Precigen (PGEN) 10-Q 9 Nov 17 2017 Q3 Quarterly report Financial data

Document and Entity Information

Document and Entity Information - shares	9 Months Ended
	Sep. 30, 2017	Oct. 31, 2017
Document And Entity Information [Abstract]
Document Type	10-Q
Amendment Flag	false
Document Period End Date	Sep. 30, 2017
Document Fiscal Year Focus	2,017
Document Fiscal Period Focus	Q3
Trading Symbol	XON
Entity Registrant Name	INTREXON CORP
Entity Central Index Key	1,356,090
Current Fiscal Year End Date	--12-31
Entity Filer Category	Large Accelerated Filer
Entity Common Stock, Shares Outstanding		120,720,505

Consolidated Balance Sheets

Consolidated Balance Sheets - USD ($) $ in Thousands	Sep. 30, 2017	Dec. 31, 2016
Current assets
Cash and cash equivalents	$ 64,216	$ 62,607
Restricted cash	6,987	6,987
Short-term investments	44,502	174,602
Receivables
Trade, net	18,134	21,637
Related parties	17,866	16,793
Notes, net	0	1,500
Other	2,253	2,555
Inventory	17,730	21,139
Prepaid expenses and other	8,052	7,361
Total current assets	179,740	315,181
Long-term investments	0	5,993
Equity securities	26,642	23,522
Investments in preferred stock	148,499	129,545
Property, plant and equipment, net	102,876	64,672
Intangible assets, net	240,897	225,615
Goodwill	166,821	157,175
Investments in affiliates	22,942	23,655
Other assets	9,844	3,710
Total assets	898,261	949,068
Current liabilities
Accounts payable	7,852	8,478
Accrued compensation and benefits	11,206	6,540
Other accrued liabilities	18,960	15,776
Deferred revenue	48,289	53,364
Lines of credit	234	820
Current portion of long term debt	439	386
Deferred consideration	0	8,801
Related party payables	816	440
Total current liabilities	87,796	94,605
Long term debt, net of current portion	7,673	7,562
Deferred revenue, net of current portion	227,998	256,778
Deferred tax liabilities, net	15,868	17,007
Other long term liabilities	5,747	3,868
Total liabilities	345,082	379,820
Commitments and contingencies (Note 16)
Total equity
Common stock, no par value, 200,000,000 shares authorized as of September 30, 2017 and December 31, 2016; 120,624,346 and 118,688,770 shares issued and outstanding as of September 30, 2017 and December 31, 2016, respectively	0	0
Additional paid-in capital	1,370,917	1,325,780
Accumulated deficit	(820,554)	(729,341)
Accumulated other comprehensive loss	(16,750)	(36,202)
Total Intrexon shareholders' equity	533,613	560,237
Noncontrolling interests	19,566	9,011
Total equity	553,179	569,248
Total liabilities and total equity	$ 898,261	$ 949,068

Consolidated Balance Sheets (Pa

Consolidated Balance Sheets (Parenthetical) - shares	Sep. 30, 2017	Dec. 31, 2016
Statement of Financial Position [Abstract]
Common stock, shares authorized	200,000,000	200,000,000
Common stock, shares issued	120,624,346	118,688,770
Common stock, shares outstanding	120,624,346	118,688,770

Consolidated Statements of Oper

Consolidated Statements of Operations - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2017	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016
Revenues
Collaboration and licensing revenues, including $24,492 and $26,688 from related parties during the three months ended September 30, 2017 and 2016, respectively, and $77,937 and $70,299 during the nine months ended September 30, 2017 and 2016, respectively	$ 28,155	$ 30,590	$ 89,384	$ 82,144
Product revenues	7,670	9,260	25,780	28,699
Service revenues	9,975	8,706	37,890	33,298
Other revenues	216	429	899	783
Total revenues	46,016	48,985	153,953	144,924
Operating Expenses
Cost of products	8,001	9,156	25,625	29,471
Cost of services	7,013	5,803	21,805	17,807
Research and development	36,472	29,035	104,663	83,266
Selling, general and administrative	39,277	33,812	113,258	106,956
Total operating expenses	90,763	77,806	265,351	237,500
Operating loss	(44,747)	(28,821)	(111,398)	(92,576)
Other Income (Expense), Net
Unrealized and realized appreciation (depreciation) in fair value of equity securities and preferred stock	2,175	412	9,240	(45,388)
Interest expense	(138)	(227)	(498)	(759)
Interest and dividend income	5,070	4,494	14,437	5,817
Other income (expense), net	(1,021)	(32)	4,453	1,205
Total other income (expense), net	6,086	4,647	27,632	(39,125)
Equity in net loss of affiliates	(2,993)	(6,255)	(11,273)	(16,951)
Loss before income taxes	(41,654)	(30,429)	(95,039)	(148,652)
Income tax benefit	818	418	2,164	3,290
Net loss	(40,836)	(30,011)	(92,875)	(145,362)
Net loss attributable to the noncontrolling interests	1,147	1,029	3,123	2,887
Net loss attributable to Intrexon	$ (39,689)	$ (28,982)	$ (89,752)	$ (142,475)
Net loss attributable to Intrexon per share, basic and diluted (in usd per share)	$ (0.33)	$ (0.24)	$ (0.75)	$ (1.21)
Weighted average shares outstanding, basic and diluted (in shares)	120,518,885	118,346,782	119,741,291	117,785,160

Consolidated Statements of Ope5

Consolidated Statements of Operations (Parenthetical) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2017	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016
Related Party Transaction [Line Items]
Collaboration and licensing revenues	$ 28,155	$ 30,590	$ 89,384	$ 82,144
Related Parties, Aggregated
Related Party Transaction [Line Items]
Collaboration and licensing revenues	$ 24,492	$ 26,688	$ 77,937	$ 70,299

Consolidated Statements of Comp

Consolidated Statements of Comprehensive Loss - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2017	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016
Statement of Comprehensive Income [Abstract]
Net loss	$ (40,836)	$ (30,011)	$ (92,875)	$ (145,362)
Other comprehensive income (loss):
Unrealized gain (loss) on investments	79	(151)	74	588
Gain (loss) on foreign currency translation adjustments	7,410	(3,495)	19,405	(13,167)
Comprehensive loss	(33,347)	(33,657)	(73,396)	(157,941)
Comprehensive loss attributable to the noncontrolling interests	1,129	1,024	3,096	2,916
Comprehensive loss attributable to Intrexon	$ (32,218)	$ (32,633)	$ (70,300)	$ (155,025)

Consolidated Statements of Shar

Consolidated Statements of Shareholders' and Total Equity - 9 months ended Sep. 30, 2017 - USD ($) $ in Thousands	Total	Common Stock	Additional Paid-in Capital	Accumulated Other Comprehensive Loss	Accumulated Deficit	Total Intrexon Shareholders' Equity	Noncontrolling Interests
Balances (in shares) at Dec. 31, 2016	118,688,770	118,688,770
Balances at Dec. 31, 2016	$ 569,248	$ 0	$ 1,325,780	$ (36,202)	$ (729,341)	$ 560,237	$ 9,011
Increase (Decrease) in Stockholders' Equity
Cumulative effect of adoption of ASU 2016-09	0		1,461		(1,461)	0	0
Stock-based compensation expense	31,949		31,914			31,914	35
Exercises of stock options (in shares)		109,971
Exercises of stock options	867		839			839	28
Shares issued as payment for services (in shares)		439,200
Shares issued as payment for services	8,440		8,440			8,440	0
Shares and warrants issued in acquisition (in shares)		684,240
Shares and warrants issued in acquisition	16,997		16,997			16,997	0
Shares issued to acquire noncontrolling interests (in shares)		221,743
Shares issued to acquire noncontrolling interests	(913)		5,082			5,082	(5,995)
Shares issued as payment of deferred consideration (in shares)		480,422
Shares issued as payment of deferred consideration	0		0			0	0
Adjustments for noncontrolling interests	(13)		2,789			2,789	(2,802)
Noncash dividend	0		(22,385)			(22,385)	22,385
Net loss	(92,875)				(89,752)	(89,752)	(3,123)
Other comprehensive income	$ 19,479			19,452		19,452	27
Balances (in shares) at Sep. 30, 2017	120,624,346	120,624,346
Balances at Sep. 30, 2017	$ 553,179	$ 0	$ 1,370,917	$ (16,750)	$ (820,554)	$ 533,613	$ 19,566

