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COLLABORATIONS AND CONSORTIA
Partnerships play a dual role in our operations. In alignment with our vision, we work on projects that help adapt single-cell applications to diagnostic and therapeutic purposes. Meanwhile, we access resources and experience that fuel our own evolution.
Our services
We currently offer single-cell, spatial and bulk transcriptomics.
Our R&D team is actively testing new single-cell multi-omic technologies and spatial
modalities to offer additional insight into our clients' biological questions.
Single-cell sequencing
SORT-Seq
Single-cell transcriptomics method utilizing 384-well plates, ideal for low cell counts, FACS sorted populations, and pilot projects. Developed by our founder, exclusively offered by us.
VASA-Seq
Single-cell RNA sequencing method for full- length and total RNA, ideal for analyzing non- coding RNA and complete transcriptomes. Developed by one of our team members, exclusively offered by us.
Spatial transciptomics
Pooled cells
Bulk RNA Sequencing
Comprehensive transcriptome analysis of pooled cell populations, ideal for limited starting material and large projects requiring cell population data.
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
- 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.
Data Analysis
- 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.
Applications
Cell Type Identification
Identify novel or rare cell types by analyzing gene expression profiles of individual cells and grouping them based on similarities in their transcriptional signatures.
Drug Discovery
By identifying differentially expressed genes in specific cell types, disease states, and responders/non-responders, single cell sequencing can accelerate target and biomarker discovery.
Immune Profiling
High-resolution immune profiling provides insight into functional states of immune cells in response to antigenic stimulation and treatment; BCR and TCR repetoire sequencing can provide starting points for immuno-oncology therapeutic development of monoclonal antibodies or cell therapies.
Research areas
Oncology
Revolutionize cancer research and discover new treatments by measuring the heterogeneity of the tumor microenvironment and probing the molecular mechanisms underlying cancer development and disease progression.
Immunology
Unlock new insights into the mechanisms underlying immune system function, response to stimuli, and involvement in immuno-oncology treatments.
Developmental Biology
Unravel developmental processes to discover molecular mechanisms behind development, genetic diseases, and regeneration.
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Get the Ultimate Guide
Our ultimate guide is a crash-course in single-cell sequencing and will get you up to speed with how it was developed and how you can use it to level up your research.
Why choose SCD?
We are single-cell sequencing experts
We are 100% focused on single-cell and spatial transcriptomics, enabling us to take on both large-scale projects and create customized solutions for each client project.
Our experience is unmatched in the field
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.
We help you stay ahead of the curve
We are committed to continuously integrating leading-edge technologies into our service offerings to ensure clients have access to the latest advancements. Our R&D department works to both internalize the best commercial platforms and advance our own single-cell innovations.
We work with you 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.
"The service of Single Cell Discoveries guarantees a smooth process between customer and company. In case of problems or questions, the scientists reacted competently and immediately, so that answers could be found quickly and flexibly.."
"The service of Single Cell Discoveries guarantees a smooth process between customer and company. In case of problems or questions, the scientists reacted competently and immediately, so that answers could be found quickly and flexibly.."
"Fantastic job made by a really professional and friendly team. I strongly recommend Single Cell Discoveries for sequencing services."
"The service of Single Cell Discoveries guarantees a smooth process between customer and company. In case of problems or questions, the scientists reacted competently and immediately, so that answers could be found quickly and flexibly.."
"Fantastic job made by a really professional and friendly team. I strongly recommend Single Cell Discoveries for sequencing services."
"Donec id lacus ipsum. Integer facilisis nunc quis tellus fermentum malesuada. Nam tristique id ipsum vitae lobortis. Interdum et malesuada fames ac ante ipsum primis in faucibus."
Interested? Connect with
our scientists to get started
History
Ever a sole focus on single-cell science
What is now an industry-leading single-cell laboratory was once nothing more than a bold idea.
Single Cell Discoveries co-founder Mauro Muraro, PhD, started working on some of the earliest single-cell technologies in the Van Oudenaarden lab at the Hubrecht Institute. Back then, single cells were moved by mouth pipette. The procedure was so laborious and the empty pipette boxes so numerous that Mauro committed himself to develop a higher-throughput, standardized protocol. Recruiting several robots, Mauro was able to replace manual mouth pipetting with mechanized liquid handling and accomplish in an afternoon what used to take a year. This protocol was published in 2016 as SORT-seq.
