10x Genomics Inc.

11/07/2025 | Press release | Distributed by Public on 11/07/2025 05:01

Quarterly Report for Quarter Ending September 30, 2025 (Form 10-Q)

Management's Discussion and Analysis of Financial Condition and Results of Operations.
You should read the following discussion of our financial condition and results of operations in conjunction with our unaudited condensed consolidated financial statements and the related notes and other financial information included elsewhere in this Quarterly Report and our audited consolidated financial statements and notes thereto and the section titled "Management's Discussion and Analysis of Financial Condition and Results of Operations" in our Annual Report on Form 10-K for the fiscal year ended December 31, 2024 filed with the SEC on February 12, 2025 (our "Annual Report"). As discussed in the section titled "Special Note Regarding Forward-Looking Statements," the following discussion and analysis, in addition to historical financial information, contains forward-looking statements that involve risks and uncertainties. Our actual results could differ materially from those anticipated in these forward-looking statements as a result of various factors, including those set forth in the section titled "Risk Factors" in this Quarterly Report, in Part II, Item 1A of our Quarterly Report on Form 10-Q for the quarter ended March 31, 2025 and in Part I, Item 1A of our Annual Report.
In addition, statements that "we believe" and similar statements reflect our beliefs and opinions on the relevant subject. These statements are based upon information available to us as of the date of this Quarterly Report and while we believe such information forms a reasonable basis for such statements, such information may be limited or incomplete, and our statements should not be read to indicate that we have conducted an exhaustive inquiry into, or review of, all potentially available relevant information. These statements are inherently uncertain and investors are cautioned not to unduly rely upon these statements.
Overview
We are a life sciences technology company focused on building innovative products and solutions to interrogate, understand and master biology. Our integrated research solutions include instruments, consumables and software for analyzing biological systems at resolution and scale that matches the complexity of biology. Our commercial product portfolio includes our Chromium instruments and our Visium CytAssist and our Xenium Analyzer, which we refer to as "Spatial instruments," and our proprietary microfluidic chips, slides, reagents and other consumables for our Chromium, Visium and Xenium solutions, which we refer to as "consumables." We bundle our software with these products to guide customers through the workflow, from sample preparation through analysis and visualization. Customers purchase instruments and consumables from us for use in their experiments. In addition to instrument and consumable sales, we derive revenue from post-warranty service contracts for our instruments.
Since our inception in 2012, we have incurred net losses in each year. Our net losses were $27.5 million and $27.3 million for the three and nine months ended September 30, 2025 and net losses were $35.8 million and $133.6 million for the three and nine months ended September 30, 2024, respectively. As of September 30, 2025, we had an accumulated deficit of $1.5 billion and cash and cash equivalents, and marketable securities totaling $482.1 million. We expect to continue to incur significant expenses for the foreseeable future and to incur operating losses in the near term.
Acquisition
On August 7, 2025, we entered into an agreement to acquire all outstanding shares of common stock of Scale Biosciences, Inc., a single cell genomics technology company ("Scale"). Upon closing the transaction on August 11, 2025, we made an upfront payment consisting of $9.2 million in cash and $13.5 million (1,099,992 shares) in shares of our Class A common stock. In the first quarter of 2026, we expect to pay $20.0 million, subject to any adjustments, in connection with the technology transfer completed in the third quarter of 2025 and in the future may pay up to $30.0 million of contingent consideration if certain milestones are met.
The transaction was accounted for as an asset acquisition because substantially all of the fair value of the assets acquired is concentrated in the developed technology. We determined that the contingent consideration was within the scope of ASC 480, Distinguishing Liabilities from Equity, because the contingent consideration is payable in cash or shares of our Class A common stock, at our election. The contingent consideration was recorded at fair value as of the acquisition date. Upon closing, we recognized $22.4 million for the fair value of the contingent consideration. Refer to Note 3, Asset Acquisition, in the Notes to condensed consolidated financial statements included in this report, for a description of the fair value measurement of the contingent consideration.
