10x Genomics Chromium
Single Cell 3’ Assays


The Chromium Single Cell 3’ Solution delivers a scalable microfluidic platform for 3’ digital gene expression profiling of up to 80,000+ cells per run. The technology permits high throughput single cell transcriptomics from a variety of cell types (up to 50 μm in diameter) as well as single-nuclei profiling using 10X Genomics approved protocols. The 10x GemCode Technology samples a pool of ~750,000 barcodes to separately index the transcriptome of each cell. It does so by partitioning thousands of cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs) where all generated cDNAs share a common barcode. Libraries are generated and sequenced from the cDNA and the barcodes are then used to associate individual reads back to the individual partitions. Up to 8 samples can be processed in parallel in the Chromium. We are currently offering services for 3’RNA-Seq. Immune repertoire profiling (with or without 3’ RNA-Seq) is also available upon request. More information about Chromium technology and technical resources can be found on the 10X Genomics Website.

Chromium Single Cell 3’ Solution

Chromium Single Cell 3’ Solution. Formation of GEMs. RT reaction takes place inside each GEM, which is then pooled for cDNA amplification and library construction in bulk.

  • Cell counts and viability assessment on the Countess II
  • Cell washing and resuspension as required for input into the Chromium Single Cell Controller.
  • Cell capture and GEM formation (from 100 to 10,000 cells per sample as specified by client)
  • cDNA amplification
  • Illumina library preparation with quality assurance
  • Next generation sequencing on the Illumina NextSeq 500 or MiniSeq as required to achieve desired depth
  • Delivery of FastQ files and QC results
  • Data files can be analyzed with 10X Genomics free software solutions Cell Ranger and Cell Loupe Browser.
  • Optional data analysis services can also be provided by the OHRI Bioinformatics Facility
Countess II Cell Counter and Viability Analyzer

Countess II Cell Counter and Viability Analyzer

10X Genomics Chromium Single Cell Controller

10X Genomics Chromium Single Cell Controller

General Recommendations
  1. To initiate a project, please contact Kathy Sheikheleslamy or Pearl Campbell
  2. Please refer to the Single Cell Protocols Cell Preparation Guide for recommended best practices for washing, counting, and concentrating cells.
  3. Fifty microliters (50 ul) of each sample should be provided as a single cell suspension at a concentration of ~1,000 cells/ul in 1x PBS - 0.04% BSA with >90% viability.
  4. Clients will remain with the core technician during cell counting and viability assessment on the Countess II to provide approval to proceed with the experiment.
  5. Cells should be provided no later than 12:00 on previously scheduled analysis date.

The cost of this service is dependent on several variables including the number of samples, the number of cells targeted per sample, and the read depth per cell. A typical experiment can range from $2,700 to $6,000 (or more) per sample depending on experimental goals. We recommend that you speak with us to discuss your project requirements.

Contact Information

Kathy Sheikheleslamy
613.737.8899 x73251

Pearl Campbell PhD
613.737.8899 x73110