Exosome Omics Analysis Services - Creative Biostructure Exosome

Q: What is the minimum sample volume required for exosomal small RNA sequencing from plasma or serum?

For reliable small RNA-seq data, we recommend starting with 2-4 mL of plasma/serum to ensure sufficient exosome yield. While our low-input library preparation kits can work with as little as 1 mL, lower volumes may result in fewer detected unique miRNAs. It is critical that samples are free of hemolysis, as cellular RNA released from ruptured red blood cells can severely contaminate the exosomal RNA profile.

Q: Can your workflow detect lncRNAs and circRNAs in exosomes, or is it limited to miRNAs?

Yes, we can detect long RNA species. However, unlike standard small RNA-seq, this requires a Total RNA-seq workflow with rRNA depletion (ribo-depletion). Since exosomal RNA is often fragmented and dominated by ribosomal RNA, the depletion step is essential to maximize the reads mapping to lncRNAs and circRNAs. Please specify this requirement during the project consultation, as it affects the library preparation strategy and sequencing depth.

Q: How do you handle high-abundance protein contamination (e.g., Albumin, IgG) in exosome proteomics?

High-abundance plasma proteins can mask low-abundance exosomal markers in LC-MS/MS analysis. We strongly recommend using Size Exclusion Chromatography (SEC) or density gradient ultracentrifugation for isolation prior to proteomics, as precipitation-based kits often co-precipitate serum proteins. For samples already isolated, we can employ an additional wash step or a "top 14" protein depletion strategy to improve the depth of coverage for authentic exosomal proteins.

Q: What normalization strategy do you use for exosomal qPCR or Sequencing data, given that "housekeeping genes" are not stable in exosomes?

Standard reference genes (like GAPDH or Actin) are often unreliable in exosomes. For sequencing, we use RPM/CPM (Reads Per Million) normalization or TMM (Trimmed Mean of M-values). For qPCR validation, we recommend adding an external spike-in control (e.g., cel-miR-39) to the lysis buffer prior to RNA extraction. This allows us to normalize for technical variations in extraction efficiency and reverse transcription, ensuring the most objective relative quantification.

Q: Does the bioinformatics report for Exosome Omics include pathway prediction and target analysis?

Yes. Our standard bioinformatics package includes differential expression analysis, volcano plots, and heatmaps. For miRNA-seq, we provide target gene prediction using databases like miRBase, TargetScan, and miRDB. We then perform GO (Gene Ontology) terms and KEGG pathway enrichment analysis on these targets to help you understand the potential biological functions and signaling pathways modulated by the exosomal cargo in your specific study context.

Exosome Multi-Omics Solutions Trusted by Leading Scientists

Creative Biostructure delivers high-depth multi-omics integration services, empowering academic institutions and pharmaceutical partners to accelerate biomarker discovery and precision medicine development.

What Is Exosome Omics Analysis?

Exosome omics services profile the molecular cargo carried by exosomes to reveal what cells are doing in health and disease. Because exosomes circulate in biofluids and mirror their cells of origin, omics readouts can support biomarker discovery, patient stratification, and mechanism studies.

Each omics layer answers a different question. Exosome transcriptome profiling focuses on RNA content such as miRNA and mRNA to capture gene regulation signals. Exosome proteomics measures proteins to identify functional pathways, surface markers, and disease related changes. Exosome lipidomics characterizes lipid species that shape membrane properties and signaling. Exosome metabolomics profiles small molecules to reflect metabolic states and treatment response.

Multi omics integration combines these datasets to find consistent, cross validated signals and build pathway or network level interpretations.

Comprehensive Exosome Omics Solutions

Creative Biostructure offers an integrated portfolio of exosome omics services to help you decode exosomal cargo at multiple molecular levels. From discovery to interpretation, our workflows emphasize data quality, reproducibility, and biologically meaningful insights for biomarker research and translational studies.

Exosome Transcriptome Profiling

Uncover the complete exosomal RNA landscape, including mRNA, miRNA, lncRNA, and circRNA. We utilize high-sensitivity NGS protocols optimized for low-input samples to detect novel transcripts and analyze differential expression.

Exosome Proteomics

Achieve deep coverage of the exosomal proteome using high-resolution LC-MS/MS. Our services support Label-free, TMT, and DIA quantification strategies to identify surface markers, signaling proteins, and post-translational modifications.

Exosome Lipidomics

Characterize the lipid composition and membrane dynamics of exosomes. We perform targeted and untargeted profiling to identify lipid classes, fatty acid chains, and lipid-protein interactions crucial for vesicle stability and uptake.

Exosome Metabolomics

Analyze the small-molecule metabolic signature of exosomes. Our metabolomics profiling provides a snapshot of the parent cell's physiological state, helping to identify metabolic reprogramming and potential diagnostic metabolites.

Exosome Multi-Omics Integration

Synthesize data across molecular layers using advanced bioinformatics. We statistically correlate transcriptomic, proteomic, and metabolic datasets to map regulatory networks and identify robust, multi-dimensional biomarker signatures.