From then on, The Hubrecht Institute established the Single Cell Core Facility, one of the first of its kind in the world. Co-founder Judith Vivié was recruited to run the facility, and demand
exploded. In 2018, after one of many long weeks serving clients through the core facility, Mauro and Judith decided they could best meet the growing demand for single-cell sequencing services through an independent company. Five years later, quality service, intelligent automation, bleeding-edge technology, and hard work are still central to Single Cell Discoveries' expanding operations. Each member of the growing team is committed to advancing single-cell sequencing and empowering clients with impactful single-cell discoveries with the ultimate goal of improving the human condition.
Case studies
Immune Profiling of atherosclerosis reveals new therapeutic potential
A team of scientists uses 10x Genomics Single Cell Immune Profiling to characterize T cells in the atherosclerotic plaque. Their results redefine atherosclerosis as an autoimmune disease.
Mechanism of disease: a new hypothesis for atherosclerosis
To elucidate atherosclerosis’ mechanism of disease, Sheffield University researchers analyzed the transcriptomes of single endothelial cells.
Drug Discovery
for Precancerous Liver Disease
Here’s the story of how SORT-seq helped advance a novel drug candidate for liver cancer into clinical trials.
Our articles
10x Chromium: how does it work and what are its features?
10x Chromium is a machine, or platform, that researchers use for high-throughput single-cell RNA sequencing (scRNA-seq). It enables the analysis of gene expression profiles at single-cell resolution. Also, it can…
Biotech podcast The Single-Cell World speaks with our CEO
Our CEO and co-founder, Mauro Muraro, PhD, is the most recent guest in the biotech podcast The Single-Cell World. In the 40-minute conversation, he speaks to host Cátia Moutinho, PhD,…
What is CellRanger and How Do You Use It?
To unravel single-cell RNA sequencing data, scientists can use Cell Ranger, a tool developed by 10x Genomics that combines with most 10x Genomics services. The CellRanger software empowers researchers to…
Company news & Announcements
We have moved to our new location!
We are excited to announce that Single Cell Discoveries has moved to a new location. We have found a more spacious and modern space that will enable us to better…
Single Cell Discoveries receives first Illumina NovaSeq X Plus in the Benelux — Press Release
UTRECHT, June 6, 2023 – Single Cell Discoveries, a Contract Research Organization (CRO) dedicated to single-cell sequencing, is proud to announce the first delivery of the new Illumina NovaSeq X…
Recent publications
Blood
Neutral sphingomyelinase blockade enhances hematopoietic stem cell fitness through an integrated stress response
Clinical & Experimental Immunology
Compartment-driven imprinting of intestinal CD4 T cells in inflammatory bowel disease and homeostasis
Nature Communications
Development of Plasmodium falciparum liver-stages in hepatocytes derived from human fetal liver organoid cultures
Step 1
Consultation
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
Sample Preparation
SORT-seq is a plate-based method. There are two options here. Either you order your SORT-seq plates with us, sort your samples into the plates, and ship them back to us. Or send us your samples and we'll do the sorting for you.
Deliverables
As with all of our services, we provide ongoing support from our single-cell sequencing specialists. For each SORT-seq project, we provide the following:
- Regular updates during processing, including QC reports.
- Raw sequencing data (FASTQ files)
- Raw and filtered gene count tables
- An interactive preliminary analysis report including QC, clustering and differential gene expression analysis
- A Seurat object to do your own analysis with the Seurat pipeline
- A brief explanation from our data team about the quality of your data
FAQ
We advise two plates for each sample or condition. This ensures a technical backup plate is always available in case something goes wrong with shipment or processing.
Content
Content
Our R&D experts
Dylan Mooijman, PhD
HEAD OF R&D
The master chef in our R&D kitchen, Dylan Mooijman oversees improvements to current services and innovation on new methods. He is motivated by pioneering single-cell sequencing technology. Before taking the helm of our R&D unit, Dylan earned a HFSP fellowship to work at EMBL Heidelberg (Ephrussi lab) and a PhD degree at the Van Oudenaarden lab.
