Q: What is mim-tRNA-seq, and how does it differ from standard tRNA-seq?

mim-tRNA-seq is a next-generation sequencing approach that not only quantifies tRNA abundance but also captures modification-linked misincorporation signatures, enabling the inference of aminoacylation (charging) states. In contrast, standard tRNA-seq typically measures only total tRNA pools without addressing modifications or charging levels.

Q: Can you measure charged (aminoacylated) tRNA with this service?

Yes, our workflow includes matched protected (charged) and deacylated controls, allowing for the quantitative inference of the relative proportion of aminoacyl-tRNA (aa-tRNA) to uncharged tRNA, making it suitable for studies of translation-ready tRNA pools.

Q: What sample input is required to run aa-tRNA (mim-tRNA-seq) successfully?

We accept total RNA (≥1–2 µg) or tissue/cell inputs with preserved small RNA integrity and minimal freeze-thaw cycles. A matched biochemical preparation of charged versus deacylated tRNA is required to support charging inference, and high RIN/OD260/280 values are strongly recommended.

Q: Which organisms or sample types are supported by your service?

Our platform supports human, mouse, yeast, and plant systems using curated tRNA reference libraries and isoacceptor/isodecoder mapping. Custom support for non-model organisms is available upon consultation.

Q: How is data delivered, and what do I receive?

You receive raw FASTQ files, BAM/BAI alignments, expression and modification matrices (in TSV/CSV format), aa-tRNA charging tables, quality-control reports, and publication-ready visuals, along with complete parameter documentation for transparency and downstream analysis.

Q: How do I decide if I need aa-tRNA (mim-tRNA-seq) versus a standard tRNA-seq service?

Use aa-tRNA (mim-tRNA-seq) when your project requires measurement of tRNA charging dynamics, translation-ready pools, or modification-charging interactions. For a more comprehensive profiling of tRNA abundance, consider our standard tRNA sequencing service .

Q: What kind of research questions can aa-tRNA (mim-tRNA-seq) address?

This service supports investigation of translation bottlenecks, amino acid starvation responses, tRNA synthetase defects, tRNA modification loss and codon-usage adaptation, enabling mechanistic insight into how tRNA biology influences protein synthesis and cellular regulation.

aa-tRNA (mim-tRNA-seq) Sequencing Service for Accurate tRNA Charging Analysis

Understanding how cells regulate translation requires more than standard tRNA seq. Most workflows measure tRNA abundance but overlook two essential layers: extensive nucleotide modifications and the charging status that determines whether a tRNA is translation-ready. Our aa-tRNA (Mim-tRNA) sequencing service addresses these gaps by integrating Mim tRNA seq protocol, modification-informed signatures, and controlled biochemical steps to infer aa-tRNA charging with high precision.

This service is designed for research teams that require accurate, modification-aware tRNA profiling across various conditions, including amino acid starvation, stress responses, genetic knockouts, or drug perturbations. By combining structural relaxation, TGIRT reverse transcription, and isoacceptor-aware mapping, our workflow delivers quantitative readouts of tRNA abundance, modification patterns, and aminoacylation levels in a single experiment.

What we solve for your team

Quantify true translation-ready tRNA pools, not only total tRNA levels.
Detect modification signatures that obstruct conventional sequencing.
Compare aminoacylated vs deacylated tRNA under defined conditions.
Resolve highly similar isoacceptor and isodecoder families.

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key advantages of aa-tRNA mim-tRNA-seq sequencing, including tRNA abundance quantification, modification detection, charging inference, and isoacceptor resolution

Our aa-tRNA (mim-tRNA-seq) Sequencing Platform

What Is mim-tRNA-seq

Our aa-tRNA (mim-tRNA-seq) platform is designed to quantify tRNA molecules with high accuracy across eukaryotic systems. The method integrates structure relaxation, TGIRT-driven readthrough, and isoacceptor-aware alignment to address challenges specific to tRNA, such as extensive modifications and high gene similarity. This enables reliable detection of tRNA abundance and modification signatures, even in samples with diverse cell states or stress conditions.

Our workflow extends mim-tRNA-seq to measure aminoacylation levels through controlled biochemical treatments. By comparing protected (charged) and deacylated tRNA under matched conditions, we infer aa-tRNA charging with high sensitivity. This enables researchers to evaluate translation-ready tRNA pools and study how nutrient shifts, stress, or genetic perturbations alter charging dynamics.

