System Biosciences

Exo-NGS

Overview

Getting better insights from exosomal RNA biomarkers is as easy as S-B-I

Because we know exosomes and we know how to deliver on end-to-end service

For many researchers interested sequencing exosomal RNA—whether it’s for biomarker discovery and profiling, or addressing other research questions—it may seem like there are too many hurdles to overcome to get to the data: How much sample is required? What’s the best way to isolate exosomes? Does this data look right?

Fortunately, SBI is here to cut through your uncertainties by providing a customized service with full levels of support. Whether you’re an exosome expert or brand new to the field, SBI’s Exo-NGS^™ (Exosomal RNA-Seq) services can accelerate your biomarker discovery and profiling.

Because we’ve been working with exosomes for years, we can reliably and reproducibly isolate exosomes from almost any biofluid—from plasma and tissue culture media to CSF, synovial fluid, and even mouse bronchial alveolar fluid (a challenging sample where exosomes are concerned!).

And more importantly for exosome RNA-Seq, we routinely generate high-quality exosomal RNA libraries from as little 1 ng of total RNA, which is unparalleled given the challenges of obtaining high-quality RNA from exosomes. SBI can overcome these experimental hurdles to deliver quality and meaningful NGS data from your exosome samples.

Lastly, but not least, looking beyond the data, we can provide what your average NGS company cannot: the expertise of working with exosomes and exosomal biomarker samples. We’ve run thousands of samples and know what to expect from exosome RNA-Seq studies. We don’t just deliver raw data, we provide analyzed files and typically spend time with you reviewing your results and providing expert insights into your data, a value-add that is rare in this industry. Still not sure? Take a look at the data below, and then contact us and we’ll be happy to answer any questions before, during, or after your Exo-NGS service.

More usable reads for uncovering novel biomarkers
Any type of exosomal RNA
Low sample requirements (as little as 1ng of total RNA)
Any biofluid (we handle exosome isolation)
Unparalleled end-to-end scientific support
Have your own exosomes? We can handle them!

Supporting data

Good exosomal RNA-seq data starts with as little as 1 ng of total RNA

How do we get quality NGS data from such small amounts of RNA? It starts with the library prep. The standard methods for preparing RNA libraries often results in a large overlap between adaptor dimers and exosomal RNAs (Figure 1A). However, at SBI, we’ve modified the library prep to better separate the exosomal RNA from uninformative adaptor sequences (Figure 1B). The result is more usable sequencing reads from lower amounts of RNA as seen by the number (Figure 2) and percentage (Figure 3) of usable reads as well as the number (Figure 4) and percentages (Figure 5) of mapped reads. Fewer adaptors and more exosomal reads mean better insights from your data.

Figure 1. SBI’s exosomal RNA library preps provide better separation between exosomal RNA and the uninformative adaptor dimers.(A) Using standard library preparation methods, the adaptor dimer band overlaps with the exosomal RNA band, leading higher levels of contaminating adaptor sequence reads and fewer usable exosomal RNA reads. (B) SBI’s library preparation method leads to better separation between the adaptor sequences and the exosomal RNA, resulting in a higher percentage of usable exosomal RNA sequence reads.

Figure 2. SBI’s exosomal RNA library preps result in more total reads and more usable reads after quality assessment and control (QA/QC) filtering.

Figure 3. SBI’s exosomal RNA library preps result in a higher percentage of usable reads.

Figure 4. SBI’s exosomal RNA library preps result in a higher number of mapped reads.

Figure 5. SBI’s exosomal RNA library preps result in a higher percentage of mapped reads.

Exosome Proteomics Services

Overview

Easily expand your biomarker studies to exosomal proteins

Because we know exosomes and we know how to deliver on end-to-end service

SBI’s Proteomics Services makes it easy to profile exosomal proteins, whether you’re hunting for biomarkers, seeking easy-to-access information on the physiology of the parent cell, or studying exosome biology. Our customized services provide comprehensive support that includes a pre-service consultation and everything from exosome isolation to data acquisition, analysis, and even interpretation. The result is high quality exosomal proteomics data regardless of whether you have a lot of experience working with exosomes or are new to the field.

Because we’ve been working with exosomes for years, we can reliably and reproducibly isolate exosomes from almost any biofluid—from plasma and tissue culture media to CSF, synovial fluid, and even mouse bronchial alveolar fluid (a challenging sample where exosomes are concerned!). And importantly for researchers working with limited sample volumes, our sample input requirements are very low (Table 1).

