10x Genomics, Inc.

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1. Description of Business and Basis of Presentation

Organization and Description of Business

10x Genomics, Inc. (the “Company”) is a life sciences technology company focused on building innovative products and solutions to interrogate, understand and master biological systems at resolution and scale that matches the complexity of biology. The Company’s integrated research solutions include the Company’s Chromium instruments and the Company's Visium CytAssist and Xenium Analyzer, which the Company refers to as “Spatial instruments,” and the Company’s proprietary microfluidic chips, slides, reagents and other consumables for the Company’s Chromium, Visium and Xenium solutions, which the Company refers to as “consumables.” The Company bundles its software with these products to guide customers through the workflow, from sample preparation through analysis and visualization. The Company was incorporated in the state of Delaware in July 2012 and began commercial and manufacturing operations and selling its instruments and consumables in 2015. The Company is headquartered in Pleasanton, California and has wholly-owned subsidiaries in Asia, Europe, Oceania and North America.

Basis of Presentation

The accompanying condensed consolidated financial statements, which include the Company’s accounts and the accounts of its wholly-owned subsidiaries, are unaudited and have been prepared in accordance with U.S. generally accepted accounting principles (“GAAP”). The condensed consolidated balance sheet at December 31, 2024 has been derived from the audited consolidated financial statements of the Company at that date. Certain information and footnote disclosures typically included in the Company’s audited consolidated financial statements have been condensed or omitted. The accompanying unaudited condensed consolidated financial statements have been prepared on the same basis as the annual consolidated financial statements and, in the opinion of management, reflect all adjustments, which include only normal recurring adjustments, necessary to state fairly the Company’s financial position, results of operations, comprehensive income (loss) and cash flows for the periods presented, but are not necessarily indicative of the results of operations to be anticipated for any future annual or interim period. All intercompany transactions and balances have been eliminated. The preparation of financial statements requires management to make estimates and assumptions that affect the reported amounts of assets, liabilities, revenue and expenses, and related disclosure of contingent assets and liabilities. Actual results could differ from those estimates.

The accompanying unaudited condensed consolidated financial statements and notes should be read in conjunction with the audited consolidated financial statements and related notes for the year ended December 31, 2024 included in the Company's Annual Report on Form 10-K filed with the SEC on February 12, 2025 (our “Annual Report”).

2. Summary of Significant Accounting Policies

Except as noted below, there were no material changes in the Company’s significant accounting policies during the nine months ended September 30, 2025. See Note 2, Summary of Significant Accounting Policies, to the consolidated financial statements included in the Company’s Annual Report for information regarding the Company’s significant accounting policies.

Revenue Recognition

Products and Services Revenue

The Company generates revenue from sales of products, which consist of instruments and consumables, and services. Revenue from product sales is recognized when control of the product is transferred, which is generally upon shipment to the customer. Instrument service agreements, which relate to extended warranties, are typically entered into for aone-year term, following the expiration of the standardone-year warranty period. Revenue for extended warranties is recognized ratably over the term of the extended warranty period as a stand ready performance obligation. Revenue is recorded net of discounts, distributor commissions and sales taxes collected on behalf of governmental authorities. Customers are invoiced generally upon shipment, or upon order for services, and payment is typically due within 30 days. Cash received from customers in advance of product shipment or the provision of services is recorded as a contract liability. The Company’s contracts with its customers generally do not include rights of return or a significant financing component.

The Company regularly enters into contracts that include various combinations of products and services which are generally distinct and accounted for as separate performance obligations. The transaction price is allocated to each performance obligation in proportion to its standalone selling price. The Company determines standalone selling price using average selling prices with consideration of current market conditions. If the product or service has no history of sales or if the sales volume is not sufficient, the Company relies upon prices set by management, adjusted for applicable discounts.

License and Royalty Revenue

The Company has agreements with third parties that include up-front fees and royalties. Revenue related to the delivery of intellectual property is recognized when the license is delivered to the third parties. Royalty revenue is recognized when the underlying sales occur. If the timing of the reporting of the actual sales from our licensees is after our reporting date, we estimate the royalty revenue receivable at period end and adjust for any changes in estimates in the following period.