Consolidated Statements of Cash

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2017	Sep. 30, 2016
Cash flows from operating activities
Net loss	$ (92,875)	$ (145,362)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	22,881	17,657
Loss on disposal of property, plant and equipment	1,311	297
Unrealized and realized (appreciation) depreciation on equity securities and preferred stock	(9,240)	45,388
Noncash dividend income	(12,303)	(3,676)
Amortization of premiums on investments	411	862
Equity in net loss of affiliates	11,273	16,951
Stock-based compensation expense	31,949	30,631
Shares issued as payment for services	8,440	8,284
Provision for bad debts	1,093	1,609
Deferred income taxes	(2,294)	(2,967)
Other noncash items	(1,848)	1,259
Changes in operating assets and liabilities:
Restricted cash	0	(6,987)
Receivables:
Trade	2,491	2,118
Related parties	(1,073)	7,438
Notes	0	(42)
Other	537	381
Inventory	3,418	4,683
Prepaid expenses and other	(516)	(985)
Other assets	(1,036)	2,134
Accounts payable	(3,756)	2,901
Accrued compensation and benefits	3,291	(8,001)
Other accrued liabilities	1,554	7,771
Deferred revenue	(35,281)	(14,099)
Deferred consideration	(313)	(630)
Related party payables	356	479
Other long term liabilities	1,271	126
Net cash used in operating activities	(70,259)	(31,780)
Cash flows from investing activities
Purchases of investments	0	(75,246)
Maturities of investments	136,300	71,987
Purchases of equity securities, preferred stock and warrants	(1,161)	(2,308)
Proceeds from sales of equity securities	235	0
Cash acquired in a business combination	2,054	0
Investments in affiliates	(10,639)	(9,415)
Cash paid in asset acquisition	(14,219)	(7,244)
Purchases of property, plant and equipment	(32,675)	(20,197)
Proceeds from sale of property, plant and equipment	1,423	243
Issuance of note receivable	(2,400)	(2,964)
Proceeds from repayment of note receivable	1,500	0
Net cash provided by (used in) investing activities	80,418	(45,144)
Cash flows from financing activities
Acquisitions of noncontrolling interests	(913)	0
Advances from lines of credit	4,563	2,308
Repayments of advances from lines of credit	(5,149)	(2,320)
Proceeds from long term debt	285	547
Payments of long term debt	(385)	(848)
Payments of deferred consideration for acquisitions	(8,678)	(6,705)
Proceeds from stock option exercises	867	18,180
Payment of stock issuance costs	(10)	0
Net cash provided by (used in) financing activities	(9,420)	11,162
Effect of exchange rate changes on cash and cash equivalents	870	(313)
Net increase (decrease) in cash and cash equivalents	1,609	(66,075)
Cash and cash equivalents
Beginning of period	62,607	135,782
End of period	64,216	69,707
Supplemental disclosure of cash flow information
Cash paid during the period for interest	534	875
Cash paid during the period for income taxes	497	0
Significant noncash financing and investing activities
Stock received as consideration for collaboration agreements	0	18,766
Preferred stock received as consideration for collaboration amendments	0	120,000
Stock and warrants issued in business combinations	16,997	0
Stock issued to acquire noncontrolling interest	5,082	0
Stock issued in asset acquisition	0	4,401
Contingent consideration assumed in asset acquisition	0	3,660
Noncash dividend to shareholders	22,385	0
Purchases of equipment included in accounts payable and other accrued liabilities	$ 2,137	$ 926

Organization

Organization	9 Months Ended
	Sep. 30, 2017
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Organization	Organization Intrexon Corporation ("Intrexon"), a Virginia corporation, forms collaborations to create biologically based products and processes using synthetic biology. Intrexon's primary domestic operations are in California, Florida, Maryland, and Virginia, and its primary international operations are in Belgium and Hungary. There have been no commercialized products derived from Intrexon's collaborations to date. Trans Ova Genetics, L.C. ("Trans Ova"), a provider of bovine reproductive technologies and other genetic processes to cattle breeders and producers, is a wholly owned subsidiary of Intrexon with primary operations in Iowa, Maryland, Missouri, Oklahoma, and Texas. Oxitec Limited ("Oxitec"), a pioneering company in biological insect control solutions, is a wholly owned subsidiary of Intrexon with primary operations in England and Brazil. Intrexon Produce Holdings, Inc. ("IPHI") is a wholly owned subsidiary of Intrexon. Okanagan Specialty Fruits, Inc. ("Okanagan"), a company which developed and received regulatory approval for the world's first non-browning apple without the use of any flavor-altering chemical or antioxidant additives, is a wholly owned subsidiary of IPHI with primary operations in Canada. Fruit Orchard Holdings, Inc. ("FOHI") is a wholly owned subsidiary of IPHI with primary operations in Washington. ViaGen, L.C. ("ViaGen"), a provider of genetic preservation and cloning technologies, and Exemplar Genetics, LLC ("Exemplar"), a provider of genetically engineered swine for medical and genetic research, are wholly owned subsidiaries with primary operations in Texas and Iowa, respectively. In March 2017, Intrexon acquired the remaining 49% of the equity of Biological & Popular Culture, Inc. ("BioPop"), a California company developing artwork, children's toys and novelty goods that are derived from living organisms or enabled by synthetic biology for $900 in cash and 221,743 shares of Intrexon common stock valued at $5,082 . Upon closing this transaction, BioPop became a wholly owned subsidiary of Intrexon. As of September 30, 2017 , Intrexon owned approximately 58% of AquaBounty Technologies, Inc. ("AquaBounty"), a company focused on improving productivity in commercial aquaculture. In January 2017, in conjunction with the listing by AquaBounty of their common stock on the NASDAQ Stock Market, Intrexon purchased $25,000 of additional AquaBounty common stock and subsequently distributed shares of AquaBounty common stock as a dividend to Intrexon shareholders. See Note 14 for additional discussion. Intrexon Corporation and its consolidated subsidiaries are hereinafter referred to as the "Company."

