HEBER-seq: High-Efficiency Barcoded Extracellular RNA Sequencing

The Challenge in exRNA Research — Why Traditional Approaches Fall Short

Extracellular RNA (exRNA) has emerged as a valuable source of biological information, carrying molecular signals that reflect physiological and pathological states. Yet, researchers often encounter significant limitations when using conventional sequencing approaches to study cell-free RNA (cfRNA):

• Sample loss during vesicle enrichment — The need to isolate extracellular vesicles (EVs) adds multiple handling steps, often reducing RNA yield and introducing variability.
• High input requirements — Traditional methods demand larger sample volumes, making it difficult to work with scarce or precious biofluids.
• Incomplete RNA coverage — Many workflows focus on small RNAs, leaving longer RNA species such as mRNA and lncRNA underrepresented.
• rRNA contamination — Ribosomal RNA can dominate sequencing reads, masking the signals of interest.
• Fragmented analysis pipelines — Researchers often face the burden of piecing together quality control, expression profiling, and functional analysis across multiple tools.

For scientists aiming to identify biomarkers, explore disease mechanisms, or monitor dynamic biological processes, these limitations create barriers to discovery. A more efficient and comprehensive solution is required—one that delivers sensitive detection, broad RNA coverage, and streamlined data analysis from minimal sample input.

Introducing HEBER-seq: Our High-Efficiency Solution

Key Advantages for Researchers — Why HEBER-seq Stands Out

For researchers, the true impact of HEBER-seq lies in how it overcomes the barriers of traditional cfRNA sequencing and unlocks new opportunities for discovery:

• Low-input compatibility — Generate robust datasets even when working with limited or precious biofluid samples.
• No vesicle enrichment required — Reduce processing steps, eliminate sources of variability, and improve RNA yield.
• Comprehensive transcriptome coverage — Access long RNA species (mRNA and lncRNA) alongside small RNAs for a fuller view of extracellular biology.
• Improved reproducibility — Streamlined workflows and standardized preparation deliver consistent, comparable results.
• Research efficiency — By maximizing usable data from each sample, HEBER-seq shortens the path from sequencing to discovery.

These advantages ensure that researchers can focus less on technical hurdles and more on generating meaningful insights from cfRNA biology.

Project Workflow at CD Genomics — From Sample to Data Interpretation

Analytical Capabilities — From Raw Reads to Functional Insights

HEBER-seq is supported by a robust bioinformatics pipeline that transforms raw sequencing reads into meaningful biological insights. Each step is optimized for extracellular RNA, ensuring that researchers receive data that is both reliable and ready for interpretation.

Data Output & Deliverables — What You Receive

With HEBER-seq, researchers receive more than just sequencing data—they gain a complete package of processed results and visual outputs that are ready for exploration, publication, or integration into downstream studies. Every dataset is delivered in standardized formats to ensure usability across diverse research workflows.

Typical deliverables include:

By delivering both raw data and high-quality interpretations, HEBER-seq ensures that researchers can immediately transition from sequencing to discovery without the need for additional processing.

Demo

Sample Submission Requirements — Ensuring Reliable Results

High-quality results begin with high-quality samples. To fully leverage the sensitivity of HEBER-seq, we recommend following the guidelines below for sample preparation, preservation, and shipping.

Accepted sample types:

• Plasma
• Urine
• Cerebrospinal fluid (CSF)
• Other biofluids upon consultation

Input and quality guidelines:

• Minimal input volumes are sufficient, but samples must meet basic RNA integrity and purity standards.
• Avoid repeated freeze–thaw cycles that may compromise extracellular RNA stability.
• Samples should be free from RNase contamination and visible debris.
• Recommended starting design: For robust differential expression analysis, a study cohort of 30 vs 30 samples (case vs control) is suggested as a practical baseline.

Preservation and shipping recommendations:

• Collect samples using certified RNase-free consumables.
• Store and ship under low-temperature conditions to preserve RNA integrity.
• Provide detailed metadata (sample type, collection conditions, storage method) to support accurate interpretation.

Why Choose CD Genomics for HEBER-seq

Choosing a sequencing partner goes beyond the technology—it's about the reliability, expertise, and support behind the service. At CD Genomics, we provide:

• Specialized expertise in extracellular RNA — Our team applies validated protocols and deep RNA-seq experience to every project.
• Dedicated project support — From initial consultation to final report, we offer tailored guidance at each stage.
• Scalable solutions — Whether a pilot study or a large cohort, we adapt workflows to meet diverse research needs without compromising data quality.
• Comprehensive bioinformatics — Integrated pipelines deliver publication-ready results, with optional advanced analyses based on project goals.
• Data security and confidentiality — All projects are handled under strict QC and data protection standards.

By partnering with CD Genomics, researchers gain more than a sequencing service—they gain a trusted collaborator committed to advancing extracellular RNA research with precision and care.

