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Updated: Sep 4, 2026
High Throughput MicroRNA Profiling: Optimized Multiplex qRT-PCR at Nanoliter Scale on the Fluidigm Dynamic ArrayTM IFCs
Published on: August 3, 2011
Data on individual PCR efficiency values as quality control for circulating miRNAs
Anna Brunet-Vega1, Carles Pericay2, María Elisa Quílez3
1Oncology Service, Hospital de Sabadell, Corporació Sanitària Parc Taulí, Institut Universitari Parc Taulí-UAB, Sabadell, Spain ; Fundació Parc Taulí, Corporació Sanitària Parc Taulí, Institut Universitari ParcTaulí-UAB, Sabadell, Spain.
Abstract:
This data article contains data related to the research article entitled "Variability in microRNA recovery from plasma: Comparison of five commercial kits, doi:10.1016/j.ab.2015.07.018" Brunet-Vega (2015) [1]. PCR efficiency, along with RNA and cDNA quality, are the most important factors affecting the quality of qPCR results. Constant amplification efficiency in all compared samples is indispensable when relative quantification is used to measure changes in gene expression. An easy way to measure PCR efficiency, without the need of a standard curve, is LinRegPCR software. Individual PCR efficiency can be determined as a part of qPCR quality control. This is especially important when the initial RNA quantity is so low that cannot be accurately quantified, such as in circulating RNA extractions. This data article reports the Cqs and PCR efficiencies of 5 miRNAs quantified in RNA isolated from 4 patients with colorectal cancer (CRC) and 4 healthy donors using five commercially available kits.
Insights
This study compared five commercial kits for microRNA (miRNA) recovery from plasma. Data shows significant variability in PCR efficiency, impacting gene expression analysis in colorectal cancer patients.
Area of Science:
- Biochemistry
- Molecular Biology
- Genomics
Background:
- Accurate quantification of circulating microRNAs (miRNAs) is crucial for biomarker discovery.
- Plasma RNA extraction methods can significantly influence downstream quantitative PCR (qPCR) results.
- Variability in RNA recovery and quality affects the reliability of gene expression analysis.
Purpose of the Study:
- To compare the performance of five commercial kits for miRNA isolation from human plasma.
- To assess the impact of different kits on PCR efficiency and miRNA quantification.
- To provide data for optimizing miRNA recovery and analysis in colorectal cancer research.
Main Methods:
- RNA was isolated from plasma of colorectal cancer patients and healthy donors using five commercial kits.
- Quantification of 5 specific miRNAs was performed using qPCR.
- PCR efficiency was determined using LinRegPCR software, without requiring a standard curve.
Main Results:
- Significant variability in Cq values and PCR efficiencies was observed across the five kits.
- The choice of kit impacted the reliability of miRNA quantification.
- Data highlights challenges in standardizing miRNA recovery from low-input plasma samples.
Conclusions:
- Commercial kits differ substantially in their ability to recover and prepare plasma RNA for qPCR.
- PCR efficiency is a critical parameter to assess for reliable miRNA quantification, especially with low RNA input.
- Standardization of RNA extraction methods is essential for reproducible miRNA biomarker studies.
