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Single Cell Genomics

The ability to interrogate the mRNA content of individual cells is transformative for the Life Sciences. This is especially true for cancer research. Tumor cell heterogeneity and tumor niche/microenvironment play pivotal roles in tumor development and treatment response. The composition of both are poorly understood as yet. Part of the Holstege group is dedicated to making single cell mRNA sequencing technology available to the Princess Máxima Center research groups.
What we offer: 

Single cell mRNA sequencing technology is developing rapidly, with different types of solutions coming and going very quickly, sometimes filling complementary niches. Our standard platform is a modification of the SORT-Seq protocol (Muraro 2016), initially developed by the Yanai lab (CEL-Seq2: Hashimshony 2016) and further improved by us in collaboration with the group of Alexander van Oudenaarden. This platform involves FACS sorting of cells into 384-well plates pre-filled with well-specific oligonucleotide barcodes that incorporate unique molecular identifiers for individual transcripts (UMIs). These plates are then further processed in multiple steps using ERCC control RNAs and empty wells to evaluate reaction success and contamination, respectively. The resulting sequencing-ready library is tested and if successful can be sent off for sequencing. A standard data-processing and analysis pipeline is maintained by us. It runs on the local High Performance Computing (HPC) environment and takes care of processing and mapping reads, as well as performing general and cell-specific quality-control.

Besides the platform sketched above, there are also other platforms possible (eg Fluidigm, 10x Genomics), either directly through us or through other facilities on campus.

Our equipment:
  • TTPLabtech Mosquito Genomics nanodispenser, 5-position, humidity-controlled deck
  • PCRmax Alpha4 Thermal Cycler
  • UV HEPA PCR workstation
  • Tecan D300e nanodispenser (shared with drug screening)
  • ThermoFisher Multidrop Combi dispenser (shared with drug screening)


Contact Thanasis Margaritis
Email: A.Margaritis-2@prinsesmaximacentrum.nl