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Single Cell Genomics

The Máxima Single Cell Genomics Facility is a KiKa-funded research infrastructure dedicated to making single cell mRNA sequencing technology available to study pediatric tumors.


We provide access to two scRNA-seq platforms:

  • SORT-Seq: involves FACS sorting of cells into 384-well plates that are processed into sequencing libraries.
  • 10xGenomics Chromium Single Cell Controller: the leading microfluidics platform. Higher cell throughput per experiment, but less flexible.


Results of the facility have shown that the two platforms have their own strengths. Their output can be combined and complement each other.


The facility is actively involved in developing computational tools:

  • Ameba, a database for storing single cell experiment information and facilitating pipeline deployment in computer clusters.
  • Sharq (Candelli et al. bioRxiv 2018), a data-processing and analysis pipeline, maintained and developed by the facility. It runs on the Utrecht High Performance Computing (HPC) environment, processing and mapping reads, as well as performing general and cell-specific quality-control.
  • CHETAH (de Kanter et al. NAR 2019), an accurate cell type identification method that uses single-cell RNAseq reference data to classify cells in a hierarchical fashion. Including collaborating in analyzing scRNA-seq results.


Knowledge Transfer

Facility members educate researchers on the various equipment and bioinformaticians interested in analyzing their own single cell genomics data, both internally and abroad within the European network ELIXIR.


Internal previous teaching material, recommended webinars and documentation on our technical procedures and pipelines is maintained at our wiki:

Watch facility video: https://youtu.be/EkOLDbyXIgQ
Our equipment:
  • 10x Genomics Chromium Controller
  • TTPLabtech Mosquito Genomics nanodispenser, 5-position, humidity-controlled deck
  • PCRmax Alpha4 Thermal Cycler
  • Dedicated UV HEPA PCR workstations for RNA and DNA work
  • Bio-Rad T100 Thermal Cycler
  • Bio-Rad C1000 Touch Thermal Cycler
  • Tecan D300e nanodispenser (shared with drug screening)
  • ThermoFisher Multidrop Combi dispenser (shared with drug screening)
  • Agilent Bioanalyzer
  • Perkin Elmer LabChip GX Touch HT nucleic acid analyzer



Facility manager         Thanasis Margaritis

Bioinformaticians        Philip Lijnzaad
                                       Tito Candelli
                                       Lindy Visser

Wet lab                        Eduard Bodewes




Key publications


Kildisiute G,  Kholosy WM,  Young MD, Roberts K,  Elmentaite R,  van Hooff SR, Pacyna CN, Khabirova E, Piapi A, Thevanesan C,  Bugallo Blanco E, Burke C, Mamanova L,  Keller KM,  Langenberg-Ververgaert KPS, Lijnzaad P, Margaritis T,  Holstege FCP,  Tas ML, Wijnen HWA,  van Noesel MM, del Valle I,  Barone G,  van der Linden R,  Duncan C, John Anderson,  Achermann JC, Haniffa M,  Teichmann SA, Rampling D,   Sebire NJ,  He X, de Krijger RR,  Barker, RA  Meyer KB,  Bayraktar O,  Straathof K, Molenaar JJ, Behjati S. Tumor to normal single cell mRNA comparisons reveal a pan-neuroblastoma cancer cell. (2020) BioRxiv. doi: https://doi.org/10.1101/2020.06.22.164301

Young MD, Mitchell TJ, Custers L, Margaritis T, Morales F, Kwakwa K, Khabirova E, Kildisiute G, Oliver TRW, de Krijger RR, van den Heuvel-Eibrink MM, Comitani F, Piapi A, Bugallo-Blanco E, Thevanesan C, Burke C, Prigmore E, Ambridge K, Roberts K, Vieira Braga FA, Coorens THH, Del Valle I, Wilbrey-Clark A, Mamanova L, Stewart GD, Gnanapragasam VJ, Rampling D, Sebire N, Coleman N, Hook L, Warren A, Haniffa M, Kool M, Pfister SM, Achermann JC, He X, Barker RA, Shlien A, Bayraktar OA, Teichmann S, Holstege FC, Meyer KB, Drost J, Straathof K, Behjati S. Single cell derived mRNA signals across human kidney tumors. (2020) BioRxiv. doi: https://doi.org/10.1101/2020.03.19.998815

Calandrini C, Schutgens F, Oka R, Margaritis T, Candelli T, Mathijsen L, Ammerlaan C, van Ineveld RL, Derakhshan S, de Haan S, Dolman E, Lijnzaad P, Custers L, Begthel H, Kerstens HHD, Visser LL, Rookmaaker M, Verhaar M, Tytgat GAM, Kemmeren P, de Krijger RR, Al-Saadi R, Pritchard-Jones K, Kool M, Rios AC, van den Heuvel-Eibrink MM, Molenaar JJ, van Boxtel R, Holstege FCP, Clevers H, Drost J. An organoid biobank for childhood kidney cancers that captures disease and tissue heterogeneity. (2020) Nature Communications, 11;11(1):1310. PMID: 32161258


de Kanter JK, Lijnzaad P, Candelli T, Margaritis T, Holstege FCP. CHETAH: a selective, hierarchical cell type identification method for single-cell RNA sequencing. (2019) Nucleic Acids Research, 47(16):e95. PMID: 31226206

Schutgens F, Rookmaaker MB, Margaritis T, Rios A, Ammerlaan C, Jansen J, Gijzen L, Vormann M, Vonk A, Viveen M, Yengej FY, Derakhshan S, de Winter-de Groot KM, Artegiani B, van Boxtel R, Cuppen E, Hendrickx APA, van den Heuvel-Eibrink MM, Heitzer E, Lanz H, Beekman J, Murk JL, Masereeuw R, Holstege F, Drost J, Verhaar MC, Clevers H. Tubuloids derived from human adult kidney and urine for personalized disease modeling. (2019) Nature Biotechnology, 37(3):303-313. PMID: 30833775


Candelli T, Lijnzaad P, Muraro MJ, van Oudenaarden A, Margaritis T, Holstege F. Sharq, a Versatile Preprocessing and QC Pipeline for Single Cell RNA-Seq. (2018) BioRxiv. doi: https://doi.org/10.1101/250811