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Status |
Public on Aug 31, 2013 |
Title |
Evaluation of quantitative miRNA gene expression platforms in the microRNA Quality Control (miRQC) study |
Organisms |
Homo sapiens; Escherichia phage MS2 |
Experiment type |
Non-coding RNA profiling by high throughput sequencing
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Summary |
MiRNAs are important negative regulators of protein coding gene expression, and have been studied intensively over the last few years. Several measurement platforms, designed to determine their relative RNA abundance levels in biological samples, have been developed. In this study, we systematically compared 12 commercially available miRNA expression platforms by measuring an identical set of 20 standardized positive and negative control samples, including human universal reference RNA, human brain RNA and titrations thereof, human serum samples, and synthetic spikes from miRNA family members with varying homology. We developed novel and robust quality metrics to objectively assess platform performance of very different technologies such as small RNA sequencing, RT-qPCR and (microarray) hybridization. We assessed reproducibility, sensitivity, accuracy, specificity, and concordance of differential expression. The results indicate that each method has its strengths and weaknesses, which helps to guide informed selection of a quantitative miRNA gene expression platform in function of particular study goals.
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Overall design |
Sequencing of 20 miRQC samples on Illumina Genome Analyzer IIx System
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Contributor(s) |
Schroth G, Narayanan A, Veeramachaneni V |
Citation(s) |
24973947 |
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Submission date |
Aug 12, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Aishwarya Narayanan |
Organization name |
Strand Life Sciences
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Street address |
5th Floor, KBP, Bellary Road
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City |
Bangalore |
ZIP/Postal code |
560024 |
Country |
India |
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Platforms (2) |
GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
GPL17561 |
Illumina Genome Analyzer IIx (Enterobacterio phage MS2) |
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Samples (20)
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Relations |
BioProject |
PRJNA214981 |
SRA |
SRP028738 |