A novel nanowell system based on SmartChip™ technology for the isolation and processing of 1000s of single cells

Advances in Next-Generation Sequencing have increased our ability to work with small/precious samples and grow our understanding of basic biological principles. Such biological insights are typically derived from data “averaged” over bulk cell and tissue samples. However, single cell analyses suggest that cell-specific transcriptome differences may have profound functional consequences. While technologies to isolate and process hundreds of single cells have made progress, advancements in single cell biology require new technologies that can enhance and automate the isolation and processing of tens of thousands of individual cells in a selective and flexible manner. To satisfy this need, we have engineered a single-cell system (SCS) to accommodate a number of downstream applications including RNA-seq. The WaferGen SCS includes a 5184 nanowell array based on SmartChip™ technology, imaging station, multi-sample nano-dispenser (for accurate dispense of cells and reagents into nanowells) and an image-analysis software that can identify 1000s of single-cell containing wells in an automated fashion. Using Poisson dispense method, the WaferGen SCIS can routinely isolate up to ~1800 viable single cells. Analysis of acquired chip images by proprietary software quickly evaluates cell staining to assess cell viability. The image analysis software is then used to select viable isolated cells for further processing. Well locations of selected cell are then uploaded to the dispenser to add reagents into wells of interest. This unique selective processing of individual cell-containing wells can dramatically help to minimize data analysis noise from wells containing multiple cells. The new WaferGen SCS moves the science of single-cell analysis forward by offering: Power – up to 1800 viable cells/chip across the broadest range of cell types per sample (5-100um), Control – ability to selectively process ONLY single-cell containing wells and Insight – process up to 8 samples per chip. We present data that demonstrate the reproducible dispensing of individual cells/nuclei using preprinted oligonucleotide-barcodes and processing of the cells for RNA-seq.