Table 1. Required sample volumes for SBI’s Proteomics Services

BIOFLUID	VOLUME
Serum, plasma, ascites fluid	0.5–1 ml
Cell media, urine, CSF	5–10 ml
Other	Inquire

We can also work with already isolated exosomes, although we recommend using our proven sample preparation approaches which typically deliver cleaner peptide libraries with lower amounts of carryover protein, for more reliable exosome proteomics data.

Lastly, but not least, looking beyond the data, we can provide what your average proteomics service company cannot: the expertise of working with exosomes and exosomal biomarker samples. We’ve run thousands of samples and know what to expect from exosome proteomics studies. We don’t just deliver raw data, we provide analyzed files and typically spend time with you reviewing your results and providing expert insights into your data, a value-add that is rare in this industry. Still have questions? Ready to order? Contact us

Proteomics service highlights:

Proprietary sample cleanup procedure reduces non-specific proteins found in biofluids
Both EV total and surface protein profiling services available
Libraries prepared using standard trypsin cleavage for MASCOT compatibility
Data file compatibility with Scaffold viewer simplifies data mining and analysis
Fast turn-around times—approximately 4 weeks

Data deliverables:

Full protocol report
Raw MS spectra data
Pre-analyzed data in Scaffold format
Examples: Sample Data and Experimental Report

Exosome Lipidomics & Metabolomics Services

Overview

Take your biomarker studies to the next level with exosomal lipidomics/metabolomics

Because we know exosomes and we know how to deliver on end-to-end service

Whether you’re interested in circulating biomarker discovery, basic exosome research, or other exosome-related studies, SBI’s Exosome Lipidomics & Metabolomics Service helps you quickly and efficiently get the most information from your exosomes. Simply send us your sample or purified exosomes and we’ll send back a spreadsheet with putative identifications, mass/charge ratios, and differential analysis (if requested).

What can lipidomics of exosomes tell you?

Lipids are an important part of cellular physiology, and are increasingly being recognized for their importance in exosome biology as well. Exosomes were recently shown to have the highest lipid-to-protein ratio of all classes of extracellular vesicles¹, with lipid content that both differs from the parent cell the vesicles are shed from² and also changes as exosomes undergo a variety of physiological processes³. These unique lipid profiles can serve as novel circulating biomarkers, and recent evidence suggests that specific lipid species carried by exosomes can also modulate the function of recipient cells⁴.

With so much information revealed by lipid content, lipidomics studies of exosomes are a great way to identify lipid-based biomarkers and for understanding vesicle biogenesis and function⁵.

What can metabolomics of exosomes tell you?

In addition to lipids, exosomes carry a wide range of metabolites that can also be used for biomarker discovery. A recent study found distinctly different populations of metabolites in PANC1 cells treated with TGF-β, a known driver of cancer progression, versus a control group, suggesting that metabolite profiling can be used for differentiating cellular states⁶. Like exosomal lipids, exosomal metabolites can also take an active role in the target cell, and have been shown to reprogram metabolic machinery upon uptake by cancer cells, fueling growth⁷.

Lipidomics & Metabolomics service highlights:

Discover novel circulating biomarkers
Learn more about exosome biology
Send us your sample and receive data in 4–6 weeks

Data deliverables:

MS data will be delivered as Excel files with putative identification based on the m/z ratio of the analytes
Differential analysis of lipids and metabolites between treatment groups will be included in the Excel files

Figure 1. Exosomes affect metabolism in cancer cells. A recent study by Zhao, et al,⁷ demonstrated that exosomes from patient-derived cancer-associated fibroblasts (CAFs) can reprogram the cellular machinery in cancer cells. They used a metabolomics approach to demonstrate that exosomes shed from CAFs contain intact metabolites that fuel tumor growth. In addition, they showed that uptake of CAF exosomes inhibited mitochondrial oxidative phosphorylation, increasing glycolysis and glutamine-dependent reductive carboxylation.

