Single Cell Discoveries

What Single Cell Discoveries does

Single Cell Discoveries BV is a privately held Contract Research Organization headquartered in Utrecht, Netherlands, founded in September 2018 by Mauro Muraro (CEO) and Judith Vivié (COO). The company provides end-to-end single-cell and spatial transcriptomics services to pharmaceutical, biotechnology, and academic research customers globally, with disclosed clients including Roche, Pfizer, Almirall, Genmab, DKFZ, Mount Sinai, and Boston Children's Hospital. It operates with 11-50 employees from a laboratory at Utrecht Science Park, with a US sample logistics partnership via MLM Medical Labs in Memphis, TN.

The company's core offering is a technology-agnostic portfolio of single-cell and spatial RNA sequencing services, spanning proprietary plate-based methods (SORT-seq, VASA-seq), third-party platforms (10x Genomics, Parse Biosciences, Scale Bio, BioSkryb), and Illumina NovaSeq X Plus sequencing infrastructure — making it the first holder of that sequencer in the Benelux region. SCD holds Certified Service Provider status with all four major single-cell platform vendors and, in May 2025, became the first laboratory worldwide operationally ready to perform fully automated library preparation for 10x Genomics assays, reducing hands-on time from over five hours to one hour at a throughput of 96 samples per day. Turnaround is four weeks from sample to data for standard projects and two weeks for sequencing-only services.

The business model is professional services revenue on a per-project quote basis following PhD-level scientific consultation, with multi-year contracts common. Marketing is consultative and content-driven rather than transactional, emphasizing the firm's "white-glove" positioning as a scientific thought partner. The company holds a central operational role in the IMI-funded PERSIST-SEQ consortium (with AstraZeneca, Oncode Institute, and others), targeting characterization of 5 million cancer cells over five years, and participates in the Health Holland-funded CLEAR COVID-19 consortium. Pricing is not publicly disclosed; revenue, valuation, and ownership structure beyond founders and a single €50,000 EFRO grant in 2025 are not publicly available.

Name

Single Cell Discoveries

Legal name

Single Cell Discoveries BV

Website

https://scdiscoveries.com

Company type

Private

Founded year

2018

Operating status

Operating

Headcount range

11–50 employees

Short description

Single Cell Discoveries is a Utrecht-based CRO providing end-to-end single-cell and spatial transcriptomics services to pharma, biotech, and academic clients using a technology-agnostic platform approach spanning 10x Genomics, Parse, Scale Bio, and proprietary methods.

Ownership category

akta.pro rank

Product category

Single-Cell Sequencing Contract Research Services

NAICS

Research and Development in Biotechnology (except Nanobiotechnology) (541714), Scientific Research and Development Services (5417)

SIC

Services-Commercial Physical & Biological Research (8731)

akta.pro primary industry

Single-Cell & Spatial Omics Services (HLAGANAC)

akta.pro secondary industries

Bioinformatics & Multi-omics Analysis Software (HLAGAJAD), Bioinformatics, Multi-Omics Data Analysis & Interpretation Services (HLAGANAI)

Keywords

• Single-cell sequencing
• Spatial transcriptomics
• Bulk RNA sequencing
• Contract research organization
• Multiomics services

Headquarters

HQ city

Utrecht

HQ country

Netherlands

HQ region

Europe

Offices2 records

Markets served

GTM type

B2B

Offering type

Services

Cost components

Personnel, Technology or R&D, Operations, Infrastructure, Supply Chain, Marketing or Sales

