Ginkgo Bioworks Holdings, Inc.
For the period ended Sep 30, 2025. Filed Nov 6, 2025.
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A company's report for each of its first three quarters. The financial statements are not audited. It shows how the business has moved since the last annual report, and what management says changed.
Sep 30, 2025 · Filed Nov 6, 2025
DNA$11.29+13.4%Stored close · as of Nov 6, 2026
What changed in Management’s Discussion and Analysis?
Read the current filingPrevious report: 10-Q
Period ended 2025-06-30; filed 2025-08-07.
0001628280-25-038982
Item 2. Management’s Discussion and Analysis of Financial Condition and Results of OperationsCurrent report: 10-Q
Period ended 2025-09-30; filed 2025-11-06.
0001628280-25-050193
Item 2. Management’s Discussion and Analysis of Financial Condition and Results of OperationsThe baseline is this issuer’s latest earlier reporting period of the same form that was filed before the current report. A previous 10-Q is a different quarter, not a year-over-year comparison. Amendments are excluded.
Compared 153 previous paragraphs and 169 current paragraphs.
114 unchanged; 36 reworded; 17 added; 2 removed; 1 previous and 2 current paragraphs rearranged.
Tables are not compared: 4 previous and 4 current tables excluded. Dates, whitespace, punctuation and numbering changes are ignored; changes to financial figures remain significant.
A changed paragraph is not evidence that risk increased or decreased. An unchanged paragraph does not establish that risk stayed the same.
Added paragraphs (17)
Current report
A selection of our cell engineering tools offerings are described below.
Current report
Datapoints
Current report
Recent advances in machine-learning (ML), molecular simulation, and other computational techniques hold great promise to improve our ability to program cells. We believe our Foundry is well-positioned to build the kind of large, well-structured datasets that such computational approaches need to succeed. In time, we believe computational approaches will reduce the need for certain kinds of experiments (for example, we already use ML to make protein and enzyme design projects more efficient).
Current report
To this end, we have introduced two new data generation services to provide high-quality data at the scale, price, and speed that AI-powered drug development demands:
Current report
•Our Functional Genomics Datapoints services generate large, high fidelity transcriptomic and phenotypic datasets in the disease context of our customers’ choice to power AI models of cell and disease biology for use in target identification, target validation, and drug discovery; and
Current report
•Our Antibody Developability Datapoints services generate biophysical antibody characterization developability datasets for our customers to use in AI model training and validation.
Current report
Reconfigurable Automation Cart (“RAC”) Systems
Current report
Ginkgo Automation’s capabilities build on years of internal expertise, encompassing hardware design, software integration, and applications development, epitomized in our offering of RACs: our Reconfigurable Automation Cart systems. The modularity and flexibility of the RACs enables high walkway time, high uptime, and high throughput experimentation for high-mix biological workflows like the kinds performed in Ginkgo’s Foundry and in our partners’ labs. In addition to providing advanced automation hardware and software, Ginkgo Automation’s deployments to third party customers include access to Catalyst Flow, a fully remote, active error resolution and troubleshooting support service. Catalyst Flow’s proactive monitoring is expected to enable Ginkgo’s scientists and engineers to identify and resolve approximately 80-90% of system errors remotely, without the need for our customers to initiate tickets.
Current report
Loss on Deconsolidation of Subsidiary
Current report
Loss on deconsolidation of subsidiary pertains to our deconsolidation of our former foreign subsidiary Altar SAS (“Altar”) in the third quarter of 2024 as a result of a sale.
Current report
Cell Engineering revenue was $29.4 million for the three months ended September 30, 2025, compared to $75.1 million for the three months ended September 30, 2024, a decrease of $45.7 million. This decrease was primarily due to the recognition of $45.4 million in non-cash revenue from the release of the deferred revenue balance associated with the terminated Motif contract in the third quarter of 2024.
Current report
Gain (Loss) on Investments
Current report
Loss on Deconsolidation of Subsidiary
Current report
In the third quarter of 2024, we recorded a $7.0 million loss on our deconsolidation of our former foreign subsidiary Altar as a result of a sale.
Current report
At-The-Market Program
Current report
On August 7, 2025, we filed a universal shelf registration statement on Form S-3, which was declared effective by the SEC on August 14, 2024, on which we registered for sale up to $500 million of any combination of our Class A common stock, preferred stock, warrants, and/or units from time to time and at prices and on terms that we may determine. On September 4, 2025, the Company entered into a Sales Agreement (the “Sales Agreement”) with Allen & Company LLC (“Allen”), who is acting as the sales agent (the “Agent”), pursuant to which the Company may sell shares of its Class A common stock from time to time at prices and on terms determined by market conditions at the time of offering, up to an aggregate offering price of $100.0 million (the “Shares”) through or directly to the Agent in one or more at-the-market (“ATM”) offerings. Since inception of the Sales Agreement through September 30, 2025, the Company has issued 975,300 shares of Class A common stock under the ATM Sales Agreement for net proceeds of $9.4 million. We currently intend to use the net proceeds from this offering for general corporate purposes, which may include, but are not limited to, financing our operations, technology development, working capital and capital expenditures.
