Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Negative and positive control samples - DNA extraction

ABSTRACT: References samples to the DNA extraction

PROVIDER: PRJEB39304 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

DNA Extraction

Project description:DNA extraction method targeted loci environmental

| PRJNA315949 | ENA

DNA extraction affects metabarcoding success

Project description:DNA extraction with inhibitor removal outperforms more simple methods in DNA metabarcoding of homogenized unsorted bulk samples

| PRJEB26589 | ENA

Effect of DNA extraction method on brain DNA copy number estimation

Project description:We analysed DNA from two brain regions (cerebellum, CER and frontal cortex, FC) from 4 Parkinson's disease (PD) and 4 control brains on a custom design 8x60k Agilent aCGH targeted to PD genes. All brain DNA samples were hybridised with Agilent sex-matched reference DNA, and three CER samples were hybridised against the FC of the same brain, with a dye swap in one. Male and female reference DNA were hybridised to eachother. The samples were then re-extracted with additional protocols, and hybridisations were performed for two CER samples betwen DNA extracted from the same CER with different protocols, and for one brain between the CER and FC new extraction.

2016-02-01 | GSE71360 | GEO

Louisiana Salt Marsh soil samples - meiofauna extraction

Project description:Louisiana Salt Marsh soil samples - meiofauna extraction 18S

| PRJNA706428 | ENA

Electrochemical cell lysis of gram-positive and gram-negative bacteria: DNA extraction from environmental water samples.

Project description:Cell lysis is an essential step for the nucleic acid-based surveillance of bacteriological water quality. Recently, electrochemical cell lysis (ECL), which is based on the local generation of hydroxide at a cathode surface, has been reported to be a rapid and reagent-free method for cell lysis. Herein, we describe the development of a milliliter-output ECL device and its performance characterization with respect to the DNA extraction efficiency for gram-negative bacteria (Escherichia coli and Salmonella Typhi) and gram-positive bacteria (Enterococcus durans and Bacillus subtilis). Both gram-negative and gram-positive bacteria were successfully lysed within a short but optimal duration of 1 min at a low voltage of ∼5 V. The ECL method described herein, is demonstrated to be applicable to various environmental water sample types, including pond water, treated wastewater, and untreated wastewater with DNA extraction efficiencies similar to a commercial DNA extraction kit. The ECL system outperformed homogeneous chemical lysis in terms of reaction times and DNA extraction efficiencies, due in part to the high pH generated at the cathode surface, which was predicted by simulations of the hydroxide transport in the cathodic chamber. Our work indicates that the ECL method for DNA extraction is rapid, simplified and low-cost with no need for complex instrumentation. It has demonstrable potential as a prelude to PCR analyses of waterborne bacteria in the field, especially for the gram-negative ones.

| S-EPMC7063685 | biostudies-literature

Impact of G2 Enhancer on DNA extraction from recalcitrant soil core samples

Project description:Qualitative and quantitative evaluation of the impact of G2-Enhancer on DNA extraction from deep-soil samples

| PRJEB24676 | ENA

DNA extraction from MX-80 bentonite

Project description:DNA extraction from natural and spiked MX 80 bentonite

| PRJEB29317 | ENA

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

DNA extraction methods comparison

Project description:The impact of the DNA extraction methods on the gut bacterial and fungal microbiota community recovery

| PRJEB29363 | ENA

Comparison of DNA extraction kits for MiSeq sequencing

Project description:Comparison of DNA extraction kits for MiSeq sequencing

| PRJEB10820 | ENA