Total RNA Sequencing
What Is Total RNA Sequencing?
Total RNA sequencing offers a comprehensive view of the transcriptome by capturing both coding and non-coding RNAs. At AUGenomics, our total RNA-seq services help researchers uncover the full spectrum of RNA expression, including mRNA, lncRNA, snRNA, and other regulatory RNA species, even in low-quality or degraded samples.
Total RNA sequencing offers a comprehensive view of the entire transcriptome, including mRNA, long non-coding RNA (lncRNA), small nuclear RNA (snRNA), circular RNA (circRNA), and other regulatory species—by removing abundant ribosomal RNA (rRNA) and converting the remaining RNA into sequencing libraries. At AUGenomics, we use multiple rRNA-depletion strategies:
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Bead-Based Hybridization Capture: Biotinylated antisense probes bind rRNA, which is then pulled out of solution with streptavidin-coated magnetic beads, removing > 95% of rRNA in one step.
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RNase H–Mediated Depletion: Short DNA probes anneal to rRNA; RNase H then specifically cleaves the RNA strand of the DNA–RNA hybrid, leaving other RNAs intact.
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CRISPR-Cas9 Guided Cleavage: Programmable Cas9 and guide RNAs target and cut rRNA (or any abundant transcript) in cDNA libraries, fragmenting unwanted molecules for efficient removal (Jumpcode Genomics)
Our approach yields a truly comprehensive view of gene expression, alternative splicing patterns, novel transcript discovery (including circRNAs and fusion transcripts), RNA editing events, and allele-specific expression, even from low-quality or highly degraded inputs.
At AUGenomics, our total RNA-seq services combine optimized rRNA-depletion, strand-specific library preparation, and high-quality sequencing to help researchers uncover the full spectrum of RNA expression (including mRNA, lncRNA, snRNA, and other regulatory RNA species). We deliver complete, unbiased transcriptome profiling for your most challenging samples with support for low-quality or degraded samples.
Advantages of Total RNA Sequencing
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Comprehensive Coverage: Captures both poly(A)+ and non-poly(A) RNAs—mRNAs, lncRNAs, snRNAs, snoRNAs, circRNAs, and other regulatory species—in a single assay.
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rRNA & Abundant Transcript Removal: Multiple depletion methods (bead-based, RNase H, CRISPR-Cas9, SEQuoia) eliminate > 95% rRNA and other high-copy RNA, maximizing informative reads.
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Strand-Specific Libraries: Preserve transcript orientation to distinguish overlapping sense/antisense transcription and accurately map non-coding RNAs.
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Degraded & Low-Input Compatibility: Optimized workflows for FFPE, cell-free RNA, and samples with as little as 10 ng total RNA.
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Isoform & Splice Variant Detection: Random-primed, full-transcript coverage reveals alternative splicing events, novel exons, and fusion transcripts.
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RNA Editing & Allele-Specific Expression: Detect post-transcriptional modifications and parental-allele biases across all RNA classes.
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Scalable & Flexible: Process from single samples to hundreds in multiplexed runs, with customizable read depths (40–100 M reads/sample).
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nbiased Discovery: No reliance on poly(A) tails—enables exploration of circular RNAs, enhancer RNAs, and other emerging transcript classes.
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AUGenomics’ total RNA-Seq harnesses these advantages to deliver an all-in one, high-resolution portrait of your transcriptome, from coding messages to the vast landscape of non-coding regulators.
Total RNA sequencing is a powerful tool for:
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Comprehensive transcriptome profiling of coding and non-coding RNAs
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Discovery of novel transcripts (e.g., circular RNAs, enhancer RNAs, unannotated lncRNAs)
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Analysis of alternative splicing, isoform diversity, and alternative polyadenylation
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Gene fusion & chimeric transcript detection in cancer and other diseases
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Allele-specific expression & RNA editing studies
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Studying non-coding RNA expression & function (lncRNA, snRNA, snoRNA)
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Expression analysis from FFPE or degraded samples with rRNA-depletion methods
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Epigenetic & post-transcriptional regulation (eRNA profiling, RNA modification inference)
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Immune, cancer, and host-pathogen transcriptomics (including viral or microbial RNA detection)
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Metatranscriptomic profiling in environmental or microbiome studies
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Biomarker discovery & functional annotation for drug target identification
Our workflows are ideal for exploratory studies and for any project where poly-A selection would miss critical RNA species.
What is Total RNA Sequencing Used For?
Total RNA Sequencing with AUGenomics
Sample Submission
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Accepted Sample Types: Total RNA from tissue, cells, blood, FFPE, or challenging/degraded sources
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Input Requirement: 50–100 ng of total RNA (≥10 ng supported for ultra-low input workflows)
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Sequencing Recommendations:
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Standard depth: 30–60 million reads/sample
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rRNA depletion or exome-capture options available for ribosomal RNA removal
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Suitable for both eukaryotic and prokaryotic transcriptomes
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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 total RNA-seq and mRNA-seq?
A: Total RNA-seq captures all RNA species, including non-coding RNAs and degraded RNA fragments, whereas mRNA-seq focuses only on polyadenylated (protein-coding) transcripts.
Q: Can I use total RNA-seq for FFPE or low-quality RNA?
A: Yes. Total RNA-seq is well suited for degraded or fragmented samples where poly-A tails may be compromised.
Q: Do you offer ribosomal depletion?
A: Yes. We provide rRNA removal options using depletion kits compatible with both human and non-human samples.
Got more questions? Contact our team and get a free consultation anytime. info@augenomics.com
Glossary of Terms
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Total RNA-seq: Sequencing of all RNA species in a sample
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rRNA Depletion: Removal of ribosomal RNA to enrich informative transcripts
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Non-coding RNA: RNA molecules that are not translated into proteins but serve regulatory roles
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FFPE: Formalin-Fixed, Paraffin-Embedded—preserved tissue sample type