Comparison of the Three and Nine Months Ended September 30, 2025 and 2024
Revenue
Three Months Ended
September 30, 		Change Nine Months Ended
September 30, 		Change
(dollars in thousands) 2025 2024 $ % 2025 2024 $ %
Instruments
Chromium $ 4,927 $ 7,641 $ (2,714) (36) % $ 16,567 $ 24,283 $ (7,716) (32) %
Spatial 7,072 11,415 (4,343) (38) 24,744 44,078 (19,334) (44)
Total instruments revenue 11,999 19,056 (7,057) (37) 41,311 68,361 (27,050) (40)
Consumables
Chromium 92,519 96,536 (4,017) (4) 262,416 274,571 (12,155) (4)
Spatial 35,373 29,668 5,705 19 103,017 85,330 17,687 21
Total consumables revenue 127,892 126,204 1,688 1 365,433 359,901 5,532 2
Services 8,128 6,299 1,829 29 24,255 17,292 6,963 40
Products and services revenue 148,019 151,559 (3,540) (2) 430,999 445,554 (14,555) (3)
License and royalty revenue 983 95 888 935 45,794 210 45,584 21707
Total revenue $ 149,002 $ 151,654 $ (2,652) (2) % $ 476,793 $ 445,764 $ 31,029 7 %
Products and services revenue decreased $3.5 million, or 2%, to $148.0 million for the three months ended September 30, 2025 as compared to the three months ended September 30, 2024. Instruments revenue decreased $7.1 million, or 37%, to $12.0 million for the three months ended September 30, 2025 as compared to the three months ended September 30, 2024. Consumables revenue increased $1.7 million, or 1%, to $127.9 million for the three months ended September 30, 2025 as compared to the three months ended September 30, 2024. Services revenue increased $1.8 million, or 29%, to $8.1 million for the three months ended September 30, 2025 as compared to three months ended September 30, 2024, primarily driven by an increase in service plans for instruments coming off warranty.
Products and services revenue decreased $14.6 million, or 3%, to $431.0 million for the nine months ended September 30, 2025 as compared to the nine months ended September 30, 2024. Instruments revenue decreased $27.1 million, or 40%, to $41.3 million for the nine months ended September 30, 2025 as compared to the nine months ended September 30, 2024. Consumables revenue increased $5.5 million, or 2%, to $365.4 million for the nine months ended September 30, 2025 as compared to the nine months ended September 30, 2024. Services revenue increased $7.0 million, or 40%, for the nine months ended September 30, 2025 as compared to nine months ended September 30, 2024, primarily driven by an increase in service plans for instruments coming off warranty.
In February 2025, the Company settled its worldwide patent litigation with Vizgen, Inc. As part of that settlement, Vizgen has limited rights to certain intellectual property owned or exclusively licensed by the Company. As one part of the settlement, the Company received an upfront payment of $26.0 million and will receive royalties on Vizgen's sales of products covered by the license. The $26.0 million upfront payment was recorded as a $9.2 million gain on settlement and $16.8 million of license and royalty revenue. The amount attributed to the gain on settlement was determined by applying a royalty rate to the Vizgen historical revenues prior to the settlement.
In May 2025, the Company entered into a settlement agreement and license agreements with Bruker Corporation resolving all outstanding litigation and other proceedings between the parties across all jurisdictions around the world. Under the agreements, the Company will receive four quarterly installment payments beginning in the third quarter of 2025, which total $68.0 million and applicable interest. The Company will also receive royalties on Bruker's sales of products and services covered by the licenses. The $68.0 million was recorded as a $40.7 million gain on settlement and $27.3 million of license and royalty
revenue. The amount attributed to the gain on settlement was determined by applying a royalty rate to the historical revenues prior to the settlement.
We expect our revenues to moderately increase sequentially in the fourth quarter of 2025.