Integrated Capability: Abundance, Modifications, and Charging

Our platform provides three layers of information in a single service:

tRNA abundance: isoacceptor and isodecoder resolution
Modification profiles: derived from position-specific misincorporation
Charging levels: relative proportions of aminoacylated and deacylated tRNA

This integrated readout helps teams interpret translation efficiency, codon bias, and tRNA regulatory mechanisms more effectively than single-dimensional approaches.

Why Analyse Aminoacyl-tRNA (aa-tRNA)?

aa-tRNA reveals the translation-ready tRNA pool

Total tRNA abundance does not reflect translational capacity. Only aminoacylated tRNAs can participate in protein synthesis, making aa-tRNA a direct indicator of how efficiently a cell can translate specific codons. Measuring charging levels shows which tRNA species are functionally available under defined biological conditions.

Charging levels change rapidly during environmental and metabolic shifts

Aminoacylation responds within minutes to nutrient deprivation, oxidative stress, and metabolic perturbations. By comparing charged and deacylated tRNA profiles, researchers can identify bottlenecks in translation caused by amino acid shortages or altered metabolic states. This information complements transcriptome and proteome measurements, especially when mRNA and protein levels diverge.

aa-tRNA profiling supports enzyme and regulatory studies

Charging defects often arise from changes in tRNA synthetase activity or mutations affecting substrate recognition. Monitoring aa-tRNA levels helps determine how these changes impact translation efficiency, fidelity, and global protein output. The approach is equally valuable for investigating modification-dependent stability, as some tRNA species lose charging capacity when specific modifications are disrupted.

Applications in codon usage, translation efficiency and stress biology

Charging dynamics influence the rate at which ribosomes decode specific codons. Low charging levels for a given isoacceptor can slow ribosome movement and shape protein expression. For teams studying codon-dependent translation, metabolic regulation, or stress-responsive pathways, aa-tRNA data provide essential context for interpreting ribosome profiling, proteomics, and gene expression datasets.

Experimental Workflow

1. Sample QC: Assess RNA integrity and purity; confirm small-RNA preservation.

2. Structure relaxation: Apply conditions that reduce secondary structure without damaging modifications.

3. Reverse transcription (TGIRT): Generate cDNA while retaining modification-linked signatures.

4. Library construction: Ligate adapters and amplify under bias-controlled cycles.

5. Sequencing (Illumina): Produce high-depth reads suitable for quantitative mim-tRNA-seq.

6. Biochemical contrasts for aa-tRNA: Sequence protected and deacylated preparations under matched conditions.

Pipeline illustration showing the aa-tRNA mim-tRNA-seq workflow from sample QC to sequencing and bioinformatics analysis

Data Analysis Workflow

1. Read QC and trimming: Remove adapters; evaluate quality metrics and length profiles.

2. tRNA reference build: Use a species-matched, curated reference with mature sequences and CCA tails.

3. Multi-mapping alignment: Assign reads using strategies tailored to paralogous tRNA families.

4. Quantification: Report isoacceptor and isodecoder abundance with robust normalisation.

5. Modification calling: Derive position-specific misincorporation signatures for modification profiling.

6. Charging estimation: Compare protected versus deacylated profiles to infer aminoacylation levels.

7. Statistics and visuals: Generate differential analyses, heatmaps, and publication-ready figures.

For broader tRNA-seq needs beyond aa-tRNA analyses, you may also consider our tRNA sequencing service or focus on epitranscriptomic mapping via our tRNA modification sequencing service.

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"Pipeline illustration showing the aa-tRNA mim-tRNA-seq workflow from sample QC to sequencing and bioinformatics analysis."