Segment Information

The Company operates as a single operating segment. The Company’s chief operating decision maker (“CODM”), its Chief Executive Officer, manages the Company’s operations on a consolidated basis for the purposes of allocating resources, making operating decisions and evaluating financial performance. The measures of profitability and significant segment expenses reviewed by the CODM are consistent with the presentation and disclosure in these consolidated financial statements.

Acquisitions of intellectual property

The Company evaluates 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 the Company has acquired inputs and processes that have the ability to create outputs, which would meet the requirements of a business.

The Company accounts for asset acquisition under Accounting Standards Codification, Business Combinations, Topic 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.

If the Company has the option to pay in equity for contingent consideration related to the acquisition, a liability is recorded in accordance with the guidance of ASC 480, Distinguishing Liabilities from Equity. The contingent consideration is recorded at fair value at inception and is revalued on a quarterly basis for any adjustments and recognized in the Company’s condensed consolidated statements of operations in “Other income (expense), net.”

Reclassification

Amounts related to the royalty revenue in the condensed consolidated statements of operations for the three and nine months ended September 30, 2024 have been reclassified to conform to the current presentation. Amounts related to the other receivables in the condensed consolidated balance sheet as of December 31, 2024 have been reclassified to conform to the current presentation.

Recently Issued Accounting Pronouncement and Disclosure Rules

In December 2023, the Financial Accounting Standards Board (“FASB”) issued Accounting Standard Update (“ASU”) No. 2023-09, Income Taxes (“ASU No. 2023-09”), which prescribes standardized categories and disaggregation of information in the reconciliation of provision for income taxes, requires disclosure of disaggregated income taxes paid, and modifies other income tax-related disclosure requirements. The updated standard is effective beginning with the Company’s fiscal year 2025 annual reporting period. The Company will adopt ASU No. 2023-09 in its fourth quarter of 2025 using a prospective transition method. We are currently evaluating the impact that the updated standard will have on our financial statement disclosures.

In November 2024, the FASB issued ASU 2024-03, Disaggregation of Income Statement Expenses ("ASU 2024-03"), and in January 2025 issued ASU 2025-01, Clarifying the Effective Date ("ASU 2025-01") to provide clarification as to the effective date. ASU 2024-03 requires disaggregated disclosure of income statement expenses. ASU 2024-03 does not change the expense captions currently presented on the income statement; rather it requires disaggregation of certain expense captions into specified categories in disclosures within the footnotes to the financial statements. ASU 2024-03, as amended by ASU 2025-01, is effective for annual reporting periods beginning after December 15, 2026, and interim reporting periods within fiscal years beginning after December 15, 2027. ASU 2024-03 can be applied on a prospective basis; however, retrospective application is permitted. Early adoption is permitted. As ASU 2024-03 only requires additional disclosure, it will not have a material impact on the Company's financial condition and results of operations.

3. Asset Acquisition

On August 7, 2025, the Company 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, the

Company made an upfront payment consisting of $9.2 million in cash and $13.5 million (1,099,992 shares) in shares of the Company’s Class A common stock. In the first quarter of 2026, the Company expects 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. The Company 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 the Company’s Class A common stock, at the Company’s election. The contingent consideration was recorded at fair value as of the acquisition date. Upon closing, the Company recognized $22.4 million for the fair value of the contingent consideration.

The following table summarizes the value of assets acquired and liabilities assumed (in thousands) as of the closing on August 11, 2025:

Other assets and liabilities, net includes assumed liabilities for pre-acquisition services provided to Scale by third parties which are also measured at fair value under ASC 480. The Company expects to remeasure the contingent consideration and assumed liabilities within the scope of ASC 480 as of each applicable reporting period. Upon remeasurement as of September 30, 2025, the Company recorded a $1.1 million change in the fair value within “Other income (expense), net” in the Company’s condensed consolidated statement of operations. Measurement of the liabilities using a probability weighted discounted cash flow approach is classified as a Level 3 fair value measurement due to the use of significant unobservable inputs. The calculation relies upon the probability of achieving the milestones and approximate timing of payment based on the terms of the arrangement.

