The David H. Koch Institute for Integrative Cancer Research at MITThe David H. Koch Institute for Integrative Cancer Research at MIT

Massachusetts Institute of Technology

National Cancer Institute Cancer Center

Science + Engineering... Conquering Cancer Together

Nanowell Devices and Applications

What is a nanowell device?

An array of wells, manufactured from PDMS (a silicone-based organic polymer), using photolithography and replica molding. The device is comprised of blocks of subnanoliter wells within a 1” X 3” glass slide. Each array has roughly 85,000 wells, which can hold 1 to 5 cells each.Nanowell Arrays are manufactured by the Nanowell Cytometry Platform for use in single cell phenotyping and SeqWell single cell RNAseq.

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Targeted Single Cell Phenotyping

A process which includes two complementary methods for characterization of individual cells within a population: 1) microengraving, to probe the secretory behavior of up to 100,000 individual cells and 2) multispectral fluorescent imaging to detect and analyze surface markers (up to 14) on cells in nanowell arrays. These methods enable identification of cells with specific expression patterns and provide information about cell type distribution within a population.

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Review article on Microengraving
Profiling human antibody response
Monoclonal antibody discovery via hybridoma screening
Discovery of immunotherapy targets in tumor microenvironment
Functional analysis of Circulating Tumor Cells
Characterization of secreted factors in single human induced pluripotent stem cells
Different antibody repertoires in autoimmune disorders

Cell Recovery

Recovery of single cells from arrays by alignment of microengraving and/or imaging data sets with the array grid, identification and location of individual cells, and picking/transfer for culture and expansion or genome or expression analysis.

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A relatively high throughput, cost-effective method for single cell RNAseq developed by Koch Institute investigators Chris Love and Alex Shalek. Individual cells are seeded into nanowell arrays and lysed, and the associated mRNA is attached to polyT containing beads. We work in collaboration with the Koch Institute Integrated Genomics & Bioinformatics Core/MIT BioMicro Center to support library preparation, quality control, sequencing and analysis.

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