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 .

Financial Results

Summary P&L (GAAP)

Metric	Q1 2025	Q2 2025	Q3 2025
Revenue ($M)	$154.9	$172.9	$149.0
Gross Margin %	68%	72%	67%
Operating Expenses ($M)	$144.8	$95.0	$132.5
Operating Income (Loss) ($M)	$(39.3)	$30.1	$(32.2)
Net Income (Loss) ($M)	$(34.4)	$34.5	$(27.5)
GAAP EPS (diluted)	$(0.28)	$0.28	$(0.22)

Notes: Q2 includes $27.3M license/royalty revenue and a $40.7M gain on settlement; excluding license/royalty, Q2 gross margin was 67% .

Actuals vs S&P Global Consensus (Q3 2025)

Metric	Actual	Consensus	Surprise
Revenue ($M)	$149.0	$142.6*	+$6.4M / +4.5%
GAAP EPS	$(0.22)	$(0.284)*	+$0.06

Q4 2025 context: Company revenue guide $154–$158M vs Street $156.0M*; EPS Street -$0.224*.

Values retrieved from S&P Global.

Revenue by Source

Revenue Source ($M)	Q3 2024	Q2 2025	Q3 2025
Instruments – Chromium	$7.641	$5.727	$4.927
Instruments – Spatial	$11.415	$8.770	$7.072
Total Instruments	$19.056	$14.497	$11.999
Consumables – Chromium	$96.536	$85.788	$92.519
Consumables – Spatial	$29.668	$36.397	$35.373
Total Consumables	$126.204	$122.185	$127.892
Services	$6.299	$8.475	$8.128
Total Products & Services	$151.559	$145.157	$148.019
License & Royalty	$0.095	$27.751	$0.983
Total Revenue	$151.654	$172.908	$149.002

Revenue by Geography (Q3 point-in-time)

Region ($M)	Q3 2024	Q3 2025
United States	$84.723	$77.246
Americas ex-US	$3.099	$2.625
Total Americas	$87.822	$79.871
EMEA	$37.851	$41.624
China	$15.030	$15.189
APAC ex-China	$10.951	$12.318
Total APAC	$25.981	$27.507
Total Revenue	$151.654	$149.002

KPIs and Balance Sheet Trend

KPI	Q1 2025	Q2 2025	Q3 2025
Gross Margin %	68%	72%	67%
Services Revenue ($M)	$7.652	$8.475	$8.128
Stock-Based Comp (Total, $M)	$31.076	$27.245	$25.264
Cash & Mkt Securities ($M)	$426.9	$447.3	$482.1

Guidance Changes

Metric	Period	Previous Guidance	Current Guidance/Update	Change
Revenue	Q3 2025	$140–$144M (8/7/25)	Actual $149.0M	Beat vs guidance high end
Revenue	Q4 2025	—	$154–$158M; ~5% QoQ at midpoint; ~-6% YoY	New quarterly guide
Full-year Revenue	FY 2025	Withdrawn (5/8/25)	Still withdrawn (quarterly guidance only)	Maintained withdrawn
Other items (margins, OpEx, tax)	Q4 2025	—	No quantitative guidance; no year-end budget flush assumed; gov’t shutdown factored	N/A

