Flow Cytometry: Nanowell Cytometry

nanowell plate next to a penny for scale

The Nanowell Cytometry platform is a shared resource housed in the Flow Cytometry Core that provides Koch Institute & MIT researchers access to Microengraving and SeqWell technologies, developed in the Love and Shalek Laboratories at the Koch Institute.

The Microengraving platform enables measurement of multiple traits from individual cells derived from a wide array of tissues or cell types, such as immune cells either in their native condition or upon stimulation. The modularity of the platform allows simultaneous assessment from small or large numbers of cells. Additionally, it is possible to obtain genetic information from the individual cells of interest.To date, the platform has been employed in projects related to antibody discovery, tumor profiling from various cancer tissues, and immune cell functions in various allergic, infectious or auto-immune diseases.

Seq-Well is a portable, low-cost platform for massively-parallel single-cell RNA-Seq. Barcoded mRNA capture beads and single cells are sealed in an array of subnanoliter wells using a semi-permeable membrane, enabling efficient cell lysis and transcript capture.

Additionally, the Core offers access to the CellCelector, a tool which enables users to isolate single cells using an ultra-precise robotic micromanipulator. We also offer access to nanowell microplates which enable automated isolation of monoclonal and viable clones.


Access to the platform is available to all members of the MIT community, to the extent permitted by available capacity. Priority access is given to KI members, NCI-funded research projects and other contributing user groups in recognition of funding support. Depending on available capacity, access may be available to non-MIT users (details available on request from platform Lead Specialist Shanu Mehta).

The Nanowell Cytometry Platform is supported in part by funding provided to the Koch Institute from a National Cancer Institute Cancer Center Support Grant.

NCI Cancer Center: A Cancer Center Designated by the National Cancer Institute