Introduction
As we start a new year and reflect on 2024, it’s the perfect time to examine the types of analyses our bioinformaticians at Bridge Informatics tackled. While our most requested analyses often involve single-cell RNA-sequencing (scRNA-seq) from the 10X Chromium platform, this blog post highlights additional platforms and explores future directions for the single-cell field.
Major Platforms and Their Features
10X Chromium
The 10X Chromium platform leverages droplet microfluidics to co-encapsulate single cells with barcodes and reagents for downstream RNA-seq or ATAC-seq. It requires single-cell suspensions (or single-nuclei suspensions), with throughput largely influenced by the suspension’s cell count. Known for its high throughput—above 10,000 cells per run—10X Chromium is a leading platform for single-cell analyses.
BD Rhapsody
BD Rhapsody uses microwells to isolate individual cells, offering visual quality checks before proceeding with a run. This platform, also requiring a single-cell suspension, delivers mid-range throughput (fewer than 10,000 cells). BD Rhapsody stands out with its flexibility, offering several quality checkpoints between cell loading and sequencing.
Fluidigm
Fluidigm’s platform employs channel microfluidics, a popular approach during the early days of single-cell analysis adoption. It allows visual cell inspection and provides higher sequencing depth than 10X Chromium. However, its lower throughput (fewer than 1,000 cells per run) and single-cell suspension requirement make it suitable for specific use cases prioritizing depth and imaging.
ddSEQ (Bio-Rad)
Bio-Rad’s ddSEQ platform builds on its ddPCR technology, using droplet microfluidics for single-cell analysis. It supports high throughput and flexible downstream assays. Designed for accessibility, ddSEQ is user-friendly, requiring minimal specialized expertise. However, it relies on consumables and hands-on manipulation for downstream assays, making it a more modular yet less streamlined solution.
Cost and Accessibility
While 10X Genomics dominates the single-cell market, its high cost and reliance on skilled personnel often restrict access to well-funded research cores. Platforms like Fluidigm and BD Rhapsody, despite their price tags, have found adoption in individual labs due to their approachable workflows. On the other hand, Bio-Rad’s ddSEQ is the most affordable and accessible, though it demands more user intervention and supplementary reagents. These considerations—cost, accessibility, input requirements, and downstream capabilities—are shaping the evolving single-cell analysis landscape.
The Single-Cell Market Size
The single-cell analysis market is booming, with a valuation of USD 3.90 billion in 2022, projected to reach USD 15.8 billion by 2032 (Grand View Research). Growth drivers include the demand for cellular-level molecular biology insights, rising cancer rates, and rapid technological advancements. Established players like 10X Genomics and innovators such as Deepcell Inc. are advancing the field through AI-powered platforms and high-dimensional readouts. Robust government and industry investments further accelerate this expansion, unlocking opportunities for disease diagnosis and drug discovery.
The Competitive Landscape
Research institutions are rapidly adopting single-cell technologies, with academic and research labs leading revenue generation. Emerging players like ParseBio and SeqWell Inc. are introducing cost-effective, accessible kits, while established companies such as BD Biosciences expand their offerings through strategic acquisitions. Innovations in single-cell isolation and RNA-seq processing continue to heighten competition and widen accessibility across academic, government, and industrial labs.
Looking Ahead to Emerging Applications
The drive to contextualize -omics profiles within their spatial tissue environment has propelled spatial platforms into prominence. Examples like 10X Genomics Visium and Xenium, as well as SlideSeq, offer significant advantages, including the omission of single-cell suspension requirements. These platforms use cryosectioned tissue inputs and enable biological replicates in one assay area, addressing key limitations of traditional single-cell workflows.
Gene-targeted spatial assays, such as Xenium, Singular Genomics G4X, and MERFISH, are gaining traction for their ability to provide detailed spatial metadata. Meanwhile, platforms like Parse Biosciences emphasize accessibility, using simple workflows involving well plates and centrifuges to isolate fixed cells. These innovations are reshaping single-cell research, making it more versatile and cost-effective.
Conclusion
The single-cell field continues to flourish and diversify. Platforms like 10X Chromium, BD Rhapsody, Fluidigm, and Bio-Rad’s ddSEQ cater to varying needs for throughput, cost, and accessibility. Government and industry investments, combined with advancements in spatial analyses and new market entrants, underscore the growing importance of high-resolution data in disease biology.
Navigating this landscape requires expertise and adaptability. Partnering with service providers like Bridge Informatics ensures seamless support for data storage, analysis, visualization, and pipeline development. By overcoming common challenges in scRNA-seq data analysis, we help unlock the full potential of your research.
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