Unlock RNA Beyond Primary Sequence
Leading-edge technologies for reading, interpreting and manipulating RNA’s chemical marks
Epitranscriptomics presents paradigm-shifting opportunities for identifying novel diagnostic biomarkers, drug targets and therapeutics. Alida Biosciences’ technologies are designed to unleash the transformative potential of epitranscriptomics in basic research and applications in RNA-centered diagnostics and therapeutics.
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. Proximity barcoding requires a molecular recognition element, e.g. an antibody or other protein binder, that specifically binds the target and is associated with a DNA barcode. The barcoding reaction transfers the barcode to the nucleic acid target, thus 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 proximity barcoding chemistry is optimized for minimal crosstalk, allowing for future expansion of the 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-times smaller than antibodies, express at high yields and with reproducible quality, and they 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 of 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™ includes EpiScout™:
A Seamless Sample-to-Answer Workflow
The EpiPlex™ platform combines a robust reagent kit with advanced analysis software, providing a user-friendly end-to-end solution. The current version of the EpiPlex™ platform detects m6A and inosine.
The EpiScout™ software returns publication-quality plots, summary tables and data inputs for tertiary analysis specific to your research problem. The optimized RNA modification peak caller uses machine learning for best-in-class peak detection. The pipeline also provides quality metrics and global statistics to give a quick overview of data quality and trends, and analysis features to compare technical replicates and different biological samples. You will immediately see the loci and genes bearing RNA modifications with reports that make it easy to identify the sites most changed between biological samples. Regions of greatest interest to you can be visualized in any genome viewer.
EpiPlex™ and EpiScout™ make the epitranscriptome more accessible than ever before. EpiScout™ Analysis Software is included with the purchase of EpiPlex™ RNA Mod Encoding Kits and is available as a cloud app on DNAnexus or as a docker image.
A comprehensive workflow to deliver RNA modification and RNA expression data in a single experiment
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 sample to the prepared sequencing library. The magnetic bead based assay format offers convenient handling, scalable throughput and is compatible with 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. For the first time, you will be able to observe correlative changes across the epitranscriptome with sequence resolution.
Low RNA Input
Tolerant of low RNA input, EpiPlex™ kits enable the analysis of challenging, clinically-relevant samples—like frozen or FFPE tissues or blood biopsies. Study even degraded samples with minimal impact on data quality and learn from your precious patient samples.
Accessible Analysis
Every EpiPlex™ RNA Mod Encoding Kit includes full access to EpiScout™ Analysis Software, a custom pipeline available on DNAnexus or as a stand-alone desktop application. Whether you are bench scientist or a bioinformatician, this tool will deliver the answers you are looking for.
EpiPlex™, for combined RNA modification and RNA expression insight
AlidaBio transforms RNA modification research with next-generation epitranscriptomic tools. Our advanced 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.
