10X Genomics - Earnings Call - Q3 2025

Executive Summary

• TXG beat Street on both revenue and EPS: Q3 revenue $149.0M vs S&P consensus $142.6M (+4.5%) and GAAP EPS -$0.22 vs -$0.28, aided by spatial momentum and disciplined OpEx control; gross margin 67% (down 300 bps YoY) on mix and inventory write-downs. Consensus values marked with an asterisk are from S&P Global.*
• Underlying trajectory improved sequentially: excluding Q2’s $27.3M one-time license/royalty, revenue grew ~2% QoQ; cash/marketable securities rose by $35M to $482.1M, reinforcing liquidity in a challenged funding environment.
• Q4 revenue guide $154–$158M implies ~5% QoQ growth at the midpoint and sits around Street ($156.0M*); management does not assume a typical year-end budget flush and has factored a potential U.S. government shutdown into the outlook.
• Product catalysts: shipments of next-gen Chromium Flex (plate-based multiplexing) and launch of Xenium Protein (integrated RNA+protein spatial multiomics) support scale and multiomic adoption; Anthropic collaboration lowers analysis barriers for single-cell/spatial via natural language interfaces.

What Went Well and What Went Wrong

What Went Well

• Revenue/EPS beat and guide: Q3 revenue $149.0M exceeded both company Q3 guide ($140–$144M) and Street, with Q4 guide $154–$158M calling for ~5% QoQ growth at midpoint.
• Spatial strength: Spatial consumables $35.4M, +19% YoY, with rising runs and price per run; management highlights growing preference for image-based Xenium and early positive feedback on Xenium Protein.
• Balance sheet/cash generation: Cash and marketable securities ended Q3 at $482.1M (+$35M QoQ), providing flexibility to invest through macro uncertainty. CEO: “Our strong balance sheet and disciplined execution give us confidence… to drive long-term growth.”

What Went Wrong

• Instrument softness and gross margin pressure: Instruments $12.0M (-37% YoY) as ASPs declined; gross margin contracted to 67% (from 70%) on mix and higher inventory write-downs.
• Americas weakness and macro: Americas revenue $79.9M (-9% YoY) on U.S. academic/government funding uncertainty; management embedded no “budget flush” in Q4.
• Price headwinds in single-cell: Chromium consumables $92.5M (-4% YoY) as average reaction prices fell during Flex/On-Chip Multiplexing transitions; elasticity expected to offset over time, but near-term revenue impact persists.

Transcript

Dan Brennan (Senior Analyst)

Thank you for standing by. Welcome to the 10x Genomics Q3 2025 earnings conference call. All lines have been placed on mute to prevent any background noise. After the speaker's remarks, there will be a question-and-answer session. If you would like to ask a question during this time, simply press the star followed by the number one on your telephone keypad. If you would like to withdraw your question, please press the star once again. Thank you. I would now like to turn the conference over to Cassie Corneau, Senior Director, Investor Relations and Strategic Finance. You may begin.

Cassie Corneau (Senior Director of Investor Relations and Strategic Finance)

Thank you, and good afternoon, everyone. Earlier today, 10x Genomics released financial results for the third quarter ended September 30, 2025. If you have not received this news release or would like to be added to the company's distribution list, please send an email to [email protected]. An archived webcast of this call will be available on the Investor tab of the company's website, 10xgenomics.com, for at least 45 days following this call. Before we begin, I'd like to remind you that management will make statements during this call that are forward-looking statements within the meaning of federal securities laws. These statements involve material risks and uncertainties that could cause actual results or events to materially differ from those anticipated, and you should not place undue reliance on forward-looking statements.

Additional information regarding these risks, uncertainties, and factors that could cause results to differ appears in the press release 10x Genomics issued today and in the documents and reports filed by 10x Genomics from time to time with the Securities and Exchange Commission. 10x Genomics disclaims any intention or obligation to update or revise any financial projections or forward-looking statements, whether because of new information, future events, or otherwise. Joining the call today are Serge Saxonov, our CEO and co-founder, and Adam Taich, our Chief Financial Officer. We will host a question-and-answer session after our prepared remarks. We ask analysts to please keep to one question so that we may accommodate everyone in the queue. With that, I will now turn the call over to Serge.

