What we offer
Technologies
We facilitate both single-cell and single-nucleus RNA and DNA sequencing using three platforms. SORTseq is a technique for performing gene expression profiling of single cells that are FACS-sorted into 384-well plates. Mission Bio Tapestri offers single-cell DNA sequencing, allowing the identification of SNVs, indels, CNVs and other structural variants in individual cells. Lastly, the 10x Genomics platform allows a variety of single-cell quantification strategies:
- 3'- or 5’-end Gene Expression
- Multiome: simultaneous gene expression and chromatin-accessibility per cell
- Feature Barcoding: simultaneous gene expression and cell surface protein quantification
- Cellplex: multiplexed gene expression, in which samples are pooled for higher throughput and reduced cost
- V(D)J sequencing: simultaneous gene expression and T- and B-cell receptor sequencing
- Visium: spatial transcriptomics, measuring the local gene expression in microscopic images
Services
The Single Cell Genomics facility makes single cell technologies available to researchers of the Princess Máxima Center. After an intake meeting where goals, feasibility and mutual expectations are discussed, we can provide:
- Expertise, including advice on experimental design, planning and trouble shooting
- Library preparation
- Sequencing
- Analysis and biological interpretation
- Data management, including backup, live progress overviews, quality reports and downstream analyses
- Sample multiplexing
Training
We train researchers on the required experimental procedures and equipment. We organize courses for bioinformaticians interested in analyzing their own data, both internally and abroad within the European network ELIXIR.
Computing
All data and metadata are collected and managed in comprehensive sample and library tracking database that allows us to adhere to the FAIR principles. We are involved in developing computational tools (Candelli et al. 2018; de Kanter et al. 2019) and make extensive use of high performance computing facilities at the UBC computer cluster and cloud providers, using both traditional and virtualized environments.Video
Watch facility video: https://youtu.be/EkOLDbyXIgQ
Our equipment:
- 10x Genomics Chromium Controller
- Missio Bio Tapestri platform
- SPTLabtech 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
Personnel
Facility manager Thanasis Margaritis
Bioinformaticians Philip Lijnzaad
Tito Candelli
Lindy Visser
Wet lab Aleksandra Balwierz
Interested?
