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Single Cell Genomics

Single-cell sequencing technologies provide insight into cellular processes at an unprecedented level of detail. They overcome the shortcomings of traditional bulk sequencing and enable the identification of individual cell types and dynamic states. The Máxima Single-Cell Genomics facility makes these technologies available to study pediatric tumors.

Purpose for research

Cancer cells do not exist in isolation but are embedded within a network of healthy 'neighbors'. Blood vessels and stromal cells can support the disease via efficient nutrient delivery and cell-cell communication while immune cells can target malignant cells for destruction. Diseased cells also signal to their surrounding cells to promote cancer cell survival. Cancer cell heterogeneity makes some cells better able to survive under stressful conditions, such as nutrient deprivation, immune attack, or exposure to chemotherapy. Similarly, immune cells can either be ready to fight the disease or exhausted. Traditional bulk RNA-seq blends all these complex signals into an average that obscures the heterogeneity and interplay between cells.

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Recent technological advances have made it possible to use single-cell sequencing to measure the activity of thousands of individual cells in parallel. This enables the investigation of several unexplored aspects of cancer biology such as tumor heterogeneity and clonality, niche-cancer crosstalk, and in-depth characterization of the immune microenvironment. Additionally, multiple modalities can be measured in parallel with RNA, such as open chromatin, cell surface markers, and VDJ rearrangements. All these possibilities lead to new insights into cancer biology, tumor composition, and treatment.

Services and support

The Single-Cell Genomics facility makes single-cell technologies available to researchers of the Princess Máxima Center. 10x Genomics is used as the main platform to assist researchers in acquiring high-quality data to study pediatric cancer.

The facility provides support for single-cell data generation, including:

  • Advice on experimental design, choosing the appropriate technique and optimizing sample preparation.

  • Preparation of libraries and sequencing.

  • Analysis-ready processed data, including quality control reports.

  • Expertise on single-cell data analysis and interpretation.

Equipment

Currently, the facility is equipped with the following instruments:

  • 10x Genomics Chromium X - Advanced microfluidics system to perform single cell partitioning and barcoding for single-cell RNA-seq and multiomics

  • Mission Bio Tapestri platform - Advanced microfluidics system capable of providing single-cell targeted DNA-seq and allowing simultaneous detection of analytes incl. SNVs, CNVs and proteins.

  • SPTLabtech Mosquito Genomics nanodispenser - Precise multi-channel positive displacement pipetting from 25 nL to 1.2 μL into plates.

  • Perkin Elmer LabChip GX Touch HT nucleic acid analyzer -  High-resolution DNA and RNA quantification and sizing using automated capillary electrophoresis separation.

  • CellDrop fluorescent cell counter - Precise cell counter based on fluorescence to count both live and dead cells

“Single-cell sequencing technologies provide insight into cellular processes at an unprecedented level of detail”

Thanasis Margaritis

Team leader

Thanasis Margaritis is a single-cell biologist leading the Single-Cell Genomics facility that provides state-of-the-art single-cell technology support to over 70 researchers within the Princess Máxima Center. Margaritis has more than twenty years' experience in functional genomics, including seven years of single-cell technology experience. This expertise benefits the research efforts of the Princess Maxima Center in better understanding pediatric cancer and identifying treatment approaches. Margaritis obtained a Bachelors in Pharmacy, a Master’s in Molecular Biology and Biotechnology and a PhD degree in Gene Expression and Transcriptional Regulation. He is a member of the single cell network Netherlands (scNL) management team.

Network

The facility is part of the single cell network Netherlands (scNL). This network aims to bring together researchers interested in single-cell experimental and computational methods, as well as in their application to tackle biological and clinical questions. 

This facility is made financially possible by donations of KiKA.

Key publications

Team

Contact Single cell genomics faciliteit

scgenomics@prinsesmaximacentrum.nl