Serge Saxonov (CEO)

Thanks, Cassie. Good afternoon, everyone. We exceeded the top end of our guidance range in the third quarter with total revenue of $149 million. Our team delivered a solid quarter, executing well in the midst of continuing macro challenges. Despite ongoing funding pressures and policy uncertainty, we saw sustained enthusiasm for our products with momentum in both single-cell and spatial. The positive trends we highlighted in the first half of the year continued this quarter. 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. We frequently hear from customers how much they love Xenium, both for its exceptional performance and for the breadth of applications unlocked by the platform.

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. Both of them deliver configurations with lower price per sample, which has been opening up new customers and new use cases for single-cell. On-Chip Multiplexing is particularly well-suited for applications requiring fewer cells and for getting started with single-cell. Because of that, it has been great for bringing new customers into the ecosystem. Flex has many benefits and is becoming the default single-cell assay for many of our customers. 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. Finally, we ended the quarter with $482 million on the balance sheet, reflecting our ongoing commitment to cost management and cash generation.

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. We're staying extra close to our customers as they navigate persistent funding uncertainty. While the pace of news flow has moderated compared to earlier in the year, spending behavior remains cautious, particularly for capital expenditures. We expect these conditions to remain largely unchanged in the near term, and we will stay flexible in how we work with customers to support their ongoing research. While the macro environment remains challenging, we remain focused on advancing our innovation roadmap and driving greater adoption of our products. Our latest product launches and partnerships illustrate how we're executing on these priorities. Last week, we began shipping the next generation of Chromium Flex.

As I mentioned earlier, our Flex assay is becoming the default single-cell assay for many of our customers. It combines exceptional sensitivity, robustness, and scalability, all at a low cost. Our next generation Flex further improves these qualities and also enables streamlined, automation-friendly, plate-based workflows. The product represents a step change in scale, enabling massive perturbation screens and supporting AI-driven initiatives such as virtual cell modeling. We also developed and validated our scalable FFPE dissociation protocol, which scales easily to 96 well plates. The protocol improves efficiency and throughput for high-volume studies and strengthens the assay's value in large-scale translational research. Feedback from early-access customers has been phenomenal, and we're eager to see how more researchers apply the new Flex across a wide range of studies. We were also excited to start shipping Xenium Protein earlier in Q3.

It is a powerful new addition to the Xenium platform that allows researchers to detect RNA and proteins in the same cell and on the same tissue section, all in a single automated run. By reducing the need for separate workflows, technologies, or tissue sections, Xenium Protein simplifies experimental design and allows researchers to move more quickly from experiment to insight. As a first-of-its-kind capability, Xenium Protein represents a major leap forward, enabling comprehensive multimodal insights, streamlining workflows, and accelerating translational discovery. We're also seeing an increasing number of customers use Xenium together with Chromium Flex. The combination of highly precise spatial measurements and robust ultra-encryptome analysis provides a powerful approach for biomarker discovery in FFPE samples. This is a great example of the value that our portfolio strategy delivers to our customers. Now, stepping back, the landscape of spatial biology has evolved significantly over the past few years.

In the early days, there was broad uncertainty across the field about which applications would be best served by sequencing-based methods like Visium and which by imaging-based approaches like Xenium. Now that Xenium has been in the hands of researchers for some amount of time, that picture is becoming more clear. We now see a strong and growing preference for image-based analysis. This is a reflection of both how well Xenium works and the abundance of insights that scientists are gaining from using the platform. Based on customer feedback and the results we're seeing in the field, we increasingly see Xenium as the best solution for most of researchers' spatial needs. In addition to advancing our product roadmap, we're focused on unlocking the full potential of our current products by removing barriers to adoption and driving broader access.

Data analysis has long been one of the biggest bottlenecks in single-cell and spatial research. Our recent partnership with Anthropic helps address this issue and makes analysis more accessible by integrating it with Claude for life sciences. With Claude, researchers can now perform common analytical tasks through a conversational interface that complements our existing computational workflows. This intuitive approach makes it faster and easier for researchers to engage directly with their data. We believe this partnership is the first step towards addressing the analysis bottleneck to make our technologies more accessible to an ever-broader community of scientists. While single-cell and spatial have been the transformative engine for scientific discovery, going forward, we believe there is an especially large and growing opportunity in translational research and ultimately in clinical applications. A great example of this is our recent collaboration with CLI-SEQ and the Weizmann Institute on a periblood clinical trial.