Current report
$45.3 million of depreciation and amortization, $22.4 million non-cash lease expense, a $1.5 million change in fair values of various assets and liabilities, $2.5 million accretion of discount on marketable securities, and a $0.3 million loss on investments.
Removed paragraphs (2)
Previous report
Cell Engineering revenue was $77.4 million for the six months ended June 30, 2025, compared to $64.1 million for the six months ended June 30, 2024, an increase of $13.3 million. This increase was primarily due to the recognition of $7.5 million in non-cash revenue from the release of a deferred revenue balance associated with the terminated BiomEdit, Inc.
Previous report
Loss on Investments
Reworded paragraphs (36)
Previous wording
Our cell engineering platform is a key enabling technology and source of intellectual property for our customers’ products. We earn Cell Engineering revenue for our R&D services as well as generally through a share of the value of products created using our platform.
Current wording
Our cell engineering platform is a key enabling technology and source of intellectual property for our customers’ products. We earn Cell Engineering revenue for our R&D services.
Previous wording
We typically structure customer contracts for Cell Engineering services to include some combination of the following:
Current wording
We typically structure customer contracts for Cell Engineering services to include one or more of the following:
Previous wording
Restructuring charges are related to our restructuring plan, which was announced and commenced in the second quarter of 2024. These charges primarily include severance and other employee termination costs from a reduction in force that commenced in June 2024, as well as the impairment of a right-of-use asset due to the subleasing of a facility as part of real estate consolidation. Reductions in force are expected to be substantially completed in 2025, subject to compliance with applicable laws. While we have substantially completed the majority of our facility consolidation actions with excess space available for sublease, the actual timing for subleasing unused or underutilized facilities may extend beyond 2025 or may not occur prior to termination of such lease, depending on market conditions. Additionally, restructuring expenses related to potential asset impairments or contract amendments or terminations for any facilities no longer in use or underutilized could be material.
Current wording
Restructuring charges are related to our restructuring plan, which was announced and commenced in the second quarter of 2024. These charges primarily include severance and other employee termination costs from a reduction in force that commenced in June 2024, as well as the impairment of a right-of-use asset due to the subleasing of a facility as part of real estate consolidation. Reductions in force are expected to be substantially completed in 2025, subject to compliance with applicable laws. While we have substantially completed the majority of our facility consolidation actions with excess space available for sublease, the actual timing for subleasing unused or underutilized facilities is expected to extend into 2026 or may not occur prior to termination of such lease, depending on market conditions. Additionally, restructuring expenses related to potential asset impairments or contract amendments or terminations for any facilities no longer in use or underutilized could be material.
Previous wording
Comparison of the Three and Six Months Ended June 30, 2025 and 2024
Current wording
Comparison of the Three and Nine Months Ended September 30, 2025 and 2024
Previous wording
(“BiomEdit”) contract in the first quarter of 2025 (see Note 15 of our condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q) and an increase in revenue related to programs with large enterprise customers primarily in the pharmaceutical and biotechnology industries and with the U.S. government (healthcare and defense sectors), partially offset by the recognition of $4.5 million in non-cash revenue from the release of a deferred revenue balance associated with the termination of contract with a related party in the second quarter of 2024 and decreases in revenue related to programs with customers in the industrial biotechnology industry.
Current wording
Cell Engineering revenue was $106.7 million for the nine months ended September 30, 2025, compared to $139.2 million for the nine months ended September 30, 2024, a decrease of $32.4 million. This decrease was primarily due to the recognition of $45.4 million in non-cash revenue from the release of the deferred revenue balance associated with the terminated Motif contract in the third quarter of 2024, the recognition of $4.5 million in non-cash revenue from the release of a deferred revenue balance associated with the termination of contract with a related party in the second quarter of 2024, and decreases in revenue for certain programs with customers in the industrial biotechnology industry. These decreases were partially offset by the recognition of $7.5 million in non-cash revenue from the release of a deferred revenue balance associated with the terminated BiomEdit, Inc. (“BiomEdit”) contract in the first quarter of 2025 (see Note 15 of our condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q) and an increase in revenue related to programs with large enterprise customers primarily in the pharmaceutical and biotechnology industries and with the U.S. government (healthcare and defense sectors).
