Sample Submission Guidelines
Why tRNA Sequencing Matters
While traditional transcriptomics and ribosome profiling have transformed our understanding of gene expression, the complexity of transfer RNA (tRNA) biology remains an underexplored frontier. tRNAs are essential molecules that bridge mRNA codons and amino acids, directly controlling protein synthesis. However, subtle changes in tRNA abundance, chemical modifications, or charging status can significantly influence translational regulation, impacting health and disease.
Modern tRNA sequencing methods have opened new possibilities to study these molecules in unprecedented detail. By leveraging technologies such as tRNA sequencing nanopore platforms, researchers can analyze the tRNA sequence length, detect critical post-transcriptional modifications, and explore how tRNA populations shift in response to stress, cancer progression, metabolic disorders, or viral infections.
Moreover, insights from tRNA sequencing services contribute to building comprehensive tRNA sequence databases, supporting advanced studies in genomics, translational medicine, and therapeutic development. Profiling the tRNAome has become essential for decoding cellular adaptation and uncovering novel biomarkers or therapeutic targets.
In research and drug development, the ability to accurately characterize the tRNA sequence length and modification landscape ensures precise interpretation of cellular responses, helping avoid misinterpretation and accelerating discoveries.
Service Overview
At CD Genomics, we provide a comprehensive tRNA sequencing service designed to illuminate the complexities of translational regulation and cellular adaptation. Leveraging both traditional tRNA sequencing methods and innovative tRNA sequencing nanopore technologies, we offer unparalleled insight into tRNA dynamics across various biological contexts.
Our services capture critical data on:
- tRNA abundance: Quantify levels across tissues, cell types, or experimental conditions.
- tRNA modifications: Identify and locate chemical changes that affect tRNA stability and function.
- tRNA sequence length: Detect full-length tRNA molecules for precise mapping and analysis.
- Aminoacylation status: Measure the charging state of tRNAs, vital for understanding translation efficiency.
CD Genomics' expertise ensures:
- Direct sequencing of native tRNA without cDNA or PCR, minimizing bias and preserving natural modifications.
- Creation of reliable, high-quality tRNA sequence databases for downstream research.
- Powerful bioinformatics solutions delivering publication-ready visualizations, including volcano plots, heatmaps, and scatter plots.
Why Choose CD Genomics for tRNA Sequencing?
✅ Advanced tRNA Sequencing Methods
We offer both traditional protocols and tRNA sequencing nanopore solutions, enabling single-molecule resolution and direct detection of native modifications without the need for cDNA conversion or PCR. This ensures highly accurate and comprehensive tRNA profiling.
✅ Full-Length tRNA Sequencing
Capture complete tRNA sequence length information for precise mapping and variant detection, crucial for understanding translational regulation and identifying disease-specific changes.
✅ Comprehensive Modification Detection
Detect diverse post-transcriptional modifications, such as methylation and pseudouridylation, revealing how these chemical changes impact tRNA stability, folding, and function.
✅ Aminoacylation Analysis
Measure charged vs. uncharged tRNA pools to explore how aminoacylation dynamics affect translation efficiency—a key factor in disease studies and therapeutic research.
✅ High Sensitivity with Low Input Requirements
Our optimized workflows deliver high-quality results from minimal starting material, making tRNA sequencing services accessible for precious or limited samples.
✅ Extensive tRNA Sequence Database Integration
Benefit from our curated and authoritative tRNA sequence databases, which enhance annotation accuracy and enable robust bioinformatic analysis.
✅ Publication-Ready Data Visualizations
We provide high-quality figures, including volcano plots, heatmaps, and scatter plots, suitable for publications, presentations, or regulatory submissions.
✅ Expert Bioinformatics Support
Our team of bioinformatics specialists offers end-to-end data analysis, delivering insights tailored to your specific research objectives.
Workflow / How It Works
Sample Preparation
Extraction and purification of total RNA or small RNA from diverse sample types.
tRNA Processing
Deacylation and adapter ligation, ensuring high efficiency for full-length tRNA sequence length capture.
Library Construction
Creation of libraries suitable for high-throughput sequencing or direct native RNA sequencing.
Sequencing
High-resolution sequencing using either Illumina platforms or nanopore-based systems for direct RNA analysis.
Bioinformatics Analysis
Comprehensive data processing, annotation against authoritative tRNA sequence databases, and generation of publication-ready visualizations.