Using Chromium to profile thousands of individual cells from blood samples, this new study built on a groundbreaking discovery recently published in Nature Medicine, where CLI-SEQ and Weizmann researchers identified a unique circulating cell signature capable of detecting hematologic disorders with remarkable accuracy. Their clinical trial uses single-cell to validate, refine, and amplify that proof of concept, uncovering molecular signals that traditional blood tests may miss and determining whether bone marrow biology can be accurately assessed through circulating cells. This work represents a promising step toward more accessible and less invasive diagnostics and improving clinical decision-making. Finally, we're continuing to see increasing momentum around virtual cell efforts and large perturbation studies. Described as a holy grail of science, the virtual cell is an AI model trained on massive amounts of data meant to simulate the workings of individual cells.

Multiple groups are now generating large-scale 10X single-cell data to train algorithms as initial steps toward the virtual cell vision. There are strong reasons to expect that scaling of data will result in vastly more capable models, as it has in just about every other application of artificial intelligence. These models hold the promise of transforming science, drug discovery, and ultimately human health. We believe that virtual cell efforts represent one of the most important trends in biology in the coming years. We anticipate that our technologies will keep powering these efforts as they keep scaling by orders of magnitude. The strong resonance of our innovations with customers and the expansion of our tools into translational research and large-scale experiments reinforces our conviction in the foundational role of single-cell and spatial in advancing science and health. We firmly believe that this is still very early days for our technologies.

With that, I'll turn the call over to Adam to review the financials.

Adam Taich (CFO)

Thank you, Serge. 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. As anticipated, revenue from scale was not material and accounted for less than $1 million. Total consumables revenue was $127.9 million, up 1%. Chromium consumables revenue was $92.5 million, down 4%, primarily driven by lower average selling prices. Spatial consumables revenue was $35.4 million, up 19%, primarily driven by Xenium consumables revenue.

Moving on to instruments, total instrument revenue was $12 million, down 37%. Chromium instrument revenue was $4.9 million, down 36%, and spatial instrument revenue was $7.1 million, down 38%, both driven primarily by lower average selling prices. Services revenue was $8.1 million, up 29%, primarily due to an increase in Xenium service plans. Looking at our revenue by geography, Americas revenue was $79.9 million, down 9% from the prior year, driven by continued uncertainty in the U.S. academic and government funding environment. Excluding settlement impacts from Q2, Americas was up 1% sequentially. AMEA revenue was $41.6 million, up 10% from the prior year, and up 20% sequentially, primarily driven by strong spatial consumables performance. APAC revenue was $27.5 million, up 6% year-over-year and down 14% sequentially due to the previously mentioned Q2 customer-driven pull forward in China.

Turning to the rest of the income statement, gross profit for the third quarter was $100.3 million compared to $106.4 million for the prior year period. Gross margin decreased to 67% from 70% the prior year, primarily driven by changes in product mix and higher inventory write-downs, partially offset by lower royalties and lower warranty costs. Total operating expenses for the third quarter decreased to $132.5 million compared to $147.9 million for the prior year period, driven by lower personnel expenses and lower outside legal expenses. Operating loss for the third quarter was $32.2 million compared to an operating loss of $41.5 million in the third quarter of last year. Net loss for the period was $27.5 million compared to a net loss of $35.8 million for the third quarter of last year.

We ended the quarter with $482 million in cash, cash equivalents, and marketable securities, up $35 million from the prior quarter. Turning to our outlook for the fourth quarter, we anticipate revenue to be in the range of $154 million-$158 million, representing 5% growth compared to Q3 at the midpoint. This outlook reflects the continuation of the key positive drivers of performance that we've seen throughout this year. We do not anticipate a material change in customer purchasing behavior and do not anticipate the year-end budget acceleration we have previously experienced in the fourth quarter. Our balance sheet remains strong, providing the flexibility to invest in innovation, advance our strategic initiatives, and support long-term growth. We are confident in our ability to execute with discipline and agility as market conditions evolve, and we remain focused on creating durable value for our customers and shareholders.

With that, I'll turn the call back to Serge.