Previous wording
As discussed above in Components of Results of Operations, Cell Engineering revenue comprises both cash and non-cash consideration. Cell Engineering revenue recognized relating to non-cash consideration decreased from $8.2 million for the three months ended June 30, 2024 to $1.2 million for the three months ended June 30, 2025, and from $12.1 million for the six months ended June 30, 2024 to $9.9 million for the six months ended June 30, 2025, primarily due to the recognition of $4.5 million from the release of a deferred revenue balance associated with the termination of contract with a related party in the second quarter of 2024 and lower non-cash revenue from other customers, offset by the recognition of $7.5 million in non-cash revenue from the release of the deferred revenue balance associated with the terminated BiomEdit contract in the first quarter of 2025.
Current wording
As discussed above in Components of Results of Operations, Cell Engineering revenue comprises both cash and non-cash consideration. Cell Engineering revenue recognized relating to non-cash consideration decreased from $48.0 million for the three months ended September 30, 2024 to zero for the three months ended September 30, 2025, and from $60.1 million for the nine months ended September 30, 2024 to $9.9 million for the nine months ended September 30, 2025, primarily due to the recognition of $45.4 million in non-cash revenue from the release of the deferred revenue balance associated with the terminated Motif contract in the third quarter of 2024, and the recognition of $4.5 million from the release of a deferred revenue balance associated with the termination of contract with a related party in the second quarter of 2024, offset by the recognition of $7.5 million in non-cash revenue from the release of the deferred revenue balance associated with the terminated BiomEdit contract in the first quarter of 2025.
Previous wording
Biosecurity revenue was $10.5 million for the three months ended June 30, 2025, compared to $20.0 million for the three months ended June 30, 2024, a decrease of $9.5 million. This decrease was primarily due to lower revenue related to a program with the U.S. government.
Current wording
Biosecurity revenue was $9.5 million for the three months ended September 30, 2025, compared to $14.0 million for the three months ended September 30, 2024, a decrease of $4.5 million. This decrease was primarily due to lower revenue related to programs with the U.S. government and a foreign government.
Previous wording
Biosecurity revenue was $20.6 million for the six months ended June 30, 2025, compared to $30.1 million for the six months ended June 30, 2024, a decrease of $9.5 million. This decrease was primarily due to lower revenue related to a program with the U.S. government.
Current wording
Biosecurity revenue was $30.0 million for the nine months ended September 30, 2025, compared to $44.0 million for the nine months ended September 30, 2024, a decrease of $14.0 million. This decrease was primarily due to lower revenue related to a programs with the U.S. government and a foreign government.
Previous wording
The cost of Biosecurity revenue was $9.4 million for the three months ended June 30, 2025, compared to $11.8 million for the three months ended June 30, 2024, a decrease of $2.4 million. This decrease was primarily due to cost reductions implemented during the first quarter of 2025 as well as a reduction in activities supporting a program with the U.S. government.
Current wording
The cost of Biosecurity revenue was $8.2 million for the three months ended September 30, 2025, compared to $10.0 million for the three months ended September 30, 2024, a decrease of $1.8 million. This decrease was primarily due to cost reductions implemented during 2025 as well as a reduction in activities supporting a program with the U.S. government.
Previous wording
The cost of Biosecurity revenue was $17.4 million for the six months ended June 30, 2025, compared to $21.0 million for the six months ended June 30, 2024, a decrease of $3.6 million. This decrease was primarily due to cost reductions implemented during the first quarter of 2025 as well as a reduction in activities supporting a program with the U.S. government.
Current wording
The cost of Biosecurity revenue was $25.6 million for the nine months ended September 30, 2025, compared to $31.0 million for the nine months ended September 30, 2024, a decrease of $5.4 million. This decrease was primarily due to cost reductions implemented during 2025 as well as a reduction in activities supporting a program with the U.S. government.
Previous wording
The cost of other revenue was $5.4 million for the three months ended June 30, 2025, compared to $1.9 million for the three months ended June 30, 2024, an increase of $3.5 million. This increase was primarily due to an increase in activity to support Datapoints contracts. These costs relate to our cell engineering customer offerings, Datapoints and lab automation solutions, which began in the second quarter of 2024. Costs associated with our end-to-end cell engineering solutions offering are included in research and development expenses.
Current wording
The cost of other revenue was $4.6 million for the three months ended September 30, 2025, compared to $2.0 million for the three months ended September 30, 2024, an increase of $2.6 million. This increase was primarily due to an increase in activity to support Datapoints contracts. These costs relate to our cell engineering customer offerings, Datapoints and lab automation solutions, which commenced in the second quarter of 2024. Costs associated with our end-to-end cell engineering solutions offering are included in research and development expenses.
Previous wording
The cost of other revenue was $9.5 million for the six months ended June 30, 2025, compared to $1.9 million for the six months ended June 30, 2024, an increase of $7.6 million. This increase was primarily due to an increase in activity to support Datapoints contracts. These costs relate to our cell engineering customer offerings, Datapoints and lab automation solutions, which began in the second quarter of 2024. Costs associated with our end-to-end cell engineering solutions offering are included in research and development expenses.
