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Updated: May 16, 2026
09:29
A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools
Published on: August 21, 2019
YM500: a small RNA sequencing (smRNA-seq) database for microRNA research
Wei-Chung Cheng1, I-Fang Chung, Tse-Shun Huang
1Division of Pediatric Neurosurgery, Neurological Institute, Taipei Veterans General Hospital, Taipei 11217, Taiwan.
Nucleic Acids Research
|December 4, 2012
Summary
Researchers developed YM500, a database integrating 609 small RNA sequencing datasets for microRNA (miRNA) analysis. It aids in miRNA quantification, isomiR identification, and novel miRNA discovery, with high validation accuracy.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- MicroRNAs (miRNAs) are key regulators in biological processes and diseases.
- High-throughput small RNA sequencing (smRNA-seq) has revolutionized miRNA research.
- Existing resources often lack integrated analysis pipelines for diverse miRNA data.
Purpose of the Study:
- To establish YM500, an integrative database for analyzing human and mouse smRNA-seq data.
- To provide comprehensive analysis results including miRNA quantification, isomiR identification, arm switching, and novel miRNA prediction.
- To offer a user-friendly web interface for accessing and exploring these analyses.
Main Methods:
- Collected and analyzed 609 human and mouse smRNA-seq datasets from public (GEO) and private sources.
- Developed integrated analysis pipelines for miRNA quantification, isomiR identification (including RNA editing), arm switching, and novel miRNA prediction.
- Validated miRNA profiling results against RT-qPCR, achieving a high correlation (R = 0.84).
Main Results:
- YM500 database established, hosting analysis results for 609 smRNA-seq datasets.
- Interactive web interface allows searching miRNA quantification, isomiR identification, arm switching, and novel miRNA predictions.
- IsomiR identification criteria are definable, with dbSNP integration to differentiate from SNPs.
Conclusions:
- YM500 provides a valuable resource for miRNA research by integrating diverse datasets and analyses.
- The database facilitates discovery of novel miRNAs and isomiRs with potential biotech applications.
- High correlation between database profiling and RT-qPCR validates the reliability of the YM500 analysis.
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