Use scRNA-seq to
your research

Single-cell RNA sequencing (scRNA-seq) is revolutionizing the field of biology by providing a powerful tool to identify cell types, dissect heterogeneous disease responses, and comprehensively profile the immune system. What benefits does it have for your research?

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SORT-seq services for Single Cell RNA at Single Cell Discoveries

When to use scRNA-seq

As a scientist, you have probably come across the use of scRNA-seq in your field. How can you apply it to your research? Which technology should you choose? And what do you need to think about before starting your project?


Cell Type Identification

scRNA-seq technology can capture gene expression profiles of all individual cells in a tissue at high read depth and increasing scalability. You can thus identify all (even rare) cell types and subtypes and map out the components of highly heterogeneous tissues like brains, tumors, or developing tissue.

In-depth sequencing can reveal cell states and lineages in developing tissues or model systems and characterize how tissues respond to drugs or disease at single-cell resolution.

scRNA-seq is compatible with many species, including all common pharmaceutical model systems and non-animal species.

Immune Profiling

Characterize all functional states of an immune cell population through their gene expression profiles and gain insights into how a body responds to infection or treatment. Moreover, additional T cell receptor sequencing (alpha-beta or gamma-delta), immunoglobulin sequencing, B cell receptor sequencing, and, more broadly, cell-surface protein sequencing (CITE-seq) further contribute to a high-resolution assessment of immune cell clonality.

Highly suitable for drug immunogenicity assessment and immunotherapy, cell therapy (e.g., CAR T-cell therapy), or stem cell therapy development


Integrate single-cell transgene detection into scRNA-seq full transcriptome profiling to measure the transfection efficiency of gene therapy (e.g. for AAV biodistribution measurements or capsid design) and viral therapy platforms.

Moreover, optimize safety and efficacy of gene editing by validating transgene expression in cells, revealing cell tropism, and studying transcriptomic response after administration. Or measure CRISPR guide RNA transfection at high throughput.

Drug Discovery

Flexible scalability makes scRNA-seq highly compatible with (pre)clinical drug development experiments. For example, compare cell-type compositions or differentially expressed genes in specific cell types between disease states, or responders versus non-responders, and gain insight into drug efficacy and mechanism of action.

Accelerate target and biomarker discovery with high-resolution identification of differentially expressed genes in cells of interest.

scRNA-seq in Drug Discovery

Take a deep dive in the applications of scRNA-seq in specific areas of drug development: Download our eBook.

Mechanism of Disease

Detect cell type-specific marker genes

Target Identification

Measure gene expression changes at high throughput

Mechanism of Action

Deconvolute heterogeneous
drug responses

Lead Identification and Optimization

Optimize cell and gene therapy efficiency


Integrate scRNA-seq as a readout in drug testing

Clinical Trials

Make the most use of valuable patient material


Get to know the
scRNA-seq portfolio

Tissue type, sample volume, number of cells, fixation state, RNA biotype, and required read depth all influence which technology best suits a project. Explore multiple single-cell RNA sequencing technologies to determine which fits your demands.


Our seRvices


ATAC-seq for single cells at Single Cell Discoveries

Study the Information Guide

Download our information guide to access an overview of Single Cell Discoveries, explore our single-cell sequencing services, learn how to get started, and gain more valuable insights.


Custom scRNA-seq solutions

Pioneering new technologies

Protocol development is at the heart of many single-cell scientists. At Single Cell Discoveries, we have pioneered the SORT-seq and VASA-seq methodologies and are driven to keep finding new ways to employ single-cell sequencing to another biological challenge.

What is possible with scRNA-seq?

You do not know what is impossible with single-cell sequencing until you try it. Our Research & Development unit is delighted to work on innovative, non-standard project, whether it is a novel application, a tough tissue, or an uncommon species requiring technological tinkering.

How to start

How we supercharge
your research

Project Design

  • Strategize with our PhD-level account executives to decide between multiple single-cell technologies, including two exclusively offered by us.
  • Leverage our experience with 200+ clients over 1000+ unique projects.

Sample Processing

  • Run in our purpose-built single-cell lab with Illumina Novaseq X.
  • Benefit from our experience with 8500+ samples sequenced in 40+ organisms and 30+ tissue types with over 10M single cells sequenced.

Data Analysis

  • Gain quick insights into your single-cell data with our preliminary analysis report with QC, clustering, and differential gene expression.
  • Uncover biological insights through custom data analysis with our bioinformaticians who have processed over 50 terabytes of single-cell data.
Step 1 - Consultation with our clients
Step 1


Every project starts with one or more free consultations because no two single-cell projects are the same. Our experienced PhD-level team discusses your biological question, sample type, planning, data analysis options, and other wishes. This will ensure you select the best method for your project and can hit the ground running.

Step 2 - Preparation of the client samples
Step 2

Sample Preparation

For 10x Genomics, create a single-cell suspension from your sample and either cryopreserve or methanol-fix the cells. For plate-based methods, FACS-sort the single cells into the wells of our cell capture plates. Then, send your samples to our lab on dry ice. In the case of nuclei, the sample preparation depends on the project. 

Single cell sequencing Illumina NovaSeq scientist places samples in the new NovaSeq X machine
Step 3

Processing in Our Lab

Our experienced team performs the sequencing protocol in our facility. We sequence the libraries on our Illumina NovaSeq X Plus or NextSeq 2000. We'll do multiple QC checks and keep you informed of the status of your project.

Exploring data analysis
Step 4

Data Analysis

Our data consulting team is ready to assist with further guidance or tailored analysis projects such as pseudotime and gene set enrichment analysis.

Why choose SCD?

We are scRNA-seq experts

A 100% focus on single-cell and spatial transcriptomics in our team enables us to take on both large-scale projects and create customized solutions for each client project.

Single-cell sequencing service provider

You will access unmatched experience

We have been working in the single-cell field since 2012. Our co-founder and CEO Mauro Muraro published our SORT- seq technology, and our R&D consultant is the mind behind VASA-seq. We have experience in over 40 organisms and 30 tissues and are able to quickly adapt workflows for novel samples.

You stay ahead of the curve

You can follow our continuous integration of leading-edge technologies into our portfolio and get access to the latest advancements. Our R&D department works to both internalize the best commercial platforms and advance our own single-cell innovations.

Work with us as a collaborative partner

We are dedicated to maintaining a high-touch, collaborative relationship with clients as we scale our capacity to accommodate larger projects. We act as a thought partner and a catalyst for biological discovery.

Which scRNA-seq technology is the best?

What's the best (most suitable) scRNA-seq technology depends on your biological question, sample type, and budget. Schedule a meeting with one of our experts to discuss your project in more detail. We'll make sure to advise you on the best platform for your project.

Information Guide

Discover our single-cell sequencing solutions

Download our information guide to access an overview of Single Cell Discoveries, explore our single-cell sequencing services, learn how to get started, and gain more valuable insights.