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What is Single Cell RNA Sequencing? 

5’
Protocol and guide Single cell sequencing

The basics of single-cell RNA sequencing

As biologists, we know biology is anything but uniform. Every tissue is a mosaic of diverse cell types, each with unique transcriptional profiles that shift dynamically in response to developmental cues, disease states, and environmental signals. While bulk RNA sequencing provides valuable global data, it inherently averages gene expression across mixed populations: masking rare cell types, transitional states, and critical regulatory interactions. 

That is the reason why single-cell RNA sequencing (scRNA-seq) has become a game-changer in fields like oncology, immunology, neuroscience, and beyond. It offers resolution that bulk approaches simply can’t deliver, allowing us to dissect cellular heterogeneity, identify novel subpopulations, and better understand how tissues function and change over time. At Singleron Biotechnologies, our scRNA-seq products are designed to capture complexity at the single-cell level, so researchers can drive more precise insights and uncover biology that would otherwise be missed.

The SCOPE-chip®: How We Capture Cellular Diversity

At the heart of Singleron’s products is the SCOPE-chip®, which separates individual cells into thousands of microwells: no pressure, no droplets, just gravity. Barcoded paramagnetic beads capture polyadenylated mRNA as cells are lysed directly in the wells. During reverse transcription, each cDNA molecule is tagged with a unique cell barcode and UMI, making it easy to trace every read back to its cell of origin and correct for amplification bias.

From there, our library prep workflow gets your samples sequencing-ready. But we don’t stop at data generation: Singleron’s user-friendly bioinformatics tools guide you through data analysis, from raw reads to clustering, cell type annotation, visualization, and more. 

The Workflow at a Glance

Tissue Dissociation

Single Cell Suspension | (Nuclei Isolation)

Capture: 10 000 cells on SD chip | 30 000 cells on HD chip

Library Generation

Sequencing

Bioinformatics Analysis

Why Choose Singleron’s Approach?

  • Gentle: Gravity-based capture preserves fragile cells
  • Flexible: Capture a few thousand cells or scale up to 30,000; even large cell types
  • Easy and cost-effective: All you need is a standard 200 µL pipette

Unlock a World of Possibilities with Singleron’s Single-Cell Assays

Singleron offers a broad portfolio of single-cell assays tailored to your research needs. For transcriptomic profiling, our Single Cell RNA Library kit is ideal for freshly dissociated tissues where intact cells are abundant, while our Single Nucleus RNA Library kit enables robust analysis of frozen samples, or hard-to-dissociate tissues, and large cells such as neurons or muscle cells that are difficult to isolate intact.

If your study requires full-length transcript coverage for detailed analysis of splice variants, SNPs, or fusion genes, the MobiuSCOPE® product combines 3’ and 5’ capture strategies to deliver high-resolution, full-length RNA profiles—while still using cost-effective short-read sequencing. Planning a larger study? The CLindex® Sample Multiplexing kit allows you to pool and process multiple samples in a single run, increasing throughput, reducing batch effects, and lowering costs.

Unique Single Cell Solutions For Your Research

If your research goes beyond transcriptomics, Singleron has you covered with multiomic solutions that layer additional biological insights. If you’re targeting specific mutations, gene fusions, or microbial transcripts, our FocuSCOPE product portfolio allows enrichment of lowly expressed sequences at the transcript level. Choose from pre-validated panels for blood cancer, lung cancer, clonal hematopoiesis, Epstein–Barr virus, intracellular bacteria, or work with us to create a custom panel tailored to your research.

Specialized applications include our Single Cell ProMoSCOPE kit, which profiles post-translational glycosylation on cell surfaces at single-cell resolution, revealing important aspects of cell signaling and immune regulation. For researchers working with non-mammalian species, our Microbial Single Cell RNA Library kit is optimized to accurately capture transcriptomes of organisms like yeast.

When timing matters, the DynaSCOPE® kit enables time-resolved single-cell transcriptomics, capturing gene expression dynamics across multiple time points; ideal for studying developmental processes, drug responses, or circadian rhythms. To explore gene regulation, our Single Cell ATAC-seq assay maps chromatin accessibility and regulatory element activity across individual cells, offering valuable insights into transcriptional control.

What is the difference between single cell rna sequencing and single nucleus rna sequencing?

While single cells provide more information (transcripts in the nucleus and the cytoplasm), sometimes they are difficult to isolate and process due to several factors (for instance, freezing tissues damages the integrity of the cell membrane and adipocytes are too light and large to be captured in the microwells). In these cases, it is beneficial to isolate single nuclei. In turn, some cell types might be more difficult to isolate, creating a bias towards the easy-to-isolate cells. Using single nucleus RNA seq, this bias is reduced.

When should I use single nuclei RNA sequencing?

When should I use single nuclei RNA sequencing?

You do not have any fresh tissue on hand? Are you working with big or complex cells?

Then you can utilize the power of single-nucleus sequencing for your research questions. Single-nucleus sequencing can be used amongst others in the following instances:

  • The tissue has been frozen and therefore the integrity of the cell membrane may have been compromised.
  • The cells are very big or have a complex structure (e.g. neurons or osteoclasts).
  • The cells are difficult to dissociate without impacting the cell viability.

Start your single cell journey with us

Whether you’re new to single-cell or looking to take your research further, starting with the Singleron technology is easy. If you want to run everything in your own lab, we offer intuitive, ready-to-use kits that integrate seamlessly into your workflows. Prefer a more hands-off approach? Our end-to-end services take care of everything from sample prep to data analysis, so you can focus on the biology.

Not sure which kit or workflow is right for you?

Our application support team is here to help you design the best experiment for your samples and research goals. Get in touch with us and let’s bring single-cell clarity to your next project!

A post by Melanie Dostert

Melanie Dostert, Ph.D. is a microbiologist specializing in biofilm-associated antibiotic resistance. She completed her doctorate at the University of British Columbia and has conducted research at the Max Planck Institute for Dynamics of Complex Technical Systems. Her work bridges microbiology, systems biology, and clinical applications, with a growing interest in single-cell technologies.

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