Summary of Significant Accounti

Summary of Significant Accounting Policies	9 Months Ended
	Sep. 30, 2017
Accounting Policies [Abstract]
Summary of Significant Accounting Policies	Summary of Significant Accounting Policies Basis of Presentation The accompanying interim consolidated financial statements are unaudited and have been prepared in accordance with accounting principles generally accepted in the United States of America ("U.S. GAAP"). Certain information and footnote disclosures normally included in the Company's annual financial statements have been condensed or omitted. These interim consolidated financial statements, in the opinion of management, reflect all normal recurring adjustments necessary for fair statement of the Company's financial position as of September 30, 2017 and results of operations and cash flows for the interim periods ended September 30, 2017 and 2016 . The year-end consolidated balance sheet data was derived from the Company's audited financial statements but does not include all disclosures required by U.S. GAAP. These interim financial results are not necessarily indicative of the results to be expected for the year ending December 31, 2017 , or for any other future annual or interim period. The accompanying interim unaudited consolidated financial statements should be read in conjunction with the audited consolidated financial statements and related notes thereto included in the Company's Annual Report on Form 10-K for the year ended December 31, 2016 . The accompanying consolidated financial statements reflect the operations of the Company and its subsidiaries. All intercompany accounts and transactions have been eliminated. Investments in Preferred Stock The Company holds preferred stock in certain of its collaborators which may be converted to common stock as described in Note 7 . The Company elected the fair value option to account for its investments in preferred stock whereby the value of preferred stock is adjusted to fair value as of each reporting date and unrealized gains and losses are reported in the consolidated statement of operations. These investments are subject to fluctuation in the future due to, among other things, the likelihood and timing of conversion of the preferred stock into common stock, the volatility of each collaborator's common stock, and changes in general economic and financial conditions of the collaborators. The investments are classified as noncurrent in the consolidated balance sheet since the Company does not intend to sell the investments nor expect them to be converted into shares of common stock within one year. Until such time as the Company converts the preferred stock into common stock, the Company is entitled to monthly dividends and records dividend income as described in Note 7 . Equity Method Investments The Company accounts for its investments in each of its joint ventures and for its investments in start-up entities backed by the Harvest Intrexon Enterprise Fund I, LP ("Harvest"), a related party, (Note 17 ) using the equity method of accounting based upon relative ownership interest. The Company's investments in these entities are included in investments in affiliates in the accompanying consolidated balance sheets. The Company accounts for its investment in Oragenics, Inc. ("Oragenics"), one of its collaborators, using the fair value option. The fair value of the Company's investment in Oragenics was $5,634 and $7,244 as of September 30, 2017 and December 31, 2016 , respectively, and is included as equity securities in the accompanying consolidated balance sheets. The Company's ownership of Oragenics was 29.4% and 29.5% as of September 30, 2017 and December 31, 2016 , respectively. Unrealized appreciation (depreciation) in the fair value of these securities was $827 and $(455) for the three months ended September 30, 2017 and 2016 , respectively, and was $(1,610) and $(11,597) for the nine months ended September 30, 2017 and 2016 , respectively. See Note 19 for additional discussion regarding Oragenics. Summarized financial data as of September 30, 2017 and December 31, 2016 and for the three and nine months ended September 30, 2017 and 2016 , for the Company's equity method investments are shown in the following tables. September 30, December 31, Current assets $ 68,021 $ 77,761 Non-current assets 12,856 11,040 Total assets 80,877 88,801 Current liabilities 9,032 11,588 Non-current liabilities 2,400 — Total liabilities 11,432 11,588 Net assets $ 69,445 $ 77,213 Three Months Ended Nine Months Ended 2017 2016 2017 2016 Revenues $ 58 $ 65 $ 175 $ 394 Operating expenses 9,693 18,363 33,128 50,406 Operating loss (9,635 ) (18,298 ) (32,953 ) (50,012 ) Other (145 ) 75 37 1,502 Net loss $ (9,780 ) $ (18,223 ) $ (32,916 ) $ (48,510 ) Variable Interest Entities As of September 30, 2017 and December 31, 2016 , the Company determined that certain of its collaborators and joint ventures as well as Harvest were variable interest entities ("VIE" or "VIEs"). The Company was not the primary beneficiary for these entities since it did not have the power to direct the activities that most significantly impact the economic performance of the VIEs. The Company's aggregate investment balances of these VIEs as of September 30, 2017 and December 31, 2016 were $187,555 and $159,115 , respectively, which represents the Company's maximum risk of loss related to the identified VIEs. Self-insurance Reserves Effective January 1, 2017, the Company commenced a self-insurance program for a significant portion of its employee health benefit programs. The Company maintains stop-loss coverage with third party insurers to limit its individual claims and total exposure under those programs. The Company estimates its accrued liability for the ultimate costs to close known claims, including claims incurred but not yet reported to the Company, as of the balance sheet date. The Company's recorded estimated liability for self-insurance is based on the insurance company's incurred loss estimates and management's judgment, including assumptions and factors related to the frequency and severity of claims and the Company's claims development history. The assessment of self-insurance reserves is a highly subjective process that requires judgments about future events. Self-insurance reserves are reviewed at least quarterly to determine the adequacy of the accruals and related financial statement disclosure. The ultimate settlement of self-insurance reserves may differ significantly from amounts the Company has accrued in its consolidated financial statements. Segment Information While the Company generates revenues from multiple sources, including collaboration agreements, licensing, and products and services associated with bovine reproduction, management is organized around a singular research and development focus to further the development of the Company's underlying synthetic biology technologies. Accordingly, the Company has determined that it operates in one segment. As of September 30, 2017 and December 31, 2016 , the Company had $19,335 and $13,265 , respectively, of long-lived assets in foreign countries. The Company recognized revenues derived in foreign countries totaling $4,448 and $3,502 for the three months ended September 30, 2017 and 2016 , respectively, and $11,773 and $8,678 for the nine months ended September 30, 2017 and 2016 , respectively. Use of Estimates The preparation of financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, the disclosure of contingent assets and liabilities at the date of the financial statements, and the reported amounts of revenues and expenses during the reporting periods. Actual results could differ from those estimates. Recently Adopted Accounting Pronouncements In January 2017, the Financial Accounting Standards Board ("FASB") issued Accounting Standards Update ("ASU") 2017-01, Business Combinations (Topic 805) - Clarifying the Definition of a Business ("ASU 2017-01"). The provisions of ASU 2017-01 clarify the definition of a business to assist entities with evaluating whether transactions should be accounted for as acquisitions (or disposals) of assets or businesses. The Company adopted this standard in the second quarter of 2017, and the implementation of this standard did not have a material impact on the Company's consolidated financial statements. In October 2016, the FASB issued ASU 2016-17, Consolidation (Topic 810) - Interests Held through Related Parties That Are under Common Control ("ASU 2016-17"). The provisions of ASU 2016-17 amend the consolidation guidance on how a reporting entity that is the single decision maker of a VIE should treat indirect interests in the entity held through related parties that are under common control with the reporting entity when determining whether it is the primary beneficiary of that VIE. The Company adopted this standard effective January 1, 2017, and the implementation of this standard did not have a material impact on the Company's consolidated financial statements. In March 2016, the FASB issued ASU 2016-09, Stock Compensation (Topic 718) - Improvements to Employee Share-Based Payment Accounting ("ASU 2016-09"). The provisions of ASU 2016-09 simplify various aspects of the accounting for employee share-based payment transactions, including the income tax consequences, classification of awards as either equity or liabilities, and classification on the statement of cash flows. The Company adopted this standard effective January 1, 2017. Upon adoption in the first quarter of 2017, the Company elected to recognize forfeitures as they occur and recorded an opening adjustment to additional paid-in capital and accumulated deficit for previously unrecognized stock-based compensation costs due to estimating forfeitures on unvested shares totaling $1,461 . The Company also recognized deferred tax assets of approximately $17,900 related to the excess tax benefits that previously arose directly from tax deductions related to equity compensation greater than stock-based compensation costs recognized in the consolidated financial statements and the cumulative adjustment for forfeitures. These deferred tax assets were fully offset by a valuation allowance (Note 13 ). The adoption was on a modified retrospective basis and had no impact on prior periods. In March 2016, the FASB issued ASU 2016-07, Investments-Equity Method and Joint Ventures (Topic 323) - Simplifying the Transition to the Equity Method of Accounting ("ASU 2016-07"). The provisions of ASU 2016-07 eliminate the requirement that when an investment qualifies for use of the equity method as a result of an increase in the level of ownership interest or degree of influence, an adjustment must be made to the investment, results of operations, and retained earnings retroactively on a step-by-step basis as if the equity method had been in effect during all previous periods that the investment had been held. The Company adopted this standard effective January 1, 2017, and the implementation of this standard did not have a material impact on the Company's consolidated financial statements. In July 2015, the FASB issued ASU 2015-11, Inventory (Topic 330) - Simplifying the Measurement of Inventory ("ASU 2015-11"). The provisions of ASU 2015-11 provide guidance for simplifying the calculation for subsequent measurement of inventory measured using the first-in-first-out or average cost methods. The Company adopted this standard effective January 1, 2017, and the implementation of this standard did not have a material impact on the Company's consolidated financial statements. Recently Issued Accounting Pronouncements In July 2017, the FASB issued ASU 2017-11, Earnings Per Share (Topic 260), Distinguishing Liabilities from Equity (Topic 480) and Derivatives and Hedging (Topic 815): I. Accounting for Certain Financial Instruments with Down Round Features; II. Replacement of the Indefinite Deferral for Mandatorily Redeemable Financial Instruments of Certain Nonpublic Entities and Certain Mandatorily Redeemable Noncontrolling Interests with a Scope Exception ("ASU 2017-11"). The amendments in Part I of ASU 2017-11 change the classification analysis of certain equity-linked financial instruments (or embedded features) with down round features. When determining whether certain financial instruments should be classified as liabilities or equity instruments, a down round feature no longer precludes equity classification when assessing whether the instrument is indexed to an entity's own stock. The amendments also clarify existing disclosure requirements for equity-classified instruments. As a result, a freestanding equity-linked financial instrument (or embedded conversion option) no longer would be accounted for as a derivative liability at fair value as a result of the existence of a down round feature. For freestanding equity-classified financial instruments, the amendments require entities that present earnings per share ("EPS") in accordance with Topic 260 to recognize the effect of the down round feature when it is triggered. That effect is treated as a dividend and as a reduction of income available to common shareholders in basic EPS. Convertible instruments with embedded conversion options that have down round features are now subject to the specialized guidance for contingent beneficial conversion features (in Subtopic 470-20, Debt-Debt with Conversion and Other Options ), including related EPS guidance (in Topic 260). The amendments in Part II of ASU 2017-11 re-characterize the indefinite deferral of certain provisions of Topic 480 that now are presented as pending content in the FASB codification, to a scope exception. Those amendments do not have an accounting effect. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2018, with early adoption permitted, and is effective for the Company for the year ended December 31, 2019. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. In May 2017, the FASB issued ASU 2017-09, Compensation-Stock Compensation (Topic 718) – Scope of Modification Accounting ("ASU 2017-09") . The provisions of ASU 2017-09 provide guidance about which changes to the terms or conditions of a share-based payment award require an entity to apply modification accounting in Topic 718. An entity should account for the effects of a modification unless (a) the fair value of the modified award is the same as the fair value of the original award, (b) the vesting conditions of the modified award are the same as the vesting conditions of the original award and (c) the classification of the modified award as an equity instrument or a liability instrument is the same as the classification of the original award immediately before the original award is modified. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2017, with early adoption permitted, and is effective for the Company for the year ending December 31, 2018. The amendments in ASU 2017-09 should be applied prospectively to an award modified on or after the adoption date. As this standard is prospective in nature, the impact to the Company's consolidated financial statements will depend on the nature of any future award modifications. The Company does not intend to early adopt this standard. In January 2017, the FASB issued ASU 2017-04, Intangibles-Goodwill and Other (Topic 350): Simplifying the Test for Goodwill Impairment ("ASU 2017-04"). The provisions of ASU 2017-04 simplify how an entity is required to test goodwill for impairment by eliminating Step 2 from the goodwill impairment test. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2019, with early adoption permitted, and is effective for the Company for the year ending December 31, 2020. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. In November 2016, the FASB issued ASU 2016-18, Statement of Cash Flows (Topic 230) - Restricted Cash (A Consensus of the FASB Emerging Issues Task Force) ("ASU 2016-18"). The provisions of ASU 2016-18 require amounts generally described as restricted cash and restricted cash equivalents to be included with cash and cash equivalents when reconciling the total beginning and ending balances for the periods presented on the statement of cash flows. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2017, with early adoption permitted, and is effective for the Company for the year ending December 31, 2018. The implementation of this standard is not expected to have a material impact on the Company's consolidated financial statements. In August 2016, the FASB issued ASU 2016-15, Statement of Cash Flows (Topic 230) - Classification of Certain Cash Receipts and Cash Payments ("ASU 2016-15"). The provisions of ASU 2016-15 address eight specific cash flow issues and how those certain cash receipts and cash payments are presented and classified in the statement of cash flows under Topic 230, Statement of Cash Flows , and other Topics. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2017, with early adoption permitted, and is effective for the Company for the year ending December 31, 2018. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. In February 2016, the FASB issued ASU 2016-02, Leases (Topic 842) ("ASU 2016-02"). The provisions of ASU 2016-02 set out the principles for the recognition, measurement, presentation and disclosure of leases for both parties to a contract (i.e. lessees and lessors). The new standard requires lessees to apply a dual approach, classifying leases as either finance or operating leases based on the principle of whether or not the lease is effectively a financed purchase by the lessee. This classification will determine whether lease expense is recognized based on an effective interest method or on a straight-line basis over the term of the lease, respectively. A lessee is also required to record a right-of-use asset and a lease liability for all leases with a term of greater than 12 months regardless of their classification. Leases with a term of 12 months or less will be accounted for in a similar manner as under existing guidance for operating leases today. ASU 2016-02 supersedes the previous lease standard, Topic 840, Leases . The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2018, and is effective for the Company for the year ending December 31, 2019. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. In January 2016, the FASB issued ASU 2016-01, Financial Instruments - Overall (Subtopic 825-10) - Recognition and Measurement of Financial Assets and Financial Liabilities ("ASU 2016-01"). The provisions of ASU 2016-01 make targeted improvements to enhance the reporting model for financial instruments to provide users of financial statements with more decision-useful information, including certain aspects of recognition, measurement, presentation, and disclosure of financial instruments. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2017, and is effective for the Company for the year ending December 31, 2018. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. In May 2014, the FASB issued ASU 2014-09, Revenue from Contracts with Customers ("ASU 2014-09"). The FASB issued ASU 2014-09 to clarify the principles for recognizing revenue and to develop a common revenue standard for U.S. GAAP. The standard outlines a single comprehensive model for entities to use in accounting for revenue arising from contracts with customers and supersedes the most current revenue recognition guidance. This guidance was originally effective for annual periods and interim periods within those annual periods beginning after December 15, 2016 and early adoption was not permitted. In August 2015, the FASB issued ASU 2015-14, Revenue from Contracts with Customers (Topic 606) - Deferral of the Effective Date , which deferred the effective date of the guidance in ASU 2014-09 by one year to December 15, 2017 for interim and annual reporting periods beginning after that date and permitted early adoption of the standard, but not before the original effective date of December 15, 2016, and is effective for the Company for the year ending December 31, 2018. In 2016 and 2017, the FASB clarified the implementation guidance on principal versus agent, identifying performance obligations, licensing, narrow-scope improvements, practical expedients, and to expedite improvements to ASU 2014-09 by issuing ASU 2016-08, Revenue from Contracts with Customers (Topic 606) - Principal versus Agent Considerations , ASU 2016-10, Revenue from Contracts with Customers (Topic 606) - Identifying Performance Obligations and Licensing , and ASU 2016-12, Revenue from Contracts with Customers (Topic 606) - Narrow-Scope Improvements and Practical Expedients , ASU 2016-20, Technical Corrections and Improvements to Topic 606, Revenue from Contracts with Customers , and ASU 2017-13, Revenue Recognition (Topic 605), Revenue from Contracts with Customers (Topic 606), Leases (Topic 840), and Leases (Topic 842) . The Company continues to progress in the evaluation of its collaborations and licensing agreements and product and service revenue arrangements to determine the impact, if any, that the implementation of this standard will have on the Company's consolidated financial statements. The Company has completed its review of collaboration and licensing agreements and product and service revenue arrangements and plans to finalize its analysis in the fourth quarter of 2017 to determine the impact, if any, this standard may have on its financial position, results of operations and disclosures. Additionally, any revenue arrangements entered into subsequent to December 31, 2017 with financial or other significant terms which differ from the financial or other significant terms of the Company's existing revenue arrangements will be evaluated under this new standard.