Current wording
The cost of other revenue was $14.1 million for the nine months ended September 30, 2025, compared to $3.9 million for the nine months ended September 30, 2024, an increase of $10.2 million. This increase was primarily due to an increase in activity to support Datapoints contracts. These costs relate to our cell engineering customer offerings, Datapoints and lab automation solutions, which commenced in the second quarter of 2024. Costs associated with our end-to-end cell engineering solutions offering are included in research and development expenses.
Previous wording
Our research and development expenses principally relate to the development of new offerings and the operation, expansion and enhancement of our existing service offerings utilizing our proprietary platform, which includes our Foundry and Codebase assets, to our cell engineering customers. Research personnel costs, including stock-based compensation, is our largest expense, totaling $23.7 million and $58.3 million for the three months ended June 30, 2025 and 2024, respectively, and $54.4 million and $120.5 million for the six months ended June 30, 2025 and 2024, respectively. We also acquired and expensed in-process research and development primarily through the issuance of our equity, aggregating to zero and $3.0 million for the three months ended June 30, 2025 and 2024, respectively, and zero and
Current wording
Our research and development expenses principally relate to the development of new offerings and the operation, expansion and enhancement of our existing service offerings utilizing our proprietary platform, which includes our Foundry and Codebase assets, to our cell engineering customers. Research personnel costs, including stock-based compensation, is our largest expense, totaling $19.3 million and $31.2 million for the three months ended September 30, 2025 and 2024, respectively, and $73.3 million and $152.5 million for the nine months ended September 30, 2025 and
Previous wording
$19.8 million for the six months ended June 30, 2025 and 2024, respectively. Our remaining research and development costs are comprised primarily of rent and related facilities costs, information technology costs, depreciation pertaining to facilities and equipment, laboratory consumables, contract services, and routine costs and fees.
Current wording
2024, respectively. We also acquired and expensed in-process research and development primarily through the issuance of our equity, aggregating to zero for both the three months ended September 30, 2025 and 2024, respectively, and zero and $19.8 million for the nine months ended September 30, 2025 and 2024, respectively. Our remaining research and development costs are comprised primarily of rent and related facilities costs, information technology costs, depreciation pertaining to facilities and equipment, laboratory consumables, contract services, and routine costs and fees.
Previous wording
Research and development expenses were $124.3 million for the six months ended June 30, 2025, compared to $270.7 million for the six months ended June 30, 2024, a decrease of $146.4 million. This decrease was primarily driven by reductions of $39.5 million in personnel-related compensation and benefits expenses (net of $2.6 million tax credit), $27.0 million in stock-based compensation expense (inclusive of employer payroll taxes), $22.3 million in rent and facilities expenses, $19.8 million in acquired in-process research and development expense, $13.6 million in laboratory supplies, $11.6 million in information technology expenses, $6.4 million in allocated overhead expenses (reclassified from R&D to G&A and cost of sales), and $6.2 million in other operating expenses.
Current wording
Research and development expenses were $69.4 million for the three months ended September 30, 2025, compared to $77.0 million for the three months ended September 30, 2024, a decrease of $7.7 million. This decrease was primarily driven by reductions of $15.0 million in personnel-related compensation and benefits expenses, $8.0 million in rent and facilities expenses, $4.4 million in depreciation and amortization, $2.2 million in laboratory supplies, $2.0 million in allocated overhead expenses (reclassified from R&D to G&A and cost of sales), $1.1 million in temporary labor and contractors, and $0.6 million in other operating expenses. These decreases were partially offset by an increase of $22.5 million in information technology expenses primarily due to a shortfall in contractually committed spending related to our strategic cloud and AI partnership with Google Cloud (see Note 10 of our condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q) and $3.1 million in stock-based compensation expense (inclusive of employer payroll taxes).
Previous wording
Research and development expenses were $53.4 million for the three months ended June 30, 2025, compared to $134.2 million for the three months ended June 30, 2024, a decrease of $80.9 million. This decrease was primarily driven by reductions of $23.0 million in personnel-related compensation and benefits expenses (net of $2.6 million tax credit), $15.7 million in rent and facilities expenses, $12.0 million in stock-based compensation expense (inclusive of employer payroll taxes), $8.4 million in laboratory supplies, $5.9 million in information technology expenses, $3.0 million in acquired in-process research and development expense, $2.9 million in depreciation and amortization, $2.2 million in outside services, $1.8 million in allocated overhead expenses (reclassified from R&D to G&A and cost of sales), and $6.0 million in other operating expenses.
