Single-Cell Sequencing Do You Need It

Single-cell sequencing is transforming how we understand cancer, immunology, and complex diseases—giving researchers insight into cellular heterogeneity that bulk RNA-seq can’t touch.

But setting it up in-house is a big commitment. Beyond the cost of platforms like 10x Genomics’ Chromium, you’ll need the right sample prep workflows, bioinformatics support, and infrastructure to handle high-throughput data.

This post breaks down when it makes sense to bring single-cell capabilities into your lab—and when outsourcing might be the smarter move. We’ll cover core use cases, key requirements, and how leasing can make the tech more accessible without blowing your budget.

What Makes Single Cell-Sequencing So Powerful?

Single-cell RNA sequencing (scRNA-seq) represents a major advancement in genomics, offering unprecedented resolution by capturing gene expression profiles at the level of individual cells. Unlike bulk RNA-seq—which averages transcriptomic data across a population—scRNA-seq reveals the full complexity and heterogeneity within cell populations.

That level of detail enables breakthroughs across life sciences and biotech. With scRNA-seq, researchers can:

• Identify rare cell types or subpopulations: Essential in oncology, immunology, and stem cell research where minority populations often drive disease progression, immune escape, or therapeutic resistance.
• Track dynamic changes in response to treatment: Allows researchers to assess how individual tumor or immune cells evolve under drug pressure, supporting translational research and drug development.
• Map cellular differentiation and lineage trajectories: Especially valuable in developmental biology, regenerative medicine, and cell therapy manufacturing, where knowing how cells change over time is critical.

The technology stack behind scRNA-seq is as powerful as it is intricate. High-throughput microfluidics systems, like those from 10x Genomics (Chromium), enable droplet-based barcoding and simultaneous profiling of tens of thousands of cells per run. When paired with tools for single-cell ATAC-seq, proteomics, or multiomic profiling, these workflows deliver multi-dimensional insights at the single-cell level.

But this resolution comes at a cost. From sample preparation and nuclei isolation to library preparation, amplification, and bioinformatics, single-cell sequencing requires precision across each step. Technical challenges—like maintaining high-quality RNA, preventing cell doublets, and achieving sufficient sequencing depth—can derail experiments if not carefully managed. On top of that, data analysis pipelines must handle massive, complex datasets while preserving reproducibility and specificity.

Without the right infrastructure, trained personnel, and computational resources, labs risk burning through budget, reagents, and precious samples—without generating usable insights.

In-House Or Outsourced? Choosing the Right Option

For many early-stage biotech companies, translational research groups, and precision medicine teams, the biggest question isn’t what single-cell sequencing can do—it’s how to access it.

You’re likely already running pilot studies, publishing data, or exploring novel biology. The challenge now is deciding whether to build internal sequencing capacity or rely on external partners like core facilities or CROs. And that decision has implications for everything from workflow timelines to IP strategy and cost efficiency.

Outsourcing to a core facility or CRO can make sense if:

• Your current needs are project-based, exploratory, or limited in scale
• You lack in-house expertise in library preparation, barcoding, or bioinformatics
• You’re validating new assays or testing unfamiliar sample types (e.g., fixed tissue, low-input samples)
• Budget constraints make a capital investment hard to justify
• You’re trying to de-risk platform selection or compare technologies like 10x Genomics, BD Rhapsody, or Mission Bio’s Tapestri before committing

In these scenarios, outsourcing gives you access to trained operators, established protocols, and advanced instrumentation—without the burden of maintenance, training, or long-term commitment.

Bringing single-cell sequencing in-house may be the better move if:

• Your company’s core IP, drug discovery platform, or diagnostic development depends on high-throughput single-cell analysis
• You need tight control over sample prep, turnaround time, and data security
• Your team is generating enough volume to make leasing or purchasing a platform more cost-effective
• You’re building a competitive edge around proprietary workflows, datasets, or algorithms
• You want to shorten iteration cycles and avoid external bottlenecks

In-house sequencing gives you the power to prototype, test, and refine on your timeline—not someone else’s. And with the right leasing structure, you can scale infrastructure without massive upfront costs, improving cash flow and avoiding long-term equipment obsolescence.

