You’re considering a gene expression profiling technology for your next research project. But which one should you choose? 

We’ve discussed the [technical differences](https://www.10xgenomics.com/blog/what-is-the-difference-between-bulk-and-single-cell-rna-sequencing) between the big two—single cell and bulk RNA-seq—and their different [biological applications](https://www.10xgenomics.com/blog/bulk-vs-single-cell-rna-seq-when-averages-arent-enough). Those are both great places to start to understand which platform may best fit your experimental goals. 

But you may have other practical considerations: how much does it cost? How long does it take? How challenging is the protocol or data analysis? In other words, are there trade-offs that you’ll have to make, paying a cost in one way to take greater advantage in another. 

Like buying a car, you may need to test it out and see. But this blog will give you a head start to know what to expect. Typically, you're going to compare bulk and single cell RNA-seq on factors like cost, data resolution and quality, and cellular or sample throughput—all of which affect your potential for biological discovery and real-world impact.   

We’ll start generally. Jump ahead to explore a quick breakdown of:

- <a href="#Advantages_and_disadvantages_of_bulk_RNA_seq">Advantages and disadvantages of bulk RNA-seq</a>
- <a href="#Advantages_and_disadvantages_of_single_cell_RNA_seq">Advantages and disadvantages of single cell RNA-seq</a>

Then, we’ll get into the specifics and look at the latest single cell capabilities from 10x, like new assays and automation that <a href="#lower_costs">lower costs</a>, <a href="#simplify_hands_on_workflows">simplify hands-on workflows</a>, and <a href="#accelerate_data_analysis">accelerate data analysis</a>. 

### <div id="Advantages_and_disadvantages_of_bulk_RNA_seq">Advantages and disadvantages of bulk RNA-seq</div>

Bulk RNA-seq is a lower-cost option for whole transcriptome analysis. It provides an averaged, sample-level view of gene expression rather than resolving individual cell differences. Lower sequencing depth cuts costs, and simpler sample prep with lower-resolution output makes for an easier workflow and analysis. 

But these advantages come with major tradeoffs in _resolution and the potential for discovery_. Because bulk RNA-seq provides an average readout of gene expression across all the cells in a sample, it can’t tease apart the cellular origins of gene expression readouts. It’s impossible to know from a bulk readout if one or a few cell types are the majority producers of a certain gene or unique transcript. 

In short: a bulk readout can’t reveal the cellular heterogeneity of a sample, while single cell sequencing reveals the breadth of cell types in a complex tissue (Figure 1), even resolving rare, low-abundance cell types that could be driving unique gene expression profiles.

![Figure 1. Resolution of gene expression readouts from bulk versus single cell RNA-seq. (Left) Bulk RNA-seq shows average expression levels for six genes across a sample. (Right) Single cell RNA-seq of the same sample resolves expression at cellular resolution, revealing the individual cell types and subpopulations underlying each gene's average expression signal.](https://cdn.10xgenomics.com/image/upload/v1728499489/blog/Why%20single%20cell%20matters/Screenshot_2024-10-09_at_2.41.30_PM.png)

### <div id="Advantages_and_disadvantages_of_single_cell_RNA_seq">Advantages and disadvantages of single cell RNA-seq</div>

Single cell RNA-seq delivers whole transcriptome cellular profiles for individual cells, which uncovers cellular heterogeneity in a way that bulk simply can’t. Single cell technology from 10x Genomics comes with the added benefits of a robust, reproducible, instrument-enabled workflow that reduces error by automating steps, ensuring the highest data quality. [Automation](https://www.10xgenomics.com/instruments/chromium-family/single-cell-automation) also enables greater scale, which can reduce cost per cell to run single cell assays. 

But there’s a tradeoff: single cell workflows carry perceived barriers of _cost and complexity_. Single cell RNA-seq usually costs more than bulk partly because it requires deeper sequencing to capture rare features. You also have to dissociate samples into a single cell suspension with high cell viability, or jump into unfamiliar data analysis techniques, making scRNA-seq a more advanced experiment. 

