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Omics Research // Single-Cell/Spatial Omics

Single-Cell Analysis

Advance gene expression research in suspensions, biological fluids, tissues, or cell populations with Psomagen’s single-cell sequencing technologies.

What Is Single-Cell Sequencing?

Single cell sequencing allows us to isolate the transcriptome or DNA of each individual cell, enabling cell type identification and deconvolution of a heterogeneous population of cells. 

Researchers use single-cell RNA sequencing to examine the small complexities of each region of the transcriptome.  Single-cell DNA sequencing can identify mutations and chromatin accessibility in individual cells.

Single cell sequencing recognizes that every cell is as different as the person it belongs to.  By isolating the components of an individual cell, researchers are better able to understand how and why that cell responds to stimuli and direct diagnosis, drug discovery, and treatment.


Why Is Single Cell Sequencing Important?

Traditional RNA sequencing relies on extraction of RNA from tissue, a heterogeneous mix of cell types.  RNA extraction from cell culture or sorted cell types include cells at different stages of their development.  Sequencing results yield an average gene expression across all cell types and stages.  A dying cell’s transcriptome influences data just as much as a live, differentiating cell. 

Bulk RNA sequencing does not yield a transcriptomic profile representative of any individual cell in that sample.  Single cell sequencing allows us to isolate the transcriptome of each individual cell, enabling cell type identification and deconvolution of a heterogeneous population of cells. 


Is Single-Cell Right for Me?

Selecting the right technology for your research question is the first step toward success. Our recent article walks through important differences between single-cell, spatial, and in situ technologies.

What Can You Do?

Cancer Research

Tumors are a mix of healthy and cancerous cells, as well as potential immune infiltrate.  Differentiating transcriptomic profiles of healthy versus cancerous cells can yield potential targets for treatment therapies, in hopes of developing treatment options which will leave healthy tissues unaffected.  Similarly, identification of immune cell populations provide insight into innate immune response, presenting additional pathways for treatment.



The nervous system is a highly complex system composed of a variety of cell types.  Single cell sequencing allows for the identification of the cellular composition of brain and CNS tissues, including cellular subtypes.  Over 3,000 different cell types have been identified in the human brain, emphasizing the delicate balance that cellular composition plays in human development.  Transcriptional changes can contribute to neurodegenerative and neurological diseases. 



An organism’s immune system relies on a wide variety of cell types.  However, the specificity of the adaptive immune system comes from genetic mutations and recombination events, meaning each lymphocyte can have a unique transcriptomic profile. Single cell sequencing can isolate an individual T or B cell and identify its VDJ regions.  This provides a more complete picture of an organism’s immune response, guiding treatments and understanding of conditions from autoimmunity to aging.


...And More

  • Targeted sequencing
  • CRISPR screening
  • Dermatology
  • Gastroenterology

We're Certified!

Did you know we're a 10x Genomics Certified Service Provider (CSP)? When you sequence with us, you can be confident that your samples will be processed by efficient, effective, and well trained scientists. Optimized SOPs developed over years of experience allow our labs to adapt to the complexities of single cell protocols. 

Our expert team makes your research their priority! We’ve been fully trained and are committed to yearly recertification for all our 10x services.

  • 3’ Gene Expression
  • 5’ Gene Expression
  • Flex Fixed Gene Expression
  • Immune Profiling
  • Multiome ATAC + Gene Expression*
  • ATAC

Single-Cell Sequencing Workflows from 10x Genomics®

10x technologies provide a diverse portfolio of single-cell options.

Microfluidics encapsulate an individual cell along with a Gel Bead, coated in uniquely barcoded oligo-dT primers for mRNA capture.

This process creates full length cDNA suitable for long read sequencing.

Capture up to 20,000 cells/sample with high throughput assays.

Standard gene expression capture. Use gene expression levels to identify cell subtypes and cell trajectories.  Compatible with full length cDNA sequencing.

Gene expression capture, compatible with  immune profiling for human and mouse TCR and BCR enriched sequencing and targeted enrichment.

Compatible with 3' and 5' gene expression assays.

Compatible with 3' and 5' gene expression assays.

Combine multiple pre-labeled samples into a single lane. 

Chromatin accessibility from a single nucleus, assessing its availability for interaction with proteins, namely transcription factors. Determine the prevalence of subpopulations and their overall impact on a heterogeneous cell sample – a critical area of regulatory pathway discovery.

3' gene expression plus ATAC from the same nucleus. A good choice for solving research and discovery problems at a systems biology level. Determine what gene expression is occurring and how the structure of that DNA may regulate that expression.

Psomagen was the first 10x Certified Service Provider for scATACSeq in the US and the second worldwide.

Probe-based capture from fixed or FFPE human and mouse cells or nuclei.