The following table discloses the summary of changes in the contingent consideration and assumed liabilities measured at fair value using Level 3 inputs (in thousands):

4. Restructuring

On May 6, 2025, the Company implemented a reduction in force plan in order to decrease costs and maintain a streamlined organization to support the business. Restructuring charges of $6.0 million associated with this plan, comprised primarily of severance-related costs, were recorded in the second quarter of 2025.

The following table is a summary of restructuring costs for the nine months ended September 30, 2025 (in thousands):

Restructuring costs of $0.4 million, $3.9 million and $1.7 million were recorded in cost of revenue, research and development expense, and selling, general and administrative expense, respectively, in the Company's condensed consolidated statements of operations during the second quarter of 2025. The restructuring activities were substantially completed by the end of the third quarter of 2025.

5. Other Financial Statement Information

Available-for-sale Securities

Available-for-sale securities consisted of the following (in thousands):

The contractual maturities of marketable securities as of September 30, 2025 were all less than one year.

The Company incurredno material gross realized gains or losses from available-for-sale debt securities during the three and nine months ended September 30, 2025 or September 30, 2024.

The available-for-sale debt securities are subject to a periodic impairment review. For investments in an unrealized loss position, the Company determines whether a credit loss exists by considering information about the collectability of the instrument, current market conditions and reasonable and supportable forecasts of economic conditions. The Company recognizes an allowance for credit losses, up to the amount of the unrealized loss when appropriate, and writes down the amortized cost basis of the investment if it is more likely than not that the Company will be required or will intend to sell the investment before recovery of its amortized cost basis. Allowances for credit losses and write-downs are recognized in “Other income (expense), net,” and unrealized losses not related to credit losses are recognized in “Accumulated other comprehensive income (loss).” There are no allowances for credit losses for the periods presented.

Inventory

Inventory was comprised of the following (in thousands):

Property and Equipment, Net

Property and equipment, net consisted of the following (in thousands):

Intangible Assets, Net

During the three months ended September 30, 2025, the Company recorded developed technology of $51.6 million and assembled workforce of $0.7 million in connection with the Scale acquisition. Subsequently, the Company recorded an impairment charge of $0.7 million related to the assembled workforce during the same period. The amortization of developed technology is recorded in cost of revenue. See Note 3, Asset Acquisition, for details related to intangibles acquired.

Compensation and Related Benefits

Accrued compensation and related benefits were comprised of the following (in thousands):

Accrued Expenses and Other Current Liabilities

Accrued expenses and other current liabilities were comprised of the following (in thousands):

Product Warranties

Changes in the reserve for product warranties were as follows (in thousands):

Revenue and Deferred Revenue

As of September 30, 2025, the aggregate amount of remaining performance obligations related to separately sold extended warranty service agreements or allocated amounts for extended warranty service agreements bundled with sales of instruments was $33.0 million, of which approximately $22.1 million is expected to be recognized to revenue in the next 12 months, with the remainder thereafter. The contract liabilities of $33.0 million and $33.2 million as of September 30, 2025 and December 31, 2024, respectively, consisted of deferred revenue related to extended warranty service agreements.

The following revenue recognized for the periods indicated were included in deferred revenue as of December 31, 2024 and 2023, respectively (in thousands):

The following table represents revenue by source for the periods indicated (in thousands). Chromium products include the Company’s single cell products and spatial products include the Company’s Visium and Xenium products:

The following table presents revenue by geography based on the location of the customer for the periods indicated (in thousands):

(1) Includes license and royalty revenue.

License and Royalty Revenue

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 has the right to 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 license. 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. As of September 30, 2025, the Company had received one quarterly payment, and the remaining balance was recognized under other receivables which is presented separately on the Company’s condensed consolidated balance sheets.

Other Income (Expense), Net

Gains or losses from foreign currency remeasurement are included in “Other income (expense), net” in the condensed consolidated statements of operations. The Company recognized foreign currency transaction loss of $0.6 million for the three months ended September 30, 2025, and foreign currency transaction income of $3.1 million for the nine months ended September 30, 2025. The Company recognized foreign currency transaction income of $1.3 million and $0.3 million for the three and nine months ended September 30, 2024, respectively.

The change in fair value of contingent consideration are included in “Other income (expense), net” in the condensed consolidated statements of operations. The company recognized the $1.1 million loss due to change in fair value of contingent consideration for the three and nine months ended September 30, 2025.

