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Single Cell Sequencing

Single cell RNA seq: Explore and interpret single cell gene expression profiles

Transcriptomics of individual cells can allow researchers to gain insights into cellular heterogeneity, identify rare cell types, and uncover new biomarkers for diseases.

SAGC has a Chromium Controller and Chromium X Series from 10X Genomics to enable multiomic analysis through droplet GEM-based single cell partitioning and sequencing.

Applications available:

  • Single cell RNA expression
  • Single cell ATAC
  • Single cell CNV
  • Cell surface marker tagging can be incorporated into some of these techniques and quantified during sequencing. 




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Chromium single cell gene expression

  • Comprehensive RNA-seq profiling from single cells
    High throughput and workflow efficiency:
    run 1 to 128 samples, or up to 1 million cells per run.
  • Compatible with fixed, fresh, and frozen samples, as well as whole cells and nuclei.


  Chromium X Series Chromium Controller
Assay Compatibility
  • Single Cell Gene Expression LT
  • Single Cell Gene Expression
  • Single Cell Immune Profiling
  • Single Cell ATAC
  • Single Cell Multiome ATAC + Gene Expression
  • Single Cell Gene Expression Flex
  • Single Cell Gene Expression HT
  • Single Cell Immune Profiling HT
  • Single Cell Gene Expression LT
  • Single Cell Gene Expression
  • Single Cell Immune Profiling
  • Single Cell ATAC
  • Single Cell Multiome ATAC + Gene Expression
Cell Throughput Low, Standard, and High
100-730,000 singlets per run*
Single Cell Gene Expression Flex - 500-1,024,000 singlets per run*
Low and Standard
100–140,000 singlets per run
Additional Resources from 10X
Grant Application Resources - Chromium Single Cell Gene Expression

Other single cell technologies (such as EvercodeTM from Parse Biosciences) leverage serial plating as an alternative to 10X, which relies on microfluidics. This can offer some advantages with certain cell types and achieve higher throughput at a lower cost.

Parse Biosciences: leverages combinatorial barcoding

  • Scalable: 10K to 1M cells or nuclei
  • Flexible: Fix and store samples collected on different days for the same run

Considerations for deciding between split-pool (combinatorial barcoding) and droplet-based (microfluidics):
  • Time course study
  • Collection of cells across different sites
  • Very high-throughput experiments
  • Sensitive detection of very rare cell types



Single cell experiments 'at scale' - the million cell experiment

"The range of single cell technologies on offer and the improvements in throughput are allowing researchers to rethink their experimental design and run a lot more samples."
Dr. Renee SmithSenior Genomics Scientist
  • Single Cell RNA (scRNA-seq)

Single Cell RNA (scRNA-seq)

Submit Fresh Cells in sterile microcentrifuge tubes.  Cell Submission ~ 700 – 1200 cells/µl


Bioinformatics Support - single cell pipelines and analysis