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== CEES metagenomics wiki ==
 
 
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= CEES metagenomics wiki =
 
  
 
This wiki is meant as a resource for people performing metagenomics work in CEES. The website contains protocols for DNA extraction, PCR, library preps, sequencing etc., in addition to relevant literature.
 
This wiki is meant as a resource for people performing metagenomics work in CEES. The website contains protocols for DNA extraction, PCR, library preps, sequencing etc., in addition to relevant literature.
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== Protocols ==
 
== Protocols ==
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DNA extraction and 16S rDNA amplification are performed according to the protocols of the [http://www.earthmicrobiome.org/ Earth MIcrobiome Project] (EMP). The protocols can be found [http://www.earthmicrobiome.org/emp-standard-protocols/ here].
  
 
=== DNA extraction ===
 
=== DNA extraction ===
  
For the above mentioned materials, the main procedure for DNA extraction is a modified version of the DNeasy Blood & Tissue Kit, including an initial bead beating step.
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MoBio Powersoil HTP 96-well Soil DNA isolation kit, slightly modified by EMP: [http://press.igsb.anl.gov/earthmicrobiome/emp-standard-protocols/dna-extraction-protocol/ http://press.igsb.anl.gov/earthmicrobiome/emp-standard-protocols/dna-extraction-protocol/]
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=== 16S rDNA PCR amplification ===
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EMP protocol: [http://press.igsb.anl.gov/earthmicrobiome/emp-standard-protocols/16s/ http://press.igsb.anl.gov/earthmicrobiome/emp-standard-protocols/16s/]
  
[http://www.qiagen.com/no/resources/download.aspx?id=6b09dfb8-6319-464d-996c-79e8c7045a50&lang=en DNeasy 96 Blood & Tissue Kit handbook]
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== Helpful tips ==
  
Paper describing the modified protocol: "[http://www.google.no/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0CCQQFjAA&url=http%3A%2F%2Fwww.researchgate.net%2Fprofile%2FChristopher_Allender%2Fpublication%2F8167483_High-throughput_extraction_of_arthropod_vector_and_pathogen_DNA_using_bead_milling%2Flinks%2F09e4150871fd43c853000000.pdf&ei=5NS8VPvjCMn2OoCygYgF&usg=AFQjCNFwgGWnboyaAEUiNdOUSxuccghlsQ&bvm=bv.83829542,d.ZWU High-throughput extraction of arthropod vector and pathogen DNA using bead milling]" (Allender et al. 2004)
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== Relevant articles ==

Latest revision as of 10:53, 5 March 2015

CEES metagenomics wiki

This wiki is meant as a resource for people performing metagenomics work in CEES. The website contains protocols for DNA extraction, PCR, library preps, sequencing etc., in addition to relevant literature.

Tips for adding a page (from the bioinf-wiki of Lex).

Material

The starting material currently includes cod gut samples, human stool samples and (...?).

Protocols

DNA extraction and 16S rDNA amplification are performed according to the protocols of the Earth MIcrobiome Project (EMP). The protocols can be found here.

DNA extraction

MoBio Powersoil HTP 96-well Soil DNA isolation kit, slightly modified by EMP: http://press.igsb.anl.gov/earthmicrobiome/emp-standard-protocols/dna-extraction-protocol/

16S rDNA PCR amplification

EMP protocol: http://press.igsb.anl.gov/earthmicrobiome/emp-standard-protocols/16s/

Helpful tips

Relevant articles