Earnings Call Themes & Trends

Topic	Previous Mentions (Q1 & Q2 2025)	Current Period (Q3 2025)	Trend
Funding/NIH, macro	Deteriorating U.S. academic/government funding; withdrew FY guide; limited visibility	Shutdown risk factored; no year-end budget flush; visibility still limited	Stable-challenged
Single-cell elasticity/pricing	Reaction volumes up with GEM-X/Flex; price headwinds persist	Double-digit reaction growth again; ~20–30% avg reaction price drop with new Flex configs; volume expected to offset over time	Improving volumes; pricing headwind persists
Spatial momentum (Xenium)	Strong Xenium utilization; per-instrument use rising	Spatial consumables +19% YoY; preference shifting to image-based Xenium; 5K panel tailwind; Xenium Protein launched	Improving
China & tariffs	~$4M pull-forward into Q2; APAC +41% YoY	APAC +6% YoY; sequential down 14% on Q2 pull-forward; go-to-market improved	Normalizing
Product roadmap	Visium HD, Flex v2 teased; Xenium RNA+protein planned	Shipping next-gen Flex (plate-based, automation); Xenium Protein launched	Accelerating
AI/data analysis	ARC Virtual Cell; billion-cell efforts	Emphasis on “virtual cell”; Anthropic/Claude collaboration to ease analysis	Expanding
CapEx/instrument pricing	Discounting to overcome CapEx constraints	Instrument ASP pressure; slight Q4 instrument uptick possible	Stable-challenged
Biopharma demand	Mixed; biotech under pressure; pharma reprioritizing	Cautious near term; large-scale translational and AI-driven screens are promising	Mixed

Management Commentary

CEO Serge Saxonov: “We exceeded the top end of our guidance range in the third quarter with total revenue of $149 million…we saw sustained enthusiasm for our products with momentum in both single-cell and spatial.”
On product cadence: “We began shipping the next generation of Chromium Flex…[and] started shipping Xenium Protein… enabling simultaneous RNA and protein detection on the same tissue section” .
On strategic context: “We increasingly see Xenium as the best solution for most of researchers’ spatial needs…we believe virtual cell efforts represent one of the most important trends in biology in the coming years.”
CFO Adam Taich: “We anticipate [Q4] revenue to be in the range of $154–$158 million…We do not anticipate a material change in customer purchasing behavior and do not anticipate the year-end budget acceleration we have previously experienced.”

Q&A Highlights

Q4 mix and shutdown: Modest instrument uptick versus Q3; shutdown risk is incorporated; NIH intramural exposure is a small % of business .
Pricing elasticity: New Flex lowers average reaction prices ~20–30% but expected to be offset by higher volumes over time; elasticity strategy appears to be working with reaction growth .
Spatial dynamics: Growing preference for Xenium; rising runs and spend per run; per-box usage trending up though no pull-through disclosed .
China: Q2 tariff-driven pull-forward (~$4M) weighed on Q3 sequentially; underlying demand solid; improved visibility from GTM changes .
Instruments/discounting: Temporary discounts used to overcome CapEx constraints; not intended to set long-term ASP precedent .

Estimates Context

Q3 2025 beat: $149.0M revenue vs $142.6M*; GAAP EPS -$0.22 vs -$0.284* .
Q4 2025: Company guides $154–$158M vs Street $156.0M*; Street EPS -$0.224*; company provided no EPS guidance .
Implications: Street models likely lift for spatial consumables and total revenue given Q3 outperformance and Q4 midpoint in line with consensus; EPS revisions modest given GM pressure and continued OpEx discipline .

Values retrieved from S&P Global.

Key Takeaways for Investors

Spatial momentum remains the growth engine (Xenium consumables +19% YoY with rising run counts and spend per run); integrated RNA+protein (Xenium Protein) and plate-based Flex scale should support multiomic adoption and larger studies .
The revenue/EPS beat and a balanced Q4 guide near consensus suggest stabilizing execution despite macro headwinds; lack of a year-end budget flush keeps expectations grounded .
Single-cell pricing headwinds are strategic (to drive elasticity and volume); management sees reaction growth offsetting price over time, aided by Flex V2 scale and automation .
Gross margin compression (67%) reflects mix and inventory write-downs; mix normalization and consumables growth (versus instruments) are key levers to watch into 2026 .
Cash inflected higher to $482.1M; coupled with OpEx control, TXG can continue to invest through uncertainty and pursue strategic M&A/partnerships (Scale Biosciences IP, Anthropic collaboration) .
Macro/funding caution persists (U.S. academic/government), with shutdown risk embedded; watch EMEA spatial strength and APAC normalization post China pull-forward .
Near-term catalysts: broader uptake of new Flex and Xenium Protein, AI-enabled analysis via Claude, and potential translational wins as customers scale projects .

10x Genomics, Inc. (TXG)·Q3 2025 Earnings Summary