Darina Šikrová, PhD
R&D SCIENTIST
Darina Šikrová is focused on optimizing our technologies. She is motivated by solving "impossible problems" and her capabilities earned her a PhD on rare genetic causes and gene therapy for muscular dystrophy disease FSHD.
Our experts
Dylan Mooijman
HEAD OF R&D
The master chef in our R&D kitchen, Dylan Mooijman oversees improvements to current services and innovation on new methods. He is motivated by pioneering single-cell sequencing technology. Before taking the helm of our R&D unit, Dylan earned a HFSP fellowship to work at EMBL Heidelberg (Ephrussi lab) and a PhD degree at the Van Oudenaarden lab.
Darina Šikrová
R&D SCIENTIST
Darina Šikrová is focused on optimizing our technologies. She is motivated by solving "impossible problems" and her capabilities earned her a PhD on rare genetic causes and gene therapy for muscular dystrophy disease FSHD.
Dylan Mooijman
HEAD OF R&D
The master chef in our R&D kitchen, Dylan Mooijman oversees improvements to current services and innovation on new methods. He is motivated by pioneering single-cell sequencing technology. Before taking the helm of our R&D unit, Dylan earned a HFSP fellowship to work at EMBL Heidelberg (Ephrussi lab) and a PhD degree at the Van Oudenaarden lab.
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Buying guide
Which technology is suitable for my project?
Use the buying guide to receive instant advice on what technology is a good candidate for your project.
How can we help?
Want to supercharge your project with SORT-seq insights?
Connect with our PhD-level scientists to discuss your biological question, timeline, sample types, and other customizations for your SORT-seq analysis.
How can we help?
Want to supercharge your project with single-cell insights?
Connect with our PhD-level scientists to discuss your biological question, timeline, sample types, and other customizations for your single-cell analysis.
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Classes (you can add these classes to widgets and rows):
- slim < makes the widget or row content slimmer
- slim-r < makes the widget or row content slightly slimmer to right
- slim-l < makes the widget or row content slightly slimmer to left
- slimmer < makes the widget or row content slightly slimmer
- intro < makes the normal text slightly larger
- line-top < gives the widget a gradient line at the top
Primary menu classes (not for mobile menu):
- mega < makes the parent menu item compatible for mega menu classes
- kol-x2 < makes the head submenu items 2 columns
- stack < makes the submenu items visible below their parent item without needing to hover
- title < gives the menu item alternative title styling
- grey < makes the menu item background a tint colour
- arrow < adds an arrow button behind the menu name
To add more space to your row use the dropdowns "Margin bottom" and "Padding inside" when editing a row.
To make text a light colour check "Text light" on when editing a row.
Buttons:
Buttons light:
You can add the following css classes to the "dark back" row:
- corners < adds rounded corners top-right and bottom-left
- corners-inv < adds rounded corners top-left and bottom-right
- corner-tl < adds rounded cornertop-left
- corner-br < adds rounded corner bottom-right
- pt-xl < adds padding to the top of the back
You can also drop the Gradient back section inside the layout builder of the dark back layout builder.
You should switch the checkbox "Light text" on if you want the text to be white.
You can add the following css classes to the "gradient back" row:
- corners < adds rounded corners top-right and bottom-left
- corners-inv < adds rounded corners top-left and bottom-right
- corner-tl < adds rounded cornertop-left
- corner-br < adds rounded corner bottom-right
- pt-xl < adds padding to the top of the back
You can also drop the Dark back section inside the layout builder of the gradient back layout builder.
You can add the following css classes to the "dark back" row:
- corners < adds rounded corners top-right and bottom-left
- corners-inv < adds rounded corners top-left and bottom-right
- corner-tl < adds rounded cornertop-left
- corner-br < adds rounded corner bottom-right
- pt-xl < adds padding to the top of the back
You should switch the checkbox "Light text" on if you want the text to be white.
You can add the following css classes to the "gradient back" row:
- corners < adds rounded corners top-right and bottom-left
- corners-inv < adds rounded corners top-left and bottom-right
- corner-tl < adds rounded cornertop-left
- corner-br < adds rounded corner bottom-right
- pt-xl < adds padding to the top of the back
How can we help?
Want to supercharge your project with single-cell insights?
Connect with our PhD-level scientists to discuss your biological question, timeline, sample types, and other customizations for your single-cell analysis.