6. Commitments and Contingencies

Lease Agreements

The Company leases office, laboratory, manufacturing, distribution and server space in various locations worldwide.

As of September 30, 2025, the Company recorded $1.8 million in right of use asset and lease liabilities in connection with Scale acquisition. See Note 3, Asset Acquisition, for details related to right of use assets and lease liabilities acquired.

The payments due under the Company’s operating lease liabilities as of September 30, 2025 are as follows (in thousands):

The following table summarizes additional information related to operating leases as of September 30, 2025:

Litigation

The Company is regularly subject to lawsuits, claims, arbitration proceedings, administrative actions and other legal and regulatory proceedings involving intellectual property disputes, commercial disputes, competition and other matters, and the Company may become subject to additional types of lawsuits, claims, arbitration proceedings, administrative actions, government investigations and legal and regulatory proceedings in the future. As of September 30, 2025, the Company has concluded that a loss is not probable and a contingent liability has not been recorded.

Parse

In August 2022, the Company filed suit against Parse Biosciences, Inc. (“Parse”) in the U.S. District Court for the District of Delaware alleging that Parse’s Evercode Whole Transcriptomics products and ATAC-seq products infringe U.S. Patent Nos. 10,155,981 (the “981 patent”), 10,697,013 (the “013 patent”), 10,240,197 (the “197 patent”), 10,150,995 (the “995 patent”), 10,619,207 (the “207 patent”) and 10,738,357 (the “357 patent”). In February 2025, the Court entered a consent judgment and permanent injunction against Parse with respect to the 995, 207 and 357 patents relating to ATAC-seq. Parse filed petitions for Inter Partes Review (“IPR”) of the 981, 197 and 013 patents which were found unpatentable by the Patent Trial and Appeals Board in February 2025. The Company strongly disagrees with those decisions and has appealed. The Court has stayed the litigation pending the outcome of the appeals.

In August 2025, the Company acquired Scale. Scale and Parse are parties in a litigation in the U.S. District Court for the District of Delaware in which Scale is asserting that Parse’s Evercode products infringe U.S. Patent Nos. 10,626,442, 10,982,256, 11,512,341 and 11,634,752 (the “752 patent”) and Parse is asserting the Scale’s single cell sequencing products infringe U.S. Patent Nos. 10,900,065, 11,168,355 and 11,427,856 (the “Asserted Parse Patents”). On February 13, 2025 the parties filed a stipulation agreeing that Scale’s High Throughput Assay and methods of using such assays do not infringe the Asserted Parse Patents, and dismissing such claims. In October 2025, the Court entered summary judgment that the 752 patent is invalid. The Company disagrees with this decision and plans to appeal. In November 2025, the Court entered summary judgment that the accused Scale products do not infringe the Asserted Parse Patents. Additional summary judgment motions are pending and a trial date has not been set.

Curio

In December 2023, the Company filed suit against Curio Bioscience, Inc. (“Curio”) in the U.S. District Court for the District of Delaware alleging that the Curio Seeker Spatial Mapping Kit and associated products and services infringe U.S. Patent Nos. 10,480,022, 10,662,468, 11,001,879, 11,549,138 and 11,761,030. Trial on the Company’s claims is scheduled for May 2026.

In December 2023, the Company filed a request for a preliminary injunction in the Dusseldorf Local Division of the UPC alleging that the Curio Seeker Spatial Mapping Kit and associated products and services infringe EP Patent No. 2697391 (the “EP 391 patent”). In April 2024, the UPC granted the Company’s request and issued a preliminary injunction requiring Curio to stop offering, marketing, using or possessing these Curio Seeker products and services in Germany, France and Sweden. Curio did not appeal the preliminary injunction. On March 25, 2024, the Company filed a main request in the Dusseldorf Local Division of the UPC alleging that the Curio Seeker Spatial Mapping Kit and associated products and services infringe the EP 391 patent. In June 2025, the UPC found that Curio directly infringes one of the patent’s claims and issued a permanent injunction ordering Curio to cease and desist from selling the Seeker products in Germany, France and Sweden.

