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Assesing an improved protocol for plasma microRNA extraction

ABSTRACT: The first step in biomarkers discovery is to identify the best protocols for their purification and analysis. We have identified an optimal RNA extraction method of microRNAs from human plasma samples. We also report that the addition of low doses of carrier RNA before starting RNA extraction improves microRNA extraction and quantification.

ORGANISM(S): synthetic construct Homo sapiens

PROVIDER: GSE51375 | GEO | 2013/10/18

SECONDARY ACCESSION(S): PRJNA222852

REPOSITORIES: GEO

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Assesing an improved protocol for plasma microRNA extraction

Project description:The first step in biomarkers discovery is to identify the best protocols for their purification and analysis. We have identified an optimal RNA extraction method of microRNAs from human plasma samples. We also report that the addition of low doses of carrier RNA before starting RNA extraction improves microRNA extraction and quantification. Human plasma and matched biopsies were obtained from healthy donors and patients attended at the Hospital Universitari i Politècnic La Fe (Valencia, Spain). RNA was extracted by different preanalytal conditions and reagents, testing the suitable of carrier addition at differnt doses. The best protocol was followed up by hybridation on Affymetrix microarrays.

2013-10-18 | E-GEOD-51375 | biostudies-arrayexpress

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2017-04-20 | GSE80589 | GEO

Assessing an improved protocol for plasma microRNA extraction.

Project description: Not available

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A comparison of RNA extraction and sequencing protocols for detection of small RNAs in plasma

Project description:We compared 3 small RNA library prep kits (CleanTag, NEXTflex, QIAseq) and two RNA extraction methods (miRNeasy and MagnaZol) on plasma. We report that library preparation has a significant effect upon the miRNA profile detected, with QIAseq libraries exhibiting the least sequencing bias of the three library kits. RNA extraction methods also contribute, to a lesser extent, to the miRNA profile detected, with MagnaZol RNA extraction increasing the percentage of reads mapping to miRNAs and the number of individual miRNAs detected.

2019-05-21 | GSE118125 | GEO

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2019-01-28 | PXD012517 | iProX

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Project description:We demonstrate a method for the DNA, RNA and Protein extraction of plasma extracellular vesicles.

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Optimization of Extraction of Circulating RNAs from Plasma

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A unified protocol for simultaneous extraction of DNA and proteins from archaeological dental calculus

Project description:Archaeological materials are a finite resource, and efforts should be made to minimize destructive analyses. This can be achieved by using protocols combining extraction of several lines of evidence, which decreases the material needed for analyses while maximizing the information yield. Archaeological dental calculus is a source of several different types of biomolecules, as well as microfossils, and can tell us about the human host, microbiome, diet, and even occupational activities. Here, we present a unified protocol allowing for simultaneous extraction of DNA and proteins from archaeological dental calculus. We evaluate the protocol on dental calculus from a range of ages and estimated preservation states, and compare it against standard DNA-only and protein-only protocols. We find that most aspects of downstream analyses are unaffected by the unified protocol, although minor shifts in the recovered proteome can be detected. Protein recovery depends on both the amount of starting material and choice of extraction protocol, whereas DNA recovery is significantly lowered through the unified protocol. However, DNA recovery from dental calculus is generally very high, and we found no differences in DNA fragment characteristics or taxonomic profile. In conclusion, the unified protocol allows for simultaneous extraction of two complementary lines of evidence from archaeological dental calculus without compromising downstream analyses, thereby minimizing the need for destructive analysis of this finite resource.

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Wood extraction protocol evaluation_W219_2023

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Identification of extracellular miRNA in archived serum samples by next-generation sequencing from RNA extracted using multiple methods

Project description:MicroRNAs (miRNA) are non-coding RNAs that negatively regulate gene expression by preventing the translation of specific mRNA transcripts. Since miRNAs are stably expressed in bodily fluids, there is growing interest in profiling these miRNAs, as it is minimally invasive and cost-effective as a diagnostic matrix. A technical hurdle in studying miRNA dynamics is the ability to reliably extract miRNA as small sample volumes and low RNA abundance create challenges for extraction and downstream applications. The purpose of this study was to develop a pipeline for the recovery of miRNA using small volumes of archived serum samples. The RNA was extracted employing several widely utilized RNA isolation kits with and without addition of a carrier. We were able to profile miRNA levels in serum samples using the small RNA sequencing method on the Illumina platform and observed that successful sequencing cannot be predicted by substrate RNA quality. Although the carrier RNA had a significant impact on miRNA measurement, it did not enhance the mapping of any miRBase annotated sequences. However, some of the extraction procedures offer certain advantages: RNA extracted by TRIzol seemed to align to the miRBase best; extractions using TRIzol with carrier yielded higher miRNA-to-small RNA ratios and higher numbers of processed reads, but the majority of the reads were not aligning to miRBase. Our findings illustrate that miRNA extraction and quantification is influenced by the choice of methodologies and by careful selection of an extraction method, permitting archived serum samples to become valuable resources for high-throughput applications.

2016-08-01 | GSE80274 | GEO

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