Bioinformatics Deliverables
Analysis Pipeline
- Differential Expression Analysis
Identifies significant differences in tRNA sequence length and abundance across conditions. Visual outputs include volcano plots, scatter plots, and heatmaps. - Modification Detection and Mapping
Detects and annotates post-transcriptional modifications within tRNA sequences, revealing their functional impact on translation and disease processes. - Aminoacylation Status Profiling
Measures charged vs. uncharged tRNA pools, providing insights into translation efficiency and metabolic adaptation. - Variant and Isoform Identification
Detects sequence variants, mutations, and novel isoforms using curated tRNA sequence databases, supporting disease biomarker research and therapeutic development. - Custom Reports
Delivers interactive, publication-ready reports formatted for scientific presentations, publications, or regulatory submissions. - Data Integration Support
Integrates tRNA-seq results with other omics data sets (e.g., transcriptomics, proteomics) for deeper biological insights.
Data Output
- Formats: FASTQ, BAM, VCF, tab-delimited expression tables
- Visualizations: heatmaps, scatter plots, volcano plots, variant plots
- Annotation files: GFF3, BED, or custom formats upon request
- Reports: PDF summaries, interactive Excel sheets
Supported Sample Types
- Total RNA from tissues, cells, fluids
- Low-input RNA samples
- Purified tRNA fractions
- Challenging samples with high modification levels
Computing Infrastructure
- High-performance computing clusters
- Dedicated bioinformatics pipelines optimized for:
tRNA sequencing nanopore data
- Traditional short-read tRNA-seq
- Custom analysis environments available upon request
Bioinformatics Expertise
Support for:
- Experimental design consultation
- Statistical analysis and interpretation
- Figure and table preparation for publication
- Specialized knowledge in tRNA biology and modification analysis
Applications
🔬 Cancer Research & Tumor Biology
Investigate how alterations in tRNA sequence length, abundance, and modifications drive oncogenesis, metastasis, and therapy resistance. Identify potential tRNA-based biomarkers for diagnostics or therapeutic targets.
🧬 Translational Regulation Studies
Understand how cells fine-tune gene expression through dynamic changes in tRNA populations, modifications, and aminoacylation status under different physiological or pathological conditions.
🧪 Biomarker Discovery & Personalized Medicine
Leverage tRNA sequencing service data to discover novel biomarkers and develop precision medicine strategies tailored to patient-specific translational profiles.
🦠 Infectious Disease & Virology
Explore how viruses manipulate host tRNA sequence databases and tRNA pools to optimize viral protein translation and evade immune responses.
🧠 Neurodegenerative & Metabolic Diseases
Analyze tRNA dysregulation implicated in disorders like Huntington's disease, neurodegeneration, and metabolic syndromes, supporting therapeutic research.
🧫 Synthetic Biology & Biotechnology
Optimize codon usage and translation efficiency by mapping tRNA sequencing nanopore data, improving gene editing designs and synthetic constructs.
⚙️ Gene Therapy & ATMP Development
Gain insights into tRNA dynamics critical for designing advanced therapeutic medicinal products (ATMPs), enhancing translation efficiency and safety profiles.
Sample Requirements
| Sample Type | Minimum Amount | Notes |
|---|---|---|
| Cells | 2 × 10⁶ cells | Harvested under RNase-free conditions. |
| Tissue | 50 mg | Fresh or frozen; stored at -80°C. |
| Whole Blood / Serum / Plasma | 2–3 mL | Collect in EDTA or heparin tubes; store at -80°C. |
| Cerebrospinal Fluid (CSF) | 5 mL | Store at -80°C; avoid freeze-thaw cycles. |
| Urine | 50 mL | Centrifuge to pellet cells if required; store pellet at -80°C. |
| Total RNA | ≥ 2 µg | OD260/280 ≥ 1.8; OD260/230 ≥ 1.5; intact RNA with clear bands on electrophoresis. |
Storage & Shipping Recommendations:
- Ship samples on dry ice to prevent degradation.
- Avoid repeated freeze-thaw cycles.
- For RNA samples, dissolve in RNase-free water or ethanol, and store at -80°C.
- Contact us if your sample type is not listed or if you have limited material; we offer custom solutions for challenging projects.
Frequently Asked Questions (FAQ)
Q1. What is tRNA sequencing, and how is it different from other RNA-seq methods?
A1. tRNA sequencing focuses specifically on transfer RNA molecules (~70–90 nt), capturing their abundance, post-transcriptional modifications, and aminoacylation (charging) status. Unlike standard RNA-seq, which emphasizes mRNAs and may overlook tRNA modifications and nuanced processing, our tRNA sequencing nanopore and traditional tRNA sequencing methods are optimized to handle the structured and chemically modified nature of tRNAs, enabling full-length and modification-aware profiling.