Mergers and Acquisitions

Mergers and Acquisitions	9 Months Ended
	Sep. 30, 2017
Mergers and Acquisitions [Abstract]
Mergers and Acquisitions	Mergers and Acquisitions GenVec Acquisition In June 2017, pursuant to an Agreement and Plan of Merger (the "GenVec Merger Agreement"), the Company acquired 100% of the outstanding shares of GenVec, Inc. ("GenVec"), a clinical-stage company and pioneer in the development of AdenoVerse gene delivery technology. Pursuant to the GenVec Merger Agreement, the former shareholders of GenVec received an aggregate of 684,240 shares of the Company's common stock and have the right to receive contingent consideration equal to 50% of any milestone or royalty payments received under one of GenVec's collaboration agreements, provided such payments are received within three years after the closing of the transaction. The Company also assumed warrants held by certain former shareholders of GenVec. The results of GenVec's operations subsequent to the acquisition date have been included in the consolidated financial statements. The fair value of the total consideration transferred was $17,582 . The acquisition date fair value of each class of consideration transferred is presented below: Common shares $ 15,616 Warrants 1,381 Contingent consideration 585 $ 17,582 The fair value of the shares of the Company's common stock issued was based on the quoted closing price of the Company's common stock immediately prior to the closing of the acquisition. The fair value of the warrants assumed was estimated using the Black-Scholes option-pricing model. The fair value of the contingent consideration was determined using a probability weighted discounted cash flows model and is considered a freestanding financial instrument and recorded at fair value each reporting period. The estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown below: Cash and cash equivalents $ 2,054 Short term investments 542 Trade receivables 75 Other receivables 97 Prepaid expenses and other 227 Property and equipment 250 Intangible assets 14,000 Other non-current assets 58 Total assets acquired 17,303 Accounts payable 2,158 Accrued compensation and benefits 1,226 Other accrued expenses 856 Other long term liabilities 92 Deferred tax liabilities 239 Total liabilities assumed 4,571 Net assets acquired 12,732 Goodwill 4,850 Total consideration $ 17,582 The acquired intangible assets include developed technology, the fair value of which was determined using the multi-period excess earning method, which is a variation of the income approach that converts future cash flows to single discounted present value amounts. The intangible assets are being amortized over a useful life of eleven years . Goodwill, which is not deductible for tax purposes, represents the assembled workforce and the anticipated buyer-specific synergies arising from the combination of the Company's and GenVec's technology. As of September 30, 2017, the Company had incurred $519 of acquisition related costs, of which $9 and $507 is included in selling, general and administrative expenses in the accompanying consolidated statements of operations for the three and nine months ended September 30, 2017 , respectively. Condensed Pro Forma Financial Information GenVec's results of operations subsequent to the acquisition are included in the consolidated statements of income. The following condensed pro forma financial information for the three months ended September 30, 2016 and the nine months ended September 30, 2017 and 2016 is presented as if the acquisition had been consummated on January 1, 2016: Three Months Ended Nine Months Ended 2016 2017 2016 Pro forma Revenues $ 49,158 $ 154,185 $ 145,413 Loss before income taxes (31,954 ) (102,305 ) (153,868 ) Net loss (31,536 ) (100,330 ) (150,389 ) Net loss attributable to the noncontrolling interests 1,029 3,123 2,887 Net loss attributable to Intrexon (30,507 ) (97,207 ) (147,502 )