Explore Advanced Exosome Multi-Omics Technologies

Creative Biostructure applies fit for purpose omics platforms and rigorous quality control to generate reproducible, publication ready exosome datasets. We support discovery, targeted validation, and multi layer interpretation for biomarker and mechanism studies.

Category	Techniques	Key Advantages	Best Use Cases
Transcriptomic Profiling (RNA)	Next-Generation Sequencing (NGS)	Captures full RNA diversity (mRNA, miRNA, lncRNA, circRNA) with high sensitivity for low-input samples.	Novel transcript discovery, differential expression analysis, and non-coding RNA regulatory studies.
	Long-Read Sequencing (PacBio/Nanopore)
	Single-Cell RNA Sequencing (scRNA-seq)
Proteomic Analysis (Protein)	Label-Free Quantification (LFQ)	Achieves deep proteome coverage and high quantitative accuracy without labeling bias.	Global protein profiling, post-translational modification (PTM) analysis, and biomarker identification.
	TMT/iTRAQ Labeling
	Data-Independent Acquisition (DIA)
Lipidomics & Metabolomics	UPLC-MS/MS (Targeted/Untargeted)	Provides precise structural identification and quantification of diverse lipid classes and polar metabolites.	Membrane dynamics research, metabolic reprogramming analysis, and lipid-protein interaction studies.
	Shotgun Lipidomics
	GC-MS
Bioinformatics & Integration	Multi-Omics Factor Analysis (MOFA)	Mathematically integrates heterogeneous datasets to reveal hidden sources of variation.	Systems biology modeling, multi-dimensional biomarker signature discovery, and pathway network construction.
	Weighted Gene Co-expression Network Analysis (WGCNA)
	Machine Learning Algorithms

Applications of Exosome Omics and Multi-Omics Analysis

Precision Biomarker Discovery

• Identifies robust multi-analyte signatures (RNA + Protein).
• Enhances diagnostic sensitivity and specificity.
• Distinguishes comorbidities through complex profiles.

Disease Mechanism Elucidation

• Maps intricate regulatory networks and signaling pathways.
• Links gene expression changes to metabolic outputs.
• Uncovers novel pathogenesis in cancer and neurodegeneration.

Therapeutic Target Identification

• Reveals "druggable" nodes within disease networks.
• Identifies mechanisms of drug resistance.
• Validates therapeutic targets using systems biology.

Liquid Biopsy Development

• Accelerates the development of non-invasive diagnostic tests.
• Enables longitudinal monitoring of patient response.
• Supports patient stratification for personalized medicine.

By integrating genomic, proteomic, and metabolic data, researchers can move beyond simple correlation to understanding causation. Creative Biostructure supports projects from initial multi-omics screening to rigorous validation and translation.

State-of-the-Art Multi-Omics Analytical Platforms

Creative Biostructure employs a suite of cutting-edge high-throughput technologies to drive multi-omics discovery. Our facility is equipped with Illumina NovaSeq and PacBio sequencing systems for comprehensive transcriptomics, alongside Thermo Scientific Orbitrap and Bruker timsTOF mass spectrometers for high-resolution proteomics, lipidomics, and metabolomics. Supported by our High-Performance Computing clusters for advanced bioinformatics integration, these platforms deliver exceptional data depth, sensitivity, and reproducibility for systems biology research.

Image Source: Illumina

Image Source: Thermo Fisher Scientific

Image Source: Bruker

Our Integrated Exosome Multi-Omics Workflow

At Creative Biostructure, our multi-omics workflow transforms complex samples into actionable insights. We use an optimized pipeline to preserve fragile cargo—RNA, proteins, lipids, and metabolites—ensuring high-quality data for biomarker discovery.

1

Sample Pre-processing and Quality Control

Perform rigorous quality checks and pre-treatment to remove cellular debris, ensuring optimal preservation of fragile RNA and metabolite markers.

2

Exosome Isolation and Cargo Extraction

Isolate high-purity exosomes using tailored methods (e.g., SEC) and employ specialized protocols for simultaneous extraction of RNA, proteins, and lipids to maximize yield.

3

High-Throughput Multi-Omics Profiling

Execute parallel data acquisition using NGS for transcriptomics and High-Resolution LC-MS/MS for proteomics, lipidomics, and metabolomics.

4

Integrated Bioinformatics Analysis

Perform statistical integration of multi-omics datasets to uncover regulatory networks and identify robust composite biomarker signatures.

5

Biological Interpretation and Reporting

Deliver publication-ready reports with interactive visualizations, offering deep biological interpretation that connects data to functional mechanisms.

Creative Biostructure offers flexible service options: choose individual omics profiling (e.g., RNA-seq only) or a fully integrated multi-omics package tailored to your specific research questions.

Starting a Project with Creative Biostructure

Sample Requirements

• Minimum Volume: Varies by omics combination; typically 3-5 mL for biofluids (plasma/serum) or >50 mL for cell culture supernatants to ensure sufficient yield for simultaneous RNA/Protein/Lipid extraction.
• Acceptable Sample Types: Cell culture media, plasma (EDTA preferred), serum, urine, CSF, or pre-purified exosome pellets.
• Storage and Transport: Samples must be snap-frozen in liquid nitrogen and shipped on dry ice to prevent RNA degradation and metabolic changes.
• Critical Handling: Strictly avoid repeated freeze-thaw cycles and hemolysis, as these significantly alter the exosomal multi-omics profile.