Q2. What sequencing platforms do you use?
A2. CD Genomics employs both short-read platforms (e.g., Illumina) for traditional tRNA sequencing and third-generation nanopore sequencing (e.g., Oxford Nanopore) for direct, full-length tRNA sequence and modification detection—without cDNA or PCR biases.
Q3. What sample types and input amounts are required?
A3. We accept cells, tissue, body fluids (e.g., blood, CSF, urine), and purified total RNA. Minimum inputs are: 2×10⁶ cells, 50 mg tissue, 2–3 mL blood/serum/plasma, 5 mL CSF, 50 mL urine, or ≥ 2 μg total RNA (OD260/280 ≥ 1.8; OD260/230 ≥ 1.5). Samples should be shipped on dry ice and stored at –80 °C to preserve integrity for trna sequencing service. (As detailed in the Sample Requirements section.)
Q4. What turnaround times and deliverables can I expect?
A4. We work efficiently to ensure timely delivery of your results. Clients receive: interactive bioinformatics reports, raw sequencing data (FASTQ/BAM), quantitative counts, volcano and heatmap visualizations, modification mapping, aminoacylation profiling, and publication-quality graphics. We'll confirm a detailed timeline when you place your order.
Q5. How many samples or replicates should I include?
A5. We recommend at least three biological replicates per group to support robust differential expression and statistical analysis. While technical replicates are not required, we offer library multiplexing to minimize costs without sacrificing quality.
Q6. What quality controls are in place?
A6. We perform stringent QC throughout the workflow using:
- Sample QC (Qubit, NanoDrop, Bioanalyzer)
- Library QC (Bioanalyzer, qPCR)
- Sequencing QC (platform-specific controls)
- Data QC with tools like FastQC
All QC results are provided with your data package.
Q7. Can you detect all tRNA modifications and measure aminoacylation?
A7. Yes—we detect a wide variety of modifications (e.g., methylation, pseudouridylation) through comparison of modified and unmodified signals in tRNA sequencing nanopore data. Charged vs. uncharged tRNAs are distinguishable via signature signals in dedicated protocols like aa-tRNA-seq.
Q8. How do you annotate tRNA sequences?
A8. Sequences are aligned against our curated tRNA sequence database, leveraging tools like tRNAscan-SE alongside modification-aware algorithms, ensuring accurate isoform and variant annotation.
Q9. Is low-input or challenging sample available?
A9. Definitely. We support low-input workflows and custom library prep for limited or precious samples, utilizing demethylation and adaptor strategies to maximize yield and data quality.
Q10. How can I get started?
A10. Contact our team to discuss project goals, sample type, and research context. We'll propose a tailored plan, provide a quote, and guide you through sample preparation. Once agreed, you ship samples on dry ice, and we'll handle the rest—delivering high-quality data and expert interpretation.
Nano-tRNAseq: Quantitative tRNA Abundance & Modification Profiling
1. Background
Traditional methods for tRNA analysis suffer from significant biases due to reverse transcription, PCR amplification, and inability to detect tRNA modifications. As tRNAs carry ~13 modifications per molecule impacting translation and disease, an accurate method to simultaneously quantify abundance and modifications is essential .
2. Methods
The authors developed Nano-tRNAseq, a direct RNA nanopore sequencing protocol that includes:
- Double-ligation of 5' and 3' adapters to mature tRNAs
- Demethylation and deacylation to enhance adapter ligation
- Re-processing raw MinKNOW signals to recover tRNA reads
- Comparative sequencing of in vitro transcribed (IVT) and native tRNAs from S. cerevisiae
Fig. 1b featuring the library prep schematic showing adapter ligations on tRNA. Label this immediately below the schematic.
3. Results
- 12-fold increase in tRNA reads using custom MinKNOW parameters vs. default.
- High reproducibility of native tRNA measurements (Spearman's ρ = 0.984).
- Accurate abundance quantitation compared to Illumina-based techniques (ρ = 0.93).
- Detection of modification interdependencies (e.g., Ψ55 loss affecting m¹A58, m⁵U54) and CCA tail deadenylation under oxidative stress.
Fig. 1d scatter plot showing replicability
Fig. 9a heatmap of base-call errors in PUS4 knockout.
4. Conclusions
Nano-tRNAseq offers a cost-effective, high-throughput approach with single-molecule resolution to accurately quantify tRNA abundance and modification states. It overcomes biases of traditional methods and establishes a framework for studying the "tRNAome" in disease, stress response, and biomarker discovery .