Current wording
Research and development expenses were $193.6 million for the nine months ended September 30, 2025, compared to $347.7 million for the nine months ended September 30, 2024, a decrease of $154.0 million. This decrease was primarily driven by reductions of $54.6 million in personnel-related compensation and benefits expenses (net of $2.6 million tax credit), $30.3 million in rent and facilities expenses, $23.8 million in stock-based compensation expense (inclusive of employer payroll taxes), $19.8 million in acquired in-process research and development expense, $15.8 million in laboratory supplies, $8.4 million in allocated overhead expenses (reclassified from R&D to G&A and cost of sales), $6.3 million in depreciation and amortization, $4.5 million in temporary labor, and contractors and $1.5 million in other operating expenses. These decreases were partially offset by an increase of $11.0 million in information technology expenses primarily due to a shortfall in contractually committed spending related to the our strategic cloud and AI partnership with Google Cloud (see Note 10 of our condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q).
Previous wording
General and administrative expenses were $43.3 million for the three months ended June 30, 2025, compared to $66.3 million for the three months ended June 30, 2024, a decrease of $23.0 million. This decrease was primarily driven by reductions of $9.4 million in personnel-related compensation and benefits expenses (net of $0.9 million tax credit), $6.1 million in earnout remeasurement expenses, $6.1 million in professional fees, $6.0 million of stock-based compensation expense (inclusive of employer payroll taxes), $1.9 million in temporary labor and contractors, and $5.2 million in other operating expenses. These decreases were partially offset by an increase of $11.6 million in rent and facilities expenses primarily due to a new lease that commenced in the second quarter of 2024 and remains unoccupied.
Current wording
General and administrative expenses were $45.0 million for the three months ended September 30, 2025, compared to $52.3 million for the three months ended September 30, 2024, a decrease of $7.3 million. This decrease was primarily driven by reductions of $6.4 million in personnel-related compensation and benefits expenses, $1.9 million in allocated overhead expenses (reclassified from R&D to G&A), $1.2 million of stock-based compensation expense (inclusive of employer payroll taxes), $1.4 million in earnout remeasurement expenses, $1.4 million in professional fees, and $0.7 million in other operating expenses. These decreases were partially offset by an increase of $5.7 million in rent and facilities expenses primarily due to a new lease that commenced in the second quarter of 2024 and remains unoccupied.
Previous wording
General and administrative expenses were $92.3 million for the six months ended June 30, 2025, compared to $136.6 million for the six months ended June 30, 2024, a decrease of $44.3 million. This decrease was primarily driven by reductions of $18.3 million in professional fees, $15.1 million in personnel-related compensation and benefits expenses (net of $0.9 million tax credit), $14.4 million in stock-based compensation expense (inclusive of employer payroll taxes), $6.5 million in earnout remeasurement expenses, $4.2 million in temporary labor and contractors, and $9.0 million in other operating expenses. These decreases were partially offset by an increase of $23.2 million in rent and facilities expenses primarily due to a new lease that commenced in the second quarter of 2024 and remains unoccupied.
Current wording
General and administrative expenses were $137.3 million for the nine months ended September 30, 2025, compared to $188.9 million for the nine months ended September 30, 2024, a decrease of $51.6 million. This decrease was primarily driven by reductions of $21.4 million in personnel-related compensation and benefits expenses (net of $0.9 million tax credit), $19.7 million in professional fees, $15.6 million in stock-based compensation expense (inclusive of employer payroll taxes), $7.9 million in earnout remeasurement expenses, $5.7 million in allocated overhead expenses (reclassified from R&D to G&A), $4.4 million in temporary labor and contractors, and $5.9 million in other operating expenses. These decreases were partially offset by an increase of $29.0 million in rent and facilities expenses primarily due to a new lease that commenced in the second quarter of 2024 and remains unoccupied.
Previous wording
During both the three and six months ended June 30, 2024, we recorded a full impairment of the $47.9 million goodwill balance related to our Cell Engineering reporting unit.
Current wording
During the nine months ended September 30, 2024, we recorded a full impairment of the $47.9 million goodwill balance related to our Cell Engineering reporting unit.
Previous wording
Restructuring charges were $3.7 million and $17.1 million for the three months ended June 30, 2025 and 2024, respectively, and $8.9 million and $17.1 million for the six months ended June 30, 2025 and 2024, respectively. Restructuring charges relate to our restructuring plan, which was announced and commenced in the second quarter of 2024, primarily affecting the Cell Engineering segment. These charges primarily consisted of employee termination costs from the reduction in force. See Note 3 of our condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q for further details.
Current wording
Restructuring charges were $1.7 million and $2.9 million for the three months ended September 30, 2025 and 2024, respectively, and $10.7 million and $20.0 million for the nine months ended September 30, 2025 and 2024, respectively. Restructuring charges relate to our restructuring plan, which was announced and commenced in the second quarter of 2024, primarily affecting the Cell Engineering segment. These charges primarily consisted of employee termination costs from the reduction in force. See Note 3 of our condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q for further details.
