Single-Cell Sequencing

“Every cell is a data point with a story. What we’ve built here is a system that gives researchers the tools to hear that story clearly - whether it’s in development, immunity, or disease.” - Ashot Harutyunyan

Single-cell sequencing enables high-resolution profiling of gene expression, chromatin accessibility, and immune repertoires at the level of individual cells. Unlike bulk methods that average signals across populations, single-cell approaches reveal cellular heterogeneity, capture rare subpopulations, and trace developmental disease trajectories. At the McGill Genome Centre, we support a wide range of single-cell workflows - from high-throughput droplet-based platforms to plate-based full-length transcriptomics - making it possible to interrogate cellular identity, dynamics and function across tissues and conditions. Common applications include tumour heterogeneity analysis, immune profiling, developmental biology, and stem cell research. Our services, offered by the Advanced Genomic Technologies laboratory, integrate experimental design, platform selection, and computational analysis, offering tailored support for both discovery and translational studies.

Common Applications

  • Profiling transcriptomes at single-cell resolution

  • T-cell and B-cell receptor profiling

  • Measuring regulatory landscape at the single-cell level

  • Detecting genomic alterations in individual cells

  • Targeted sequencing of coding regions in single cells

  • Simultaneous profiling of gene expression and chromatin accessibility

  • Integrating RNA and protein expression using antibody barcodes

  • Custom RNA capture in preserved or archived samples

Technologies at the McGill Genome Centre

10x Genomics Chromium
(droplet-based platform)

  • Single-cell 3’ / 5’ RNA-Seq: Gene expression profiling, with optional immune repertoire sequencing (5’)

  • ATAC-Seq: Chromatin accessibility analysis

  • Multiome: Simultaneous RNA and ATAC profiling from the same cell

  • CITE-seq / Feature Barcoding: Integrated transcript and protein profiling

  • Fixed RNA Profiling (10x Flex): High-throughput custom RNA capture from preserved samples

Plate-based and alternative platforms

  • SmartSeq4: Full-length, high-sensitivity RNA sequencing with well-level control

  • Hive (3’): Customisable, high-throughput 3’ RNA-seq platform optimised for scale

Single-cell DNA / CNV / Exome platforms

  • Single-cell DNA/Exome Sequencing: Targeted detection of coding-region variants

  • CNV Analysis: Single-cell-level assessment of copy number variations

Platform deliverables

  • All our single cell services, offered by the Advanced Genomic Technologies laboratory, include sample quality control (QC), sequencing QC metrics, and single cell metrics. Data are delivered in fastq format along with outputs from the appropriate single-cell pipeline for the application (e.g., cellranger count, cellranger multi, cellranger arc, space ranger, beenet for Hive libraries, etc …)

  • For project-level single-cell analysis, deeper bioinformatics support is available through the Canadian Centre for Computational Genomics (C3G). These services are offered as an add-on and ensure fully integrated support from sample to data interpretation