Ultra Low Input RNA Sequencing
What Is Ultra Low Input RNA Sequencing?
Ultra Low Input RNA Sequencing empowers transcriptome analysis from picogram- to nanogram-scale RNA—or as few as 1–1,000 cells—unlocking insights from exceptionally rare or precious samples such as circulating tumor cells, laser-capture microdissected biopsies, early embryos, or brain tissue micro-regions. AUGenomics’ SMART-Seq Stranded Kit with random-primed reverse transcription and integrated rRNA-cDNA removal delivers:
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Full-length cDNA from both coding and non-coding RNAs (mRNA, lncRNA, snRNA, circRNA)
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Strand specificity to distinguish sense/antisense transcripts
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Ultra-sensitive detection down to 10 pg total RNA or 1 cell
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Unbiased amplification via template-switching SMART technology, preserving the true representation of original transcripts
Whether you’re mapping gene expression in tiny cell populations, profiling degraded FFPE archives, or exploring the non-coding RNA landscape, our ultra low input RNA-Seq workflows provide the data quality and reproducibility you need.
Advantages of Ultra Low Input RNA Sequencing
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Minimal Input Requirements: Reliable performance from as little as 500 pg–5 ng total RNA (equivalent to 10–50 cells).
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Degraded & FFPE Compatibility: Optimized for samples with DV200 ≥ 30%, ensuring high library complexity from fragmented RNA.
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Strand-Specific Libraries: Preserve transcriptional orientation to distinguish sense/antisense expression.
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Low Amplification Bias & High Complexity: Consistently low duplication rates and broad transcript representation even at ultra-low inputs.
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Exceptional Sensitivity: Reliable data from 10 pg–10 ng RNA or 1–1,000 cells
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Full Transcriptome Coverage: Random-primed RT captures poly(A)+ and non-poly(A) RNAs, including lncRNAs and circRNAs
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Integrated rRNA Removal: Removes >95% rRNA-derived cDNA without extra kits
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UMI-Enabled Quantitation: Unique Molecular Identifiers collapse PCR duplicates for accurate molecule counts
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Small RNA Compatibility: Optional small-RNA protocols deliver complex libraries from as little as 1 ng input
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High Throughput & Cost Efficient: Dual-index barcoding supports 96–384 samples per run and reduces per-sample costs
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Rapid Turnaround: Complete from RNA receipt to data delivery in 7–10 business days, rush options available
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AUGenomics’ ultra low input RNA-Seq combines these advantages to unlock rich transcriptomic insights from the most challenging samples.
Ultra Low Input RNA Sequencing is particularly valuable for:
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Profiling rare cell populations or limited biopsy samples
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FFPE-derived RNA samples with heavy degradation
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Organoids & 3D Cultures: Gene expression in micro-tissues and organoid models
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Low-Volume Biofluids: CSF, synovial fluid, BAL, or exosome-rich plasma/serum
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Non-Coding RNA Discovery: lncRNAs, circular RNAs, snRNAs, and other regulatory transcripts
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Small RNA Profiling: miRNAs, piRNAs, tRFs from ultra-low input small-RNA libraries
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Preclinical & Translational Research: Biomarker discovery and pathway analysis in limited material
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Single-cell or near single-cell resolution RNA studies (outside of full single-cell platforms)
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Early-stage embryo or small-organism research
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Archived samples and low-concentration biofluids
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Preclinical models with limited sample access
Our optimized protocols help you generate high-quality data even when sample material is minimal or partially degraded.
What is Ultra Low Input RNA Sequencing Used For?
Ultra Low Input RNA Sequencing with AUGenomics
Sample Submission
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Accepted Sample Types: Cells or RNA extracted from FFPE tissue, microdissected cells, biopsies, or low-volume fluids (e.g., CSF, serum)
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Input Requirement: As low as 10 pg to 10 ng total RNA or 1-1,000 sorted cells
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Sequencing Recommendations:
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10–30 million reads/sample for standard applications
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Enzymatic cDNA amplification protocols with UMI support for bias correction
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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 minimum RNA input required for ultra low input RNA-seq?
A: We can work with as little as 10 picograms of total RNA. However, input amount and integrity impact library complexity and should be assessed before submission.
Q: Is this method suitable for FFPE or degraded samples?
A: Yes. This service is designed specifically for samples with low yield or compromised integrity, including FFPE tissues.
Q: How do UMIs improve data quality?
A: UMIs tag each original cDNA molecule prior to PCR, enabling accurate collapse of duplicates and reducing amplification bias—crucial for low-input workflows.
Q: Can I profile small RNAs in the same workflow?
A: Yes—ask about our ultra-low input small RNA-Seq protocols, which generate complex libraries from as little as 1 ng total RNA.
Q: What depth do you recommend?
A: 10–30 million paired-end reads per sample for full-length transcriptome and isoform analysis; lower depths may suffice for targeted or 3′-end methods.
Q: Why random priming instead of oligo(dT)?
A: Random primers capture non-poly(A) RNAs and degraded fragments, providing full transcriptome coverage.
Got more questions? Contact our team and get a free consultation anytime. info@augenomics.com
Glossary of Terms
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Ultra Low Input RNA-seq: RNA sequencing performed on minimal RNA quantities
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UMI: Unique Molecular Identifier used to correct amplification bias
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FFPE: Formalin-Fixed Paraffin-Embedded tissue—commonly degraded RNA source
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Amplification Bias: Skew in data caused by unequal amplification of RNA fragments during library prep