Revenue model

1. Single-Cell Sequencing Services: Contract research organization providing single-cell and spatial transcriptomics services on a project basis. Services include single-cell RNA sequencing, immune profiling, ATAC-seq, multiomics, plate-based methods (SORT-seq, VASA-seq), and high-throughput options via Parse Biosciences and Scale Biosciences platforms. Revenue generated through per-project pricing with consultation and custom assay development options.
2. Spatial Transcriptomics Services: 10x Genomics Visium HD spatial gene expression services enabling whole transcriptome analysis at single-cell resolution with continuous tissue coverage. Includes sample preparation, library construction, and data analysis.
3. Bulk RNA Sequencing: Low input, high-quality transcriptome data services including Total Bulk RNA sequencing leveraging Cel-seq2 barcoding. Both normal and low input options available.
4. Sequencing Service: Standalone sequencing service using Illumina NovaSeq X Plus. Fastest sequencing service in Europe delivering high-quality data in 2 weeks. Accepts ready-to-sequence libraries from clients.
5. Data Analysis Consulting: Custom data analysis services beyond standard exploratory analysis included with projects. Specialized bioinformatics support, custom pipelines, and integration with third-party tools like BioTuring BBrowserX.
6. Custom Assay Development: R&D team continuously customizes existing methods to fit unique experimental needs. Proprietary assay development for specific customer requirements.

Pricing tiers

Go-to-market motion1 record

Distribution channels3 records

Marketing channels6 records

Core offering

Single Cell Discoveries is a Contract Research Organization providing end-to-end single-cell and spatial transcriptomics services on a project basis. Offerings span single-cell RNA sequencing (using proprietary SORT-seq and VASA-seq, plus 10x Genomics, Parse Biosciences, and Scale Biosciences platforms), spatial transcriptomics (10x Genomics Visium HD), bulk RNA sequencing, and standalone Illumina NovaSeq X Plus sequencing. Every project includes exploratory data analysis with optional custom bioinformatics consulting.

Product overview

Single Cell Discoveries is a Contract Research Organization (CRO) offering a comprehensive portfolio of single-cell and bulk RNA sequencing services. The core offerings include multiple single-cell platforms (SORT-seq plate-based, VASA-seq full-length, 10x Genomics microfluidics, Parse Biosciences scalable, and Scale Biosciences high-throughput), spatial transcriptomics (Visium HD), and bulk RNA sequencing (including Discovery-seq/DRUG-seq for drug discovery). Data analysis is included with all services, with advanced custom bioinformatics available. The company positions itself as a technology-agnostic, scientist-led organization that helps researchers select the right workflow for their specific needs, delivering fully analyzed data within four weeks.

Differentiator

Problem solved

Functional benefit

Brands

• SORT-seq: Plate-based single-cell sequencing service compatible with many sample types and low cell input.
• VASA-seq
• Discovery-seq

Products and services

• Single-Cell Sequencing End-to-end single-cell RNA sequencing CRO service using plate-based SORT-seq, Parse Biosciences scalable workflows, and 10x Genomics microfluidics platforms for high-throughput single-cell analysis. Customers include pharma, biotech, and academic research groups needing expert-led experimental design through data analysis.
• SORT-seq Proprietary plate-based single-cell sequencing service compatible with many sample types and low cell input. Delivered as a CRO service to researchers needing flexible plate-based workflows.
• VASA-seq Proprietary full-length single-cell RNA sequencing service offering enhanced sensitivity for isoform and splice variant detection. Suitable for complex neural tissues and applications requiring complete transcript characterization. Developed by SCD's Fredrik Salmén.
• 10x Genomics Single-Cell Services Certified 10x Genomics service provider offering Single Cell Gene Expression, Single Cell Immune Profiling, Single Cell Gene Expression Flex, Single Cell ATAC-seq, and Epi Multiome workflows with annual recertification.
• Parse Biosciences Single-Cell Services Certified Parse Biosciences service offering Evercode Single Cell Whole Transcriptome solutions that scale to millions of cells for high-throughput single-cell analysis projects.
• Discovery-seq (DRUG-seq) Higher-sensitivity DRUG-seq alternative service providing high-throughput RNA sequencing for drug discovery applications. Enables rapid hit-finding to validation workflow in combination with single-cell sequencing and spatial transcriptomics.
• Bulk RNA Sequencing Low input, high-quality transcriptome data service using standard bulk or Total Bulk RNA sequencing with Cel-seq2 barcoding. Available in normal and low input options.
• Visium HD Spatial Transcriptomics Whole transcriptome spatial gene expression analysis at single-cell resolution with continuous tissue coverage using 10x Genomics Visium HD. Includes sample preparation, library construction, and data analysis.
• BioSkryb Genomics Multi-omic Sequencing Services ResolveDNA and ResolveOME multi-omic sequencing services for simultaneous measurement of genomic and transcriptomic information from single cells, delivered as the first European Certified Service Provider of BioSkryb Genomics.
• Sequencing Service (Illumina NovaSeq X Plus) Standalone sequencing service on Illumina NovaSeq X Plus, described as the fastest sequencing service in Europe delivering high-quality data in 2 weeks. Accepts ready-to-sequence libraries from clients with expert support and flexible data formats.
• Scale Biosciences High-Throughput Sequencing Solutions High-throughput, cost-effective single-cell sequencing using Scale Biosciences' QuantumScale chemistry with Single Cell Methylation kit and Single Cell CRISPR Guide Enrichment kit, with advanced multiplexing.
• Data Analysis Consulting Custom bioinformatics and data consulting services beyond the standard exploratory analysis included with all SCD projects. Includes integration with BioTuring BBrowserX for interactive visualization and ImmuneWatch DETECT for TCR epitope prediction from sequencing data.
• Custom Assay Development Bespoke assay development service where SCD's R&D team customizes existing methods and develops new assays to fit unique experimental requirements for individual customers.

