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Small RNA Sequencing

tRF&tiRNA Sequencing Service — Comprehensive tRF&tiRNA Expression Profiling

tRFs and tiRNAs, generated through precise biogenesis processes from tRNA, perform many biological functions as small non-coding RNAs and are associated with many diseases and conditions. Arraystar tRF&tiRNA sequencing service offers a sample-to-data solution, from performance-optimized tRF&tiRNA-seq with the rtStar™ tRF&tiRNA Pretreatment Kit to comprehensive bioinformatics.

End-to-end sample-to-data service · Bonus microRNA expression analysis included

Overview

Sample-to-data tRF&tiRNA profiling with precise annotation and focused bioinformatics

Arraystar tRF&tiRNA sequencing service offers the sample-to-data solution. With the wealth of information from our tRF&tiRNA-seq profiling, investigators can easily advance their next step research in this new field of study, following the approaches and applications in the Roadmap for tRF & tiRNA studies.

The composition and abundance of tRFs&tiRNAs are highly dependent on the cell type and disease condition, making them excellent biomolecules for biomarkers [1]. For example, the ratio of tRFs&tiRNAs is a good indicator of cancer progression-free survival and a candidate prognostic marker [2]. Arraystar uses a performance-optimized tRFs&tiRNA sequencing method with the rtStar™ tRF&tiRNA Pretreatment Kit (Cat. No. AS-FS-005), and a precise annotation and classification system based on tRNA topology and statistical significance.

What is tRF&tiRNA sequencing?

tRF&tiRNA sequencing profiles tRNA-derived fragments (tRFs) and tRNA halves (tiRNAs), small non-coding RNAs generated through precise biogenesis processes from tRNA. Their composition and abundance depend on cell type and disease condition, making them promising biomarker molecules for many diseases.

Service at a Glance

Standard tRF&tiRNA sequencing project — custom designs and add-on analyses available on request

Service NamePrice
tRF&tiRNA Sequencing Service

Benefits

Why researchers choose Arraystar for tRF&tiRNA sequencing

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rtStar™ Pretreatment

Performance-optimized tRFs&tiRNA sequencing method with Arraystar rtStar™ tRF&tiRNA Pretreatment Kit (Cat. No. AS-FS-005).

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Precise Annotation

Precise annotation and classification system based on tRNA topology and statistical significance.

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Comprehensive Collection

Comprehensive tRF & tiRNA collection from all databases.

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Focused Bioinformatics

tRFs&tiRNAs focused bioinformatics and statistics analyses with publication quality graphics.

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Bonus miRNA Analysis

Additional miRNA/piRNA*/sdRNA* expression and differential analyses (* for human, mouse, and rat species only).

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Integrated tRNA Solutions

Works together with our m7G TRAC-sequencing to uncover how m7G modification regulates tRF/tiRNA expression levels.

Background

tRF&tiRNA biology — biogenesis, functions, and biomarker potential

tRFs and tiRNAs, generated through precise biogenesis processes from tRNA, perform many biological functions as small non-coding RNAs and are associated with many diseases and conditions (Fig. 1). They are known to act as microRNAs in RNA interference; bind protein factors to regulate target mRNA stability; interact with cytochrome c to modulate apoptosis; alter embryonic transcriptional cascades as paternal epigenetic factor in intergenerational inheritance of metabolic disorders; and assemble stress granules in response to stress conditions.

The composition and abundance of tRFs&tiRNAs are highly dependent on the cell type and disease condition, making them excellent biomolecules for biomarkers [1]. For example, the ratio of tRFs&tiRNAs is a good indicator of cancer progression-free survival and a candidate prognostic marker [2]. Also tRNA and tRF&tiRNA populations are highly enriched in biofluids, much more so than microRNAs [3-4].

Figure 1. tRF&tiRNA functions and association with diseases.
Figure 1. tRF&tiRNA functions and association with diseases.

Arraystar tRF&tiRNA sequencing service offers the sample-to-data solution. With the wealth of information from our tRF&tiRNA-seq profiling, investigators can easily advance their next step research in this new field of study, following the approaches and applications in the Roadmap for tRF & tiRNA studies.

