Single Cell Genomics
Single cell genomics has revolutionized the study of cellular heterogeneity. New approaches, including single cell RNA sequencing (RNA-seq), help identify and define cell subtypes. Single cell RNA-seq workflows fall into two primary methodological categories: droplet-based and plate-based.
Droplet-based RNA-seq
(such as 10x Genomics’ Chromium system) captures more cells per assay than plate-based methods, but is limited to covering only the 3’ UTRs of transcripts, resulting in libraries where only ~1,000 genes per cell are detected. Consequently, this approach cannot capture rare or lowly-expressed transcripts.
Plate-based RNA-seq
Entails sequencing full-length transcripts and enables detection of more than 10,000 genes per cell. To isolate single cells in plates, traditional FACS instruments are too harsh, damaging cell integrity and inducing stress-related transcriptional changes. Namocell’s Single Cell Dispensers operate at low pressure, dramatically improving library quality for plate-based single cell RNA-seq.
Following sample collection, single cells are easily isolated by loading the cell suspension into Namocell’s proprietary microfluidic cartridges and dispensing into 96- or 384-well plates pre-loaded with lysis buffer. Following single cell isolation, cells are ready for multiple downstream genomic applications, including single cell RNA-seq.
Namocell Benefits
Gentle
Gentle sorting (< 2 psi) preserves cell integrity
Benefit
Easy to use, no need for in-house technical experts
Fast
Dispense single cells into 96-well plate in 1 min, or 384-well plate in 6 min
Affordable
Reduce reaction volume, cut reagent costs by 90
Easy
Easy to use, no need for in-house technical experts
Dispensing Efficiency
Following sample collection, single cells are easily isolated by loading the cell suspension into Namocell’s proprietary microfluidic cartridges and dispensing into 96- or 384-well plates pre-loaded with lysis buffer. Following single cell isolation, cells are ready for multiple downstream genomic applications, including single cell RNA-seq.
Namocell vs. FACS
Namocell’s Hana Single Cell Dispenser was used to sort cells for single cell RNA-seq alongside a traditional FACS instrument. Cells sorted with Hana showed markedly higher numbers of reads and genes detected per cell (post-filtering), higher mapping rates, and lower fractions of mitochondrial reads.
Cells sorted with a FACS instrument showed induction of cell stress genes such as Ubiquitin C (Ubc), likely owing to high-pressure sorting conditions (20-70 psi). Cells sorted on the low-pressure Hana system (<2 psi) showed much lower expression of these stress-related transcripts.
Namocell’s Namo Single Cell Dispenser was used to sort CHO cells for clonal outgrowth alongside both limiting dilution (LDC) and a FACS. Cells sorted with Namo showed higher cloning efficiencies than LDC and FACS.
What Scientists are Saying
Here at Cytovance, we love our Namocell. This machine has increased our plating capacity and efficiency nearly four-fold. The accuracy of Namocell’s 384-well plating coupled with the easy changes between samples has been a game changer for our workflow.
Mike Brem
Namocell Hana single cell dispenser provides a great solution for gentle single cell cloning using sterile disposable cartridges. The system is easy to use and quick to initialize. Hana combines the advantages of FACS and microfluidic cell dispensing to enable high assurance of monoclonality with high throughput and great cell viability.
Mandy Yim
We’ve been using the Namo to do single cell sorting for genomics/ transcriptomics applications as well as for colony selection for tissue culture. We’re overall very satisfied with our results and find the setup to be very easy, as well as standard maintenance. After sterility protocols (which can take an hour), being able to immediately jump to sorting in less than ten minutes has saved us time and precious samples.
Noelani Kamelamela
The Hana has had a positive impact on our workflow. We are now able, with a high degree of confidence, to generate clonal populations of cells with reduced cytotoxicity (compared to FACS) while simultaneously saving hands-on time due to not needing to immediately screen for single cells after manual limited dilutions. In many cell lines, we see a significantly higher efficiency of clonality from plate to plate compared to our previous methods.
Pawel Bialk
The instrument works very well for our purposes of single-cell dispensing, primarily gene-edited lines. Easy to use; the setup and dispensing time is very short. It has the benefits of a FACS machine (binning by forward/side scatter), with lower pressure to help increase cell survival.
Michael Parsons
Namocell’s disposable cartridges have allowed us to increase the throughput of the validation of our CRISPR engineered cell lines since we can sort a full plate in less than 3 minutes, and can move to the next plate without the hassle of cleaning. This outstanding product is paired with Namocell’s exceptional customer service that has been responsive and attentive to our needs. While evaluating different FACS machines, we simply did not find a rival that combined Namocell’s simplicity, performance and value, all while occupying a small footprint.
Trang Dickson
Our stem cell core facility was looking for ways to speed up our human induced pluripotent cell cloning to generate clonal cell lines and to analyze our gene editing efficiencies in single cells. Our criteria for an instrument for single cell dispensing was 1) sterility, 2) gentle on cells, 3) ease of use, and 4) reasonable cost. The Namocell fitted our criteria perfectly. We are able to reduce the time and effort for generating clonal CRISPR-engineered iPSC lines significantly. The instrument requires very little maintenance and users do not need to be highly trained with the main requirement being good aseptic technique. We are excited to use the Namocell potentially for other single cell applications.
Po-Lin So