But don’t discount the value that single cell analysis can bring to your research—**revealing hidden cells, disease mechanisms, and biomarkers, while supplying high-resolution data to train AI models**, to list a few possibilities. 

Plus, the apparent challenges with single cell approaches are steadily being addressed, making the technique more accessible than ever. See how we're tackling:

- <a href="#lower_costs">Cost</a>
- <a href="#simplify_hands_on_workflows">Experimental difficulty</a> 
- <a href="#accelerate_data_analysis">Data analysis</a> 

### <div id="lower_costs">Cost</div>

Cost is often the biggest barrier for researchers moving from bulk to single cell. But the low per-sample cost of bulk analysis doesn't always translate to long-term savings. Without high resolution, you could miss a new cell type or a low-level transcript key to moving your project forward (or publishing in a high-impact journal).

With 10x Genomics technologies, you not only get single cell resolution, but also higher gene sensitivity, fewer errors, and the confidence to get it right the first time. And we’re continuously innovating to lower costs: 

- The [Flex Apex](https://www.10xgenomics.com/products/flex-gene-expression) assay is bringing down cost per cell by enabling high-throughput single cell experiments, including the ability to run up to 384 samples a week in a 96-well format. Plus, Flex maximizes your sequencing budget with highly sensitive transcript detection.
- [GEM-X Universal 3’ and 5’ Multiplex](https://www.10xgenomics.com/products/universal) assays are lowering per-sample costs with smaller kit options that let you input less of your sample and use fewer reagents.
- The [Chromium Xo](https://www.10xgenomics.com/instruments/chromium-xo) instrument offers an affordable entry point to high-performance single cell profiling with our Universal 3' Gene Expression assay.
- [Automation capabilities](https://www.10xgenomics.com/instruments/chromium-family/single-cell-automation), compatible with the range of 10x single cell assays, can drive up the scale of your single cell experiments while driving down cost per cell. 
- The [QuantumScale Single Cell RNA Sequencing Kit](https://www.10xgenomics.com/products/scale/single-cell-rna-sequencing-kit) enables large-scale single cell studies that require reverse transcription, including high sample or plate-based screens. Again, greater scale brings down costs per cell or sample.  

### <div id="simplify_hands_on_workflows">Experimental difficulty</div>

New sample prep requirements and an unfamiliar instrument-based workflow may seem daunting, but, in reality, every single cell experiment follows three common steps that are similar to a bulk experiment: sample prep, running the assay, and data analysis (Figure 2).

![Figure 2. Three basic steps in every single cell experiment.](https://cdn.10xgenomics.com/image/upload/v1788984386/blog/Bulk%20vs%20Single%20Cell%20blog%20cuts/sc-workflow_3.svg)

And you’re not alone to figure it out. You have [40+ Demonstrated Protocols](https://www.10xgenomics.com/support) across our Chromium Single Cell portfolio, explainer videos, and detailed User Guides to help you succeed. Your local 10x Field Application Scientist can give you expert guidance through sample prep and experimental design, too. 

Then, push a button and walk away. That’s what the [Chromium X instrument series](https://www.10xgenomics.com/instruments/chromium-family) gives you:  confidence to spend your time on other things and superior reproducibility. Automating the partitioning steps of a single cell workflow (Figure 3) minimizes errors from manual workflow pipetting. If you aren’t ready to own an instrument, you can work with one of the many core facilities that offer Chromium Single Cell services.

![Figure 3. Video of GEM (Gel-Bead-in-emulsion) formation within a microfluidic channel inside the Chromium X instrument.](https://cdn.10xgenomics.com/image/upload/v1761606541/product-family/flex%20family%20page/Flex-fam_Performance.gif)

The results speak for themselves: you get more from every sample with up to 80% cell recovery, even from low cell inputs or samples with fragile cells. And you get consistent performance with an R² of 0.97 across runs, users, and timepoints. 

