<hide>
&bull; [[Flow Calibration|<font style="color:#000000">Flow Calibration</font>]] <BR>
</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]
&bull; [[Design a Microfluidic Chip|<font style="color:#000000">Design Microfluidic Chip</font>]] <BR>
*[http://www.myjove.com/ JoVE] Journal of Visualized Experiments: An online research journal for publishing visualized (video-based) biological experiments.
&bull; [[Order a Microfluidic Chip from the Foundry|<font style="color:#000000">Order Microfluidic Chip from Foundry</font>]] <BR>
*[http://protocol-online.org Protocol-online] Useful protocols and a popular discussion section.
&bull; [[Operate Microfluidic Chemostat|<font style="color:#000000">Operate Microfluidic Chemostat</font>]] <BR>
*[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}}
&bull; [[Agarose Pads for Microscopy|<font style="color:#000000">Agarose Pads</font>]] <BR>
}}
&bull; [[Quantitative Microscopy|<font style="color:#000000">Quantitative Microscopy</font>]] <BR>
&bull; [[Silver: Time-Lapse Microscopy|<font style="color:#000000">Time-Lapse Microscopy</font>]] <BR>
</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}}
&bull; [[Endy:Victor3 plate reader|<font style="color:#000000">Perkin Elmer Victor<sup>3</sup></font>]]<font size=1><BR>Plate reader usage protocols</font> <BR>
}}
</hide>
</showhide>


{{size|2|'''General resources'''}}<BR>
{{protocols group|Microfluidics|2=
&bull; [http://protocol-online.org <font style="color:#000000">Protocol-online</font>] <font size=1><BR>Contains a lot of useful protocols and a popular discussion section.</font> <BR>
<!--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}}
}}


</div>
{{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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<sitesearch>
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Revision as of 14:35, 30 July 2015


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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

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