Cost of Products and Services Revenue, Gross Profit and Gross Margin
Three Months Ended
September 30, 		Change Nine Months Ended
September 30, 		Change
(dollars in thousands)
2025 2024 $ % 2025 2024 $ %
Cost of products and services revenue $ 48,695 $ 45,261 $ 3,434 8 % $ 145,957 $ 142,237 $ 3,720 3 %
Gross profit $ 100,307 $ 106,393 $ (6,086) (6) % $ 330,836 $ 303,527 $ 27,309 9 %
Gross margin 67 % 70 % 69 % 68 %
Cost of products and services revenue increased $3.4 million, or 8%, to $48.7 million for the three months ended September 30, 2025 as compared to the three months ended September 30, 2024. The increase was primarily driven by higher manufacturing costs of $5.8 million and higher inventory write-downs of $3.5 million due to changes in product mix, partially offset by lower royalties of $4.1 million and lower warranty costs of $1.8 million. Gross margin decreased to 67% primarily due to changes in product mix and higher inventory write-downs, partially offset by lower royalties and lower warranty costs.
Cost of products and services revenue increased $3.7 million, or 3%, to $146.0 million for the nine months ended September 30, 2025 as compared to the nine months ended September 30, 2024. The increase was primarily driven by higher inventory write-downs of $12.3 million and higher manufacturing costs of $5.5 million due to change in product mix, partially offset by lower royalties of $10.3 million and lower warranty costs of $3.8 million. Gross margin increased to 69% primarily due to higher license and royalty revenue and lower royalties and warranty, partially offset by changes in product mix and higher inventory write-downs.
We expect our gross margin to fluctuate through the remainder of 2025 due to the non-recurring benefit in license and royalty revenue experienced in the first half of the year, as well as changes in product mix through the remainder of the year.
Operating Expenses
Three Months Ended
September 30, 		Change Nine Months Ended
September 30, 		Change
(dollars in thousands)
2025 2024 $ % 2025 2024 $ %
Research and development $ 57,194 $ 66,174 $ (8,980) (14) % $ 182,663 $ 197,730 $ (15,067) (8) %
Selling, general and administrative 75,355 81,704 (6,349) (8) 239,517 250,517 (11,000) (4)
Gain on settlement - - - N/A (49,900) - (49,900) N/A
Total operating expenses $ 132,549 $ 147,878 $ (15,329) (10) % $ 372,280 $ 448,247 $ (75,967) (17) %
Research and development expenses decreased $9.0 million, or 14%, to $57.2 million for the three months ended September 30, 2025, as compared to the three months ended September 30, 2024. The decrease was primarily driven by a $5.9 million decrease in personnel expenses, including a $4.7 million decrease in stock-based compensation expense, a $1.9 million decrease in laboratory materials, supplies and equipment, and a $0.9 million decrease in allocated costs for facilities and information technology.
Research and development expenses decreased $15.1 million, or 8%, to $182.7 million for the nine months ended September 30, 2025, as compared to the nine months ended September 30, 2024. The decrease was primarily driven by a $11.3 million decrease in personnel expenses, including a $12.7 million decrease in stock-based compensation expense, a $3.1 million decrease in allocated costs for facilities and information technology and a $1.2 million decrease in depreciation and amortization costs. In May 2025, we had a reduction in force that resulted in restructuring costs of $3.7 million.
Selling, general and administrative expenses decreased $6.3 million, or 8%, to $75.4 million for the three months ended September 30, 2025, as compared to the three months ended September 30, 2024. The decrease was primarily driven by a reduction of $4.9 million in outside legal expenses, a $1.1 million decrease in marketing expenses related to conferences and seminars, and a $0.7 million decrease in personnel expenses, partially offset by a $0.3 million increase in other expense. The three months ended September 30, 2025 includes the Scale assembled workforce impairment of $0.7 million.
Selling, general and administrative expenses decreased $11.0 million, or 4%, to $239.5 million for the nine months ended September 30, 2025, as compared to the nine months ended September 30, 2024. The decrease was primarily driven by a reduction of $9.5 million in outside legal expenses, a $1.2 million decrease in marketing expenses related to conferences and seminars, and a $0.9 million decrease in other expense, partially offset by a $0.5 million increase in personnel expenses. The three months ended June 30, 2025 includes restructuring cost of $1.9 million. The three months ended September 30, 2025 includes the Scale assembled workforce impairment of $0.7 million.