Previous wording
Interest income, net was $6.1 million for the three months ended June 30, 2025, compared to $10.3 million for the three months ended June 30, 2024, a decrease of $4.2 million primarily due to lower average cash balances invested in money market funds and marketable debt securities.
Current wording
Interest income, net was $5.7 million for the three months ended September 30, 2025, compared to $9.3 million for the three months ended September 30, 2024, a decrease of $3.5 million primarily due to lower average cash balances invested in money market funds and marketable debt securities.
Previous wording
Interest income, net was $12.2 million for the six months ended June 30, 2025, compared to $22.0 million for the six months ended June 30, 2024, a decrease of $9.9 million primarily due to lower average cash balances invested in money market funds and marketable debt securities.
Current wording
Interest income, net was $17.9 million for the nine months ended September 30, 2025, compared to $31.3 million for the nine months ended September 30, 2024, a decrease of $13.4 million primarily due to lower average cash balances invested in money market funds and marketable debt securities.
Previous wording
Loss on investments was $0.2 million and $6.8 million for the three months ended June 30, 2025 and 2024, respectively, and $3.9 million and $9.4 million for the six months ended June 30, 2025 and 2024, respectively. The change was primarily driven by fluctuations in the stock prices of marketable equity securities, partially offset by lower impairment losses on our non-marketable equity investments in privately held companies, compared to the same periods in 2024. We assess our non-marketable equity investments quarterly for potential impairment and remeasure them to fair value when events or changes in circumstances indicate that their carrying value may not be recoverable.
Current wording
Gain on investments was $3.7 million for the three months ended September 30, 2025. Loss on investments was $6.9 million for the three months ended September 30, 2024. Loss on investments was $0.2 million and $16.3 million for the nine months ended September 30, 2025 and 2024, respectively. The change was primarily driven by fluctuations in the stock prices of marketable equity securities, partially offset by lower impairment losses on our non-marketable equity investments in privately held companies, compared to the same periods in 2024. We assess our non-marketable equity investments quarterly for potential impairment and remeasure them to fair value when events or changes in circumstances indicate that their carrying value may not be recoverable.
Previous wording
The change in fair value of warrant liabilities was zero for both the three and six months ended June 30, 2025, compared to gains of $3.2 million and $4.2 million for the three and six months ended June 30, 2024, respectively. The fair value of warrant liabilities is primarily driven by fluctuations in the value of our common stock. An increase or decrease in the value of our common stock results in a loss or gain, respectively, in the fair value of warrant liabilities. As of June 30, 2025, these warrant liabilities had substantially no value.
Current wording
The change in fair value of warrant liabilities was zero for both the three and nine months ended September 30, 2025, compared to gains of $1.5 million and $5.7 million for the three and nine months ended September 30, 2024, respectively. The fair value of warrant liabilities is primarily driven by fluctuations in the value of our common stock. An increase or decrease in the value of our common stock results in a loss or gain, respectively, in the fair value of warrant liabilities. As of September 30, 2025, these warrant liabilities had substantially no value.
Previous wording
We recorded a net other expense amount of $0.9 million for the three months ended June 30, 2025, compared to a net other expense amount of $0.8 million for the three months ended June 30, 2024, a decrease of $0.1 million.
Current wording
We recorded a net other expense amount of $0.2 million for the three months ended September 30, 2025, compared to a net other income amount of $1.6 million for the three months ended September 30, 2024, a decrease of $1.7 million.
Previous wording
We recorded a net other expense amount of $5.2 million for the six months ended June 30, 2025, compared to a net other income amount of $1.2 million for the six months ended June 30, 2024, a decrease of $6.4 million. This decrease was primarily due to losses on the change in fair value of a note receivable accounted for under the fair value option recorded in 2025.
Current wording
We recorded a net other expense amount of $5.3 million for the nine months ended September 30, 2025, compared to a net other income amount of $2.8 million for the nine months ended September 30, 2024, a decrease of $8.2 million. This decrease was primarily due to losses on the change in fair value of a note receivable accounted for under the fair value option recorded in 2025.
Previous wording
(1)All periods include non-cash revenue when earned, including $7.5 million recognized in the six months ended June 30, 2025, pursuant to the release of deferred revenue related to the mutual termination of a customer agreement.
Current wording
(1)All periods include non-cash revenue when earned, including $7.5 million recognized in the nine months ended September 30, 2025, pursuant to the release of deferred revenue related to the mutual termination of a customer agreement.
Previous wording
(2)Includes $0.3 million and $1.1 million in employer payroll taxes for the three months ended June 30, 2025 and 2024, respectively, and $0.6 million and $2.7 million for the six months ended June 30, 2025 and 2024, respectively.