Analysis module What it includes

Read QC and tracking Adapter trimming, base-quality profiles, duplication, length distributions

Reference mapping Multi-mapping–aware alignment to curated isoacceptor/isodecoder sets

tRNA abundance Normalised counts at isoacceptor and isodecoder resolution

Modification signatures Position-specific misincorporation profiles from mim-tRNA-seq

aa-tRNA charging estimation Protected vs deacylated model; per-tRNA charging proportion

Differential analyses Condition comparisons for abundance, modifications, and charging

Structure-aware mapping Read and signature overlays on cloverleaf schematics

Quality metrics Replicate correlations, saturation curves, library complexity

Integrated report Methods, QC, key results, and interpretation guidance

Analysis module	What it includes
Read QC and tracking	Adapter trimming, base-quality profiles, duplication, length distributions
Reference mapping	Multi-mapping–aware alignment to curated isoacceptor/isodecoder sets
tRNA abundance	Normalised counts at isoacceptor and isodecoder resolution
Modification signatures	Position-specific misincorporation profiles from mim-tRNA-seq
aa-tRNA charging estimation	Protected vs deacylated model; per-tRNA charging proportion
Differential analyses	Condition comparisons for abundance, modifications, and charging
Structure-aware mapping	Read and signature overlays on cloverleaf schematics
Quality metrics	Replicate correlations, saturation curves, library complexity
Integrated report	Methods, QC, key results, and interpretation guidance

Sample Requirements

Sample type	Minimum input	Quality criteria	Storage & shipping	Notes
Total RNA	≥ 1–2 µg per sample	OD260/280 1.8–2.1; RIN ≥ 7; intact small RNAs	Aliquoted, RNase-free tubes; ship on dry ice	Preferred for mim-tRNA-seq and aa-tRNA-seq
Cultured cells	≥ 1×10⁶ cells	High viability before harvest; rapid lysis or extraction	Pellets snap-frozen; ship on dry ice	Avoid RNase contamination and repeated freeze–thaw
Tissue	10–20 mg	Prompt stabilisation after collection; no thaw cycles	Cryopulverised or intact pieces; ship on dry ice	Use RNase-free homogenisation methods
Model organisms	Human, mouse, yeast, plants	Species-matched references available	Coordinate for strain or ecotype details	Non-model species supported on request
Control sets	Protected + deacylated	Same biology, matched handling	Ship together with distinct labels	Required for aa-tRNA charging estimation
Not recommended	FFPE or heparinised material	May impair reverse transcription or mapping	—	Contact us for feasibility checks

Technology Comparison

Selecting the right method is essential when working with highly structured, heavily modified RNAs. The table below compares aa-tRNA (mim-tRNA-seq) with common approaches used to study tRNA abundance, modification, and aminoacylation. The goal is to help research teams choose a strategy aligned with experimental questions such as modification mapping, charging estimation, or isoacceptor-level quantification.
For background on the strengths and limitations of each workflow, you may also refer to our educational article on tRNA sequencing methods and technical challenges.

Feature	Standard RNA-seq	Small RNA-seq	LC-MS/MS	mim-tRNA-seq (our platform)
tRNA abundance	Low accuracy due to RT stops	Partial detection	Not suitable	High accuracy (isoacceptor & isodecoder)
Modification detection	No	No	Direct modification IDs	Yes, via misincorporation signatures
Aminoacylation (charging)	No	No	No	Yes, using protected vs deacylated designs
Resolution	Gene-level	Fragment-level	Modification-level	Single tRNA species (isoacceptor/isodecoder)
Secondary structure handling	Poor	Moderate	Not applicable	TGIRT readthrough preserves accuracy
Comparative studies	Limited	Limited	Moderate throughput	Ideal for stress, KO, drug, and metabolic studies
Throughput & scalability	High	High	Low	High (Illumina)
Typical use cases	Transcriptomics	Small RNA profiles	Modification mapping	Integrated abundance + modification + charging

How to choose the correct workflow

Use standard RNA-seq when the goal is to identify global transcriptome trends.
Use small RNA-seq when profiling miRNAs or tRNA fragments.
Use LC-MS/MS when you need direct chemical identification of specific modifications.
Choose mim-tRNA-seq when you require a tRNA-focused analysis that integrates abundance, modification signatures, and aminoacylation in a single dataset.

Applications

Translation efficiency and codon-dependent decoding

Charging levels influence how rapidly ribosomes decode specific codons. Projects examining codon usage, elongation bottlenecks, or proteome shifts can use aa-tRNA data to determine whether limited charging contributes to reduced translation of selected transcripts.

Nutrient sensing and metabolic regulation

Aminoacylation responds to amino acid availability and metabolic flux. Comparing protected and deacylated preparations reveals how nutrient restriction, metabolic inhibitors, or signalling pathway perturbations reshape translation-ready tRNA pools.

