Fast, Gentle and Easy Single Cell Isolation for CRISPR & Cell Engineering

CRISPR technology enables quick and easy modification of any gene in a given cell type. In a typical CRISPR workflow, target cells are transfected with a plasmid containing both the CRISPR editing construct and a fluorescent reporter, enabling easy identification of successful transfections. Edited cells are then isolated for clonal expansion. Single cell isolation has traditionally been done with two approaches, both of which have inherent drawbacks.

Limiting dilution can be extremely inefficient and costly for clonal cell isolation, particularly when transfection efficiency is low. In the event of low transfection rates, it is nearly impossible to isolate clones via limiting dilution. Moreover, single cell isolation efficiency is highly variable with limiting dilutions, resulting in many empty wells or multiple cells per well.

Fluorescence-Activated Cell Sorters (FACS), while faster and higher throughput than limiting dilutions, operate at high system pressure (up to 70 psi) that can easily damage or kill the sorted cells. Induced pluripotent stem (iPS) cells, a commonly used cell type for CRISPR cloning, are particularly sensitive to the high pressure and have low survival rates following isolation. Additionally, FACS is difficult to operate and prone to contamination.

Take Your CRISPR & Cell Engineering Research to the Next Level

Fluorescently-labeled CRISPR transfected cells are identified and dispensed with Namocell’s Single Cell Dispenser.

For CRISPR workflows, cells are transfected with a CRISPR construct and fluorescent reporter, then cultured during a recovery period. Following recovery, fluorescently-labeled transfected cells are identified and dispensed with Namocell’s Single Cell Dispenser. After clonal expansion, colonies are analyzed via PCR to identify which clones contain the desired genotype.

Namocell Benefits

Hana Single Cell Dispenser
Gentle Single Cell Sorting


- Gentle sorting (<2 psi) preserves cell viability
- Higher clonality
- Better outgrowth

Rapid single cell isolation


- 96-well plate in 1 min
- 384-well plate in 6 min

Automate Isolation Cell Analysis


- Quick setup in under 3 min
- No calibration and no maintenance

Isolate Single Cells Easily


- Compact size fits in tissue culture hood
- Sterile and disposable cell cartridge

Dispensing Efficiency

Namocell Single Cell Dispensers are highly efficient and consistent at dispensing single cells. With dispensing efficiency (percentage of dispensed wells with single cells) of 80-90% for CHO cells compared to ~30% using manual pipetting.

CHO cell dispensing using Namocell compared to manual pipetting for cho cell line development

Cloning Efficiency

• Sorting CHO cells for clonal outgrowth compared to LDC and a FACS
• CHO Cells sorted with Namocell show higher cloning efficiencies than LDC and FACS

Clonal growth of mammalian cells sorted using the Namocell Single Cell Dispenser alongside both limiting dilution (LDC) and FACS. Cells sorted with the Namocell showed higher cloning efficiencies than LDC and FACS.

CRISPR & Cell Engineering Resources


High-throughput and automation advances for accelerating single-cell cloning, monoclonality and early phase clone screening steps in mammalian cell line development for biologics production. Tejwani V, et al. Biotechnol Prog. 2021 Nov;37(6):e3208. doi: 10.1002/btpr.3208. Epub 2021 Sep 20. PMID: 34478248.

Efficient and safe single-cell cloning of human pluripotent stem cells using the CEPT cocktail. Tristan, C.A., et al. Nat Protoc 18, 58–80 (2023).

Integrating Micro and Nano Technologies for Cell Engineering and Analysis: Toward the Next Generation of Cell Therapy Workflows Prithvijit Mukherjee, et al. ACS Nano 2022 16 (10), 15653-15680. DOI: 10.1021/acsnano.2c05494

Age-Related Low Bone Mineral Density in C57BL/6 Mice Is Reflective of Aberrant Bone Morphogenetic Protein-2 Signaling Observed in Human Patients Diagnosed with Osteoporosis. Halloran D, et al. Int J Mol Sci. 2022 Sep 23;23(19):11205. doi: 10.3390/ijms231911205. PMID: 36232525; PMCID: PMC9570292.

Coexpression network and trans-activation analyses of maize reproductive phasiRNA loci. Zhan, J., et al. (2023), Plant J, 113: 160-173.

Identification of Inhibitors of Tubulin Polymerization Using a CRISPR-Edited Cell Line with Endogenous Fluorescent Tagging of β-Tubulin and Histone H1. Khachatryan H, et al. Biomolecules. 2023; 13(2):249.

A versatile polypharmacology platform promotes cytoprotection and viability of human pluripotent and differentiated cells. Chen, Y., et al. Nat Methods 18, 528–541 (2021).

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