Project description:Effect of DNA extraction methods on the determination of the structure of microbial communities in the phosphogypsum waste heap soil

| PRJEB12454 | ENA

Detection of Human Viruses from wastewater sewage extracts

Project description:Sewage samples were collected and concentrated for Human and animal viruses. Viruses were cultured on Buffalo Green Monkey Cells (BGMK) and their genomic DNA/RNA were extracted and labeled with Cy3 and Cy5 respectively. Labeled DNA/RNA were hybridized unto the array and signals generated were analyzed to indicate the presence of target viruses. Keywords: Detection of pathogens within environmental sample (Viruses) Environmental viruses were concentrated using organic flocculation with Beef Extract supplemented with glycine. Viruses were concentrated using 2 successive rounds of centrifugation and resuspended in Sodium Phosphate buffer. Viral nucleic acid was extracted, labeled and hybridized unto the microarray to determine the presence of target viruses within the sample.

2008-04-18 | E-GEOD-11195 | biostudies-arrayexpress

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

Project description: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.

2010-01-01 | GSE18420 | GEO

Viruses

Project description:Detection of Human Viruses from wastewater sewage extracts

| PRJNA106787 | ENA

Examination and comparison of the RNA extraction methods using mouse serum

Project description:Examination and comparison of the RNA extraction methods using mouse serum

| PRJNA1032931 | ENA

Evaluation of lysis methods for the extraction of bacterial DNA for analysis of the broiler chicken cecal microbiota

Project description:Methods for the extraction of bacterial DNA

| PRJEB25932 | ENA

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

2010-05-16 | E-GEOD-18420 | biostudies-arrayexpress

Evaluating the protein extraction methods for gut metaproteomics

Project description:Human stool samples were collected, microbial cells were harvested and subjected to protein extraction using different protocols for metaproteomics analyses. The protein extraction methods differ from the usage of different lysis buffer (SDS, urea and commercially available B-Per reagent), bead beating, ultrasonication and heating. The impacts of different protein extraction methods on metaproteomics results were evaluated with multiple criteria including protein yields, peptide identifications, taxonomic compositions and functional compositions.

2017-07-17 | PXD005969 | Pride

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