Quantifiable outcome

• Processing capacity increased to 96 samples per day with automated library preparation
• +4 more outcomes

Named customers12 records

Segments4 records

Ideal customer profiles2 records

Technology focussed Yes

API detail

Has API

No

API docs

API detail

Core technology

AI maturity

App detail

Integration3 records

AI capability2 records

Feature5 records

Partnerships

Twelve partnerships are on record, tiered supporting, core and flagship.

• MLM Medical LabssupportingOthers · 29 May 2026Partnership to streamline sample shipping from the U.S. Domestic shipping address in Memphis, TN enables American clients to send samples more easily with greater reliability.
• Parse BiosciencescoreTechnology or Integration · 30 September 2025Parse Biosciences certified Single Cell Discoveries as a service provider, expanding global access to scalable, high-quality single cell analysis for researchers. SCD offers Parse Biosciences' Evercode Single Cell Whole Transcriptome solutions.
• ImmuneWatchcoreTechnology or Integration · 10 September 2025Partnership to expand TCR single-cell sequencing services by integrating ImmuneWatch's DETECT tool into data consulting services, enabling epitope prediction from TCR sequencing data. Combined with 10x Genomics 5' TCR Immune Profiling for seamless workflow.
• Beckman Coulter Life SciencescoreTechnology or Integration · 8 May 2025Collaboration since 2023 to automate single-cell gene expression workflows. SCD is the first laboratory trained by both 10x Genomics and Beckman Coulter for fully automated library preparation, enabling 96 samples/day throughput.
• BioSkryb GenomicscoreTechnology or Integration · 25 March 2025SCD became the first European Certified Service Provider of BioSkryb Genomics' multi-omic sequencing services, offering ResolveDNA and ResolveOME solutions for genomic analysis.
• Illumina (Genome-wide Perturb-Seq)supportingTechnology or Integration · 4 September 2024Partnership with Illumina to deliver genome-wide Perturb-Seq experiment using NovaSeq X Plus System, pushing boundaries of functional genomics research.
• IlluminacoreTechnology or Integration · 6 June 2023First delivery of Illumina NovaSeq X Plus in Benelux. Partnership enables 2.5x greater throughput and reduced sequencing costs. SCD featured in Illumina video highlighting impact on therapy research customers like VectorY.
• 10x GenomicscoreTechnology or Integration · 1 January 2023Collaboration since 2023 to automate single-cell gene expression workflows. SCD is 10x Genomics certified service provider for Single Cell Gene Expression, Single Cell Immune Profiling, and other 10x solutions.
• BioTuringsupportingTechnology or Integration · 19 January 2022Collaboration to improve single-cell sequencing research by integrating BioTuring's BBrowserX single-cell data analysis platform. SCD clients receive free access to BBrowserX for data visualization and interactive exploration.
• PERSIST-SEQ ConsortiumflagshipStrategic or Co-development Partner · 1 September 2021Five-year public-private partnership funded by IMI, led by Oncode Institute and AstraZeneca. SCD central role: single-cell library prep, sequencing, and pre-processing for all consortium samples. Goal: characterize 5 million cancer cells to understand drug resistance. Partners include Oncode Institute, Hubrecht Institute, Netherlands Cancer Institute, Wellcome Sanger Institute, and multiple pharma companies.
• Scale BiosciencescoreTechnology or IntegrationSCD is an endorsed provider for Scale Biosciences' Single-Cell RNA and CRISPR Guide Enrichment Kits, offering high-throughput, cost-effective sequencing with advanced multiplexing.
• CLEAR COVID-19 ConsortiumsupportingStrategic or Co-development PartnerPublic-private partnership funded by Health Holland. SCD contributes single-cell RNA sequencing expertise to assess viral replication and epithelial gene expression in nasal airway cell cultures for COVID-19 drug screening. Partners include UMCU, First Health Pharmaceuticals, QVQ Holding, and Vossensteyn Biomedical.