Gain on settlement is a result of the Company settling its worldwide patent litigation with Vizgen in the first quarter of 2025 and Bruker in the second quarter of 2025.
We expect our operating expenses to trend lower in 2025 versus the prior year as a result of our actions to reduce operating costs including our May 2025 reduction in force that resulted in the termination of approximately 8% of our global workforce and additional planned reductions in non-headcount operating expenses.
Other Income (Expense), Net
Three Months Ended
September 30, 		Change Nine Months Ended
September 30, 		Change
(dollars in thousands)
2025 2024 $ % 2025 2024 $ %
Interest income $ 5,199 $ 4,971 $ 228 5 % $ 13,156 $ 14,422 $ (1,266) (9) %
Interest expense 3 (2) 5 (250) - (4) 4 (100)
Other income (expense), net (1,165) 2,078 (3,243) (156) 3,574 982 2,592 264
Total other income $ 4,037 $ 7,047 $ (3,010) (43) % $ 16,730 $ 15,400 $ 1,330 9 %
Interest income increased by $0.2 million, or 5%, to $5.2 million for the three months ended September 30, 2025 as compared to the three months ended September 30, 2024. Interest income decreased by $1.3 million, or 9%, to $13.2 million for the nine months ended September 30, 2025 as compared to the nine months ended September 30, 2024. The decrease was primarily due to lower interest rate, partially offset by higher marketable securities balance during the three and nine months ended September 30, 2025.
Other income (expense), net decreased by $3.2 million to $1.2 million other expense, net for the three months ended September 30, 2025 as compared to $2.1 million other income, net, for the three months ended September 30, 2024. The decrease in other income (expense), net was driven by loss from foreign currency rate measurement fluctuations and the $1.1 million change in fair value of contingent consideration due to the completion of the technology transfer in the third quarter of 2025.
Other income (expense), net increased by $2.6 million to $3.6 million other income, net for the nine months ended September 30, 2025 as compared to $1.0 million other income, net, for the nine months ended September 30, 2024. The increase in other income (expense), net was driven by gain from foreign currency rate measurement fluctuations, offset by the $1.1 million change in fair value of contingent consideration related to the Scale acquisition.
As explained above, we will remeasure the contingent consideration and assumed liabilities related to the Scale acquisition within the scope of ASC 480 as of each applicable reporting period. Upon remeasurement, we expect to record the change in the fair value of the contingent consideration within "other income (expense), net" in the Company's condensed consolidated statement of operations. We expect other income (expense), net, to fluctuate, potentially significantly, from quarter to quarter due to changes in the fair value of the contingent consideration.
Provision for Income Taxes
The Company's provision for income taxes was a tax benefit of $0.7 million and an expense of $2.6 million, respectively, for the three and nine months ended September 30, 2025 and an expense of $1.3 million and $4.3 million respectively, for the three and nine months ended September 30, 2024. The decrease in income tax expense for the 2025 periods was primarily due to the enactment of the One Big Beautiful Bill Act ("OBBBA") on July 4, 2025. Among its provisions, OBBBA restored the immediate deductibility of U.S. research and experimental expenditures, resulting in lower U.S. taxable income and a corresponding reduction in the Company's provision for income taxes.
Liquidity and Capital Resources
As of September 30, 2025, we had approximately $482.1 million in cash and cash equivalents, and marketable securities which were primarily held in U.S. banks. We have generated negative cumulative cash flows from operations since inception through September 30, 2025, and we have generated losses from operations since inception as reflected in our accumulated deficit of $1.5 billion.
We currently anticipate making aggregate capital expenditures of between approximately $15 million and $20 million during the next 12 months, which we expect to include, among other expenditures, equipment to be used for manufacturing and research and development.
In the first quarter of 2026, we expect to pay $20.0 million, subject to any adjustments, in connection with the technology transfer completed in the third quarter of 2025 related to the Scale acquisition. In the future, we may pay up to $30.0 million of contingent consideration if certain milestones are met. The payment is payable in cash or equity at our election.
