Single-Cell Genomics & DNA Sequencing

Single-Cell Genomics

With over 40 trillion cells in the human body and hundreds of cell types, cells have nevertheless traditionally been studied using bulk methods at the cell population or tissue level rather than single-cell level. However, the field of genomics and computational biology has progressed immensely over the last decade and new single-cell genomics approaches and techniques are advancing our understanding of human disease and many other biological problems. Following the emergence of next-generation sequencing (NGS), high-throughput genomics and transcriptomics measurements using DNA and RNA sequencing developed rapidly. Single-cell RNA sequencing (RNA-Seq) has also provided new insight into gene expression and epigenetic mechanisms behind important biological processes.

Sample preparation is a significant yet underappreciated step that allows for high-quality sequencing and single-cell analysis, which is critical to achieving breakthroughs in medicine, agriculture, and other industries.

NanoCellect’s microfluidic cell sorter, the WOLF®, allows the cell’s integrity to be maintained for numerous sequencing and multi-omics techniques. The WOLF’s ability to flexibly fit into any genomic researcher’s lab makes it a key step to any cell suspension genomic data analysis and cell sequencing analysis workflow.

WOLF Benefits

Even if genomic researchers are flow cytometry beginners, the WOLF has an intuitive and simple software workflow. It takes a day of training before novice users are up and running in their own lab.

The WOLF provides a quick solution for cleaning up samples prior to genomic studies. Scientists can be assured they will save money on reagent cost because reads are not wasted on dead cells and debris, which are eliminated on the WOLF.

Avoid stressing cells prior to transcriptomic studies. Researchers can be confident that, by utilizing a gentle sort upstream of library prep and sequencing, the readout will be unaffected by this sample prep process. Good quality sample prep up front, leads to clearer biological insight.

Many laboratories do not have space for a large, conventional cell sorter. Save on space by implementing the WOLF into a sequencing workflow, at only 2 cubic feet.

Researchers often need to sort many different cell types, and sample cross-contamination can be a huge issue while sequencing. The WOLF utilizes 100% disposable microfluidic cartridges and eliminates the issue altogether.

Researchers can use the WOLF when it is convenient for them, at any time, to get the right cells for the best quality sequencing data.

Bulk Sorting

Single Cell genomics has revolutionized the sequencing space by being able to decipher cell-to-cell differences from a large and diverse starting population. For systems biology studies of single-cell variations, such as immune cell populations, microfluidic-based cell sorting can allow users to sort a specific group of cells to complete single-cell or spatial views of genomics. The sorted population can be loaded into a partitioning library prep-based platform, like 10x Genomics RNA-seq or other single-cell transcriptome technologies. By sorting upstream of single-cell genomic-based experiments, users will achieve better resolution of their cells of choice by eliminating wasted reads on dead cells or debris. Researchers don’t need to worry about cell sorting affecting the stress of cell health and thus influencing RNA transcription—the WOLF operates at a low, gentle pressure maintaining endogenous expression profiles.

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Single-Cell Sorting on PCR Plates

Some researchers need to complete 3’ transcriptome NGS on populations of cells or on individual cells. In the case of single-cell 3’ RNA-Seq, the WOLF and N1 are especially well-suited to gentle deposition into PCR plates. Utilizing the WOLF and N1’s capability of employing flow cytometry-based cell sorting, researchers can dispense single cells of interest into 96- or 384-well PCR plates in order to complete library preparation. 3’ RNA-Seq allows users the flexibility and convenience of single-cell analysis by tagging individual cells for library construction to be performed in a single tube. For example, users can complete tissue dissociation of a tumor sample, and study the heterogeneity of progenitor or tumor cells by using single-cell RNA sequencing. In combination with the WOLF and N1 single-cell dispensing, researchers have a flexible, cost-efficient, and simple method to complete single-cell transcriptome analysis.

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Whole Genome

Single-cell sequencing is generally used to find multi-omics of an individual cell genome or transcriptome.

Scientists can complete varying types of whole-genome sequencing methods by easily sorting for specific populations by bulk sorting on the WOLF. Researchers can sort cells with extremely large genomes, like human, plant, or animal cells, and learn a variety of information regarding population genetics or disease. Users also can complete small genome sequencing by sorting for microorganisms like yeast and bacteria. By bulk sorting for a variety of cell types, genomics researchers can complete other whole-genome techniques like de novo and phased sequencing, where reference genomes may not be available or the comparison of alleles may be critical for genetic disease studies. The WOLF allows labs to be completely flexible when it comes to sequencing research and eliminate carryover with a 100% disposable fluidic cartridge.

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ATAC-seq

By sorting away dead cells or debris using flow cytometry on a microfluidic cell sorting platform, users will be left with a high-quality sample that can be prepared for an ATAC-seq assay. ATAC-seq detects open chromatin regions and allows researchers to analyze chromatin accessibility within the dataset at a population-wide or single-cell level. The WOLF prepares samples of high quality such that specialty genomic techniques like ATAC-seq can be easily accomplished. The epigenomic landscape of many different populations of cells or single cells can be elucidated simply by completing sample prep with the WOLF cell sorter.

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The WOLF is a technology that enables small companies to do things they could not do before.” “The microfluidics capability is something that I have been excited about. The nature of how the WOLF works is being extremely attractive to us. Some of the experiments we’d like to do in the future could not be done on any other device.

Justin Chartron, Ph.D. Protabit LLC

Neurons are extremely delicate so the selection step should be the least disturbing of all if we want to have reliable results. When we tried the WOLF, we were extremely surprised that our cells were very healthy and viability was above 90%, sometimes above 95% which is very impressive.

Dorota Skowronska-Krawczyk, M.Sc.,Ph.D. University of California Irvine

A great machine that has helped us take our cell-engineering pipeline to the next level!

Ronan O'Connell Rice University

The NanoCellect team and technical specialist have been awesome. After two test runs with very involved training/assistance, we have been very pleased with the results. The equipment is intuitive and the sorts have been very clean.

B. Davenport, Ph.D. University of Colorado

NanoCellect Customer Support team has been fantastic in helping us get up and running. The instrument is a helpful tool in our cell line development workflow.

Douglas Austen Takeda Pharmaceuticals

The NanoCellect customer support team is really helpful, knowledgeable and efficient; the WOLF is a great tool in our stem cell research workflow

Helen Miranda, Ph.D. Case Western Reserve University