References

Osteikoetxea X, et al. Improved characterization of EV preparations based on protein to lipid ratio and lipid properties. PLoS One. 2015;10(3):e0121184. PMCID: PMC4370721.
Llorente A, et al. Molecular lipidomics of exosomes released by PC-3 prostate cancer cells. Biochim Biophys Acta. 2013;1831(7):1302-9. PMID: 24046871.
Carayon K, et al. Proteolipidic composition of exosomes changes during reticulocyte maturation. J Biol Chem. 2011;286(39):34426-39. PMCID: PMC3190795.
Subra C, et al. Exosomes account for vesicle-mediated transcellular transport of activatable phospholipases and prostaglandins. J Lipid Res. 2010;51(8):2105-20. PMCID: PMC2903822.
Subra C, et al. Exosome lipidomics unravels lipid sorting at the level of multivesicular bodies. Biochimie. 2007;89(2):205-12. PMID: 17157973.
Altadill T, et al. Enabling Metabolomics Based Biomarker Discovery Studies Using Molecular Phenotyping of Exosome-Like Vesicles. PLoS One. 2016 Mar 14;11(3):e0151339. PMCID: PMC4790956.
Zhao H, et al. Tumor microenvironment derived exosomes pleiotropically modulate cancer cell metabolism. Elife. 2016 Feb 27;5. pii: e10250. PMCID: PMC4841778.

How it works

Ordering Exosome Proteomics Services is easy

Step 1. Contact us for a quote.

Step 2. Send us your samples.

Step 3. Get your data files in 4–6 weeks.

Our standard service offers UPLC-FTMS analysis of very polar metabolites in the aqueous phase, with lipids and other metabolites in the organic phase. Non-polar analysis also available upon request.

Note that all IDs are based only on retention time, accurate mass measurement, and preliminary MS/MS data, and cannot be guaranteed. Not all peaks will be identified, and we recommend that any peaks of interest—either due to the identity of the compound reported and/or change in intensity between samples—MUST be verified by additional targeted analysis at additional cost.

Input sample requirements

BIOFLUID	VOLUME
Serum	500μl–1ml
Plasma	500μl–1ml
Cell Media	5ml–10ml
Urine	5ml–10ml
Spinal Fluid	5ml–10ml
Ascites Fluid	500μl–1ml
Other	Inquire

NTA-based Exosome Characterization

Overview

Get the confidence to move forward with SBI’s NTA Services

Because we know exosomes and we know how to deliver on end-to-end service

When you use SBI’s NTA-based Exosome Characterization Services, you can get a clearer picture of the quality of your exosomes in as little as two weeks and without needing to invest in your own NTA instrument. Send us your biofluid or prepared exosomes, choose conventional or fluorescent nanoparticle tracking analysis (NTA), and we’ll send back a report with the particle analysis data—the mean and mode diameter size, particle concentration, and video of the collected data, all gathered in triplicate.

Why choose SBI for NTA characterization of exosome preps?

Because we’ve been working with exosomes for years, and can reliably and reproducibly isolate exosomes from almost any biofluid—from plasma and tissue culture media to CSF, synovial fluid, and even mouse bronchial alveolar fluid (a challenging sample where exosomes are concerned!).

And because SBI is the only company that can provide fluorescent NTA using our proprietary ExoGlow™-NTA reagents (learn more about conventional and fluorescent NTA below, in the How It Works section).

Nanoparticle Tracking Analysis-based Exosome Characterization Services highlights:

Understand the quality of your exosome preps
Leverage SBI’s long-term experience working with exosomes
Send us your biofluid or exosome prep and receive data in about 2 weeks

How it works

Ordering NTA-based Exosome Characterization Services is easy

Step 1. Contact us for a quote.

Step 2. Send us your biofluid or exosome prep.

Step 3. Get your data files in approximately 2 weeks.

What’s NTA?

SBI uses NTA measurements that rely on light scattering to extract particle size and the number of particles in a sample (Figure 1A). Briefly, a laser is directed at the sample and the particles in the sample scatter the light, which is imaged by a camera attached to a microscope and operating at 30 frames per second. The NTA software collects data on multiple particles simultaneously, and calculates the hydrodynamic diameter of each particle using the Stokes-Einstein equation.

Figure 1. The ExoGlow-NTA dye only binds to membranes of intact EVs. Unlike conventional NTA (A), which collects data on all particles in a solution based on light scattering, the fluorescence mode of the NTA instrument selectively detects only the fluorescently-labeled particles—in this case, the ExoGlow-NTA-labeled EVs (B)—and only the data from fluorescently-labeled particles is reported.

What is fluorescent NTA and how is it different from conventional NTA?

Making a great exosome research tool even better, SBI has developed ExoGlow-NTA, a proprietary dye for fluorescent NTA* that enables data collection for only the extracellular vesicles present in a heterogenous sample. The result is more accurate EV/exosomal NanoSight data that ignores protein aggregates, membrane fractions, and other background particles to provide EV-specific particle size and concentration.

