Office of Technology Transfer – University of Michigan

Hydro-Seq: High Sample Efficiency Single Cell Whole Transcriptome Analysis Technology

Technology #7243

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Euisik Yoon
Managed By
Joohee Kim
Licensing Specialist, Physical Sciences & Engineering 734-764-8202
Patent Protection
US Patent Pending
Scaling and automation of a high-throughput single-cell-derived tumor sphere assay chip
Lab Chip, 2016,16, 3708-3717, 2016

To adequately diagnose and treat cancer, cancer cells are studied for particular gene expressions. Research has shown that the most important cells to look for are circulating tumor cells (CTCs) as these give rise to cancer. Traditional technologies for studying gene expression look at a population average, which masks diversity that is often seen in cancer patients. It is estimated that CTCs make up only 1-5% of the cell population and therefore can get lost in a population average. Therefore, technologies have focused on single-cell analysis to identify these cells. Many of these technologies still have draw-backs including being labor intensive and high cost of reagents. Some automated technologies that reduce the amount of labor needed can cause stress on cells that change gene expression or cause cell damage. The most advanced single cell sorters now use microfluidics to trap and analyze single cells. These technologies also have set backs since a large number of cells is needed and a large portion of cells are not captured through these technologies. Therefore, better devices to capture and study single cells are needed to find and study CTCs.

Microfluidic device for the capture and analysis of single cells

The Hydro-Seq device allows efficient capture of single cells (76%) on a small microfluidic chip even with as few as 50 cells loaded. The cells can be lysed and the mRNA extracted right on the chip. With the addition of barcoded beads, the mRNA can bind and be extracted for full transcriptome analysis. These chips are available in 800 wells/chip to 32,000 wells/chip and can be made with a single chamber form that mixes single cells with a single bead, or in a dual chamber form that keeps cells and beads separate. With a custom imaging process software, each individual well can be analyzed for quality control as well as to extract information such as number of cells, cell size, and cell shape to provide additional information when searching for CTCs. The small size of the chip allows for little reagents to be used making it cost effective for research labs as well as a diagnostic tool. Additionally, the use of the device requires very little manual labor. This device has the potential to speed up high throughput diagnostics and research to analyze single cells for the identification of CTCs. Furthermore, these microfluidic chips can be customized for other assays such as ELISAs, migration assays, and metabolic assays by varying the types of beads used.


  • New diagnostic
  • Research tool


  • Cost effective
  • Labor efficient
  • Analysis of single cells
  • High capture rate