Single-Cell Genomics

One of the most rapidly-moving areas of genomics is “single cell genomics” (SCG), the study of individual cells. Using SCG instruments such as those we have at the UMGC, researchers worldwide have begun to map cellular heterogeneity in genome structure and function. The UMCG has two instrument platforms for single-cell genomics (SCG): the Fluidigm C1 and 10X Genomics Chromium platforms.

There are significant differences between our two SCG platforms. Please inquire with UMGC staff to discuss the ways in which these technologies can benefit your research.

Fluidigm C1


The Fluidigm C1 enables microfluidic single-cell capture of 96 or 800 living cells for analysis by quantitative real-time PCR (Fluidigm BioMark HD) or Next-generation Sequencing (RNA-Seq, DNA-Seq, and ATAC-Seq).

Instrument and Applications

There are two different scales of capture available, depending on the “Integrated Fluidic Circuit” (IFC) consumable chosen. The Single-cell Auto Prep IFC captures up to 96 cells for downstream quantitative PCR, RNA-Seq, or DNA-Seq. The Single-Cell mRNA Seq IFC captures up to 800 cells for downstream RNA-Seq only.

Cell Size

For the Single-cell Auto Prep IFC (96 cells), there are three cell size ranges: 1) 5-10 micron, 2) 10-17 micron, or 3) 17-25 micron. All three capture size ranges are compatible with all downstream on-chip processing chemistries, of which there are three: 1) targeted gene expression, 2) RNA-Seq, and 3) whole-genome amplification (for DNA-Seq). For the Single-cell mRNA Seq IFC (800 cells), only cells of size 10-17 micron may be captured.

Capture Performance

Under ideal capture conditions, > 90% “occupancy” of capture sites is possible, but results vary significantly as a function of cellular factors. Consequently, capture performance is an experimental variable that is beyond the UMGC’s control. UMGC staff work with users to optimize capture efficiency when necessary. Note that in the case of capture failure, it is possible to abort an experiment and avoid downstream expenses (please inquire).

10X Genomics Chromium


The 10X Genomics Chromium instrument and chemistry captures and processes from 200-80,000 cells per run for affordable and high-throughput single-cell RNA-Seq.

Instrument and Applications

The Chromium instrument can carry out from 1-8 cell captures in parallel, with each capture targeting between 200-10,000 cells. The exact number of cells captured is probabilistic, determined by the input cell density.

Cell Size

Compared to the Fluidigm C1, the 10X Genomics platform has less strict size requirements, but cells must be less than ≈ 50 µm in diameter.

Please contact our single-cell team at single-cell@umn.edu for assistance with determining the right platform and application for your experimental goals.