Investments in Joint Ventures

Investments in Joint Ventures	9 Months Ended
	Sep. 30, 2017
Equity Method Investments and Joint Ventures [Abstract]
Investments in Joint Ventures	Investments in Joint Ventures S & I Ophthalmic In September 2013, the Company entered into a Limited Liability Company Agreement ("Sun LLC Agreement") with Caraco Pharmaceutical Laboratories, Ltd. ("Sun Pharmaceutical Subsidiary"), an indirect subsidiary of Sun Pharmaceutical Industries Ltd. ("Sun Pharmaceutical"), an international specialty pharmaceutical company focused on chronic diseases, to form S & I Ophthalmic, LLC ("S & I Ophthalmic"). The Sun LLC Agreement governs the affairs and the conduct of business of S & I Ophthalmic. S & I Ophthalmic leverages experience and technology from both the Company and Sun Pharmaceutical. Both the Company and Sun Pharmaceutical Subsidiary made an initial capital contribution of $5,000 in October 2013 for a 50% membership interest in S & I Ophthalmic. S & I Ophthalmic is governed by a board of managers ("S & I Ophthalmic Board") which has four members, two each from the Company and Sun Pharmaceutical Subsidiary. In cases in which the S & I Ophthalmic Board determines that additional capital contributions are necessary in order for S & I Ophthalmic to conduct business and comply with its obligations, each of the Company and Sun Pharmaceutical Subsidiary has committed to making additional capital contributions to S & I Ophthalmic subject to certain limits defined in the Sun LLC Agreement. Each has the right, but not the obligation, to make additional capital contributions above the defined limits when and if solicited by the S & I Ophthalmic Board. In 2015, both the Company and Sun Pharmaceutical Subsidiary made subsequent capital contributions of $5,000 . Beginning on the seventh anniversary of the effective date of the Sun LLC Agreement, and upon the second anniversary thereafter, the Company, as well as Sun Pharmaceutical Subsidiary, may make a cash offer to purchase all of the other party's interest in S & I Ophthalmic. Upon receipt of such an offer, the other party must either agree to tender its interests at the offered price or submit a counteroffer at a price higher than the original offer. Such offer and counteroffer may continue until one party agrees to the other's price. The Company's investment in S & I Ophthalmic was $2,621 and $3,236 as of September 30, 2017 and December 31, 2016 , respectively, and is included in investments in affiliates in the accompanying consolidated balance sheets. OvaXon In December 2013, the Company and OvaScience, Inc. ("OvaScience"), a life sciences company focused on the discovery, development, and commercialization of new treatments for infertility, entered into a Limited Liability Company Agreement ("OvaXon LLC Agreement") to form OvaXon, LLC ("OvaXon"), a joint venture to create new applications for improving human and animal health. Both the Company and OvaScience made an initial capital contribution of $1,500 in January 2014 for a 50% membership interest in OvaXon. OvaXon is governed by the OvaXon board of managers ("OvaXon Board") which has four members, two each from the Company and OvaScience. In cases in which the OvaXon Board determines that additional capital contributions are necessary in order for OvaXon to conduct business and comply with its obligations, each of the Company and OvaScience has the right, but not the obligation, to make additional capital contributions to OvaXon subject to the OvaXon LLC Agreement. Through September 30, 2017 , both the Company and OvaScience have made subsequent capital contributions of $3,800 . The Company's investment in OvaXon was $(401) and $65 as of September 30, 2017 and December 31, 2016 , respectively, and is included in other accrued liabilities and investments in affiliates, respectively, in the accompanying consolidated balance sheets. Intrexon Energy Partners In March 2014, the Company and certain investors (the "IEP Investors"), including an affiliate of Third Security, LLC ("Third Security"), entered into a Limited Liability Company Agreement which governs the affairs and conduct of business of Intrexon Energy Partners, LLC ("Intrexon Energy Partners"), a joint venture formed to optimize and scale-up the Company's gas-to-liquid bioconversion platform for the production of certain fuels and lubricants. The Company also entered into an ECC with Intrexon Energy Partners providing exclusive rights to the Company's technology for the use in bioconversion, as a result of which the Company received a technology access fee of $25,000 while retaining a 50% membership interest in Intrexon Energy Partners. The IEP Investors made initial capital contributions, totaling $25,000 in the aggregate, in exchange for pro rata membership interests in Intrexon Energy Partners totaling 50% . In addition, Intrexon has committed to make capital contributions of up to $25,000 , and the IEP Investors, as a group and pro rata in accordance with their respective membership interests in Intrexon Energy Partners, have committed to make additional capital contributions of up to $25,000 , at the request of Intrexon Energy Partners' board of managers (the "Intrexon Energy Partners Board") and subject to certain limitations. As of September 30, 2017 , the Company's remaining commitment was $6,011 . Intrexon Energy Partners is governed by the Intrexon Energy Partners Board which has five members. Two members of the Intrexon Energy Partners Board are designated by the Company and three members are designated by a majority of the IEP Investors. The Company and the IEP Investors have the right, but not the obligation, to make additional capital contributions above the initial limits when and if solicited by the Intrexon Energy Partners Board. The Company's investment in Intrexon Energy Partners was $144 and $(477) as of September 30, 2017 and December 31, 2016 , respectively, and is included in investments in affiliates and other accrued liabilities, respectively, in the accompanying consolidated balance sheets. Intrexon Energy Partners II In December 2015, the Company and certain investors (the "IEPII Investors"), including Harvest, entered into a Limited Liability Company Agreement which governs the affairs and conduct of business of Intrexon Energy Partners II, LLC ("Intrexon Energy Partners II"), a joint venture formed to utilize the Company's natural gas bioconversion platform for the production of 1,4-butanediol, an industrial chemical used to manufacture spandex, polyurethane, plastics, and polyester. The Company also entered into an ECC with Intrexon Energy Partners II which provides exclusive rights to the Company's technology for use in the field, as a result of which the Company received a technology access fee of $18,000 while retaining a 50% membership interest in Intrexon Energy Partners II. The IEPII Investors made initial capital contributions, totaling $18,000 in the aggregate, in exchange for pro rata membership interests in Intrexon Energy Partners II totaling 50% . In December 2015, the owners of Intrexon Energy Partners II made a capital contribution of $4,000 , half of which was paid by the Company. Intrexon has committed to make additional capital contributions of up to $10,000 , and the IEPII Investors, as a group and pro rata in accordance with their respective membership interests in Intrexon Energy Partners II, have committed to make additional capital contributions of up to $10,000 , at the request of Intrexon Energy Partners II's board of managers (the "Intrexon Energy Partners II Board") and subject to certain limitations. Intrexon Energy Partners II is governed by the Intrexon Energy Partners II Board which has five members. One member of the Intrexon Energy Partners II Board is designated by the Company and four members are designated by a majority of the IEPII Investors. The Company and the IEPII Investors have the right, but not the obligation, to make additional capital contributions above the initial limits when and if solicited by the Intrexon Energy Partners II Board. The Company's investment in Intrexon Energy Partners II was $698 and $1,414 as of September 30, 2017 and December 31, 2016 , respectively, and is included in investments in affiliates in the accompanying consolidated balance sheets. EnviroFlight In February 2016, the Company entered into a series of transactions involving EnviroFlight, LLC ("Old EnviroFlight"), Darling Ingredients Inc. ("Darling") and a newly formed venture between the Company and Darling ("New EnviroFlight"). The Company determined that the series of integrated transactions to acquire substantially all of the assets of Old EnviroFlight for cash, common stock, and contingent consideration should be accounted for as a single transaction, which constituted a business, and considered New EnviroFlight to be the accounting acquirer. Consideration paid to Old EnviroFlight was $4,244 in cash, 136,340 shares of the Company's common stock valued at $4,401 and contingent consideration estimated at $3,660 . Contemporaneously, all the assets acquired from Old EnviroFlight, with the exception of certain developed technology, and $3,000 of cash were contributed to New EnviroFlight in exchange for a non-controlling, 50% membership interest in New EnviroFlight. The Company's contributions to New EnviroFlight included an exclusive license to the developed technology that was retained by the Company. Darling received the remaining 50% membership interest in New EnviroFlight as consideration for terminating rights previously held in the developed technology with Old EnviroFlight. New EnviroFlight was formed to generate high-nutrition, low environmental impact animal and fish feed, as well as fertilizer products. The Company and Darling as members have each agreed to make additional capital contributions of up to $5,000 to fund ongoing operations of New EnviroFlight. As of September 30, 2017 , the Company's remaining commitment was $250 . All of the employees of Old EnviroFlight became employees of New EnviroFlight. The Company determined that its investment in New EnviroFlight should be accounted for using the equity method of accounting. The Company recorded an estimated fair value of $5,425 for its investment in New EnviroFlight and $9,880 for the retained developed technology intangible asset. The developed technology is being amortized over a period of twenty-one years . The contingent consideration liability payable to the members of Old EnviroFlight is considered a freestanding financial instrument and is recorded at fair value each reporting period. New EnviroFlight met a regulatory milestone, as defined in the asset purchase agreement, and the members of Old EnviroFlight received a portion of the contingent consideration consisting of 59,337 shares of the Company's common stock valued at $1,583 in October 2016. The members of Old EnviroFlight may receive up to $4,000 of additional shares of the Company's common stock if certain commercial milestones are met prior to February 2019. The value of this liability was estimated at $2,326 as of September 30, 2017 (Note 8 ). The Company's investment in New EnviroFlight was $7,687 and $4,189 as of September 30, 2017 and December 31, 2016 , respectively, and is included in investments in affiliates in the accompanying consolidated balance sheets. Intrexon T1D Partners In March 2016, the Company and certain investors (the "T1D Investors"), including affiliates of Third Security, entered into a Limited Liability Company Agreement which governs the affairs and conduct of business of Intrexon T1D Partners, LLC ("Intrexon T1D Partners"), a joint venture formed to utilize the Company's proprietary ActoBiotics platform to develop and commercialize products to treat type 1 diabetes. The Company also entered into an ECC with Intrexon T1D Partners which provides the exclusive rights to the Company's technology for use in the field, as a result of which the Company received a technology access fee of $10,000 while retaining a 50% membership interest in Intrexon T1D Partners. The T1D Investors made initial capital contributions, totaling $10,000 in the aggregate, in exchange for pro rata membership interests in Intrexon T1D Partners totaling 50% . Intrexon has committed to make capital contributions of up to $5,000 , and the T1D Investors, as a group and pro rata in accordance with their respective membership interests in Intrexon T1D Partners, have committed to make additional capital contributions of up to $5,000 , at the request of Intrexon T1D Partners' board of managers (the "Intrexon T1D Partners Board") and subject to certain limitations. As of September 30, 2017 , the Company's remaining commitment was $2,900 . Intrexon T1D Partners is governed by the Intrexon T1D Partners Board, which has five members. Two members of the Intrexon T1D Partners Board are designated by the Company and three members are designated by a majority of the T1D Investors. The Company and the T1D Investors have the right, but not the obligation, to make additional capital contributions above these limits when and if solicited by the Intrexon T1D Partners Board. The Company's investment in Intrexon T1D Partners was $51 and $806 as of September 30, 2017 and December 31, 2016 , respectively, and is included in investments in affiliates in the accompanying consolidated balance sheets.

