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) is a high throughput and cost-effective single cell RNA-seq approach that can profile up to tens of thousands of cells per assay. It can be used on live cells or nuclei from tissue samples. It is critical to obtain high quality cell or nuclei suspension with minimal aggregates and debris for droplet-based RNA-seq. Using the bulk sorting mode, Namocell's Single Cell Dispensers can be used to isolate live cells or high quality nuclei, removing dead cells, debris and clumps from the sample and improving overall RNA-seq data quality.
Unlike droplet-based RNA-seq that can be limited to covering only the 3' portion of transcripts, plate-based RNA-seq entails sequencing full-length transcripts from single cells partitioned in microplates. Thus, plate-based RNA-seq approach offers the advantages of more complete profiling of the transcriptome and better detection of rare or lowly expressed genes. 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.
In a droplet-based workflow (above) using fresh frozen tissue sample, a nuclei suspension is prepared, stained for nucleic acid, and loaded on the Namocell Single Cell Dispenser to bulk sort fluorescently labeled intact nuclei, leaving debris, and degraded nucleic acid behind. The purified nuclei can proceed with droplet-based cDNA synthesis and sequencing.
In plate-based workflow (below), a cell suspension is prepared, loaded into a Namocell’s microfluidic cartridge, and dispensed 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.
Gentle sorting (< 2 psi) preserves cell integrity
Work with cell density ranging from 100 cells/mL to 150M cells/mL
Dispense single cells into 96-well plate in 1 min, or 384-well plate in 6 min
Reduce reaction volume, cut reagent costs by 90%
Easy to use, no need for
in-house technical experts
Easily isolate rare cells (<0.1% of population)
Namocell's Single Cell Dispensers are highly efficient and consistent at dispensing single cells (80-90% singlets with mammalian cells).
Namocell vs. FACS
Namocell’s HanaTM 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.
B Cell Isolation for Single Cell Genomics
Single Cell Dispensing Efficiency
Single Cell Dispensing with Minimal Input
Protocols & Resources
SMART-Seq Protocol for 1/4 Reaction Volume
Unlabeled Sample Prep Protocol
Practical Tips for Single Cell Isolation
Webinar: Fast, Gentle and Easy Single Cell Isolation
Webinar: Utilizing RNA and DNA Plate-Seq Workflows for Low-Input or Rare Single-Cell Genomics
Coexpression network and trans-activation analyses of maize reproductive phasiRNA loci. Zhan, J., et al. (2023), Plant J, 113: 160-173. https://doi.org/10.1111/tpj.16045
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.
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.
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.
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.
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.
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.
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.