Stress response and adaptive regulation

Environmental stresses—including oxidative stress, heat shock, and hypoxia—affect both modification patterns and charging behaviour. aa-tRNA (mim-tRNA-seq) helps quantify these changes and supports integration with ribosome profiling or proteomics.

tRNA synthetase function and fidelity studies

Mutations or inhibitors that affect tRNA synthetase activity can lead to reduced charging or altered selectivity. Monitoring aa-tRNA levels provides direct insight into enzyme fidelity, substrate competition, and global impacts on translation.

Modification-dependent stability and decay pathways

Certain modifications stabilise tRNA structures or facilitate accurate aminoacylation. Defects in these modifications can cause rapid decay or reduced charging. Combining modification signatures with aa-tRNA measurements clarifies how modification loss affects tRNA lifespan.

Disease models and cell-state transitions

Projects analysing cancer progression, neurodegeneration, stem cell differentiation, or immune activation can quantify shifts in the tRNA landscape and determine whether misregulation of charging contributes to altered protein synthesis.

Why CD Genomics

Specialised expertise in tRNA sequencing

We focus on structured and heavily modified RNAs. Our team is experienced in mim-tRNA-seq optimisation, TGIRT-based readthrough, and biochemical designs required for accurate aa-tRNA analysis.

Accurate mapping of complex tRNA families

We maintain curated, species-specific tRNA references and apply multi-mapping strategies tailored to isoacceptor and isodecoder groups. This ensures reliable quantification across highly similar tRNA genes.

Integrated laboratory and bioinformatics workflow

Our platform provides coordinated wet-lab and computational support. Each project includes standardised QC, modification-aware alignment, charging estimation, differential analysis, and publication-ready visuals.

CRO-grade quality and project support

We offer consistent quality control, clear communication, and transparent documentation. Each project is assigned a dedicated coordinator, ensuring smooth sample handling and on-time delivery.

FAQ

- Q: What is mim-tRNA-seq, and how does it differ from standard tRNA-seq?
  - mim-tRNA-seq is a next-generation sequencing approach that not only quantifies tRNA abundance but also captures modification-linked misincorporation signatures, enabling the inference of aminoacylation (charging) states. In contrast, standard tRNA-seq typically measures only total tRNA pools without addressing modifications or charging levels.
- Q: Can you measure charged (aminoacylated) tRNA with this service?
  - Yes, our workflow includes matched protected (charged) and deacylated controls, allowing for the quantitative inference of the relative proportion of aminoacyl-tRNA (aa-tRNA) to uncharged tRNA, making it suitable for studies of translation-ready tRNA pools.
- Q: What sample input is required to run aa-tRNA (mim-tRNA-seq) successfully?
  - We accept total RNA (≥1–2 µg) or tissue/cell inputs with preserved small RNA integrity and minimal freeze-thaw cycles. A matched biochemical preparation of charged versus deacylated tRNA is required to support charging inference, and high RIN/OD260/280 values are strongly recommended.
- Q: Which organisms or sample types are supported by your service?
  - Our platform supports human, mouse, yeast, and plant systems using curated tRNA reference libraries and isoacceptor/isodecoder mapping. Custom support for non-model organisms is available upon consultation.
- Q: How is data delivered, and what do I receive?
  - You receive raw FASTQ files, BAM/BAI alignments, expression and modification matrices (in TSV/CSV format), aa-tRNA charging tables, quality-control reports, and publication-ready visuals, along with complete parameter documentation for transparency and downstream analysis.
- Q: How do I decide if I need aa-tRNA (mim-tRNA-seq) versus a standard tRNA-seq service?
  - Use aa-tRNA (mim-tRNA-seq) when your project requires measurement of tRNA charging dynamics, translation-ready pools, or modification-charging interactions. For a more comprehensive profiling of tRNA abundance, consider our standard tRNA sequencing service.
- Q: What kind of research questions can aa-tRNA (mim-tRNA-seq) address?
  - This service supports investigation of translation bottlenecks, amino acid starvation responses, tRNA synthetase defects, tRNA modification loss and codon-usage adaptation, enabling mechanistic insight into how tRNA biology influences protein synthesis and cellular regulation.