Background References

  1. Telonis AG, et al. Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies. Oncotarget, 2015. PMID: 26325506
  2. Olvedy M, et al. A comprehensive repertoire of tRNA-derived fragments in prostate cancer. Oncotarget, 2016. PMID: 27015120
  3. Schageman J, et al. The complete exosome workflow solution: from isolation to characterization of RNA cargo. BioMed Research International, 2013. PMID: 24205503
  4. Dhahbi JM, et al. 5′ tRNA halves are present as abundant complexes in serum, concentrated in blood cells, and modulated by aging and calorie restriction. BMC Genomics, 2013. PMID: 23638709

tRF&tiRNA Sequencing Workflow

Sample-to-data tRF&tiRNA-seq in five steps

1

Sample QC

RNA quality and quantity assessment before the project proceeds, with small-RNA-retaining purification for tRNA-derived small RNA classes.

2

rtStar™ Pretreatment

Pretreatment of small RNAs with the rtStar™ tRF&tiRNA Pretreatment Kit (Cat. No. AS-FS-005) to prepare tRFs&tiRNAs for efficient downstream library construction.

3

Library Construction

Small RNA library construction from the pretreated tRF&tiRNA-enriched fraction.

4

High-Throughput Sequencing

High-throughput sequencing of the tRF&tiRNA library.

5

Bioinformatics

Precise annotation and classification based on tRNA topology and statistical significance, tRF&tiRNA-focused statistics, and data visualization with publication quality graphics.

Bioinformatics & Deliverables

Detailed tRF&tiRNA-focused analyses included in every project

The tRF&tiRNA-seq provides a wealth of bioinformatics analyses to better understand their biology and facilitate biomarker applications. As a bonus, microRNA expression analysis is also included.

Standard Deliverables

Figure 1. Differential analysis data tables with detailed annotation of tRF&tiRNA sequences, type, length and cleavage sites in tRNAs.
Figure 1. Differential analysis data tables with detailed annotation of tRF&tiRNA sequences, type, length and cleavage sites in tRNAs.
Figure 1 (second panel). Differential analysis data tables with detailed annotation of tRF&tiRNA sequences, type, length and cleavage sites in tRNAs.
Figure 1 (second panel). Differential analysis data tables with detailed annotation of tRF&tiRNA sequences, type, length and cleavage sites in tRNAs.
Figure 2. The distribution of tRF & tiRNA subtypes. The colors represent the tRF & tiRNA subtypes. The values in brackets represent the numbers of tRF & tiRNA subtypes.
Figure 2. The distribution of tRF & tiRNA subtypes. The colors represent the tRF & tiRNA subtypes. The values in brackets represent the numbers of tRF & tiRNA subtypes.

Research Applications

tRF&tiRNA research across biology and disease

Cancer Biomarkers

The ratio of tRFs&tiRNAs is a good indicator of cancer progression-free survival and a candidate prognostic marker (Oncotarget, 2016).

RNA Interference

tRFs act as microRNAs in RNA interference, participating in small RNA-mediated gene silencing pathways.

mRNA Stability Regulation

tRFs bind protein factors to regulate target mRNA stability.

Apoptosis Modulation

tRFs interact with cytochrome c to modulate apoptosis.

Intergenerational Inheritance

tRFs alter embryonic transcriptional cascades as paternal epigenetic factors in intergenerational inheritance of metabolic disorders.

Stress Response

tRFs assemble stress granules in response to stress conditions, linking tRNA cleavage to cellular stress signaling.

Sample Requirements

Official Arraystar sample submission requirements for tRF&tiRNA sequencing

RNA Amount & Quality

  • Total RNA input: > 1 µg per sample (official recommended minimum for the entire experiment in a single attempt, including sample QC). Supply twice the recommended minimum to avoid project delays.
  • Purification: TRIzol / RNA precipitation or an RNA isolation kit. Because tRF&tiRNA are < 200 nt, use a kit specified to retain small RNAs (e.g. Qiagen miRNeasy).
  • Concentration: > 20 ng/µL by Nanodrop; OD260/280 ~2.0 (acceptable 1.7–2.1); OD260/230 > 1.8.
  • Integrity: sharp 18S/28S rRNA bands by gel, or RIN > 7.0 by Bioanalyzer (serum/plasma/exosome/FFPE RNA exempt).
  • DNase treatment: optional for gDNA removal; required if the sample is also used for qPCR.

