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Effect of DNA extraction methods

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

PROVIDER: PRJEB12454 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1223810_1.fastq.gz	Fastqsanger.gz
	ERR1223810_2.fastq.gz	Fastqsanger.gz
	ERR1223820_1.fastq.gz	Fastqsanger.gz
	ERR1223820_2.fastq.gz	Fastqsanger.gz
	ERR1223830_1.fastq.gz	Fastqsanger.gz

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DNA extraction methods comparison

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

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Examination and comparison of the RNA extraction methods using mouse serum

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

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Methods for the concentration and extraction of viruses

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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.

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Extraction of Entamoeba histolytica membrane proteins using three extraction methods

Project description:Entamoeba histolytica membrane proteins are important players in the parasite’s pathogenicity. However, most of the proteins have not been identified. This study reports the membrane proteins extracted using three extractions methods: two commercial kits (ProteoExtract® from Calbiochem and ProteoPrep® from Sigma), and a conventional laboratory method. The resulting membrane fractions (MF) and cytosolic fractions (CF)were analysed using LC-ESI-MS/MS. The proteins identified in at least two out of three biological replicates revealed a total of 490, 492, and 587 MF proteins extracted using the ProteoExtract® kit, ProteoPrep® kit and conventional method, respectively. Meanwhile, 487, 611 and 343 proteins were identified in the CF extracted using the ProteoExtract® kit, ProteoPrep® kit and conventional method, respectively. Analysis of the identified MF and CF proteins extracted by the respective extraction kits suggests that the ProteoPrep® extraction kit was the most selective in separating MF and CF among the three extraction methods.

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Examination and comparison of the RNA extraction methods using mouse serum

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.

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Project description:Influence of RNA extraction methods and library selection schemes on RNA-seq data

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