Collaboration and Licensing Rev

Collaboration and Licensing Revenue	9 Months Ended
	Sep. 30, 2017
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Collaboration and Licensing Revenue	Collaboration and Licensing Revenue The Company generates revenue through contractual agreements with collaborators (known as exclusive channel collaborations, "ECC" or "ECCs") and licensing agreements whereby the collaborators or the licensees obtain exclusive access to the Company's proprietary technologies for use in the research, development and commercialization of products and/or treatments in a contractually specified field of use. Upfront and milestone payments are typically deferred and recognized over the expected life of the Company's technology platform using a straight-line approach. The Company recognizes the reimbursement payments received for research and development services in the period in which the services are performed and collection is reasonably assured. The following tables summarize the amounts recorded as revenue in the consolidated statements of operations for each significant counterparty to a collaboration or licensing agreement for the three and nine months ended September 30, 2017 and 2016 . Three Months Ended September 30, 2017 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 4,843 $ 5,530 $ 10,373 Oragenics, Inc. 262 213 475 Fibrocell Science, Inc. 604 1,079 1,683 Genopaver, LLC 68 1,354 1,422 S & I Ophthalmic, LLC — 376 376 OvaXon, LLC — 262 262 Intrexon Energy Partners, LLC 625 1,278 1,903 Persea Bio, LLC 125 141 266 Ares Trading S.A. 1,597 759 2,356 Intrexon Energy Partners II, LLC 500 316 816 Intrexon T1D Partners, LLC 287 1,175 1,462 Harvest start-up entities (1) 616 3,404 4,020 Other 979 1,762 2,741 Total $ 10,506 $ 17,649 $ 28,155 (1) For the three months ended September 30, 2017 , revenue recognized from collaborations with Harvest start-up entities include Thrive Agrobiotics, Inc.; Exotech Bio, Inc.; Relieve Genetics, Inc.; AD Skincare, Inc.; Genten Therapeutics, Inc.; and CRS Bio, Inc. Three Months Ended September 30, 2016 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 4,843 $ 5,586 $ 10,429 Oragenics, Inc. 262 294 556 Fibrocell Science, Inc. 604 563 1,167 Genopaver, LLC 68 1,625 1,693 S & I Ophthalmic, LLC — 2,782 2,782 OvaXon, LLC — 709 709 Intrexon Energy Partners, LLC 625 4,230 4,855 Persea Bio, LLC 125 208 333 Ares Trading S.A. 1,597 719 2,316 Intrexon Energy Partners II, LLC 500 372 872 Intrexon T1D Partners, LLC 276 511 787 Harvest start-up entities (1) 425 868 1,293 Other 895 1,903 2,798 Total $ 10,220 $ 20,370 $ 30,590 (1) For the three months ended September 30, 2016 , revenue recognized from collaborations with Harvest start-up entities include Thrive Agrobiotics, Inc.; Exotech Bio, Inc.; Relieve Genetics, Inc.; and AD Skincare, Inc. Nine Months Ended September 30, 2017 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 14,527 $ 16,795 $ 31,322 Oragenics, Inc. 786 733 1,519 Fibrocell Science, Inc. 1,814 3,561 5,375 Genopaver, LLC 205 4,410 4,615 S & I Ophthalmic, LLC — 751 751 OvaXon, LLC — 1,966 1,966 Intrexon Energy Partners, LLC 1,875 7,034 8,909 Persea Bio, LLC 375 446 821 Ares Trading S.A. 4,791 3,683 8,474 Intrexon Energy Partners II, LLC 1,500 1,421 2,921 Intrexon T1D Partners, LLC 823 3,059 3,882 Harvest start-up entities (1) 1,823 10,012 11,835 Other 3,735 3,259 6,994 Total $ 32,254 $ 57,130 $ 89,384 (1) For the nine months ended September 30, 2017 , revenue recognized from collaborations with Harvest start-up entities include Thrive Agrobiotics, Inc.; Exotech Bio, Inc.; Relieve Genetics, Inc.; AD Skincare, Inc.; Genten Therapeutics, Inc.; and CRS Bio, Inc. Nine Months Ended September 30, 2016 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 6,687 $ 17,693 $ 24,380 Oragenics, Inc. 786 1,083 1,869 Fibrocell Science, Inc. 1,814 2,604 4,418 Genopaver, LLC 205 4,703 4,908 S & I Ophthalmic, LLC — 6,326 6,326 OvaXon, LLC — 2,211 2,211 Intrexon Energy Partners, LLC 1,875 11,180 13,055 Persea Bio, LLC 375 613 988 Ares Trading S.A. 4,791 2,148 6,939 Intrexon Energy Partners II, LLC 1,500 816 2,316 Intrexon T1D Partners, LLC 554 543 1,097 Harvest start-up entities (1) 776 1,890 2,666 Other 4,684 6,287 10,971 Total $ 24,047 $ 58,097 $ 82,144 (1) For the nine months ended September 30, 2016 , revenue recognized from collaborations with Harvest start-up entities include Thrive Agrobiotics, Inc.; Exotech Bio, Inc.; Relieve Genetics, Inc.; and AD Skincare, Inc. There have been no significant changes to arrangements with our collaborators and licensees in the nine months ended September 30, 2017 . See Note 5 in the Company's Annual Report on Form 10-K for the year ended December 31, 2016 for additional details of the Company's existing collaboration and licensing agreements. Deferred Revenue Deferred revenue primarily consists of consideration received for upfront and milestone payments in connection with the Company's collaborations and licensing agreements, prepayments for research and development services performed for collaborators and licensees, and prepayments for product and service revenues. Deferred revenue consists of the following: September 30, December 31, Upfront and milestone payments $ 269,649 $ 297,867 Prepaid research and development services 1,718 6,015 Prepaid product and service revenues 4,869 5,554 Other 51 706 Total $ 276,287 $ 310,142 Current portion of deferred revenue $ 48,289 $ 53,364 Long-term portion of deferred revenue 227,998 256,778 Total $ 276,287 $ 310,142 The following table summarizes the remaining balance of deferred revenue associated with upfront and milestone payments for each significant collaboration and licensing agreement. September 30, December 31, ZIOPHARM Oncology, Inc. $ 124,282 $ 138,809 Oragenics, Inc. 6,980 7,766 Fibrocell Science, Inc. 17,212 19,026 Genopaver, LLC 1,772 1,977 Intrexon Energy Partners, LLC 16,250 18,125 Persea Bio, LLC 3,625 4,000 Ares Trading S.A. 42,387 47,178 Intrexon Energy Partners II, LLC 14,333 15,833 Intrexon T1D Partners, LLC 8,628 8,653 Harvest start-up entities (1) 18,953 20,208 Other 15,227 16,292 Total $ 269,649 $ 297,867 (1) As of September 30, 2017 and December 31, 2016 , the balance of deferred revenue for collaborations with Harvest start-up entities includes Thrive Agrobiotics, Inc.; Exotech Bio, Inc.; Relieve Genetics, Inc.; AD Skincare, Inc.; Genten Therapeutics, Inc.; and CRS Bio, Inc.