Shipping Instructions

  • Ship RNA in nuclease-free water (> 20 ng/µL), freeze-dried, or in ethanol; store at −80 °C or in liquid nitrogen.
  • Use nuclease-free certified, screw-cap 1.5 mL microtubes; seal caps with Parafilm; place tubes in a plastic bag.
  • Use 10 kg dry ice as refrigerant; include a signed Project Form and the sample list.
  • Ship to: Arraystar Inc., 9430 Key West Avenue #128, Rockville, MD 20850, USA. Contact us before shipping.

FAQ

Common questions about tRF&tiRNA sequencing

What is the difference between tRFs and tiRNAs?
tRFs (tRNA-derived fragments) and tiRNAs (tRNA halves) are generated through precise biogenesis processes from tRNA. They are classified based on tRNA topology and statistical significance. Arraystar provides a precise annotation and classification system, and every project includes differential expression profiling with detailed annotation of sequence, type, length, and cleavage sites in tRNAs.
What sample types are compatible with tRF&tiRNA sequencing?
We accept total RNA extracted from cultured cells, tissues, whole blood, plasma, serum, or other biological sources. Purified RNA should be intact with an OD260/280 of ~2.0 (acceptable 1.7–2.1), OD260/230 above 1.8, and a RIN above 7.0 where applicable. If you are unsure whether your sample type is suitable, please contact us for a free evaluation.
What is the minimum amount of RNA required?
We recommend more than 1 µg of total RNA per sample — the official Arraystar recommended minimum for the entire experiment in a single attempt, including sample QC. Supplying twice the recommended minimum helps avoid project delays. RNA integrity must be preserved, because degraded RNA cannot be rescued by downstream steps.
Is microRNA expression analysis included in this service?
Yes. The tRF&tiRNA-seq provides a wealth of bioinformatics analyses to better understand their biology and facilitate biomarker applications; as a bonus, microRNA expression analysis is also included. Additional miRNA/piRNA*/sdRNA* expression and differential analyses are available for human, mouse, and rat species only.
Why are tRFs&tiRNAs considered excellent biomarkers?
The composition and abundance of tRFs&tiRNAs are highly dependent on the cell type and disease condition, making them excellent biomolecules for biomarkers. tRNA and tRF&tiRNA populations are highly enriched in biofluids, much more so than microRNAs, and the ratio of tRFs&tiRNAs is a good indicator of cancer progression-free survival.
How does tRF&tiRNA sequencing work with m7G TRAC-Seq?
Arraystar tRF&tiRNA sequencing works together with our m7G TRAC-sequencing to uncover how m7G modification regulates tRF/tiRNA expression levels. Combining both services links tRNA modification status with downstream tRF/tiRNA generation within Arraystar's integrated tRNA research portfolio, supporting epitranscriptomic and small RNA studies.

Selected Publications

Featured Client Publications in tRF&tiRNA Research

  1. Bayazit MB, et al. Small RNAs derived from tRNA fragmentation regulate the functional maturation of neonatal β cells. Cell Reports, 2022. PMID: 35830789
  2. Blaze J, et al. Neuronal Nsun2 deficiency produces tRNA epitranscriptomic alterations and proteomic shifts impacting synaptic signaling and behavior. Nature Communications, 2021. PMID: 34389722
  3. Liu YT, et al. Structure of human cytomegalovirus virion reveals host tRNA binding to capsid-associated tegument protein pp150. Nature Communications, 2021. PMID: 34535641
  4. Pereira M, et al. m5U54 tRNA Hypomodification by lack of TRMT2A Drives the Generation of tRNA-Derived Small RNAs. International Journal of Molecular Sciences, 2021. PMID: 33799331
  5. Nechooshtan G, et al. Processing by RNase 1 forms tRNA halves and distinct Y RNA fragments in the extracellular environment. Nucleic Acids Research, 2020. PMID: 32609822

Ready to Profile tRF&tiRNA Biology Accurately?

Arraystar tRF&tiRNA-seq combines rtStar™ pretreatment with precise annotation and tRF&tiRNA-focused bioinformatics — get a quote and a project timeline tailored to your study.