[Learn more about Chromium Single Cell workflows, built for your success.](https://www.10xgenomics.com/platforms/chromium/technology) 

### <div id="accelerate_data_analysis">Data analysis</div>

Single cell data can be accessible and interpretable, no bioinformatics experience needed. Our free, user-friendly software and training resources are designed to help you get straight to biological exploration:

- [Cell Ranger pipelines](https://www.10xgenomics.com/support/software/cell-ranger/latest) process scRNA-seq data in as little as an hour with free [10x Genomics Cloud Analysis](https://www.10xgenomics.com/products/cloud-analysis).
- You can easily visualize genes and clusters with [Loupe Browser software](https://www.10xgenomics.com/support/software/loupe-browser/latest).
- [Automated cell annotation](https://www.10xgenomics.com/support/software/cell-ranger/latest/algorithms-overview/cr-cell-annotation-algorithm) capabilities are also streamlining analysis.
- Our [8-week online data analysis course](https://www.10xgenomics.com/analysis-guides/level-up-your-research-10x-data-analysis-course) equips you to perform your own analysis with 10x pipelines and community tools. 
- Our [Analysis Guides](https://www.10xgenomics.com/analysis-guides?refinementList%5Bproducts.name%5D%5B0%5D=Universal%203%27&refinementList%5Bproducts.name%5D%5B1%5D=Flex&refinementList%5Bproducts.name%5D%5B2%5D=Universal%205%27) offer a variety of helpful tutorials and FAQ blogs, from the basics to advanced analysis techniques.

With these resources, you can identify cell types and states, detect rare transcripts, perform multi-sample comparisons, and explore new questions that only single cell data makes possible. 

<RowCard title={"Explore your options for single cell assays"} content={["If you want to go deeper into what’s possible with single cell RNA-seq, this next blog introduces our assay families, Flex and Universal. Explore their respective uses and practical considerations, like sample compatibility, throughput, and more, to find the right fit for your research."]} image={{ src: "https://cdn.10xgenomics.com/image/upload/v1788984436/blog/Bulk%20vs%20Single%20Cell%20blog%20cuts/10x_Chromium-Portfolio_Blog-Hero_1200x800.webp", alt: "undefined" }} cta={{ label: "Find the right solution", url: "https://www.10xgenomics.com/blog/finding-the-perfect-fit-how-to-choose-the-right-single-cell-assay" }} />

_If you’re ready to get started with single cell, reach out to a technology specialist to [talk about your projects and goals](https://www.10xgenomics.com/platforms/chromium/contact-request)._


GEM-X technology-powered assays with whole transcriptome coverage to gather broad information from diverse species

Universal 3'

Chromium X Series

Chromium

Advanced system for multiomic analysis of hundreds to millions of cells.

Gene Expression

Epigenomic Profiling

Immune Profiling

Protein co-detection

3' gene expression profiling at scale with single cell resolution.

GEM-X technology-powered assays with whole transcriptome coverage to analyze immune diversity 

Universal 5'

5' gene expression alongside V(D)J repertoire profiling and antigen specificity of T and B cells.

Plate-based sample handling brings unprecedented scale to highly sensitive single cell profiling

Flex

Fixed RNA Profiling assay for comprehensive probe-based gene expression profiling with single cell resolution.

Chromium Single Cell Gene Expression provides single cell transcriptome 3' gene expression and multiomic capabilities to profile tens of thousands of cells. Explore cellular heterogeneity, novel targets, and biomarkers with combined gene expression, cell surface protein expression, or CRISPR edits in each cell.

Cell Surface Protein

CRISPR Screening

Sample multiplexing

Reveal the full complexity of cellular diversity, <em>cell by cell</em>

Single Cell Gene Expression

QuantumScale Single Cell RNA

Scale

3' based gene expression profiling with Quantum Barcoding.

Cost, difficulty, and data are common perceived barriers to scRNA-seq. Learn how we’re lowering that barrier, plus how single cell resolution and automation offer advantages over bulk. 

10x Genomics Blog

The single cell advantage: Resolution, data quality, and throughput vs. bulk RNA-seq cost