A guide to plant EV omics

Introduction: What can omics analysis answer?

EV isolation and characterization are only the first step. To investigate what a preparation contains, what information it carries and what functions it may have, researchers use omics analysis.

Plant-derived extracellular vesicle omics research has grown rapidly: transcriptomics investigates miRNA/lncRNA regulatory networks, proteomics examines protein composition, and metabolomics identifies small-molecule constituents. These complementary approaches address different questions. This guide covers selection, method comparison, sample requirements and deliverables.

1. Choose an omics strategy in three steps

Step 1: Define the research question

Research question	Recommended approach
Which miRNAs or lncRNAs are present in EVs, and could they target particular pathways?	Transcriptomics(miRNA / LncRNA)
Which functional proteins are on or inside EVs?	Proteomics (DIA)
Which small molecules do EVs carry, such as sugars, amino acids, flavonoids and phenolics?	Metabolomics(LC-MS/MS)
Which lipids are present in EV membranes?	Lipidomics(LC-MS)
Do EVs contain nucleic acids of microbial origin?	Microbiome (Nanopore 16S)

Step 2: Check sample quantity (see the sample guide below)

Step 3: Decide whether to integrate multiple omics layers —Integrating omics layers, such as transcriptomics and proteomics, can support cross-checks at different molecular levels for mechanistic research.

2. Compare core omics methods

Omics	Method / platform	Reference price	Turnaround	Recommended sample input
miRNA sequencing	Qiaseq library preparation + Illumina sequencing (10M reads / 3G RAW)	1000 CNY/sample	20 business days	RNA 10 ng (minimum 1 ng)
lncRNA sequencing	Smart-seq library preparation + Illumina (10G raw data; standard lncRNA + mRNA analysis)	1000 CNY/sample	20 business days	RNA 10 ng (minimum 1 ng)
Proteomics	DIA technology, Thermo Astral platform	1000 CNY/sample	20 business days	EV sample / protein: 10 μg
Metabolomics	Untargeted metabolomics LC-MS/MS, QE / HF-X platform	300 CNY/sample	20 business days	EV sample / protein: 10 μg
Plant metabolomics	Untargeted metabolomics LC-MS/MS (covering sugars, amino acids, nucleotides, alkaloids, flavonoids, phenolics and more)	500 CNY/sample	20 business days	EV sample / protein: 10 μg
Lipidomics	Relative lipidomics quantification by LC-MS/MS, QE / HF-X platform	600 CNY/sample	20 business days	EV sample / protein: 10 μg

Note for plant samples

Plant metabolomics The source describes extraction and detection optimized for plant small molecules, including sugars, amino acids, nucleotides, alkaloids, flavonoids and phenolics, and recommends the plant metabolomics option for plant-derived EVs.
For plant miRNA studies, consider both species-specific and novel miRNA identification, depending on a reference genome or de novo analysis.

3. Sample submission guide

Omics	Sample type	Recommended amount	Minimum amount	Storage
Transcriptomics (miRNA / lncRNA)	EV RNA	10ng	1ng	−80°C; ship on dry ice
Proteomics (DIA)	EVs / protein	10μg	—	-80℃
Metabolomics / lipidomics	EVs / protein	10μg	—	-80℃
Microbiome (16S)	EV DNA	50 μg (or 20 ng DNA)	—	-80℃
Genome (WGS)	EV DNA	50 μg (or 20 ng DNA)	—	-80℃

The source recommends basic characterization, including particle size, concentration and markers, before submission. Supplied EV samples require RNA extraction and capillary electrophoresis quality control first (200 CNY/sample; two business days).

4. Deliverables

Raw data, data quality-control results and an overview of relationships among samples;
Expression or relative-quantification matrices and associated molecular annotations;
Differential analysis where grouping and replication are adequate;
miRNA target prediction, GO/KEGG functional analysis and candidate regulatory networks;
Suggested follow-up validation informed by plant origin, treatment conditions and existing studies.

Frequently asked questions

Q1: Can a small amount of a precious sample be used for omics?

A: The source lists a minimum RNA input of 1 ng for transcriptomics and suggests enriching low-input samples by magnetic capture or ultrasonic nanofiltration before omics.

Q2: Can transcriptomics, proteomics and metabolomics be integrated?

A: Yes. Combined analysis can cross-check different molecular layers. Confirm the analysis requirements when submitting samples.

Q3: How do plant and animal EV omics differ?

A: Analysis can use the target species’ reference genome and annotations together with its transcriptome, a related species’ genome or de novo assembly. Where high-quality references are unavailable, the report should identify data sources, alternative strategies and limitations; homology predictions should not be described as experimentally validated functions.

Q4: How long does omics analysis take?

A: The source lists approximately 20 business days for routine transcriptomics, proteomics or metabolomics, including raw data and a standard analysis report.

Q5: Can the sequencing platform be specified?

A: The source lists Illumina for transcriptomics, Thermo Astral for proteomics and QE/HF-X for metabolomics by default. Customized platform or depth requirements can be discussed for a separate quotation.

Why Lifeint?

Lifeint reports more than 20,000 EV-related projects. Its small-RNA and other omics project data cover over 300 plant species, including more than 160 medicinal plants, and analysis draws on public resources such as NCBI, Ensembl Plants, Phytozome, miRBase and PmiREN. The source also describes experience with low-input RNA, library preparation, non-model plant databases and customized functional analysis.
University–industry–research platform: A biomedical technology centre jointly established with the School of Pharmaceutical Sciences, Xiamen University, and a joint innovation centre for functional medicinal-plant vesicles.
Public platform resources: Supporting operator of a Xiamen municipal public-service platform; partner in a Fujian collaborative innovation centre.
Projects and standards: The project “Large-scale preparation and application of extracellular vesicles” was approved under the Fujian–Chinese Academy of Sciences STS program; the company participated in the expert consensus on EV research, translation and clinical application.
Company and quality systems: The source lists high-tech, specialized and innovative enterprise qualifications, and describes ISO quality management, standardized procedures and sample tracking.

Need isolation and characterization before omics? See Plant EV isolation and characterization guide; for service prices and turnaround, see Pricing; to request services, visit Omics analysis services.

Last updated: 2026-08-12

*Prepared by Xiamen Lifeint Technology. Reference prices and timelines follow Pricing ; specific terms are subject to the agreement between the parties.*