For complex multi-omics designs, please contact our technical team to discuss specific input requirements based on your target sensitivity.

Deliverables

• Comprehensive Project Report: Detailed experimental design, library preparation/sample prep methods, and rigorous QC metrics (e.g., RNA RIN, peptide coverage).
• Raw & Processed Data: Full access to raw data files (FASTQ for NGS, .raw for MS) and normalized data matrices (Excel/CSV).
• Bioinformatics Analysis: Differential expression analysis, pathway enrichment (GO/KEGG), and multi-omics integration networks.
• Visualizations: Publication-ready figures including Heatmaps, Volcano plots, PCA plots, and Circos plots.

Our data packages provide a holistic systems-biology view, equipping you with the statistical evidence needed for high-impact publications and biomarker validation.

Featured Exosome Omics Case Studies

At Creative Biostructure, we bridge the gap between raw data and biological insight. Discover how our integrated multi-omics strategies empower researchers to decipher complex disease mechanisms and secure high-impact publications.

Case Study 1: Exosome Proteomics Analysis – DIA Method

Objective: To overcome the limitations of stochastic sampling and achieve a comprehensive, systematic profile of the exosomal proteome.

Solution: We utilized the advanced Data-Independent Acquisition (DIA) proteomics technique, which is particularly well-suited for exosome research. Instead of selecting only the most abundant ions, our workflow divides the full MS scan range into fixed windows and fragments every precursor within each window.

Outcome: This approach achieved near-complete, bias-free detection of all peptides present in the sample. The method successfully captured a deep, digital map of the proteome, identifying low-abundance markers that traditional methods often miss.

Differential Protein Clustering in Exosome Proteomics Analysis.

Differential protein clustering diagram. (Creative Biostructure)

Case Study 2: Exosome Proteomics Analysis – Label-free Method

Methodology: We employed a streamlined label-free proteomic analysis strategy, an isotope-labeling-independent approach ideal for comparative profiling. In this workflow, exosomal proteins were enzymatically digested into peptides, separated by high-precision nano-LC, and analyzed by mass spectrometry.

Quantification Principle: To determine the relative abundance of proteins between samples, we utilized a quantitative approach based on two key metrics, the number of identified peptide spectra and the summed chromatographic peak areas of each protein. This method provided robust differential expression data without the complexity of chemical labeling.

Quantity distribution of identified peptides in exosome proteomics analysis.

Quantity distribution of identified peptides. (Creative Biostructure)

Case Study 3: Exosome miRNA Sequencing

Strategic Value: The comprehensive analysis of exosomal miRNA and mRNA is a cornerstone of modern translational research. This approach is of great value across multiple fields, particularly for disease diagnosis, therapeutic development, and non-invasive biomarker discovery.

Biological Insight: We target exosomes serving as critical carriers of RNA and protein cargo. By sequencing this cargo, we identify specific RNAs involved in diverse biological processes, including transcriptional regulation, cell differentiation, tumorigenesis, and immune modulation.

Quantification of miRNA expression showing normalized miRNA levels and differential abundance across samples.

Quantification of miRNA expression. (Creative Biostructure)

Why Choose Our Exosome Omics Analysis Services

Creative Biostructure leverages cutting-edge NGS and Mass Spectrometry platforms to deliver seamless multi-dimensional data integration, turning complex exosomal cargo into clear biological insights.

True Multi-Omics Integration

Seamlessly combine Transcriptomics, Proteomics, and Lipidomics under one roof to ensure datasets are perfectly aligned for robust correlation analysis.

Superior Sensitivity for Low-Input Samples

Optimized protocols allow deep profiling from limited biofluids, maximizing information retrieval and data depth without compromising sample integrity.

Advanced Systems Biology Analysis

We utilize advanced statistical models to map regulatory networks, linking gene expression to metabolic output to reveal underlying disease mechanisms.

Tailored Experimental Design

Flexible designs from discovery to validation, with expert consultation to ensure strategies align precisely with your research goals.

Next generation sequencing flow cell in sequencer.

What Our Customers Say

" We used their Label-free proteomics to map exosome surface markers. The sensitivity for low-abundance proteins was impressive and the raw data was incredibly clean. The final report was comprehensive and ready for our publication."

– Sarah Jenkins, Senior Scientist, Translational Medicine

" Their small RNA-seq workflow handled our low-input plasma samples perfectly. The bioinformatics team's pathway analysis helped us pinpoint valid miRNA biomarkers."

– Dr. Aris Thorne, Principal Investigator, Cancer Biology

" Accurate lipid profiling was vital for our engineered exosome stability. Their targeted lipidomics platform provided the quantitative resolution we lacked internally."

– Mark Davis, Lead Bioengineer, Drug Delivery Systems

Frequently Asked Questions

For any inquiries, our support team is ready to help you get technical support for your research and maximize your experience with Creative Biostructure.

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