Current wording
(2)Includes $0.3 million and $0.2 million in employer payroll taxes for the three months ended September 30, 2025 and 2024, respectively, and $0.9 million and $2.9 million for the nine months ended September 30, 2025 and 2024, respectively.
Previous wording
(4)Represents transaction and integration costs directly related to mergers and acquisitions, including: (i) legal, consulting, and accounting fees associated with acquisitions; (ii) post-acquisition employee retention bonuses; (iii) (gain)/loss from changes in the fair value of contingent consideration liabilities resulting from acquisitions; and (iv) costs associated with the Zymergen Bankruptcy, as well as securities litigation costs. Not included in this adjustment are acquired in-process research and development expenses, which totaled zero and $3.0 million for the three months ended June 30, 2025 and 2024, respectively, and zero and $19.8 million for the six months ended June 30, 2025 and 2024, respectively.
Current wording
(4)Represents transaction and integration costs directly related to mergers and acquisitions, including: (i) legal, consulting, and accounting fees associated with acquisitions; (ii) post-acquisition employee retention bonuses; (iii) (gain)/loss from changes in the fair value of contingent consideration liabilities resulting from acquisitions; and (iv) costs associated with the Zymergen Bankruptcy, as well as securities litigation costs. Not included in this adjustment are acquired in-process research and development expenses, which totaled zero for both the three months ended September 30, 2025 and 2024, respectively, and zero and $19.8 million for the nine months ended September 30, 2025 and 2024, respectively.
Previous wording
Upon the closing of our merger with SRNG in September 2021, we received net proceeds totaling approximately $1.5 billion, inclusive of $760.0 million from investments from certain accredited investors for 1.9 million shares of our Class A common stock. As of June 30, 2025, we had cash and cash equivalents and marketable securities of $473.7 million, which we believe will be sufficient to enable us to fund our projected operations through at least the next 12 months from the date of filing of this Quarterly Report on Form 10-Q.
Current wording
Upon the closing of our merger with SRNG in September 2021, we received net proceeds totaling approximately $1.5 billion, inclusive of $760.0 million from investments from certain accredited investors for 1.9 million shares of our Class A common stock. As of September 30, 2025, we had cash and cash equivalents and marketable securities of $461.9 million, which we believe will be sufficient to enable us to fund our projected operations through at least the next 12 months from the date of filing of this Quarterly Report on Form 10-Q.
Previous wording
Net cash used in operating activities for the six months ended June 30, 2025 consisted of a net loss of $151.3 million, adjusted for net change in operating assets and liabilities of $34.3 million and non-cash charges of $93.8 million. The net change in operating assets and liabilities was primarily due to (i) a $23.7 million decrease in deferred revenue primarily from one-time releases of deferred revenue balances associated with terminated customer contracts and the recognition of previously deferred revenue, (ii) a $11.6 million decrease in operating lease liabilities from rent payments, and (iii) a $0.4 million increase in accounts receivable due to timing of customer billings, partially offset by (iv) a $5.1 million increase in accounts payable, accrued expenses and other current liabilities primarily due to a loss accrual associated with a minimum purchase obligation under a supplier agreement, and (v) a $3.8 million decrease in operating lease right-of-use assets from lease incentives received. Non-cash adjustments primarily consisted of $42.7 million of stock-based compensation expense, $31.2 million of depreciation and amortization, $14.9 million non-cash lease expense, a $1.1 million change in fair values of various assets and liabilities, and a $4.0 million loss on investments.
Current wording
Net cash used in operating activities for the nine months ended September 30, 2025 consisted of a net loss of $232.0 million, adjusted for net change in operating assets and liabilities of $20.5 million and non-cash charges of $129.1 million. The net change in operating assets and liabilities was primarily due to (i) a $27.2 million decrease in deferred revenue primarily from one-time releases of deferred revenue balances associated with terminated customer contracts and the recognition of previously deferred revenue, (ii) a $18.8 million decrease in operating lease liabilities from rent payments, and (iii) a $0.3 million increase in accounts receivable due to timing of customer billings, partially offset by (iv) a $17.0 million increase in accounts payable, accrued expenses and other current liabilities primarily due to a loss accrual associated with a minimum purchase obligation, and (v) a $3.8 million decrease in operating lease right-of-use assets from lease incentives received. Non-cash adjustments primarily consisted of $60.5 million of stock-based compensation expense,
Previous wording
Net cash used in operating activities for the six months ended June 30, 2024 consisted of a net loss of $383.1 million, adjusted for net change in operating assets and liabilities of $6.2 million and non-cash charges of $203.3 million. The net change in operating assets and liabilities was primarily due to (i) a $10.9 million increase in accounts payable, accrued expenses and other current liabilities primarily due to restructuring-related accruals, (ii) a $14.4 million decrease in operating lease right-of-use assets from lease incentives received, partially offset by (iii) a $17.0 million decrease in deferred revenue and (iv) a $3.9 million decrease in operating lease liabilities from rent payments. Non-cash adjustments primarily consisted of $30.2 million of depreciation and amortization, $77.9 million of stock-based compensation expense, $9.4 million loss on investments, $13.1 million non-cash lease expense, $19.8 million in acquired in-process research and development expense, and $47.9 million of goodwill impairment.