Ultimately, it’s a question of control, capacity, and strategic alignment. The more central single-cell data is to your science and business model, the stronger the case becomes for bringing it closer to home.

What You’ll Need to Run Single-Cell Sequencing Internally

Setting up an in-house single-cell sequencing workflow isn’t trivial—it requires more than just a sequencer. Here’s what it takes to do it right:

1. Upstream prep capabilities: You’ll need clean, viable cell suspensions or nuclei isolations, depending on your sample type. This often means incorporating FACS, tissue dissociation tools, or other enrichment techniques.
2. Platform instrumentation: Most labs turn to platforms like 10x Genomics Chromium for single-cell RNA-seq, ATAC-seq, or multiome assays. These systems rely on microfluidics, barcoding, and well-optimized reagent kits.
3. Sequencing hardware: After library prep, samples are sequenced using short-read platforms (e.g., Illumina)—requiring access to high-throughput, high-fidelity NGS instruments.
4. Bioinformatics and analysis: This is where things often bottleneck. You'll need workflows for normalization, differential expression, clustering, trajectory inference, and visualization—plus robust data storage and pipeline management.
5. Skilled personnel: You’ll need people who understand both wet lab execution and dry lab interpretation—ideally a mix of molecular biologists, computational scientists, and data analysts who can speak the same language.

Why Leasing Makes In-House Easier to Set Up

Buying and maintaining single-cell platforms can quickly strain your budget—especially for early-stage teams or smaller core labs. Leasing helps change that equation:

• Lower upfront costs, greater flexibility: Outright purchases can exceed $250,000 or more, especially for platforms like 10x Genomics or Illumina-compatible systems with full automation. Leasing spreads those costs out over time, preserving cash flow for hiring, consumables, and other critical expenses—especially during early-stage growth.
• Align spending with scientific and business milestones: By structuring lease payments around your development timeline, you can fund sequencing capacity in parallel with go/no-go decision points. Need to demonstrate technical feasibility before a Series A? Or hit a translational milestone for an oncology program? Leasing helps you match infrastructure investment with progress.
• Avoid obsolescence risk: The pace of innovation in single-cell technologies is rapid. Leasing gives you the ability to upgrade or replace equipment as your needs evolve—whether you're moving from scRNA-seq to multiome, exploring spatial profiling, or adding new modalities like ATAC-seq or proteomics.
• Simplified budgeting and predictable OPEX: Leases typically bundle service contracts, preventative maintenance, and calibration into a single monthly payment. That means fewer budget surprises and less time managing upkeep. This is especially valuable when downtime translates to lost data or delays in critical experiments.
• Accelerate internal capability building: Leasing lowers the barrier to entry for labs transitioning from outsourcing to internalization. Instead of relying on external sequencing cores, you can bring experimentation in-house—gaining control over turnaround times, optimizing protocols, and training staff directly on your workflows.

Final Thoughts: Capability, Control & Cost

Single-cell sequencing has moved from the frontier of genomics into the mainstream of discovery. Its ability to profile gene expression at the level of individual cells opens up possibilities in cancer, immunology, neurology, and more. But with that power comes complexity—and cost.

Whether you're building a translational pipeline, validating new targets, or characterizing cellular heterogeneity in clinical samples, the decision to bring single-cell sequencing in-house is as much about infrastructure and workflow as it is about data.

Leasing gives labs the flexibility to adopt advanced technologies without overextending their budgets or locking themselves into systems that may not scale with their science.

If you're considering building single-cell capabilities, explore how equipment leasing can help you move faster—without sacrificing performance or control.

Chat with the team.