Short-term and Long-term Invest

Short-term and Long-term Investments	9 Months Ended
	Sep. 30, 2017
Investments, Debt and Equity Securities [Abstract]
Short-term and Long-term Investments	Short-term and Long-term Investments The Company's investments are classified as available-for-sale. The following table summarizes the amortized cost, gross unrealized gains and losses, and fair value of available-for-sale investments as of September 30, 2017 : Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Aggregate Fair Value U.S. government debt securities $ 44,000 $ 2 $ (17 ) $ 43,985 Corporate notes and bonds 242 — — 242 Certificates of deposit 275 — — 275 Total $ 44,517 $ 2 $ (17 ) $ 44,502 The following table summarizes the amortized cost, gross unrealized gains and losses, and fair value of available-for-sale investments as of December 31, 2016 : Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Aggregate Fair Value U.S. government debt securities $ 180,412 $ 5 $ (94 ) $ 180,323 Certificates of deposit 272 — — 272 Total $ 180,684 $ 5 $ (94 ) $ 180,595 For more information on the Company's method for determining the fair value of its assets, see Note 2 – "Fair Value of Financial Instruments" in the Company's Annual Report on Form 10-K for the year ended December 31, 2016 . As of September 30, 2017 , all of the available-for-sale investments were due within one year based on their contractual maturities. Changes in market interest rates and bond yields cause certain investments to fall below their cost basis, resulting in unrealized losses on investments. The unrealized losses of the Company's investments were primarily a result of unfavorable changes in interest rates subsequent to the initial purchase of these investments and are not significant as of September 30, 2017 . As of September 30, 2017 and December 31, 2016 , the Company did not consider any of its investments to be other-than-temporarily impaired. When evaluating its investments for other-than-temporary impairment, the Company reviews factors such as the length of time and extent to which fair value has been below its cost basis, the financial condition of the issuer, the Company's ability and intent to hold the security and whether it is more likely than not that it will be required to sell the investment before recovery of its cost basis.

Investments in Preferred Stock

Investments in Preferred Stock	9 Months Ended
	Sep. 30, 2017
Investment in Preferred Stock [Abstract]
Investments In Preferred Stock	Investments in Preferred Stock Investment in ZIOPHARM Preferred Stock In June 2016, the Company received 100,000 shares of Series 1 Preferred Stock (the "Preferred Shares") of ZIOPHARM Oncology Inc. ("ZIOPHARM"), a related party, with a per share stated value of $1,200 , as consideration for amending their two previously existing ECC agreements. A summary of the terms of the Preferred Shares follows. Conversion. The Preferred Shares shall automatically convert into shares of ZIOPHARM common stock upon the date the first approval in the United States of (i) a ZIOPHARM product, as defined in and developed under one of the ECC agreements, or (ii) a product, as defined and developed under the License and Collaboration Agreement with Ares Trading S.A., a subsidiary of the biopharmaceutical business of Merck KGaA, and ZIOPHARM, is publicly announced (the "Conversion Event Date"). The Preferred Shares shall convert into a number of shares of ZIOPHARM common stock equal to the stated value of such Preferred Share, divided by the greater of: (i) the volume weighted average closing price of ZIOPHARM's common stock over the twenty trading days ending on the Conversion Event Date or (ii) $1.00 . The number of converted shares is subject to certain limitations defined in the amended and restated Certificate of Designation, Preferences, and Rights of Series 1 Preferred Stock (the "A&R Certificate of Designation"). Dividend Rights. The Company shall receive a monthly dividend, payable in additional Preferred Shares, equal to $12.00 per Preferred Share held per month divided by the stated value of the Preferred Shares, which is referred to as the PIK Dividend. For any Preferred Shares that are not converted on the Conversion Event Date, the rate of PIK Dividend on these unconverted Preferred Shares will automatically increase from $12.00 to $24.00 per Preferred Share per month. Voting Rights . The Preferred Shares do not have any voting rights except for certain protective voting rights defined in the A&R Certificate of Designation. Liquidation Rights. In the event of any voluntary or involuntary liquidation, dissolution or winding up of ZIOPHARM or a deemed liquidation event, as defined in the A&R Certificate of Designation, including a change of control or the sale, lease transfer, or exclusive license of all or substantially all of ZIOPHARM's assets, the holders of the Preferred Shares shall be entitled to receive a portion of all funds to be distributed in proportion to the holders' proportionate share of ZIOPHARM's common stock on an as-converted to common stock basis (the "Series 1 Liquidation Amount"). For purposes of calculating the Series 1 Liquidation Amount, if such liquidation event occurs prior to the Conversion Event Date, each Preferred Share shall be deemed to be convertible into the number of shares of ZIOPHARM's common stock equal to (i) the stated value of each Preferred Share, divided by (ii) the volume weighted average price of ZIOPHARM's common stock for the twenty day period ending on the date of the public announcement of the liquidation event. In addition, ZIOPHARM may elect to redeem the Preferred Shares in connection with or following a deemed liquidation event at a price per share equal to the Series 1 Liquidation Amount. The investment in ZIOPHARM preferred stock is categorized as Level 3 as there are significant unobservable inputs and the Preferred Shares are not traded on a public exchange. The fair value of the investment in ZIOPHARM preferred stock is estimated using a probability-weighted expected return ("PWERM") model. The key inputs used in the PWERM model are (i) estimating the future returns for conversion of the Preferred Shares for both product approval and a change in control of ZIOPHARM (the "conversion events") using market data of the change in value for guideline companies as a result of these conversion events; (ii) estimating the expected date and likelihood of each conversion event; and (iii) discounting these estimated future returns using a discount rate for the Preferred Shares considering industry debt issuances originated by public funds and venture capital rates of return. A significant change in unobservable inputs discussed above could result in a significant impact on the fair value of the Company's investment in ZIOPHARM preferred stock. The fair value of the Company's investment in ZIOPHARM preferred stock, including additional Preferred Shares received as dividends, was $146,637 and $129,545 as of September 30, 2017 and December 31, 2016 , respectively. During the three and nine months ended September 30, 2017 , the Company received 3,414 shares and 9,943 shares, respectively, of additional Preferred Shares and recognized $4,311 and $12,276 , respectively, of dividend income in the accompanying consolidated statements of operations. During the three and nine months ended September 30, 2016 , the Company received 3,063 shares of additional Preferred Shares and recognized $3,676 of dividend income in the accompanying consolidated statements of operations. Investment in Fibrocell Preferred Stock In March 2017, Fibrocell Science, Inc. ("Fibrocell"), one of the Company's collaborators and a related party, sold Series A Convertible Preferred Stock (the "Convertible Preferred Shares") convertible into shares of Fibrocell common stock and warrants to purchase shares of Fibrocell common stock to certain institutional and accredited investors, including the Company and affiliates of Third Security. The Company paid $1,161 in exchange for 1,161 Convertible Preferred Shares and warrants to acquire 498,843 shares of Fibrocell common stock, reflective of the 1-for-3 reverse stock split of Fibrocell's common stock effective March 10, 2017. The Convertible Preferred Shares are convertible at any time at the election of the Company and accrue dividends at 4% per annum, compounded quarterly, increasing the stated value of the shares. The investment in Fibrocell preferred stock is categorized as Level 3 as there are significant unobservable inputs and the Convertible Preferred Shares are not traded on a public exchange. The fair value of the investment in Fibrocell preferred stock is estimated using a conversion plus dividend approach utilizing the trading value of the underlying common stock and an estimated premium for the preferred stock dividend and other preferences. Market price volatility of Fibrocell's common stock and a significant change in the estimated preferred stock premium could result in a significant impact to the fair value of the investment in Fibrocell preferred stock. As of September 30, 2017 , the fair value of the Company's investment in Fibrocell preferred stock totaled $1,862 . See Note 17 for additional discussion of the warrants. Changes in the Fair Value of Investments in Preferred Stock The following table summarizes the changes in the Level 3 investments in preferred stock during the nine months ended September 30, 2017 . Nine Months Ended Beginning balance $ 129,545 Purchase of preferred stock 766 Dividend income from investments in preferred stock 12,303 Unrealized appreciation in the fair value of the investments in preferred stock 5,885 Ending balance $ 148,499

