Network Biology Collaborative Centre (NBCC)

Sinai Health System, Toronto, Ontario
What the facility does

Integrated services in functional genomics and proteomics: high-throughput screening, mass spectrometry, high-content to high-resolution imaging and next-gen sequencing

Area(s) of Expertise

The Network Biology Collaborative Centre (NBCC) operates through complementary nodes. The proteomics node specializes in functional analysis, particularly protein-protein interactions, where validated experimental approaches are combined with a robust computational platform. The high-throughput screening (HTS) node incorporates automated robotics and sample management enabling physical and functional interrogation of mammalian systems by applying extensive collections of cDNA, RNA interference and small molecule libraries. A complementary suite of high-content, automated imaging and high spatial-temporal resolution instruments permits various screening modalities. The next-gen sequencing node specializes in transcriptomics and CRISPR pooled screening support. The NBCC provides not only its extensive expertise in the design and application of sophisticated screening strategies, but also its ability to integrate these screens to drive biological insights. Customers often enter the NBCC through one node, e.g. HTS that identifies genes with interesting phenotypes, then move to imaging to obtain detailed phenotypical readouts and proteomics to identify interaction partners; this enables rapid transition from target identification to functional insight; a unique strength of the NBCC.

Research Services
  • Proteomics: identification and quantification of proteins, interaction partners, post-translational modifications by mass spectrometry;
  • High-throughput screening: design, validation and execution of screening strategies for cell-free and cell-based assays;
  • High-content screening: high-speed automated imaging of multi-well plates and slides at low or high resolution;
  • High-resolution imaging: live or fixed cell imaging at high- or super-high resolution;
  • Next-gen sequencing: broad range of DNA or RNA-based applications. 
  • Integrated data analysis available within and across screening nodes.
Sectors of Application
  • Life sciences, pharmaceuticals and medical equipment

Name of specialized facility

Name of equipment in use

Description of function

Proteomics

Thermo Scientific Orbitrap Fusion Lumos Mass Spectrometer with electron transfer dissociation (ETD) and Eksigent 425 nano-High Performance Liquid Chromatography (HPLC)

For low-abundance samples, post-translational modifications, sample multiplexing (tandem mass tag (TMT)-labeled) & targeted assays.

 

Three (3) SCIEX TripleTOF 6600 Mass Spectrometers each with an Eksigent 425 nano-HPLC

Identification and quantitation of proteins from complex mixtures using global (data-independent acquisition (DIA)/ sequential window acquisition of all theoretical spectra (SWATH)) or targeted approaches (multiple reaction monitoring-high resolution (MRM-HR)).

 

SCIEX TripleTOF 5600 Mass Spectrometer with an Eksigent Ultra nano-HPLC

Identification and quantitation of proteins from complex mixtures using global (DIA/SWATH) or targeted approaches (MRM-HR).

 

Thermo Scientific Orbitrap Elite Mass Spectrometer with an Eksigent Ultra nano-HPLC

Identification of proteins from complex mixtures and quantification of stable isotope labeling of amino acids in cell culture (SILAC)-labeled samples.

High-Throughput Screening (HTS)

Fully-integrated, HTS Platform (ThermoFisher F7) with 4 liquid handlers, 2 detectors, 2 incubators & ancillary devices

Configured to ensure high capacity, throughput and flexibility for the largest array of screening assays. Level 2 biosafety.

 

Two (2) Hamilton Robotics Sample Management Systems for -20oC storage and robotic retrieval of >400,000 screening samples

 

For storage, retrieval and re-arrangement of library reagents into customized collections ready for screens. F7-integrated.

 

ThermoFisher Dimension4 Modular Automation Platform with 3m conveyor belt and robotic flip movers connected to specific peripherals

Versatile system for multistep/multiday screening methods based on cell-free and cell-based assays. Level 2 Biosafety.

 

Labcyte Echo 555 (F7-integrated)

Acoustics-based, can touchlessly dispense nanoliter volumes. Used to handle sensitive reagents (e.g. small interfering ribonucleic acid (siRNA)).

 

 

Hamilton STARplus liquid handler (standalone)

For liquid dispensing (any viscosity, 2 to 250 ul) into multi-well plates, custom scripting, cherry picking capabilities

 

Biomek FX liquid handler (standalone)

For liquid dispensing (any viscosity, 2 to 250 ul) into multi-well plates, custom scripting, cherry picking capabilities

 

BlueCatBio BlueWasher (standalone)

Uses centrifugation instead of aspiration to delicately, yet effectively, perform sensitive washing procedures

High-content screening

Two (2) GE Healthcare IN Cell Analyzer 6000 confocal imagers, one equipped with a robotic arm and stacker

Automated confocal microscope for high-throughput imaging of cell monolayers and spheroids/organoids. Live or fixed cell assays.

 

Nexcelom Bioscience Celigo Imaging Cytometer

Automated micro-well plate based, bright field and fluorescent imaging of cell monolayers/ spheroids/organoids at 4x

High-spatio temporal resolution imaging

Two (2) GE Healthcare DeltaVision Elite high-resolution optical microscopes

For wide-field fluorescence, time-lapse live cell imaging, multi-point cell tracking and differential interference contrast

 

GE Healthcare OMX Blaze 4 multi-mode super-resolution optical microscope with 3D structured illumination (3D-SIM)

For simultaneous, multi-channel, super-resolution imaging of live and fixed cells. Ideal for cellular organelle dynamics.

Next-generation sequencing

Illumina HiSeq 3000

High-throughput, 2.4 billion reads, used for genome analysis, transcriptomics, and single cell sequencing.

 

Illumina NextSeq 500

Mid-throughput, 400 million reads, used for genome analysis, transcriptomics, and clustered regularly interspaced short palindromic repeats (CRISPR) bar code reading.