Current wording
Net cash used in operating activities for the nine months ended September 30, 2024 consisted of a net loss of $439.5 million, adjusted for a net decrease in cash due to changes in operating assets and liabilities of $91.8 million and non-cash charges of $254.2 million. The net change in operating assets and liabilities was primarily driven by a $31.1 million decrease in accounts payable, accrued expenses and other current liabilities primarily due to the payment or release of restructuring-related accruals and litigation costs, a $67.8 million decrease in deferred revenue primarily from a one-time release of a deferred revenue balance associated with a terminated customer contract, and a $11.4 million decrease in operating lease liabilities from rent payments, partially offset by a $19.2 million decrease in operating lease right-of-use assets from lease incentives received. Non-cash adjustments primarily consisted of $47.4 million in depreciation and amortization, $91.8 million in stock-based compensation expense, $16.3 million loss on investments, $20.6 million non-cash lease expense, $19.8 million in acquired in-process research and development expense, and $47.9 million in goodwill impairment.
Previous wording
Net cash used in investing activities for the six months ended June 30, 2025 primarily consisted of purchases of marketable debt securities of $320.1 million, maturities of marketable debt securities of $65.0 million, and purchases of property and equipment of $7.7 million related to the build-out of new office and laboratory space near our headquarters.
Current wording
Net cash used in investing activities for the nine months ended September 30, 2025 primarily consisted of purchases of marketable debt securities of $401.8 million, maturities of marketable debt securities of $73.6 million, and purchases of property and equipment of $7.7 million related to the build-out of new office and laboratory space near our headquarters.
Previous wording
Net cash used in investing activities for the six months ended June 30, 2024 primarily consisted of purchases of property and equipment of $33.7 million associated with Foundry capacity and capability investments and $5.4 million paid for the acquisition of Zymergen.
Current wording
Net cash used in investing activities for the nine months ended September 30, 2024 primarily consisted of $48.8 million in purchases of property and equipment related to Foundry capacity and capability investments, $5.4 million paid for the acquisition of certain Zymergen assets, and $4.0 million in proceeds from the sale of investment securities.
Previous wording
Net cash used in financing activities for the six months ended June 30, 2025 primarily consisted of principal payments on finance leases.
Current wording
Net cash provided by financing activities for the nine months ended September 30, 2025 primarily consisted of $10.0 million in net proceeds from an ATM offering and $0.3 million of principal payments on finance leases.
Previous wording
Net cash used in financing activities for the six months ended June 30, 2024 primarily consisted of principal payments on finance leases and payments of contingent consideration related to business acquisitions.
Current wording
Net cash used in financing activities for the nine months ended September 30, 2024 primarily consisted of $0.7 million of principal payments on finance leases and $0.9 million in payments of contingent consideration related to business acquisitions.
Rearranged current paragraphs (2)
Current report — wording carried from elsewhere
For each of our end-to-end cell engineering programs, we charge customers fees for the services we provide, typically structured as fixed fees, although we also have cost reimbursement arrangements. Additionally, we have historically negotiated a value share with our customers (in the form of royalties, milestones, and/or equity interests) in order to align our economics with the success of the programs enabled by our platform. Commencing in the second quarter of 2024, we announced changes in prospective commercial terms, including the removal of downstream value share from certain program types.
Current report — wording carried from elsewhere
We charge customers fees for the services we provide in our cell engineering tools offerings. Typically, these fees are structured as a fixed fee for a fixed scope of work. Fees for our data generation products (“Datapoints”), which provide large, biological datasets for customers to train their AI models, synthesizing and testing the output of customer existing models, and generating datasets for lead selection, hit selection, or a variety of other data science applications, are typically earned over a shorter period of time (weeks to months) than for end-to-end cell engineering solutions which may be multi-year programs. Fees for our automation solutions are typically earned over a period that covers design, build, and deployment and range from six to twelve months. In addition, we offer support services with fixed fees covering the support periods.
Rearranged previous paragraphs (1)
Previous report — wording carried elsewhere
Cell Engineering revenue was $39.1 million for the three months ended June 30, 2025, compared to $36.2 million for the three months ended June 30, 2024, an increase of $2.9 million. This increase was primarily due to an increase in revenue related to programs with large enterprise customers primarily in the pharmaceutical and biotechnology industries and with the U.S. government (healthcare and defense sectors), partially offset by the recognition of $4.5 million in non-cash revenue from the release of a deferred revenue balance associated with the termination of contract with a related party in the second quarter of 2024.