The ExoGlow-NTA reagent works by binding specifically and efficiently to the membranes of intact EVs, including exosomes. During data collection for fluorescent NTA, only the light scattering from fluorescently-labeled particles is obtained, resulting in EV-specific signal that ignores membrane fragments, protein aggregates, and other background particles since they do not bind the ExoGlow-NTA dye (Figure 1B). Thus, with the ExoGlow-NTA Kit, the data delivered by the NTA analysis more accurately reports on the EVs in your sample, rather than all of the particles in your sample.

Supporting data

Get Better NTA data on EVs using ExoGlow-NTA

SBI’s ExoGlow-NTA Fluorescent Labeling Kit delivers highly accurate EV quantitation in a quick and easy workflow. The proprietary dye offers highly efficient labeling (Figure 2), very low background (Figure 3), and is compatible with a wide range of EV isolation techniques (Figure 4).

Figure 2. ExoGlow-NTA-labeled liposomes deliver consistent NTA data whether in light scattering or fluorescent mode. The high concordance of NTA and fluorescent NTA data collected from the ExoGlow-NTA Kit internal standards (ExoGlow-NTA-labeled synthetic liposomes) demonstrates the labeling efficiency of the ExoGlow-NTA Dye and accuracy of the fluorescent NTA method for characterizing EVs.

Figure 3. ExoGlow-NTA exhibits undetectable background signal. Conventional NTA and Fluorescent NTA of ExoGlow-NTA dye in the absence of EVs shows bias-free undetectable autofluorescence, based on (A) particle counts and (B) imaging.

Figure 4. ExoGlow-NTA demonstrates that conventional NTA overestimates EV concentration in samples irrespective of EV isolation method. Representative data comparing conventional NTA and fluorescent NTA for EVs isolated using (A) ExoQuick (10 μg serum protein), (B) ultracentrifugation and wash (1 μg serum protein), or (C) column based (1 μg serum protein), shows how much of the conventional NTA signal is due to non-EV particles.

Exosome Isolation & Manufacturing

Overview

Accelerate discovery and development with SBI’s Exosome Isolation & Manufacturing Services

Because we know exosomes and we know how to deliver on end-to-end service

Need exosomes? SBI’s Exosome Isolation & Manufacturing Services can deliver. We’ve been working with exosomes for years, and can reliably and reproducibly isolate exosomes from almost any biofluid—from plasma and tissue culture media to CSF, synovial fluid, and even mouse bronchial alveolar fluid (a challenging sample where exosomes are concerned!). Choose your scale and choose your biofluid, and choose your isolation method. If you have any questions, our experienced services team can provide a customized scientific consultation.

Exosome Engineering

Overview

Are you ready to put exosomes to work? Let SBI help!

Because we know exosomes and we know how to deliver on end-to-end service

Used by cells to transport specific cargoes of active biomolecules, exosomes can be a powerful tool for labeling cells, delivering therapeutics, studying biological processes, and other applications. But you first need to load your cargo—whether protein, miRNA, or small molecules—and/or encode cell type specificity. Which is where SBI’s Exosome Engineering Services can help. Provided by the experienced team that makes SBI’s Exosome Engineering products, our scientists are ready to produce custom-engineered exosomes for you and can provide as much support as you need, including scientific consultation about engineering methods and exosome design.

What kind of engineering can SBI do?

SBI can use one of more of our Exosome Engineering Products to create customized exosomes for you:

Label exosomes
- General protein labeling
- General RNA labeling
- Specific protein or RNA labeling

Load cargo into exosomes
- Proteins
- Nucleic acids, including mRNA, miRNA, lncRNA, DNA
- Small molecules

Tag exosomes for uptake by specific cell types

Don’t see what you need or not sure what would be best for your application? Contact the services team to set up an in-depth phone consultation.

Why choose SBI for engineering exosomes?

Because we’ve been working with exosomes for years. Not only can we reliably and reproducibly isolate exosomes from almost any biofluid, we’ve got the experience to understand the little experimental details, such as cargo loading efficiency, cell uptake efficiency, and more.