Illumina

In October 2025, the Company filed two lawsuits against Illumina, Inc. (“Illumina”) in the United States District Court for the District of Delaware. In the first suit, the Company alleges Illumina’s announced spatial technology program infringe U.S. Patent Nos. 11,008,607, 11.549,138, 12,234,505 and 12,297,487 (collectively, the “Asserted Spatial Patents”). In the second suit, the Company alleges Illumina’s single cell kits and workflow infringe U.S. Patent Nos. 11,692,214, 11,932,902, 12,275,993, 12,305,239 and 12,416,192 (collectively, the “Asserted Single Cell Patents”). No case schedule has been set.

7. Capital Stock

As of September 30, 2025, the number of shares of Class A common stock and Class B common stock issued and outstanding were 116,460,674 and 10,078,872, respectively.

The following table represents the number of shares of Class B common stock converted to shares of Class A common stock upon the election of the holders of such shares during the periods:

8. Equity Incentive Plans

Stock-based Compensation

The Company recorded stock-based compensation cost for the periods presented as follows (in thousands):

Restricted Stock Units

Restricted stock units (“RSUs”) activity for the nine months ended September 30, 2025 is as follows:

Stock Options

Stock option activity for the nine months ended September 30, 2025 is as follows:

Performance Stock Awards

In March 2025, the Company granted 561,603 performance stock units (“PSUs”) under the 2019 Omnibus Incentive Plan (“2019 plan”) to certain members of management which are subject to the achievement of certain performance conditions established by the Company’s Compensation Committee of the Board of Directors as described below:

i.50% of target PSUs earned will be based on the Company’s compound annual growth rate (“CAGR”) of the Company’s Revenue over atwo-year performance period from January 1, 2025 to December 31, 2026. Holders may earn from 0% to 200% of the target amount of shares and earned PSUs will then be subject to service-based vesting; and

ii.50% of target PSUs earned will be based on the relative Total Shareholder Return (“TSR”) of the Company’s Class A common stock as compared to the TSR of the members of the Russell 3000 Medical Equipment and Services Sector Index over athree-year performance period from January 1, 2025 to December 31, 2027. Depending on the results relative to the TSR market condition, the holders may earn from 0% to 200% of the target amount of shares which will vest at the end of the performance period.

The PSUs will be forfeited if the performance conditions are not achieved at the end of the relative performance periods as described above. The vesting of the PSUs can also be triggered upon certain change in control events or in the event of death or disability.

The weighted-average grant date fair values of the PSUs relating to CAGR and TSR components were $10.76 and $13.94 per share, respectively. Stock-based compensation expense recognized for the PSUs relating to TSR components were approximately $0.3 million and $0.7 million for the three and nine months ended September 30, 2025, respectively. The PSUs relating to CAGR components were not deemed probable of vesting as of September 30, 2025, and no expenses were recognized for 2025.

The Company estimated the fair values of shares granted under the market-based TSR PSUs using a Monte Carlo simulation model with the following assumptions:

In March 2024, the Company granted 219,168 PSUs under the 2019 Plan to certain members of management, which are subject to the achievement of certain market-condition and performance-condition goals established by the Company’s Compensation Committee of the Board of Directors.

As of September 30, 2025, the measurement periods for the 2025 and 2024 PSUs were not completed and the market and performance criteria for the stock awards was not met and therefore no shares vested or became exercisable.

2019 Employee Stock Purchase Plan

A total of 4,909,589 shares of Class A common stock were reserved for issuance under the 2019 Employee Stock Purchase Plan (“ESPP”). The price at which Class A common stock is purchased under the ESPP is equal to 85% of the fair market value of the common stock on the first day of the offering period or purchase date, whichever is lower.

During the nine months ended September 30, 2025 and 2024,446,766 and 192,869 shares of Class A common stock, respectively, were issued under the ESPP. There wereno shares of Class A common stock issued under the ESPP during the three months ended September 30, 2025 and 2024. As of September 30, 2025, there were 3,481,248 shares available for issuance under the ESPP.

9. Net Loss Per Share

The following outstanding shares of common stock equivalents were excluded from the computation of diluted net loss per share for the periods presented because including them would have had an anti-dilutive effect: