Webinars featuring the CellRaft AIR® technology and applications to research, including CRISPR, genome editing, and single cell sorting and analysis.

Cloning in the Third Dimension: Breakthroughs in 3D Biology

Dr. Allysa Stern Scientist II, Product Applications, Cell Microsystems
Dr. Scott Magness, Associate Professor – UNC/NCSU Joint Departments of Biomedical Engineering

Traditional organoid culture presents challenges in downstream analysis of single organoids. In this webinar, Dr. Allysa Stern reviewed a unique workflow that enables clonal organoid development, monitoring of iPSC differentiation over time, and automated isolation of single organoids.

Dr. Scott Magness presented a case study related to his group’s work investigating tumor cell heterogeneity through clonal organoid morphology and transcriptomics. He discussed new approaches using single organoid transcriptomics to evaluate organoids derived from single cells from gastric dysplastic tissues and how this approach might reveal new ways to investigate tumor cell heterogeneity and evasion of some cells from cancer treatments.

In this webinar, you’ll:
– Learn how to accelerate the utility and reproducibility of iPSC-derived organoids
– Learn about clonal tumor organoid transcriptomics
– Gain an understanding of tumor cell heterogeneity

At the conclusion of this webinar, there is an engaging Q&A forum.

Download webinar video HERE.

Cloning in the Third Dimension Breakthroughs in 3D Biology Webinar 21 March 2023 at 100 PM EDT 700 × 400

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Novel methods for the development of stem cell-derived 2D and 3D models

Jessica Hartman, Ph.D. – Senior Director of Product Application, Cell Microsytems
Erin Knock, Ph.D. – Associate Director, Neural Biology, STEMCELL Technologies

Stem cells are an invaluable tool for generating multiple cell types from individual patients. However, the workflows associated with growing, differentiating and CRISPR gene editing induced pluripotent stem cells (iPSCs) in 2D and 3D culture are inefficient, low-throughput, costly, time-consuming and manually labor-intensive.

In this webinar, Dr. Jessica Hartman will discuss improving workflows that span the breadth of iPSC biology, from reprogramming to monoclonal edited colony formation to 3D models for disease.

STEMCELL’s Dr. Erin Knock will describe how to culture and differentiate choroid plexus organoids derived from hPSCs, and how they can be applied to answer specific research questions.

Key learning objectives:

  • Explore the use of hPSC-derived models to study human health, development, and disease
  • Understand the differentiation and characterization of hPSC-derived choroid plexus organoids
  • Discover a protocol that helps to get to the desired clone quickly, with demonstrated savings of valuable reagents, media and plastic

Download webinar video HERE.

Download presentation slides from this webinar HERE.

Challenge of iPS Cell Line Development 1

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Methods and best practices for the development of single cells into colonies

Jessica Hartman, Ph.D. – Senior Director of Product Application, Cell Microsystems
Lindsey Kuehm, Ph.D. – Field Applications Scientist, Cell Microsystems

Single-cell clone generation remains a major bottleneck in cell engineering. Current practices vary from manual limiting dilution, to using a variety of high-speed cell sorters, or a combination of both.

Join us for a series of case studies highlighting how scientists struggling with generating clones were able to overcome common bottlenecks in their research. Labor burden, poor cell viability, low efficiency, and lack of clonality are just some of the hurdles these investigators faced in developing the cell lines that are necessary for downstream discovery.

Key learning objectives

  • Increasing efficiency in single cell workflows
  • Understanding of different methods for developing single cells into colonies
  • How to get more colonies from the single cell workflow
  • How to get high-viability colonies


iPSC workflow3

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A roadmap to hundreds of characterized suspension cell clones using a single consumable

Jessica Hartman, Ph.D – Director of Product Application, Cell Microsytems

The most common question we receive about the AIR System is “Can we use suspension cells?”

While the AIR System excels at manipulating adherent cell types, suspension cells are vital for the success of a variety of biopharmaceutical applications, including large scale recombinant protein, vaccine, and monoclonal antibody production.

The AIR® System offers unique advantages over technologies, such as flow cytometry and droplet dispensers, designed to assess cells in suspension.

View this webinar to find out how your suspension cell applications can be adapted to the CellRaft AIR system to save you time and effort and get you the clones you need faster.