Serge Saxonov (CEO)

Thanks, Adam. Before we open the line for questions, I'd like to take a moment to thank the entire 10x team. This year has been incredibly tough for our customers. For that reason, it has also been really challenging for our team. Yet, you have worked relentlessly through the challenges, keeping focus on our customers and on advancing our mission. I deeply appreciate how our field teams work so closely and creatively with researchers, how our R&D teams keep pushing forward with new product development, and how our entire team has stepped up to the challenge with really tight execution. When I reflect back on the history of our company, going back to the earliest garage days, the periods of greatest value creation often coincided with the lowest external valuations. This feels very much like one of those moments.

Through your efforts, we have forged increasingly powerful bonds with our customers, advanced our roadmap, and made tons of progress improving our internal capabilities. We're executing from a position of strength with an unmatched innovation engine, expanding adoption, and a strong balance sheet that gives us the flexibility to invest for the long term. I'm proud of what we've achieved and confident that our best work and our greatest impact lie ahead. With that, we will now open it up for questions. Operator?

Dan Brennan (Senior Analyst)

Thank you. We will now begin the question-and-answer session. If you have dialed in and would like to ask a question, simply press the star followed by the number one on your telephone keypad to raise your hand and join the queue. If you would like to withdraw your question, simply press the star one again. With that, your first question comes from the line of Doug Schenkel with Wolfe Research. Please go ahead.

Madeline Mollman (Research Analyst)

Hi, this is Madeline Molman on for Doug. The guide calls for a 5% sequential pickup. Can you walk through how much of that is expected to come from instruments versus consumables, especially given you're not assuming a year-end budget flush? What assumptions are built into the Q4 guide regarding the government shutdown? Finally, what does this mean for 2026? Given the quarter-over-quarter improvement, it seems like you should be able to grow in 2026, adjusted for the royalties payments. Is that the right way to think about things?

Adam Taich (CFO)

Great. Thanks for the question, Madeline. I think as it relates to instruments versus consumables, we're not anticipating a big year-end budget flush, but I would anticipate potentially a little bit more of an uptick on the instrument side in Q4. If you just sort of think about that mix between consumables and instruments, it could be a little bit higher on the instrumentation side in Q4 versus what we saw in Q3. We've factored the government shutdown into our guide. To the extent that that does last to the end of this year as it relates to our Q4 guidance, that's incorporated. As a reminder, from an intramural perspective, NIH intramural is a fairly low % of our total overall business. Serge, you want to take the 26th?

Serge Saxonov (CEO)

Yeah. On 2026, so fundamentally, it's too early for us to really talk about 2026. Obviously, we're seeing great trends in the business right now. But there's also a lot of just fundamental uncertainty in the macro environment. Visibility among our customers is quite limited, and there is a lot of uncertainty still around the policy environment. We're not giving a guide. Big picture-wise, at this stage, we anticipate the first half of 2026 should look similar to the second half of 2025. We'll take it from here.

Dan Brennan (Senior Analyst)

Thank you. The next question comes from the line of Juanit Soto with Learning Partners. Please go ahead.

Juanita Soto (Assistant Service Manager)

Yeah. Hi, guys. Thanks for taking my questions. The first one is really on the spatial side. Just wanted to get a sense on how should we think about that in the fourth quarter and then potentially, especially the consumables into 2026. You came in flat to slightly down in the third quarter, so just wanted to clarify on the consumable side there. Serge, when we think about the GEM-X, the Flex V2 product that you're launching here, I just want to clarify, you have a barcode oligohybridization step that is built into it that does give significant flexibility both in terms of the number of samples that can be run and the ability to run partial plates as well. When we think about.

Customers doing lesser batching and the price per sample, which seems to be now in the sub-$300 range versus the $1,000 before, how should we think about the medium to near-term impact? I mean, I appreciate longer-term, this is going to be an elasticity of demand that could play out here. In the near to medium term, why should this not impact the revenue growth? And please let me know if any of my assumptions are wrong there. Thank you.

Serge Saxonov (CEO)

Yeah. Maybe on the spatial consumable side, first, one thing that I would just point out about this quarter is that you may remember we had a pull forward in Asia of spatial consumables into Q2 from Q3. If you kind of normalize for that, we actually had a nice sequential step up in Q3. As I mentioned, spatial has been doing quite well. Spatial consumables have been doing well. We anticipate that to continue. All the trends are pointing generally well in that direction. As far as the question on Flex V2, I mean, those are definitely astute observations around how the product works and the fact that it gives a lot of flexibility to our customers. Maybe a little bit of a step back just in terms of our overall general strategy here is merited.

We started talking about this some time ago about the fact that there's a huge elasticity potential in this market in single cell. We started lowering our prices, for example, in a very kind of careful staged manner, starting with the GEM-X introduction about a year and a half ago. Since then, with the introduction of new products like on-chip multiplexing, like the first iteration of GEM-X Flex about a year ago, kind of opening up new use cases, new configurations to drive more volume at lower prices. What we have seen is that consistently over that time, the reaction growth and volume growth has been stepping up as we've been expanding and very much in resonance with the strategy that we have put out there. The numbers line up with the strategy.

The feedback of customers also lines up with our strategy in terms of new use cases opening up, new configurations, and people running more single cell than they were doing before. The launch of the next generation of Flex now also is part of that overarching strategy where we're delivering new configurations into the marketplace to a large extent. Where it's able to be particularly impactful is enabling people to learn larger experiments. It's really at least sort of larger experiments that you do get to lower per sample and per cell prices. We want to be careful in the sense that the product, this new Flex, doesn't have exactly the same sort of configurations that the previous versions did. Overall, if you compare kind of on average, it's probably there's a 20%-30% drop in the average reaction price.

We do anticipate that this will be more than made up in volume, especially over time. That would be consistent, again, with the feedback that we've been hearing from customers and with the metrics we've been tracking internally over the course of the past year and a half.

Dan Brennan (Senior Analyst)

Thank you. The next question comes from the line of Dan Arias with Stifel. Please go ahead.

Dan Arias (Managing Director)

Yeah. Afternoon, guys. Thanks. I'll ask one since that's what you asked for. Wanted to ask a follow-up question on spatial consumables, though. Serge, can you just maybe add some color to the contributions from Xenium and Visium? I mean, I know you don't like talking about per system pull-through, but it is a tough modeling exercise for spatial just given the two product lines. Is there anything you can kind of shed light on when it comes to user dynamics per box, if possible? Anything there would be helpful just when it comes to keeping our model straight for these two product lines here. Thanks.

Serge Saxonov (CEO)

Yeah, Dan, thanks for the question. Kind of as I was alluding to in my prepared remarks, spatial in general has been a very dynamic field. There's also this broad uncertainty around how the application, the space is going to play out relative to our platforms or relative to our products, especially between Visium and Xenium. One of the things that I made sure to emphasize early is that we're seeing more and more enthusiasts for Xenium in particular. Very consistent increase in usage of the platform. Not just the broad usage, although we're seeing that in the consumable numbers, pretty consistent uptake, but also on a per instrument basis. We haven't shared pull-throughs, and it's still quite a dynamic environment for us to be able to do that.

It has been trending consistently in the right direction. Also, like I said, along sort of both the vector of more runs and also price per run. Also, back to my earlier point, in general, the trend has been more towards Xenium when you, relative to Visium and among the two products.

Dan Brennan (Senior Analyst)

Thank you. The next question comes from the line of Kyle Nixon with Kennicor. Please go ahead.

Kyle Nixon (Assistant VP)

Hey, guys. Thanks for the questions. Congrats on the quarter. I want to just address the acquisition this week from a large company about the instrument-free solution company, similar to yours in scale, a little bit larger situation now. This acquirer is going to provide access to the single cell tech to 500,000 labs globally. They're going to incorporate a 100-million-cell data set into their software and pathway analysis. They're also going to integrate single cell into pharma container diagnostics. Just would love to hear, Serge, if you have an answer to these kinds of aspirations over time. Can you do these things organically, possibly? Thanks.

Serge Saxonov (CEO)

Thanks, Kyle. Yeah. I mean, look, first of all, kind of big picture-wise. One way to look at it is that it certainly validates the space. We've been saying for a long time that single cell fundamentally has enormous potential going forward. And along multiple axes, right? It's the fundamental unit of biology. This is where biology needs to go. That's ultimately where clinical applications and drug development needs to go. Yeah, we're glad to see others agree with that assessment. Overall, the space has always been competitive. Certainly over the past several years, but even from the very, very beginning. Also, it has had quite a number of large and significant companies operate in that space.

We have consistently won with our products by virtue of our technology leadership, by virtue of the performance of our product, data quality, robustness, ease of use, just a wide breadth of applications. We certainly expect that to continue. Customers consistently choose us. There is always this sort of pattern of as new technologies come in, people trial them. The customers come back to us for all the reasons I just mentioned. We see that reflecting in our customer service, in double-blind MPS, which are off the charts, especially relative to our competitors. All of these metrics trend in our direction, and our leadership, we expect, for our leadership to continue. If anything, the gap in performance between our products and others has increased over the past several years, given all the product launches that we have had.

Yeah, we do anticipate that it's going to stay this way. I fundamentally don't anticipate, don't expect that the fundamentals of the dynamic will really change.

Dan Brennan (Senior Analyst)

Thank you. The next question comes from the line of David Westenberg with Piper Sandler. Please go ahead.

David Westenberg (Managing Director)

Hi. Thanks for taking the question. I'll just ask one short one since you have a lot in line. Can you talk about the strong spatial performance in Europe? Is there any reason to believe that there's sustainability there? Is there anything to call out in terms of one time? Thank you very much. Great job on the quarter.

Serge Saxonov (CEO)

Thanks, Kyle. Yeah. I mean, look, we want to be careful not to over-index on any particular quarter in any particular region. These things tend to be lumpy, and there tend to be fluctuations quarter to quarter. That said, yeah, for sure, we had a great quarter in terms of spatial consumables, in terms of Xenium consumables in Europe. I think that's part of the broader trend we're seeing across the world. We do expect that to generally continue.

Dan Brennan (Senior Analyst)

Thank you. The next question comes from the line of Dan Brennan with TD Cowen. Please go ahead.

Hey, good afternoon. This is Kyle on for Dan. Just wanted to ask about China, sort of what you're seeing there. I know you had some pull forward in the second quarter that you just talked about earlier. I think year over year, you still grew a little bit in China off of not an easy comp. I guess, what are you seeing over in China?

Serge Saxonov (CEO)

Yeah. I mean, good question. Just to kind of step back a little bit, you may remember that we made a number of changes to kind of our go-to-market in China a couple of years ago after a number of challenges that we faced there. That has yielded great benefits. We have a great team, great organization, great relationship with the distributors and partners over there, which has increased both visibility and execution in that region. You are seeing some of the outcomes of that. We are also seeing quite good robust demand on the ground for our products there as well. That has also been quite gratifying to see. Overall, of course, China has very different dynamics from the rest of the world. We have to be cautious about long-term visibility there.

Overall, right now, we're certainly seeing good business and good progress in the region.

Operator (participant)

Thank you. The next question comes from the line of Tycho Peterson. Hey, Jeffrey, please go ahead.

Hey, guys. This is Lauren on for Taiko. Congrats on the quarter. On the Xenium, could you maybe elaborate a little bit more on kind of early adoption trends for Xenium Protein and kind of how these multi-omic workflows are resonating with customers and kind of maybe which end markets are you seeing the strongest demand? In terms of kind of differentiation, there are other competitors kind of talking about spatial offerings and what do you think about that in terms of differentiation for Xenium? Lastly, just on single cell consumables that were down, what do you think is needed going into the end of the year, into 2026, to see recovery for single cell? Thanks.

Serge Saxonov (CEO)

Yeah. Let me start there with the protein product. That is something that obviously has been a big trend. I talked about this earlier in my prepared remarks, kind of the whole notion of multi-omics and being able to measure multiple analytes from the same sample, from the same cell, from the same tissue section. I want to kind of emphasize the fact that this is the first product of its kind that can measure both proteins and RNA expression from the same exact section using the same integrated workflow. That is something that our customers have been asking for and have been very excited to receive. The initial feedback has been very positive. People really appreciate it, really like this capability. Early days, so do not want to say any more on that point, but definitely very promising.

I think this is just kind of the first step in a long, very promising direction. I also would say that there's tremendous differentiation that Xenium has relative to other products on the market. We've talked about that before, just based on the fundamentals of the technology, based on the workflow, based on the data that we've been seeing coming back. It's not been reflected very consistently with customer feedback. All kinds of benchmarks that people have run consistently put Xenium on top. You see that in the numbers. We see that in also competitive situations out there. Our team is consistently winning in the marketplace. Xenium really stands out as a platform. As far as the question on single cell consumables, overall, we are really happy with the progress of reaction growth, volume growth.

Obviously, there are some pricing headwinds that I talked about earlier in terms of kind of new product introductions that are introducing lower price point configurations. Also, obviously, we can't forget the macro headwinds, especially when you're looking at year-over-year comparisons. If you look sequentially, there has been a really nice and robust step up in both in reaction volumes and in overall revenue for single cell consumables. I think that's a very promising sign, and we do expect these trends to continue.

Operator (participant)

Thank you. The next question comes from the line of Lou Lee with UBS. Please go ahead.

Liu Lee (Research Analyst)

Great. Thank you for taking my questions. I wanted to go back to the spatial. You mentioned that the scientists increasingly prefer Xenium over Visium. I wonder, can you talk a little bit about your kind of mobile mass for Visium going forward? Then second question, you also mentioned that people are starting to use it more like flash with the Xenium together. I wonder, can you quantify a little bit in terms of what percentage of your customers are using the two products at the same time? Thank you.

Serge Saxonov (CEO)

Yeah. I mean, in terms of the second question, it's too early to make quantifications. I certainly hear that traveling in the field, especially translational customers that have FFPE samples that they want to be analyzing, and they want to have the most comprehensive possible analysis of those samples. The two products together, the Flex together with Xenium, provides kind of the best, most comprehensive analysis. You get the whole transcriptome, single cell-based analysis using Flex, and then you have this really precise, detailed spatial analysis from Xenium. We see that as still very early in that trend, but it's a consistent theme that I've now heard, pretty consistent across multiple customers. We do expect, kind of back to your first question, the sort of trend of people really converging and being enthusiastic about Xenium. If anything, this is just kind of the beginning of.

This trajectory. We see this happening more and more as, again, researchers kind of talk to each other, where it becomes more and more clear across different applications, across different publications, just how well Xenium works and how quickly you can get from their samples to insights.

Dan Brennan (Senior Analyst)

Thank you. The next question comes from the line of Michael Riskin with Bank of America. Please go ahead.

Micheal Riskin (VP)

Great. Thanks for taking the question. You talked earlier about some of the academic and government trends and end-of-year budget flush. I want to dig a little bit more on pharma behavior, what you're seeing there as you're going into the end of the year. There's been a lot of concern on some budget constraints and just some cautious spending. Just wondering if you've noticed any change on that in the last couple of months and if you're getting just any more fruitful conversations with pharma customers. Thanks.

Serge Saxonov (CEO)

Yeah. Thanks, Mike. Yeah. Pharma has been kind of a challenging segment. We're very happy to have the full biopharma team in place, which, again, we made those changes last year. It has been very helpful to have focus teams, especially in this kind of environment. The macro has been challenging. There's just fundamental uncertainty around kind of long-term questions for pharma where to invest because of various policy questions. Especially a lot of uncertainty for them investing in early discovery, early-stage research, which is where our products have been traditionally focused on. As this sort of right now, it's a little too hard to tell precisely how the rest of the quarter is going to play out. There's definitely some areas of positive trends that we're seeing, but also plenty of reasons to be cautious as well.

Kind of in the longer term, we do see a lot of promise. As I mentioned earlier, there's tons of interest in kind of running very large-scale experiments for kind of AI-driven applications for target discovery, very large kind of screening campaigns using single cell. Big trends, still very early in that and very promising. We are also seeing a lot of promise kind of moving downstream in the drug development process into translational applications, especially given our products now with Flex and with Xenium, seeing a lot of potential there as well. We will see how sort of the rest of the quarter plays out. We are in a period of a lot of uncertainty at this point still.

Operator (participant)

Thank you. The next question comes from Justin Bowers with Deutsche Bank. Please go ahead.

Justin Bowers (CFA)

Hi, good afternoon. Sir, what's your latest thinking on the elasticity of Chromium, especially with the launch of the recent Flex assay? Have the curves crossed? In other words, absent the near-term macro headwinds, what type of growth are we thinking about for single cell in the interim?

Serge Saxonov (CEO)

Yeah. I mean, good question, right? And kind of like as I talked about earlier, we have been consistently encouraged by volume growth and how consistent it has been with our strategy. We have several elements of what we embarked on with our product launches, starting about a year and a half with the launch of GEM-X at a lower price point per sample compared to the previous architecture, NextGem. That has been kind of proceeding through the conversion through our customer base to the point where by the end of this year, we should be largely finished with that conversion. Of course, we launched new products last year as well, and also started shipping the new version of Flex. On-chip multiplexing, which kind of opens up new use cases, new customers.

Flex opens up also new use cases, large configurations, small usage, high cell volume kind of use cases. We do anticipate that we have seen that more and more volume growth. We do also see some conversion of current users, which creates headwinds on price. At this stage, it's probably too early to tell where the sort of steady state of new products is relative to kind of our previous existing products is, but we're in a, the sort of, it's been a pretty steady clip at which new products have been entering their market. We've been very happy with the progress there and the volume growth, especially.

Operator (participant)

Thank you. The next question comes from Patrick Donnelly with Citi. Please go ahead.

Patrick Donnelly (Managing Director)

Hi. This is Brendan on for Patrick. Thank you for taking our questions and congrats on the quarter. I know you guys aren't giving 2026 guidance until the next call, but I wanted to touch on the first half of 2026. Given kind of line of sight into the order funnel and visibility, is the first half of 2026 kind of looking like the first half of 2025, kind of in that mid-single-digit decline area, similar revenue levels when excluding royalties? And then just to touch on the government shutdown further, can you mind breaking out exactly what you guys have factored in for the fourth quarter? Thank you.

Serge Saxonov (CEO)

Maybe on the government shutdown. As Adam mentioned, it's factored into our guide for the quarter. The way to think about it is that at this stage for Q4, really the only material effect is likely to be on intramural NIH, which is a very small fraction of our business for this quarter. The rest of the business is sort of able to proceed independent of the shutdown. Where things start to get potentially more challenging to predict is if it sustains sort of the funding trends into 2026. This is where we are certainly refraining from giving guidance on 2026 or how it's going to play out at this stage.

Operator (participant)

Thank you. The next question comes from the line of Casey Woodring with J.P. Morgan. Please go ahead.

Casey Woodring (Equity Research Analyst)

Hi. This is Jaden on for Casey. Thank you for taking my question. Could you just touch on what impact we can see as NextGen's end-of-life is year-end as customers make that transition over and may take more time to validate an assay or incorporate it into an existing new project? What does the timeline usually look like for customers before they ramp to GEM-X? What near-term impact might that have on the P&L given the lower cost and anticipated ramp in volume? Thank you.

Serge Saxonov (CEO)

Yeah. I mean, I think on the specific question of NextGen to GEM-X transition, at this point, there is not much left for the customer base to transition. We've given people end-of-life notices, and people have been kind of running experiments with that in mind. I anticipate the bulk of the effects or sort of the effect on the P&L on the top line has already—we've already gone through it at this point. What is left is pretty marginal.

Operator (participant)

Thank you. The next question comes from the line of Sibu Nambi with Guggenheim. Please go ahead.

Hi, guys. This is Thomas on for Sibu. Thanks for taking our question. On Chromium instrument discounts, you've mentioned they'll be temporary through the macro uncertainty, but do you anticipate any resistance from customers in purchasing when you return to normalized higher pricing? Or if you can confirm if you'll choose to keep Chromium ASPs at these levels longer term? Thank you.

Serge Saxonov (CEO)

Yeah. I mean, it's a good question. Like we've said before, we have been intentionally very flexible with customers in terms of giving them creative deals and discounts when it makes sense with various products or different payment structures depending on their constraints. There have been a lot of different kinds of constraints that customers have faced over the course of this past year. Our view is that the situation has been so peculiar and so unique in a lot of instances that it really doesn't necessarily translate. Sort of the patterns and the deals that we've given customers really shouldn't set much of a precedent into kind of as we transition into more stable, more normal times.

Operator (participant)

The last question comes from Mason Carico with Stephens. Please go ahead.

Mason Carrico (Research Analyst)

Hi. Good afternoon, and thanks for taking the question. This is Ben on for Mason. Could you give us some insight into Xenium's 5K panel adoption? How much of a tailwind has this been to Xenium consumable growth this year? How much of that growth has just come from the higher pricing there? Thank you for taking the question.

Serge Saxonov (CEO)

Yeah. Good question. Like I said earlier, Xenium consumables have been growing and growing both in terms of the number of runs, number of runs per instrument, and also price per run. A large part of that increased price per run is precisely what you're referring to here, which is the adoption of the 5K panel. It's been going great. Very happy with it. We do expect it to be a good, great driver of business going forward.

Operator (participant)

This does conclude our question and answer session. I would like to thank our speakers for today's presentation, and we thank you all for joining. This now concludes today's conference call. You may now disconnect.