Genomics CORE Facility

Single Cell

Perform your next single cell gene expression analysis with our 10X Genomics Chromium Connect or Chromium iX instruments which are now available to the community for single cell RNAseq applications.

We offer many 10X library preps including :-

  • 3' single cell or nucleus gene expression
  • 5' single cell or nucleus gene expression
  • Single nucleus ATAC-Seq
  • Flex

If you're new to single cell RNASeq, here are some introductory documents from 10X Genomics.

Single cell RNA-seq: An introductory overview and tools for getting started

Getting Started: Single Cell 3’ Gene Expression

Here are some resources from 10X Genomics to help you get your samples ready.

Cell Preparation for Single Cell Protocols

Fixation of Cells & Nuclei for Chromium Fixed RNA Profiling

Tissue Fixation & Dissociation for Chromium Fixed RNA Profiling

Flow Cytometry Guidance for Single Cell Protocols

FAQ

How many cells do I need to run single cell RNASeq?

The 10X Genomics Chromium Connect system allows for the analysis of 1,000 to 20,000 cells per sample. We usually required at least 50,000 cells to start the assay.

Samples can be brought to us directly or after sorting in the Flow Core lab.

If you have fewer than 50,000 cells we may still be able to work with your sample in specific cases, you can email Genomics@dal.ca to discuss your project.

Does single cell RNASeq cover the entire transcript or just the 3' or 5' ends?

The 10X Genomics Chromium analyzes short (<100bp) reads located near the 3' or 5' ends of the transcripts. This allows you to obtain gene expression data at a low cost from up to 20,000 cells.

How many genes does the 10X detect?

This answer is complex, and is highly dependant on the cell type you're using. Cancerous cells or large, fast growing cells in culture can have 5,000 genes detected per cell. Smaller cells (eg primary immune cells, or cells that are less active) may only have 1,000-3,000 genes detected per cell.

What other RNA detection methods can I use if single cell is not suitable?

We also have a qRT-PCR instrument that's available for you to use. This is suitable if you have specific genes that you're interested in for smaller numbers of cells.

Can I use the equipment on my own?

Unfortunately we do not offer training on the single cell equipment at this time.

Can I speak to someone?

Absolutely, you can email us at Genomics@dal.ca and we'll be happy to work with you on your next project or grant application.