Our future capital requirements will depend on many factors including our revenue growth rate, research and development efforts, investments in or acquisitions of complementary or enhancing technologies or businesses, the timing and extent of additional capital expenditures to invest in existing and new facilities, the expansion of sales and marketing and international activities, legal costs associated with defending and enforcing intellectual property rights and the introduction of new products and new versions of existing products.
We take a long-term view in growing and scaling our business and we regularly review acquisition and investment opportunities, and we may in the future enter into arrangements to acquire or invest in businesses, services and technologies, including intellectual property rights, and any such acquisitions or investments could significantly increase our capital needs. We regularly review opportunities that meet our long-term growth objectives.
We expect to continue to incur operating losses for the foreseeable future. We believe that our existing cash and cash equivalents and cash generated from sales of our products will be sufficient to meet our anticipated cash needs for at least the next 12 months. However, our liquidity assumptions may prove to be incorrect, and we could exhaust our available financial resources sooner than we currently expect. We maintain the majority of our cash and cash equivalents in accounts with major U.S. and multi-national financial institutions, and our deposits at these institutions exceed insured limits. Market conditions can impact the viability of these institutions. In the event of failure of any of the financial institutions where we maintain our cash and cash equivalents, there can be no assurance that we would be able to access uninsured funds in a timely manner or at all. Any inability to access or delay in accessing these funds could adversely affect our business and financial position.
We intend to continue to evaluate market conditions and may in the future pursue additional sources of funding, such as mortgage or other financing, to further enhance our financial position and to execute our business strategy. In addition, should prevailing economic, financial, business or other factors adversely affect our ability to meet our operating cash requirements, we could be required to obtain funding though traditional or alternative sources of financing. We cannot be certain that additional funds would be available to us on favorable terms when required, or at all.
Sources of liquidity
The following table summarizes our cash flows for the periods indicated:
Nine Months Ended September 30,
(in thousands)
2025 2024
Net cash provided by (used in):
Operating activities
$ 95,273 $ 13,412
Investing activities
(11,633) 18,961
Financing activities
4,561 6,397
Effect of exchange rates changes on cash, cash equivalents, and restricted cash 441 105
Net increase in cash, cash equivalents, and restricted cash $ 88,642 $ 38,875
Operating activities
The net cash provided by operating activities of $95.3 million for the nine months ended September 30, 2025 which consisted of a net loss of $27.3 million, non-cash adjustments of $116.2 million, which included stock-based compensation expense of $83.9 million, depreciation and amortization of $26.1 million, amortization of leased right-of-use assets of $5.6 million and fair value adjustments on contingent consideration of $1.1 million, and a net cash inflow from changes in operating assets and liabilities of $6.4 million. The net cash inflow from operating assets and liabilities was primarily due to a decrease in accounts receivable of $44.5 million due to timing of collections, a decrease in inventory of $22.4 million, an increase in accounts
payable of $3.3 million, a decrease in other noncurrent assets of $2.3 million, an increase in accrued compensation and other related benefits of $2.3 million and an increase in other noncurrent liabilities of $1.3 million. The net cash inflow from operating assets and liabilities was partially offset by an increase in other receivables of $52.2 million related to the Bruker settlement, a decrease in accrued expenses and other current liabilities of $9.9 million and a decrease in the operating lease liability of $7.6 million.
The net cash provided by operating activities of $13.4 million for the nine months ended September 30, 2024 was primarily due to a net loss of $133.6 million, net cash inflow from changes in operating assets and liabilities of $2.6 million, primarily offset by stock-based compensation expense of $108.2 million, depreciation and amortization of $27.1 million, lease and asset impairment charges of $2.5 million, amortization of leased right-of-use assets of $6.0 million, and other non-cash expenses of $0.6 million. The net cash inflow from operating assets and liabilities was primarily due to a decrease in accounts receivable of $31.3 million due to timing of collections, an increase in accounts payable of $10.0 million and an increase in deferred revenue of $8.1 million. The net cash inflow from operating assets and liabilities was partially offset by a decrease in accrued expenses and other current liabilities of $17.1 million primarily driven by payments related to purchase consideration and royalty payments, an increase in inventory of $19.4 million, and a decrease in the operating lease liability of $9.8 million.
