Unlock RNA Beyond Primary Sequence
Leading-edge technologies for reading, interpreting, and manipulating RNA’s chemical marks.
Epitranscriptomics presents paradigm-shifting opportunities for novel diagnostic biomarkers, drug targets, and therapeutics. Alida Biosciences’ technologies are designed to unleash the transformative potential of epitranscriptomics in basic research and in RNA-centered diagnostics and therapeutics.
The EpiPlex assay from AlidaBio
AlidaBio’s EpiPlex Platform offers a seamless, end-to-end workflow for detection and relative quantitation of RNA modifications alongside gene expression profiling. Designed for efficiency and accuracy, the platform includes the EpiPlex RNA Mod Encoding Kit, providing all the reagents needed to go from RNA samples to sequencing-ready libraries, and the EpiScout analysis pipeline for comprehensive data analysis.
Optimized for the simultaneous detection and relative quantitation of N6-methyladenosine (m6A) and inosine, the EpiPlex platform is inherently scalable and ready to expand to additional RNA modifications in the future. With low input requirements of just 20 ng of poly(A) enriched RNA or 250 ng of total RNA, it’s compatible with a wide range of biological and clinical samples.
Key Features:
- Enrichment-based library prep using non-antibody binders to selectively enrich modified RNA fragments.
- Quantitative profiling of multiple RNA modifications (currently m6A and inosine) and gene expression in a single workflow.
- Low sample input requirements: 20 ng poly (A) enriched RNA or 250 ng total RNA.
- Rapid, streamlined workflow: ~7 hours total, including ~3 hours of hands-on time.
- Compatible with Illumina and other short-read sequencing platforms.
Unlock deeper insights into the epitranscriptome with a platform built for scalability, efficiency, and precision.
Uncover complex gene regulation dynamics with multi-target detection
AlidaBio™ proximity barcoding translates sequencing-silent RNA modifications into NGS-readable barcodes to enable multi-target detection. A molecular recognition element—such as an antibody or other protein binder—binds the target and is associated with a DNA barcode. The barcoding reaction transfers the barcode to the nucleic acid target, encoding the target identity in sequence space. While proximity barcoding is an established detection scheme for proteins, we are the first to apply this concept broadly to epigenetic markers of nucleic acids, including DNA methylation, histone and RNA modifications. Our chemistry is optimized for minimal crosstalk, allowing for future expansion of target plexity.
Capture RNA modifications with specificity using engineered molecular recognition
AlidaBio™ engineered protein binders deliver unmatched specificity, stability, and affinity compared to antibodies. Our binders are derived from small protein scaffolds using cutting-edge protein evolution techniques such as yeast, phage, or mRNA display. AlidaBio’s binders are 8× smaller than antibodies, express at high yields with reproducible quality, and can be site-specifically labeled with DNA barcodes or linkers for surface immobilization.
Novel RNA modifying enzymes
To augment our ability to detect, apply, or remove RNA modifications we established a discovery pipeline for screening RNA modifying enzymes with desirable properties. AlidaBio™ enzymes label RNA modifications with a variety of chemical handles, expanding the opportunity to detect difficult targets and to manipulate RNA.
EpiPlex™ Platform: A seamless sample-to-answer workflow
The EpiPlex™ platform combines a robust reagent kit with EpiScout™ analysis software for advanced data analysis, providing a user-friendly end-to-end solution. The current version detects m6A and inosine.
EpiScout™ returns publication-quality plots, summary tables, and data inputs for tertiary analysis. The optimized RNA modification peak caller uses machine learning for best-in-class peak detection. The pipeline provides quality metrics and global statistics for data quality and trends, and supports comparison of technical replicates and biological samples. Identify loci and genes bearing RNA modifications with reports that make it easy to spot the sites most changed between samples; regions of interest can be visualized in any genome viewer. EpiScout™ Analysis Software is available as a cloud app on DNAnexus.
A comprehensive workflow
EpiPlex™ kits use a proximity encoding assay to detect multiple targets, offer relative quantification, include gene expression analysis, and work with low RNA input—ideal for clinical samples and biomarker discovery. The assay takes 7 hours from fragmented RNA to sequencing-ready library, with a magnetic bead format that supports scalable throughput and automation on liquid handlers.
Multi-Target Detection
Simultaneous detection of multiple RNA modifications in a single experiment minimizes RNA input, lowers costs, saves analysis time, and reduces variability. Observe correlative changes across the epitranscriptome with sequence resolution.
Low RNA Input
Tolerant of low RNA input, EpiPlex™ kits enable analysis of challenging, clinically-relevant samples—frozen or FFPE tissues, blood biopsies. Study even degraded samples with minimal impact on data quality.
Accessible Analysis
EpiScout™ Analysis Software is a custom pipeline available on DNAnexus. Whether you are a bench scientist or a bioinformatician, this tool delivers the answers you need.
EpiPlex™ Platform for combined RNA modification and RNA expression insight
AlidaBio transforms RNA modification research with next-generation epitranscriptomic tools. Our technologies empower scientists and clinicians to uncover the critical role of RNA modifications in gene regulation and cellular function, driving breakthroughs in research, therapeutics, and diagnostics.