Transcriptomics

Dataset Information

2

The effects from DNA extraction methods on the evaluation of microbial diversity associated with human colonic tissue


ABSTRACT: Recent advances in (meta)genomic methods have provided new opportunities to examine host-microbe-environment interactions in the human gut. While opportunities exist to extract DNA from freshly sourced colonic tissue there are potentially valuable sources of DNA from historical studies that might also be examined. We examined how four different tissue DNA extraction methods employed in past clinical trials might impact the recovery of microbial DNA from a colonic tissue sample as assessed using a custom designed phylogenetic microarray for human gut bacteria and archaebacteria. While all methods of DNA extraction produced similar phylogenetic profiles some extraction specific biases were also observed. Real time PCR analysis targeting several bacterial groups substantiated this observation. These data suggest that while the efficacy of different DNA extraction methods differs somewhat all the methods tested produce an accurate representation of microbial diversity. This suggests that DNA samples archived in biobanks should be suitable for retrospective analyses. Three technical replicates per sample (extraction method) were analysed

ORGANISM(S): metagenome  

SUBMITTER: Mark Morrison   Páraic Ó Cuív  Daniel Aguirre de Carcer  Seungha Kang  Michelle Jones  Eline S Klaassens  Barbara A Leggett  Daniel L Worthley  Christopher S McSweeney  Vicki L Whitehall 

PROVIDER: E-GEOD-18420 | ArrayExpress | 2010-05-16

SECONDARY ACCESSION(S): GSE18420PRJNA118215

REPOSITORIES: GEO, ArrayExpress

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