SickKids Centre for Advanced Single Cell Analysis (CASCA)

CASCA provides fee-for-service access to innovative "next generation" mass cytometry and scRNA-Seq technologies for performing high content single cell analysis to advance fundamental discovery projects as well as “Precision Medicine” research initiatives. Our technology platforms and services are briefly described below.



Facility Access

  • Proof of COVID-19 Vaccination is Mandatory. External clients need to go through COVID-19 screening.
  • Elevator occupancy will be limited to 6 people
  • Please avoid high traffic times
  • Allow extra time to enter PGCRL and reach the 18th floor
  • Masking is mandatory in all areas of PGCRL. Mask will be provided to external clients at the COVID-19 screening station. 


  • CASCA operates in a Containment Level 2 (CL2) laboratory and can handle samples designated as RG1 or RG2. No samples or agents designated as RG3 and RG4 can be brought into the lab
    • Samples transported into the CASCA must be in sealed primary containers (FACS tubes, screw cap tubes, etc.). In addition, sealed primary containers must be in a sealed secondary leak proof container.
    • To minimize contact, we will implement a “no-contact” and paperless sample drop-off system
      • Use iLAB to provide all experiment information
      • Leave your samples on drop-off table (in ice box) just inside the Facility
  • All Persons must wear gown and gloves (provided by CASCA) to be donned on entry into the lab and discarded on exit.



Hyperion Imaging Mass Cytometry (IMC) 

With this innovative technology you can deeply interrogate tissues and tumors at subcellular (1 mm) resolution to define cell phenotypes, cell-cell interactions and spatial proximity within normal and diseased microenvironments.

  • Highly multiplexed immunohistochemistry analysis of tissue sections stained with metal-tagged antibodies
  • Combines a laser ablation module with the high parameter capabilities of mass cytometry (CyTOF)
  • Simultaneous analysis of up to 37 markers in a single scan
  • For more information about IMC and related regents, please visit Fluidigm  

To book a consultation or appointment please see "Request Services" tab and contact Jyh Yun Chwee 


BD Rhapsody Single Cell RNA-Sequencing & Protein "Multi-omics" Analysis Service

Download our Rhapsody service options and pricing or answers to Frequently Asked Questions

  • This microwell-based system provides the ability to simultaneously quantify RNA and surface proteins in up to 40,000 single cells in a single experiment
    • Single cells are gently deposited into wells without causing any stress on the cells
    • Each well is then matched with a BD Rhapsody™ bead that captures the mRNA and oligos from BD AbSeq reagents that were used to pre-label cell surface proteins
    • After cell separation the mRNA and BD™ Ab-Seq Oligos captured from each cell are ready for cDNA synthesis and preparation of indexed Illumina libraries
    • A unique barcode on each bead allows each captured molecule to be matched to its respective cell
    • This system provides automated cell counting, viability measurements and cell capture rates to provide quality control information prior to library preparation and sequencing
  • The BD™ Single-Cell Multiplexing Kit provides the ability to combine hematopoietic cells from 2-12 different samples in one experiment to:
    • Reduce batch effects by simultaneously running multiple controls and experimental samples at the same time
    • Substantially reduce the per sample cost
    • Improve detection and elimination of multiplets from the data
  • Use oligo-conjugated antibodies (BD™ AbSeq reagents) to provide protein expression data similar to flow cytometry
    • Cells can be pre-labelled with up to 40 Ab-Seq reagents to provide deep phenotyping of each cell sequenced
  • With BD™ Rhapsody you can choose between whole transcriptome analysis (WTA) and gene-targeted assays:
    • WTA surveys the entire transcriptome at low sensitivity, requiring high read-depths which increase sequencing costs
    • Immune gene-targeted assays use a panel of specific primer sets to amplify~400 immune genes at high sensitivity with lower sequencing costs
    • You can also purchase custom gene-targeted primers to supplement BD gene panels, or work with BD bioinformaticians to design a custom gene panel

 Download this BD Rhapsody Single-Cell Multiomics System Overview or contact Jyh Yun Chwee for more information


Mass Cytometry (CyTOF) Services 

  • Time-of-flight (TOF) mass spectrometer-coupled flow cytometers (known as CyTOFs) are used to analyze single cells stained with antibodies (Abs) or other cellular probes labeled with rare earth metals
  • CyTOF can analyze single cells stained with up to up to 50 metal-tagged probes of cell lineage, differentiation and function
  • Thus, CyTOF overcomes limitations of fluorescence flow cytometry to allow unprecedented depth for profiling single cells within heterogeneous populations from mouse models or patients
  • CASCA now operates 3 Helios instruments, which are 3rd generation CyTOFs
  • We provide biomedical researchers with scientific, technical and bioinformatics support to develop CyTOF applications for both fundamental, translational and pre-clinical research projects

     To learn more about our Mass Cytometry services, please contact Tina Chen


Using iLab to Access CASCA Services

  • First register for an iLab account by clicking HERE
  • Within one business day you will receive a password and further instructions
  • Please note that iLab functionalities work best with Chrome and Firefox
  • Please contact John Moniakis for help with iLab


Use the Request Services tab to:

  • Schedule a free Consultation for a general introduction to our CyTOF or Rhapsody services
  • Request BD Rhapsody services
  • Request Hyperion IMC services
  • Request Training to perform surface and intracellular staining of cells with metal-tagged antibodies
  • Obtain quotations for us to perform a pilot experiment so you can see the advantages of using CyTOF for high content single cell analysis 
  • Request Helios appointments to analyze your cells stained with metal-tagged Abs
  • Requests Consultations, Data Analysis, custom metal-tagging of antibodies, consumables purchases and other services


Use the Schedule Equipment tab to:

  • Book appointments on the Helios calendars
  • Note that this option is only available to experienced clients



Location and Hours of Operation

Hours Open / Hours Staffed Location

9AM- 5PM


Lab Room 18-9430
Peter Gilgan Centre for Research and Learning (PGCRL)
The Hospital for Sick Children
686 Bay Street Toronto, ON M5G 0A4