DNA extraction methods comparison
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB29363 | ENA |
REPOSITORIES: ENA
Similar Datasets
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
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. Three technical replicates per sample (extraction method) were analysed
2010-05-16 | E-GEOD-18420 | biostudies-arrayexpress
Project description:Effect of DNA extraction methods on the determination of the structure of microbial communities in the phosphogypsum waste heap soil
| PRJEB12454 | ENA
Project description:Serum miRNAs are considered useful as non-invasive biomarkers for various diseases, but the optimal method for extracting RNA from serum is currently unknown. In this study, several RNA extraction kits were used to determine which kit is the optimal method. RNA was extracted from the serum of 8-week-old C57BL/6NJcl male mice according to the protocol of each RNA extraction kit. The yield of extracted RNA samples was calculated and electrophoretic patterns were evaluated by Agilent bioanalyzer. Expression patterns of the extracted RNA samples were confirmed by Agilent mouse miRNA microarray. The results showed significant differences in RNA yields in the miRNeasy serum/plasma advanced kit, and mirVana™ PARIS™ RNA and Native Protein Purification Kit compared to almost all other samples. Furthermore, two peaks were identified in the miRNeasy serum/plasma advanced kit using small RNA kit of Agilent bioanalyzer, one at 20-40 nucleotides (nt) and the other around 40-100 nt whereas the other reagents had a single peak. In addition, a high correlation was observed between the two RNA extraction kits in microarray. These results suggest that the above two kits are suitable for miRNA extraction from mouse serum.
2024-01-01 | GSE246437 | GEO
Project description:The goal of this study was to optimize protein extraction methods to study root-associated bacteria in maize. For this we inoculated sterile maize plants with a synthetic community composed of seven different bacteria (Ben Niu et al. PNAS 2017, vol 114, n 12). Then, we extracted proteins from maize roots using eight different protein extraction methods in triplicates. These methods were a combination of different extraction buffers (SDS or Triton-based) and mechanical disruption methods (bead-beating, N2 grinding, glass homogenizer and freeze-thaw cycles). We found that vortexing maize roots with glass beads in PBS yielded the highest numbers of microbial protein identification.
2022-09-08 | PXD026369 | Pride
Project description:We present three different methods for protein extraction from fresh frozen mouse heart tissue: 1) extraction using SDS buffer followed by FASP purification, 2) extraction using SDS buffer followed by S-Trap purification, and 3) extraction using a guanidine hydrochloride buffer followed by in-solution digestion. Based on bicinchoninic acid assay, all three methods display similar recovery of total protein content. However, proteomics-based analysis identified far fewer proteins from the extraction guanidine hydrochloride. SDS-FASP identifies as many proteins as the SDS-STrap method with good coverage of proteins from different cellular compartments.
2020-07-30 | PXD020256 | Pride
Project description:The goal of this study was to optimize protein extraction methods to study root-associated bacteria in Arabidopsis. For this we inoculated Arabidopsis seedlings grown in agar plates with a synthetic community (SynSom) composed of four different strains (Variovorax paradoxus, Arthrobacter sp, Agrobacterium sp. and Pseudomonas sp.. Twelve days after inoculation we extracted proteins from the roots using six different protein extraction methods each in triplicates. These methods were a combination of different extraction buffers (SDS or Triton-based) and mechanical disruption methods (bead-beating, N2 grinding, glass homogenizer and freeze-thaw cycles) We found that bead-beating the roots with lysing matrix E in SDT lysis buffer yielded the highest numbers of microbial protein identification and enhanced the detection of proteins derived from gram positive bacteria.
2022-09-08 | PXD026330 | Pride
Project description:Methods for the extraction of bacterial DNA
| PRJEB25932 | ENA
Project description:DNA extraction method targeted loci environmental
| PRJNA315949 | ENA
Project description:Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing
| PRJEB10532 | ENA