SOP_DNA_QIAFastDNA_DTU_v3.pdf (412.56 kB)
SOP - DNA Isolation QIAamp Fast DNA Stool Modified
Version 4 2016-10-18, 16:26
Version 3 2016-10-18, 16:04
Version 2 2016-07-19, 06:55
Version 1 2016-07-09, 11:40
journal contribution
posted on 2016-10-18, 16:26 authored by Berith E. Knudsen, Lasse Bergmark, Sünje Johanna PampSünje Johanna PampThis protocol for DNA isolation is based on the Qiagen kit QIAamp Fast DNA stool mini kit (cat. no. 51604). The method has been tested using different sample matrices, e.g. human and animal feces and sewage. The protocol “Isolation of DNA from Stool for Pathogen Detection” supplied with the kit has been modified in order to increase the DNA yield from these complex samples while maintaining high quality of the DNA. The main modification to the protocol supplied with the kit is the addition of a bead-beating step in the beginning of the isolation to facilitate increasing cell lysis, e.g. of Gram-positive bacteria. Additional modifications have been included as described herein. For example, for the extraction of DNA from sewage specimens a few additional steps are included to further increase the DNA yield.
If you use this method, please cite:
Berith E. Knudsen, Lasse Bergmark, Patrick Munk, Oksana Lukjancenko, Anders Priemé, Frank M. Aarestrup, Sünje J. Pamp (2016) Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition. mSystems Oct 2016, 1 (5) e00095-16; DOI: 10.1128/mSystems.00095-16
http://msystems.asm.org/content/1/5/e00095-16
Funding
FP7 (613754), Horizon2020 (643476), Villum Fonden (VWR023052), Carlsberfondet (2013_01_0377)
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- Bacteriology
- Biogeography and phylogeography
- Bioinformatics and computational biology not elsewhere classified
- Bioinformatic methods development
- Other biological sciences not elsewhere classified
- Medical biotechnology not elsewhere classified
- Community ecology (excl. invasive species ecology)
- Evolutionary biology not elsewhere classified
- Forensic biology
- Freshwater ecology
- Genomics
- Host-parasite interactions
- Infectious agents
- Infectious diseases
- Microbial ecology
- Microbial genetics
- Microbiology not elsewhere classified
- Plant cell and molecular biology
- Animal cell and molecular biology
- Molecular evolution
- Veterinary parasitology
- Medical parasitology
- Population ecology
- Systems biology
Keywords
DNA extractionmicrobiomegenomicsmetagenomics16S rRNA gene profilinghumanpigsewagefecal sampleMicrobial community compositionsmock communityspikingQiagenDNAProtocolStandard operating procedureBacteriologyBiogeography and PhylogeographyBioinformaticsBiological TechniquesBiotechnologyCommunity Ecology (excl. Invasive Species Ecology)Computational BiologyEvolutionary BiologyForensic BiologyFreshwater EcologyGenomicsHost-Parasite InteractionsInfectious AgentsInfectious DiseasesMicrobial EcologyMicrobial GeneticsMicrobiologyMolecular BiologyMolecular EvolutionParasitologyPopulation EcologySystems Biology
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