Small RNA Sequencing
What Is Small RNA Sequencing?
Small RNA sequencing (small RNA-seq) targets the short, regulatory RNA species—typically 15–50 nucleotides—that orchestrate gene expression and genome stability. These include:
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MicroRNAs (miRNAs): ~20–24 nt RNAs guiding RISC to repress target mRNAs.
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PIWI-interacting RNAs (piRNAs): ~26–31 nt RNAs that protect genome integrity in germ cells.
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tRNA Fragments (tRFs): ~14–35 nt pieces of tRNAs with emerging regulatory roles.
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Small Nucleolar RNAs (snoRNAs) & snRNA Fragments: Processed fragments involved in RNA modification and splicing.
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Other small RNAs: siRNAs, Y-RNA fragments, vault RNAs, and novel species.
At AUGenomics, we’ve refined our small RNA-seq pipeline to turn even the tiniest RNA fragments into actionable data. From your sample—whether it’s cultured cells, plasma, or exosome isolates, we enrich precisely the 18–30 nt species you care about, then tag each molecule with a unique barcode so PCR or sequencing artifacts can be filtered out. Our tailored size-selection captures rare small RNAs without over-representing abundant ones, and our strict quality controls at each step ensure you get highly reproducible, quantitative profiles. Throughout, our specialist team guides you on sample prep, data interpretation, and biomarker discovery, so you can focus on the biology, confident that your small RNA signatures truly reflect your system, not technical noise.
Advantages of Small RNA Sequencing
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Comprehensive Class Coverage: Simultaneous profiling of miRNAs, piRNAs, tRFs, snoRNA/snRNA fragments, and emerging small RNAs.
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Ultra-Low Input Sensitivity: Reliable libraries from 1–10 ng total RNA—or EV isolates—using enhanced ligation and PCR chemistries.
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IsomiR & Variant Resolution: Single-nucleotide precision captures 5′/3′ length variants, non-templated additions, and RNA edits.
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UMI-Based Quantitation: Collapses PCR duplicates for true molecule counts and increased reproducibility.
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Reduced Adapter Bias: Randomized adapter sequences and enzyme selection minimize sequence-dependent ligation artifacts.
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High Dynamic Range: Detect abundant miRNAs and rare small RNAs in the same run with minimal saturation.
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Batch Multiplexing: Dual-index barcoding supports 96–384 samples per flow cell, ideal for large-cohort studies.
Small RNA sequencing is widely used in:
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miRNA Biomarker Discovery: Early cancer detection, cardiovascular and neurodegenerative disease markers from plasma or serum.
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Epigenetic & Post-Transcriptional Regulation: Study miRNA-mediated gene silencing, piRNA transposon control, and tRF stress responses.
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Development & Stem Cell Biology: Map dynamic small RNA expression during differentiation and lineage commitment.
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Immune & Host–Pathogen Interactions: Profile host small RNAs in infection models and viral small RNA signatures.
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Exosome & EV Small RNA Profiling: Link vesicle-encapsulated miRNAs and tRFs to intercellular communication and liquid biopsy applications.
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Agricultural & Environmental Studies: Small RNA roles in plant stress responses, microbial small RNA regulation, and cross-kingdom signaling.
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Therapeutic Response Monitoring: Track small RNA changes in response to drugs, immunotherapies, or gene-editing interventions.
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Novel Small RNA Discovery: Uncover unannotated small RNA loci and characterize their biogenesis and function.
Our workflows support a broad range of input types and are optimized for sensitivity and reproducibility.
What is Small RNA Sequencing Used For?
Small RNA Sequencing with AUGenomics
Sample Submission
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Accepted Sample Types: Total RNA or enriched small RNA from tissue, biofluids (e.g., plasma, serum, urine), exosomes, or cell cultures
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Input Requirement: 10–100 ng of total or small RNA (ultra-low input supported)
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Sequencing Recommendations:
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Read length: Single-end 50 bp or 75 bp
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10–20 million reads/sample standard for most studies
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Adapter ligation and size selection for accurate capture of short fragments
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Please refer to our Shipping Guidelines for project-specific guidance.
Turnaround Time
Typical turnaround is 7-10 business days from sample receipt. Expedited options are available depending on project scope and sequencing depth.
Frequently Asked Questions (FAQs)
Q: What’s the difference between small RNA-seq and total RNA-seq?
A: Small RNA-seq focuses specifically on short RNA molecules (typically <200 nt), while total RNA-seq captures all RNA species, including longer coding and non-coding RNAs.
Q: Can I use small RNA-seq for plasma or serum samples?
A: Yes. Our protocols are optimized for low-input and biofluid-derived RNA, including from plasma, serum, and exosomes.
Q: What types of small RNAs can I detect with this service?
A: Our workflow supports detection of miRNA, piRNA, snoRNA, snRNA, tRNA fragments, and novel small RNAs.
Q: Why use UMIs in small RNA-seq?
A: UMIs tag each original molecule pre-PCR, collapsing duplicates and providing true abundance measures, crucial when sequencing low-input or highly-amplified libraries.
Q: How do you reduce adapter-ligation bias?
A: We use randomized bases in adapters and optimized ligases to equalize ligation efficiencies across diverse small RNA sequences.
Q: Can I detect piRNAs and tRFs in the same assay?
A: Yes—our size-selection and annotation pipeline captures 18–35 nt RNAs, enabling simultaneous miRNA, piRNA, and tRF profiling.
Got more questions? Contact our team and get a free consultation anytime. info@augenomics.com
Glossary of Terms
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Small RNA: Short RNA molecules (typically <<200 nucleotides) with regulatory functions
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miRNA/piRNA/snoRNA: Classes of small non-coding RNAs that drive gene silencing, genome defense, and RNA processing
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Adapter Ligation: Library-prep step that attaches synthetic sequences to RNA fragments for amplification and sequencing
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Size Selection: Isolation of RNA fragments within a defined size range
