What Management Said
Read the full Q3 2025 transcript ↗We exceeded the top end of our guidance range in the third quarter with total revenue of $149 million. Spatial consumables had another robust quarter of double-digit year-over-year revenue growth, driven by continued strong demand for genome consumables. We again saw sustained growth in both the number of runs and the average spend per run. Within single-cell, while consumable revenue was down year-over-year, we again saw double-digit Chromium consumables reaction growth year-over-year.
Our Flex and On-Chip Multiplexing assets have been key drivers of this growth. It is also particularly well-suited for translational studies and massively scaled experiments, which are two of the most promising directions for single-cell growth going forward. This strong position provides us with both the flexibility to navigate the current environment and the resources to strategically invest in innovation and long-term growth. While the pace of news flow has moderated compared to earlier in the year, spending behavior remains cautious, particularly for capital expenditures.
I'll start by reviewing our financial results for the three months ended September 30, 2025, and then we'll provide further details on our outlook for the fourth quarter. All figures and growth rates provided will be on a year-over-year basis unless otherwise noted. As Serge mentioned, we exceeded the top end of our guidance range, and total revenue for the third quarter was $149 million. This was down 2% year-over-year and up 2% sequentially, excluding one-time license and royalty revenue in the second quarter.
What went well
- Q3 total revenue of $149 million exceeded the top end of the guidance range despite continuing macro challenges.
- Spatial consumables revenue was $35.4 million, up 19% year-over-year, driven by Xenium consumables, with sustained growth in both number of runs and average spend per run.
- Double-digit Chromium consumables reaction volume growth year-over-year, driven by Flex and On-Chip Multiplexing, opening new customers and use cases; Services revenue up 29% on Xenium service plans.
- Began shipping next-generation Chromium Flex and Xenium Protein (first-of-its-kind RNA and protein on the same section in a single run), with phenomenal early-access feedback.
- Ended the quarter with $482 million in cash, up $35 million from the prior quarter, reflecting continued cost and cash discipline.
What went wrong
- Total revenue of $149 million was down 2% year-over-year, and Chromium consumables revenue ($92.5M) declined 4% primarily on lower average selling prices.
- Total instrument revenue was $12 million, down 37% (Chromium instruments -36%, spatial instruments -38%), driven primarily by lower average selling prices amid constrained capital spending.
- Americas revenue was $79.9 million, down 9% year-over-year on continued U.S. academic and government funding uncertainty.
- Gross margin declined to 67% from 70% on changes in product mix and higher inventory write-downs; operating loss of $32.2 million and net loss of $27.5 million.
Guidance Changes
| Metric | Period | Current guidance |
|---|---|---|
| Q4 2025 revenue | Q4 2025 | $154M-$158M, representing 5% growth versus Q3 at the midpoint |
| Year-end budget flush | Q4 2025 | not anticipated this year |
| Q4 instrument vs consumables mix | Q4 2025 | potentially a bit more uptick on the instrument side than in Q3 |
| Government shutdown impact | Q4 2025 | factored into guide; only material effect likely on NIH intramural, a small fraction of business |
| First half 2026 outlook (preliminary) | H1 2026 | no formal guide; first half 2026 anticipated to look similar to second half 2025 |
Performance Breakdown
| Metric | YoY | Note |
|---|---|---|
| Total revenue | -2% ($149M; +2% sequentially ex one-time Q2 license/royalty) | Solid execution amid continuing macro and funding challenges; exceeded top end of guidance. |
| Total consumables revenue | +1% ($127.9M) | Spatial consumables strength partly offset by lower Chromium consumables. |
| Chromium consumables revenue | -4% ($92.5M) | Primarily lower average selling prices, despite double-digit reaction volume growth. |
| Spatial consumables revenue | +19% ($35.4M) | Primarily Xenium consumables, with more runs and higher spend per run including 5K panel adoption. |
| Total instrument revenue | -37% ($12M) | Chromium instruments -36% and spatial -38%, both primarily on lower average selling prices and constrained CapEx. |
| Services revenue | +29% ($8.1M) | Increase in Xenium service plans. |
| Gross margin | 67% vs 70% prior year | Changes in product mix and higher inventory write-downs, partially offset by lower royalties and warranty costs. |
| Total operating expenses | $132.5M vs $147.9M ($15.4M lower) | Lower personnel expenses and lower outside legal expenses. |
| Americas revenue | -9% ($79.9M) | Continued uncertainty in U.S. academic and government funding. |
| EMEA revenue | +10% ($41.6M; +20% sequentially) | Strong spatial consumables performance. |
| APAC revenue | +6% ($27.5M; -14% sequentially) | Year-over-year growth; sequential decline due to prior Q2 customer-driven pull forward in China. |
Earnings Call Themes & Trends
| Topic | Previous mention | Current period | Trend |
|---|---|---|---|
| Xenium vs Visium preference | Early uncertainty over sequencing vs imaging methods | Strong and growing preference for image-based Xenium; increasingly seen as the best solution for most spatial needs | — |
| Next-generation Flex / single-cell elasticity | GEM-X and first Flex driving volume at lower prices | Next-gen Flex shipping with plate-based, automation-friendly workflows; ~20-30% drop in average reaction price expected to be more than made up in volume over time | — |
| AI / virtual cell and perturbation | Emerging interest | Increasing momentum around virtual cell efforts and large perturbation studies; next-gen Flex enables massive perturbation screens | — |
| Translational and clinical applications | Growing focus | Especially large and growing opportunity; CLI-SEQ/Weizmann periblood clinical trial cited as example of single-cell in diagnostics | — |
| Anthropic / data analysis bottleneck | — | Partnership with Anthropic integrates analysis with Claude for life sciences via a conversational interface to address the analysis bottleneck | — |
Q&A Summary
The Q4 guide calls for a 5% sequential pickup; how much is instruments vs consumables, what about the shutdown, and what does it imply for 2026?