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New methods for CRISPR cell line development and screening using the CellRaft AIR® System for automated sorting and cloning

William Buchser, PhD – Assistant Professor, Department of Genetics, Washington University in St. Louis, School of Medicine
Jacquelyn DuVall, PhD – Lead for Cellular and Genomics Applications, Cell Microsystems

Cloning cells after gene editing is a labor-intensive process due to issues around cell viability, clonality and overall cell culture efficiency. The CellRaft AIR System provides an imaging-based workflow which supports single cell viability and allows independent clonal colony growth in a matter of days instead of months. The System also supports imaging-based phenotyping prior to isolation of single cells and clonal colonies for CRISPR screening applications.

Watch the webinar on demand here:

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Culture, Imaging and Isolation of Cells and Colonies using the CellRaft Array with the AIR® System

Dr. Jacquelyn DuVall, Cell Microsystems, Inc.

The CellRaft Technology is a straightforward means of culturing, sorting and isolating single cells and clonal colonies. The product relies on a single-use consumable, the CellRaft Array, a microwell cell culture dish that allows single cells to be individually analyzed and retrieved for downstream culture and analysis. At this webinar, Cell Microsystem’s Jacquelyn DuVall, PhD will review protocols recommended by Cell Microsystems for the most efficient use of the CellRaft Array. Optimized practices for cell seeding, staining and applying coatings will be presented. Finally, the use of the benchtop AIR®; System, a fully integrated instrument which supports imaging and isolation of cells with the CellRaft Array will be described.

Or, watch the webinar here:

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Making the Impossible Possible: Platform and Protocols to Develop Clonal iPSC Derived Organoids

In the last decade, several protocols and commercial kits have been launched to help differentiate iPSCs into multicellular, neuronal organoids that closely resemble human brain development, including region-specific cellular composition and functional physiology. However, the adoption of these organoid models is still limited to relatively low throughout applications, as the workflows are hampered by challenges in reproducibility and scalability, as well as being manually intensive. Here we report the use of the CellRaft® Technology, to develop and enable streamlined, reproducible organoid workflows that offer reliable imaging, software-guided selection, and automated isolation of single organoids for downstream applications.

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Taking the fear out of iPS cell line development

Despite significant strides in technology and increased access for researchers, iPSC culture remains a challenge, thereby limiting its widespread utility for therapeutic and research use. Common pain points include:

1) iPSC lines are sensitive and easily perturbed, requiring constant maintenance.

2) Poor culture conditions and cell line instability can lead to spontaneous differentiation and loss of pluripotency.

3) Generating monoclonal cell lines is incredibly challenging, with low efficiency and lack of proven clonality.

4) The labor, cost, and reagent burden associated with iPSC maintenance and workflows are incredibly high and often prohibitive for the end user.

Download this RaftNote to see how some of these challenges can be overcome.

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Image, Identify, and Isolate Single Organoids using the CellRaft AIR® System

The advancement of 3D culture systems has transformed cell-based assays for biological research and drug discovery due to their ability to re-capitulate the structure and cellular complexity of in vivo tissues. Organoids are unique due in their ability to self-organize and closely replicate in vivo pathophysiology. Most laboratory instruments employed to assess endpoints using traditional organoid cultures have limitations that preclude assessment of the heterogeneity within the population or retrieval of single, intact 3D structures for downstream applications.

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Using the CellRaft AIR® System to Image, Identify, and Isolate Suspension Cells

The AIR System offers unique advantages over technologies, such as flow cytometry and droplet dispensers, designed to assess cells in suspension. The limitations to other technologies include impacts on cell viability, inability to interrogate small numbers of cells, and reliance on fluorescent markers or staining for cell characterization. To demonstrate the value of the CellRaft technology for use in suspension cell line development, we have established methodologies for attaching suspension cells to the CellRaft Arrays during single cell expansion while still allowing the cells to expand in suspension after the clone of interest has been isolated.

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Comparison of Limiting Dilution and CellRaft® Technology for Cell Line Development

Therapeutic proteins play an essential role in the biological pharmaceutical market and are used in the treatment of many diseases, such as diabetes, cancer, and anemia. One of the main goals in recombinant protein development is the establishment of high-quality monoclonal cell lines that consistently express large amounts of the given protein. Chinese hamster ovary (CHO) cell lines have dominated the industry as commercial hosts for recombinant protein production; however, the process of generating a homogenous CHO cell line is not trivial.

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Automated Cloning for CRISPR Workflows Using the CellRaft AIR® System

Gene editing workflows require transformation of a large number of cells, followed by isolation of individual cells from the larger population to establish clonal colonies. Given the large number of gene edits required for contemporary research and the labor-intensive components of the workflow, there is an unmet need to automate post-transformation cloning.

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