Single Cell Tracker & Isolator System CellRaft AIR®
Automatically image – identify – isolate

The CellRaft Air® System is an integrated platform that uses proprietary technology to maintain cells in an unperturbed state, leading to improved viability of single cells, highly proliferative colonies, and superior clonal outgrowth, that provides a dramatic increase in the number of clones available for downstream applications.

With the system you can:

• Obtain 10 – 50X more viable monoclonal colonies
• Grow single cells in a flask-like environment, without physically separating them, eliminating perturbation to cell physiology and ensuring viability and vitality of single cells as they develop into clones
• Identify cells of interest using powerful, label-free brightfield analysis software with user-defined parameters
• Automatically and gently isolate CellRafts containing cells or colonies of interest for downstream endpoint analysis or clonal expansion
• Create a complete image-based record of all clones to support regulatory submissions

1. Seed Cells on CellRaft Array
Seeding cells on the CellRaft array is straightforward and comparable to seeding cells on any standard tissue culture dish. The dilute cell suspension is dispensed into the central reservoir, and cells settle into the microwells by gravity.

The CellRaft Arrays are designed to yield a high number of single cells with the added benefit of shared media in a flask-like environment to increase viability and monoclonal outgrowth.

3. Identify Cells of Interest in Software
CellRaft Cytometry™ allows for image-based verification of single cells to ensure monoclonality and analysis of a variety of parameters over time, ranging from morphology to gene expression. Users can easily define the characteristics of the target cells or colonies and map them for software-guided CellRaft selection for downstream isolation.

Cell Line Development
Traditionally, a limiting dilution method is used to isolate and generate single cell-derived clones, which is both time and cost prohibitive due to low efficiency of success and the manual labor input required to successfully generate a useful cell line. Several automated technologies exist that aim to improve the efficiency of single cell or colony isolation, such as FACS, colony pickers, and droplet dispensers, but they often reduce cell viability due to harsh manipulation and stress on cells that are forced through fluidic systems or to grow alone in a large volume of media.

The CellRaft technology allows for streamlined and efficient cell line development. The AIR system offers an automated solution to an otherwise labor-intensive workflow and maintains cell health, provides time-course imaging for clonal verification, and delivers automated isolation for downstream propagation, altogether providing a superior platform that is more time, labor, and costefficient for cell line development.

Stem Cell Culture
The research benefits of using iPSCs are often outweighed by the challenges of working with them. Stem cells require specialized media and growth conditions and are notoriously difficult to grow from single cell culture. With the CellRaft AIR® System, stem cells plated on the CellRaft Array show improved viability due to shared media, low culture volumes, and isolation of intact clonal colonies from single iPSCs. With the CellRaft technology, expensive media, extracellular matrix, and viability enhancers are significantly reduced, leading to cost and consumable savings as well.

CRISPR
The process of cellular cloning and sorting is a major bottleneck in the CRISPR/Cas workflow. The imaging capabilities of the CellRaft AIR® System reduces this bottleneck by providing the user with Day-0-scans to visually connect CRISPR edits to desired phenotype expression at the single cell level. The user can identify clones of interest and confirm that clonal colony propagation began from a single cell. The array is scanned and imaged over time, allowing the user to easily identify which cells to target and track through the initial colony growth phase.

Genomics
Even with the use of highly advanced FACS platforms, enriched cell populations often contain dead cells, expression negative cells, doublets, debris, or other artifacts leading to false positives and negatives. The imaging capabilities of the CellRaft AIR System provide the user with initial scans to not only see the quality and phenotype of the cells, but to choose only the best cells. Eliminate doublets and debris with automated selection of the best single cells that maintain their native phenotype for downstream genomic analysis. The system’s unique design allows users to connect downstream nucleic acid and protein profiles to a specific individual cell, providing greater value to each experiment.

Organoid Development
With this platform, CellRafts containing 3D structures of interest can be easily identified using CellRaft Cytometry™. The system enables visual verification of single cell clonality, morphology, and growth, providing critical data points for workflows requiring track and traceability for audit purposes. Identified organoids can be further evaluated and selected for phenotypic characteristics, such as organoid diameter, circularity, and fluorescence intensity.

The CellRaft AIR System offers a solution with a fully automated imaging and isolation workflow for organoid culture. Capture images in brightfield and fluorescence channels throughout the full height of the organoid Z-stack imaging. The images showing detailed phenotypic characterization are easily exported for the desired use.

Organoid grown on a CellRaft for ten days and serially imaged.

A collaborative case study in the use of a new technology platform for fast and easy cell line development

In this case study, after flow sorting failed to generate a stable double positive cell population, even after multiple rounds of sorting, CellRaft Technology was able to identify and isolate rare double positive clones that formed viable colonies.