Slightly more uptick expected on the instrument side in Q4 than Q3, with no big year-end flush assumed; the government shutdown is factored in, with NIH intramural a low percentage of business. It is too early to guide 2026, but the first half of 2026 is broadly anticipated to look similar to the second half of 2025.
How should we think about spatial consumables into Q4 and 2026, and the impact of Flex V2's pricing/flexibility?
Normalizing for the Q2 Asia pull forward, spatial stepped up sequentially in Q3 and is expected to continue. Flex V2 fits a multi-year elasticity strategy of staged price reductions (GEM-X, On-Chip Multiplexing) that has consistently lifted reaction volumes; the new Flex carries roughly a 20-30% drop in average reaction price expected to be more than made up in volume, especially over time.
Can you add color on Xenium vs Visium contributions and per-system utilization dynamics?
Pull-through is not shared given a dynamic environment, but Xenium usage has trended consistently up both broadly and on a per-instrument basis, along both more runs and higher price per run, with the overall trend favoring Xenium over Visium.
On the competitor's acquisition of an instrument-free single-cell company aiming at 500,000 labs and diagnostics, can you respond?
It validates the space and single cell's enormous potential. The space has long been competitive with large players, and 10x has consistently won on technology leadership, performance, data quality, robustness and ease of use, with off-the-charts NPS; the performance gap has widened over the years and the fundamental dynamic is not expected to change.
What drove strong spatial performance in Europe and is it sustainable?
The company cautions against over-indexing on any single quarter or region as results can be lumpy, but Q3 was a great quarter for Xenium/spatial consumables in Europe, part of a broader worldwide trend expected to generally continue.
What are you seeing in China given the Q2 pull forward?
Go-to-market changes made a couple of years ago have yielded benefits with a strong team, good distributor relationships and improved visibility and execution, plus robust on-the-ground demand; China has different dynamics requiring caution on long-term visibility, but business and progress are currently good.
What is the early feedback on Xenium Protein and differentiation, and on single-cell consumables trends?
Xenium Protein is the first product to measure RNA and protein from the same section in one integrated workflow, with very positive early feedback and seen as the first step in a promising multi-omics direction; Xenium shows tremendous differentiation and consistently tops benchmarks. Single-cell reaction and volume growth is encouraging, with pricing headwinds from lower price-point configurations and macro headwinds on year-over-year comparisons, but a nice sequential step up in reactions and revenue.
On the preference for Xenium over Visium, what is the outlook for Visium, and what share of customers use Flex and Xenium together?
It is too early to quantify combined Flex-plus-Xenium usage, but it is a consistent emerging theme especially among translational customers with FFPE samples seeking the most comprehensive analysis; the trend of customer convergence and enthusiasm toward Xenium is seen as just beginning.
What is your latest thinking on Chromium elasticity with the new Flex assay, and what interim single-cell growth?
Volume growth has been consistently encouraging and aligned with the strategy of staged price reductions (GEM-X, On-Chip Multiplexing, new Flex) opening new use cases and customers; some current users convert, creating price headwinds, and it is too early to tell where the new-product steady state sits relative to existing products, but progress and volume growth have been pleasing.
Looking at the first half of 2026 and the government shutdown specifics for Q4?
For Q4 the only material shutdown effect is likely on intramural NIH, a very small fraction of the business, with the rest able to proceed independently; the bigger risk is if funding trends persist into 2026, so the company refrains from 2026 guidance, while first half 2026 is broadly expected to resemble the second half of 2025.
What impact from NextGEM end-of-life at year-end as customers transition to GEM-X?
There is not much left for the customer base to transition; end-of-life notices were given and customers have run experiments accordingly, so the bulk of the top-line/P&L effect has already occurred and what remains is pretty marginal.
What about Xenium 5K panel adoption and how much of Xenium consumable growth is from higher pricing?
Xenium consumables have grown via more runs, more runs per instrument and higher price per run, with a large part of the increased price per run coming from 5K panel adoption, which is going great and expected to remain a strong driver.
More on 10x Genomics, Inc.
Reported 2025-11-06 · figures from the 10x Genomics, Inc. Q3 2025 earnings call.
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