Research Applications & Use Cases

The strength of HEBER-seq lies not only in its technical design but also in its versatility across diverse research areas. By enabling sensitive and comprehensive profiling of extracellular RNA, this platform opens opportunities in multiple domains of molecular biology and translational research:

• Biomarker discovery — Identify cfRNA signatures linked to early disease processes, therapeutic response, or environmental exposure.
• Disease mechanism studies — Explore how mRNA and lncRNA released into biofluids reflect underlying molecular pathways and regulatory networks.
• Viral RNA detection — Monitor circulating viral transcripts in host fluids without additional enrichment steps.
• Reproductive and developmental biology — Investigate exRNA biomarkers in pregnancy and developmental studies using non-invasive sampling.
• Comparative transcriptomics — Assess transcriptomic differences across biofluids, tissues, or experimental models to uncover system-level regulation.

By bridging sample accessibility with transcriptome-wide resolution, HEBER-seq provides researchers with a powerful approach to address complex biological questions in a non-invasive yet highly informative manner.

Frequently Asked Questions (FAQ)

• Q1: What is the minimum sample input required for HEBER-seq?
  • • A: HEBER-seq is designed to work with low-input biofluid samples. While input requirements depend on the sample type and RNA quality, we recommend a starting study design of 30 vs 30 (case vs control) to ensure sufficient statistical power in differential expression. If your samples are limited, we can discuss tailored designs to maximize yield from minimal material.
• Q2: Can HEBER-seq detect both mRNA and lncRNA, or is it limited to small RNAs?
  • • A: HEBER-seq captures both long RNAs (mRNAs, lncRNAs) and small RNAs, thanks to its library preparation workflow with rRNA depletion. This enables more comprehensive transcriptome profiling than methods focusing only on small RNAs.
• Q3: Do I need to enrich for extracellular vesicles (EVs) before sending samples?
  • • A: No. One of the key features of HEBER-seq is that EV enrichment is not required. Samples are processed directly, which reduces handling, minimizes loss, and enhances reproducibility.
• Q4: What are the guidelines for collecting, preserving, and shipping samples to ensure high data quality?
  • • A: To maintain RNA integrity:
      • Use RNase-free consumables and clean collection tubes.
      • Process samples quickly (e.g. centrifuge within hours if required) and keep them cold/frozen.
      • Avoid repeated freeze-thaw cycles.
      • Ship on dry ice or with appropriate cold‐chain arrangements.
      • Include metadata like sample type, volume, collection time, storage conditions.
• Q5: What file formats and data outputs will I receive?
  • • A: Deliverables typically include: FASTQ raw sequence files, normalized expression matrices for mRNA & lncRNA, differential expression tables, functional annotation reports (GO / KEGG), and visualization figures (heatmaps, volcano plots, ROC curves, pathway diagrams). All files are delivered in standard formats (e.g. tab-delimited, Excel / CSV, PNG or PDF for plots) to facilitate downstream analysis.
• Q6: How long does it take from sample submission to receiving full data and analyses?
  • • A: Turnaround time depends on sample number, quality, and analysis complexity. After samples pass QC, sequencing + core bioinformatics can typically be completed in a few weeks. More advanced analysis (e.g. predictive modeling, network analysis) may require additional time. We will provide you with an estimated timeline during project consultation.
• Q7: What if my RNA is partially degraded, or sample quality is not ideal?
  • • A: HEBER-seq's workflow includes special design features (e.g. rRNA depletion, robust library prep) that tolerate some level of degradation. However, very poor RNA quality can reduce sensitivity or increase noise. We can assess QC metrics on arrival and work with you to adjust expectations or suggest modifications in design.
• Q8: Is there species limitation? Can I use samples from non-human organisms?
  • • A: Currently, HEBER-seq is optimized primarily for human biofluid samples. However, with consultation, we can support other species provided there is a suitable reference genome / transcriptome assembly. Please contact us when you plan non-human studies.

Contact & Next Steps — Start Your HEBER-seq Project Today

Are you ready to unlock the full potential of extracellular RNA research with HEBER-seq? Whether your goal is biomarker discovery, disease mechanism exploration, or comparative biofluid transcriptomics, CD Genomics is here to provide expert guidance and reliable data.

We make it simple to begin:

• Request a Quote — Share your project details and receive a tailored plan with recommended sequencing depth and analysis options.
• Submit Your Samples — Follow our submission guidelines and let our team handle the library preparation, sequencing, and analysis.
• Talk to Our Specialists — Schedule a consultation to discuss your study design, sample requirements, or advanced bioinformatics needs.

Partner with CD Genomics to accelerate your cfRNA and exRNA discoveries. Our team is committed to delivering high-quality sequencing results, comprehensive data interpretation, and ongoing support throughout your project.

Start your HEBER-seq project today — [Request a Quote] or [Contact Our Specialists] to explore how we can support your research.

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