	VIRAL SYSTEMS	NON-VIRAL SYSTEMS
Integrating Vectors Great for general gene or non-coding RNA functional studies and applications where heritable expression is desired	Lentivectors High-titer and reliable • Random integration • Limited insert size • High copy number	PiggyBac™Transposon Easy, consistent transgenesis • Random integration • Unlimited insert size • High copy number
		PhiC31 Integrase System One-step single-copy integration • Site-specific integration • Unlimited insert size • Single copy number

Non-integrating Vectors Great for sensitive applications, such as gene therapy, that need to avoid potential host gene disruptions due to vector integration	AAV Vectors Effective gene delivery without viral integration • Limited insert size • High copy number	Enhanced Episomal Vectors Easy episomal expression • Unlimited insert size • High copy number
		Minicircle Technology Episomal expression free from foreign DNA • Unlimited insert size • High copy number

TITER	IFU/ML	APPLICATION
Regular Titer	>10⁷	Standard cell culture models
High Titer	>10⁸	More difficult-to-transduce cells (e.g. suspension cells)
Ultra-high Titer	>10⁹	Very difficult-to-transduce cells such as stem cells and primary cells; In vivo applications

CATALOG #	PRODUCT	SPECIES
miRNA Arrays
RA610A-1	Cancer MicroRNA “OncoMir” qPCR Array	Human
RA620A-1	Stem Cell MicroRNA Profiling Panel	Human
RA660A-1	hsa-miRNome MicroRNA Profiling Kit	Human
RA670A-1	mmu-miRNome MicroRNA Profiling Kit	Mouse
RA680B-1	rno-miRNome MicroRNA Profiling Kit	Rat

Exosomal miRNA Arrays
RA810A-1	Human SeraMir Exosome RNA 384 microRNA qPCR Profiler Assay Set	Human
RA811A-1	Mouse SeraMir Exosome RNA 384 microRNA qPCR Profiler Assay Set	Mouse
RA812A-1	Rat SeraMir Exosome RNA 384 microRNA qPCR Profiler Assay Set	Rat

lncRNA Arrays
RA900A-1	LncRNA Profiler qPCR Array Kit	Human
RA930A-1	Mouse LncRNA Profiler qPCR Array Kit	Mouse
RA950A-1	Regulatory RNA qPCR Profiler	Human

Product Categories

Exosome Labeling Kits & Products

Exosome Isolation Kits & Products

Exosome Quantitation Kits & Products

Exosome Biomarker Discovery Products

Exosome Detection Products

Exosome Engineering & Design Products

Cas9 & gRNA Delivery

HR Targeting Vectors

Multiplex gRNA Cloning

AAVS1 Safe Harbor Targeting

Cas9 Detection

CLOuD9 Gene Expression Regulation System

LentiSuite & LentiStarter High-Titer Lentivirus Kits

Viral Transduction and Transfection

Pre-packaged Positive Control Viruses

Virus Concentration Kits & Titering

Lentiviral Expression Plasmids & Lentiviral Vectors

PiggyBac Transposon

Episomal Expression Vectors (EEV)

Targeted Protein Degradation

AAV Vector Expression

Pinpoint & PhiC31 Integrase Systems

Custom mRNA Synthesis Production

Cumate Inducible Gene Expression Systems

Minicircle Technology

Cold Fusion Cloning Kit with Competent Cells

T Cell Research Tools

Signaling Pathway Reporters

Stem Cell Reporters

Bioluminescent Imaging Vectors

T Cell Research Tools

Cyto-Tracers

Lenti-miR Precursor Vectors

miRNA qPCR Profiling

Lenti-miR Libraries

lncRNA qPCR Profiling

miRZip Knockdown Vectors

Product Literature

Exo-NGS

Overview

How it works

Supporting data

Exosome Proteomics Services

Overview

How it works

Exosome Lipidomics & Metabolomics Services

Overview

How it works

Supporting data

NTA-based Exosome Characterization

Overview

How it works

Supporting data

Exosome Isolation & Manufacturing

Overview

How it works

Supporting data

Exosome Engineering

Overview

How it works

Supporting data

CRISPR/Cas9 gRNA and HR Donor Cloning

Overview

How It Works

Supporting Data

CRISPR/Cas9 Cell Line Engineering

OVERVIEW:

How it works

Supporting data

Overview

How it works

Overview

Get a Quote

Supporting data

Get custom reporter, overexpression, or other type of cell line fast and hassle-free with integrated or episomal transgene delivery, viral or non-viral vectors

Custom Overexpression Stable Cell Lines

Overview

How It Works

Supporting Data