More Single-Cell Providers


Combinatorial barcoding uniquely tags mRNA within a cell. Cells are fixed and permeabilized, enabling long term storage and collection for longitudinal studies. Oligo-dT and random RNA capture possible.

Three sizes of kits enable capture of: 

  • 12 samples, up to 10,000 total cells
  • 48 samples, up to 100,000 total cells
  • 96 samples, up to 1,000,000 total cells

Recent advancements in methodologies support a variety of projects: 

  • 3' gene expression
  • Human TCR enrichment
  • CRISPR screening
  • Targeted gene capture


High-throughput, instrument free emulsion capture uses core templated particles coated with a barcoded primer to capture mRNA. This technology is compatible with TotalSeq-A for multiplexing many samples in a single reaction. 

3' gene expression protocols are available in three sizes: 

  • T2 — up to 2,000 cells
  • T20 — up to 20,000 cells
  • T100 — up to 100,000 cells

Currently available for run-only projects at Psomagen, with more capabilities on the way. 

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One-cell-per-well method sorts each cell into a separate well for unique barcoding. A great choice for whole genome studies, because the proprietary primary-template directed amplification (PTA) yields a more accurate representation of the genome. 

Provides more efficient RNA capture within a cell, reducing the need for high cell numbers. 

Two sample type options available: 

  • ResolveDNA
  • ResolveOME

Currently available for run-only projects at Psomagen, with more capabilities on the way.

pacbio logo

Library preparation for full length, long-read cDNA generated by the 10x Genomics Kinnex single cell kit, which creates a PacBio compatible, SMRTbell library. Enables isoform and fusion detection without the need for assembly.

This methodology increases throughput 12x on Revio flow cells by concatenating individual cDNA molecules, taking advantage of long read capabilities.

Single-Cell Sequencing Best Practices

Sequencing Depth

Psomagen standardly runs single cell sequencing depth based upon the number of cells and the number of sequencing reads per cell. Please inquire for your specific experimental design.

Supported Run-Only Instruments

Illumina NovaSeq X Plus
PacBio Revio

Supported Run-Only Methodologies

10x Genomics
Parse Biosciences
Kinnex MAS-Seq


Data Delivery

All sequencing run data is delivered as demultiplexed .fastq files

If the entire flowcell or lane is purchased, the raw data can be delivered as BCL files if requested at the time of contract.

We're Ready for Your Order!

Here's what to expect in your project's life cycle. If you have a question during sequencing, it's easy to get in touch!


Request a Consultation

Create an account through our client portal and get in touch with your local field team to start designing a project.

We’ll help drive your research forward with the right tools for your research needs.


Place an Order

After finalizing the scope of work, the official quote will be issued for signing. Then, your sales representative will send specific shipping instructions.

Once all the samples and necessary documents are ready, we can start your project. Need more analysis? Reach out to our bioinformatics experts to dig deeper.


QC and Data Delivery

All Psomagen sequencing projects come with a built-in QC step to ensure you get the information you need. An account manager will update you on your project's progress in a timely manner.

You can also see some project information and securely view all valid reports on the client portal site.


Save on Single-Cell Library Prep

10x Single-Cell HT Library Prep:
- 4 or 6 samples, $500 off
- 8–16 samples, $1,000 off

10x Single-Cell Multiome Library Prep:
- 4–6 samples, $500 off
- 7–8 samples, $1,000 off
Parse V3 Library Prep and QC:
- Mini kit – $400 off
- WTK kit – $800 off
- Mega kit – $2,000 off|

See All Promotions

Why Our Clients Choose Psomagen


Superior Data Quality

Exceeds manufacturer benchmarks


Fast Turnaround

Starting at one week for sequencing projects


US-Based Processing

Sequencing and customer support in Rockville, MD


Ph.D. Level Support

Expert assistance every step of the way, with real-time project updates through our online system


Automated Workflows

Increase scalability and improve reproducibility


CLIA-Certified, CAP-Accredited Labs

Clinical research options available (inquire for more information)


Complete Sequencing Solutions

From extraction to data analysis, with many sample types accepted

Quotes From Our Clients

I chose Psomagen because of the price and US-based labs. We've used Psomagen before and were very satisfied. The people were responsive and helpful and the work done was very good.

Research Associate

Life Sciences Industry

Great service, high-quality reads, and fast turnaround time.

Christophe Cataisson, Ph.D.


Single Cell in Action

Prevalence and mechanisms of somatic deletions in single human neurons during normal aging and in DNA repair disorders
Sequential single cell transcriptional and protein marker profiling reveals TIGIT as a marker of CD19 CAR-T cell dysfunction in patients with non-Hodgkin lymphoma
Stress conditions promote Leishmania hybridization in vitro marked by expression of the ancestral gamete fusogen HAP2 as revealed by single-cell RNA-seq
PSO Comprehensive!

What forms of RNA sequencing will get you the insights you need?