Investing activities
The net cash used in investing activities of $11.6 million in the nine months ended September 30, 2025 was due to the purchase of marketable securities of $98.9 million, net cash paid for the asset acquisition of $8.6 million and purchases of property and equipment of $4.2 million, partially offset by maturities of marketable securities of $100.0 million.
The net cash provided by investing activities of $19.0 million in the nine months ended September 30, 2024 was due to proceeds from sales and maturities of marketable securities of $3.9 million and $25.8 million, respectively, partially offset by purchases of property and equipment and intangible assets of $9.7 million and $1.0 million, respectively.
Financing activities
The net cash provided by financing activities of $4.6 million in the nine months ended September 30, 2025 was primarily from proceeds related to the issuance of common stock from the exercise of stock options and employee stock purchase plan.
The net cash provided by financing activities of $6.4 million in the nine months ended September 30, 2024 was primarily from proceeds related to the issuance of common stock from the exercise of stock options and employee stock purchase plan.
Critical Accounting Estimates
Our condensed consolidated financial statements have been prepared in accordance with United States generally accepted accounting principles ("GAAP") for interim financial information and the applicable rules and regulations of the SEC. The preparation of these financial statements requires us to make estimates and assumptions that affect the reported amounts of assets and liabilities and the disclosure of contingent assets and liabilities at the date of the financial statements, as well as the reported revenues and expenses incurred during the reporting periods. Our estimates are based on our historical experience and on various other factors that we believe are reasonable under the circumstances, the results of which form the basis for making judgments about the carrying value of assets and liabilities that are not readily apparent from other sources. Actual results may differ from these estimates under different assumptions or conditions.
During the nine months ended September 30, 2025, there have been no significant changes in our critical accounting policies and estimates as compared to the critical accounting policies and estimates disclosed in the section titled "Management's Discussion and Analysis of Financial Condition and Results of Operations" included in our most recent Annual Report on Form 10-K filed with the SEC on February 12, 2025, except as follows:
Acquisitions of intellectual property
We evaluate acquisitions of assets and other similar transactions to assess whether or not the transaction should be accounted for as a business combination or asset acquisition by first applying a screen test to determine if substantially all of the fair value of the gross assets acquired is concentrated in a single identifiable asset or group of similar identifiable assets. If the screen test is met, the transaction is accounted for as an asset acquisition. If the screen test is not met, further determination is required as to whether or not we have acquired inputs and processes that have the ability to create outputs, which would meet the requirements of a business. We account for an asset acquisition under Accounting Standards Codification, Business CombinationsTopic 805, Subtopic 50, which requires the acquiring entity in an asset acquisition to recognize net assets based on the cost to the acquiring entity on a relative fair value basis, which includes transaction costs in addition to consideration given. Goodwill is not recognized in an asset acquisition and any excess consideration transferred over the fair value of the net assets acquired is allocated to the non-monetary identifiable assets based on relative fair values.
On August 7, 2025, we entered into an agreement to acquire all outstanding shares of common stock of Scale. The transaction was accounted for as an asset acquisition because substantially all of the fair value of the assets acquired is
concentrated in the developed technology. Upon closing the transaction on August 11, 2025, we made an upfront payment consisting of $9.2 million in cash and $13.5 million (1,099,992 shares) in shares of our Class A common stock. In the first quarter of 2026, we expect to pay $20.0 million, subject to any adjustments, in connection with the technology transfer completed in the third quarter of 2025 and in the future may pay up to $30 million of contingent consideration if certain milestones are met.
We determined that the contingent consideration was within the scope of ASC 480, Distinguishing Liabilities from Equity, because the contingent consideration is payable in cash or Class A common shares, at our election. The contingent consideration was recorded at fair value as of the acquisition date. Upon closing, we recognized $22.4 million for the fair value of the contingent consideration. The contingent consideration will be remeasured each reporting period, with changes in fair value recognized within "other income" in our consolidated statement of operations.
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