Scale indicators10 records

Recent moves8 records

Expansion highlights6 records

Others

• Cell Microsystems: Single-cell isolation and imaging tools provider enabling upstream sample prep workflows that feed into sequencing CROs like SCD. Adjacent ecosystem participant rather than direct competitor.
• Parse Biosciences: Single-cell technology platform vendor whose Evercode kits SCD is certified to run as a service provider. Both technology partner and indirect competitor as Parse expands its own service network.

Direct peers

• Novogene Corporation: Global genomics CRO offering single-cell sequencing, spatial transcriptomics, and bulk RNA services with significant European operations. Most direct large-scale peer to SCD's core service model.
• GENEWIZ (Azenta Life Sciences): Genomics services CRO acquired by Azenta, offering single-cell, next-gen sequencing, and synthesis services to pharma and academic customers globally. Competes for the same enterprise scRNA-seq and spatial transcriptomics projects.
• CD Genomics: Genomics CRO offering single-cell sequencing, scATAC-seq, spatial transcriptomics, and bulk RNA services. Mid-sized peer with comparable service catalog and customer base.

Broad incumbents

• BGI Group: World's largest sequencing services provider with full-stack single-cell and spatial omics offerings. Much larger and broader than SCD, but directly competes on cost-sensitive single-cell projects.
• Eurofins Genomics: Diversified European life sciences testing and genomics services business with single-cell and RNA sequencing offerings. Larger and broader portfolio, overlapping on pharma/biotech CRO work.
• Standard BioTools (formerly Fluidigm): Established single-cell platform vendor (mass cytometry, microfluidics) with services arms. Larger, broader incumbent with overlapping customer base in pharma/biotech translational research.

Emerging players

• Active Motif: Epigenetics-focused services and reagent provider offering single-cell ATAC-seq and multiomics services. Comparable in size and customer type, with overlapping applications in immunology and oncology.
• MedGenome: Genomics CRO with single-cell capabilities, particularly strong in immunology and oncology research services. Comparable service catalog with focus on translational research customers.

Market position

Strengths1 record

Weaknesses1 record

Competitive moat5 records

Key risks7 records

Key highlights7 records

Customer concentration

• Xx.com/scDiscoveries
• LinkedInlinkedin.com/company/single-cell-discoveries
• Facebookfacebook.com/singlecelldiscoveries

Compliance4 records

Revenue estimate

Valuation estimate

Number of profiles

Profiles10 records

Funding overview

Funding rounds

Investors

Funding detail is available on the Subscription and Enterprise plan.Contact sales →

M&A

Investments

M&A and investment is available on the Subscription and Enterprise plan.Contact sales →

Frequently asked questions about Single Cell Discoveries