Fair Value Measurements

Fair Value Measurements	9 Months Ended
	Sep. 30, 2017
Fair Value Disclosures [Abstract]
Fair Value Measurements	Fair Value Measurements The carrying amount of cash and cash equivalents, restricted cash, receivables, prepaid expenses and other current assets, accounts payable, accrued compensation and benefits, other accrued liabilities, and related party payables approximate fair value due to the short maturity of these instruments. The following table presents the placement in the fair value hierarchy of financial assets that are measured at fair value on a recurring basis, including the items for which the fair value option has been elected, at September 30, 2017 : Quoted Prices in Active Markets (Level 1) Significant Other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) September 30, Assets U.S. government debt securities $ — $ 43,985 $ — $ 43,985 Equity securities 19,830 6,812 — 26,642 Preferred stock — — 148,499 148,499 Other — 7,089 — 7,089 Total $ 19,830 $ 57,886 $ 148,499 $ 226,215 The following table presents the placement in the fair value hierarchy of financial assets that are measured at fair value on a recurring basis, including the items for which the fair value option has been elected, at December 31, 2016 : Quoted Prices in Active Markets Significant Other Observable Inputs Significant Unobservable Inputs December 31, Assets U.S. government debt securities $ — $ 180,323 $ — $ 180,323 Equity securities 15,544 7,978 — 23,522 Preferred stock — — 129,545 129,545 Other — 1,917 — 1,917 Total $ 15,544 $ 190,218 $ 129,545 $ 335,307 The method used to estimate the fair value of the Level 1 assets in the tables above is based on observable market data as these equity securities are publicly-traded. The method used to estimate the fair value of the Level 2 short-term and long-term investments in the tables above is based on professional pricing sources for identical or comparable instruments, rather than direct observations of quoted prices in active markets. The method used to estimate the fair value of the Level 2 equity securities in the tables above is based on the quoted market price of the publicly-traded security, adjusted for a discount for lack of marketability. The methods used to estimate the fair value of the Level 3 assets are discussed in Note 7 . There were no transfers between levels of the fair value hierarchy during the nine months ended September 30, 2017 . The carrying values of the Company's long term debt approximates fair value due to the length of time to maturity and/or the existence of interest rates that approximate prevailing market rates. The Company's contingent consideration liabilities (Notes 3 and 4 ) are measured on a recurring basis and were $2,911 and $2,081 at September 30, 2017 and December 31, 2016 , respectively. These fair value measurements were based on significant inputs not observable in the market and thus represented a Level 3 measurement. A significant change in unobservable inputs could result in a significant impact on the fair value of the Company's contingent consideration liabilities. The contingent consideration liabilities are remeasured to fair value at each reporting date until the contingencies are resolved, and those changes in fair value are recognized in earnings. The changes in the fair value of the Level 3 liabilities during the nine months ended September 30, 2017 were as follows: Nine Months Ended Beginning balance $ 2,081 Acquisition date fair value of contingent consideration liability (Note 3) 585 Change in fair value of contingent consideration recognized in selling, general and administrative expenses 245 Ending balance $ 2,911

Inventory

Inventory	9 Months Ended
	Sep. 30, 2017
Inventory Disclosure [Abstract]
Inventory	Inventory Inventory consists of the following: September 30, December 31, Supplies, embryos and other production materials $ 2,185 $ 1,835 Work in process 4,618 5,466 Livestock 8,738 11,752 Feed 2,189 2,086 Total inventory $ 17,730 $ 21,139

Property, Plant and Equipment,

Property, Plant and Equipment, Net	9 Months Ended
	Sep. 30, 2017
Property, Plant and Equipment [Abstract]
Property, Plant and Equipment, Net	Property, Plant and Equipment, Net Property, plant and equipment consist of the following: September 30, December 31, Land and land improvements $ 11,642 $ 10,904 Buildings and building improvements 15,216 8,123 Furniture and fixtures 2,220 2,176 Equipment 58,851 44,392 Leasehold improvements 22,974 15,105 Breeding stock 3,822 3,893 Computer hardware and software 9,817 6,844 Trees 5,719 2,772 Construction and other assets in progress 15,138 4,513 145,399 98,722 Less: Accumulated depreciation and amortization (42,523 ) (34,050 ) Property, plant and equipment, net $ 102,876 $ 64,672 Depreciation expense was $2,989 and $2,332 for the three months ended September 30, 2017 and 2016 , respectively, and $8,623 and $6,769 for the nine months ended September 30, 2017 and 2016 , respectively. In June 2017, AquaBounty purchased a land-based aquaculture facility to be used in the production of its AquAdvantage salmon in Indiana for $14,219 .

Goodwill and Intangible Assets,

Goodwill and Intangible Assets, Net	9 Months Ended
	Sep. 30, 2017
Goodwill and Intangible Assets Disclosure [Abstract]
Goodwill and Intangible Assets, Net	Goodwill and Intangible Assets, Net The changes in the carrying amount of goodwill for the nine months ended September 30, 2017 are as follows: Balance at December 31, 2016 $ 157,175 Acquisitions 4,850 Foreign currency translation adjustments 4,796 Balance at September 30, 2017 $ 166,821 No accumulated impairment losses existed as of September 30, 2017 and December 31, 2016 . Intangible assets consist of the following as of September 30, 2017 : Weighted Average Useful Life (Years) Gross Carrying Amount Accumulated Amortization Net Patents, developed technologies and know-how 15.7 $ 266,697 $ (43,465 ) $ 223,232 Customer relationships 6.5 10,700 (6,033 ) 4,667 Trademarks 9.3 6,800 (2,373 ) 4,427 In-process research and development 8,571 — 8,571 Total $ 292,768 $ (51,871 ) $ 240,897 Intangible assets consist of the following as of December 31, 2016 : Gross Carrying Amount Accumulated Amortization Net Patents, developed technologies and know-how $ 236,401 $ (29,748 ) $ 206,653 Customer relationships 10,700 (4,672 ) 6,028 Trademarks 6,800 (1,792 ) 5,008 Covenant not to compete 370 (339 ) 31 In-process research and development 7,895 — 7,895 Total $ 262,166 $ (36,551 ) $ 225,615 The balance of in-process research and development includes certain in-process research and development technology acquired in the Company's acquisition of Oxitec in September 2015, and amortization will begin once certain regulatory approvals have been obtained for the in-process programs. Amortization expense was $5,001 and $3,651 for the three months ended September 30, 2017 and 2016 , respectively, and $14,258 and $10,888 for the nine months ended September 30, 2017 and 2016 , respectively.

Lines of Credit and Long Term D

Lines of Credit and Long Term Debt	9 Months Ended
	Sep. 30, 2017
Debt Disclosure [Abstract]
Lines of Credit and Long Term Debt	Lines of Credit and Long Term Debt Lines of Credit Trans Ova has a $5,000 revolving line of credit with First National Bank of Omaha which matures on May 1, 2018. The line of credit bears interest at the greater of 2.95% above the London Interbank Offered Rate or 3.00% and the actual rate was 4.19% as of September 30, 2017 . As of September 30, 2017 , there were no amounts outstanding. The amount available under the line of credit is based on eligible accounts receivable and inventory up to the maximum principal amount. The line of credit is collateralized by certain of Trans Ova's assets and contains certain restricted covenants that include maintaining minimum tangible net worth and working capital and maximum allowable annual capital expenditures. Trans Ova was in compliance with these covenants as of September 30, 2017 . Exemplar has a $700 revolving line of credit with American State Bank which matures on October 30, 2018. As of September 30, 2017 , the interest rate on this line of credit was 4.50% per annum, and there was an outstanding balance of $234 . Long Term Debt Long term debt consists of the following: September 30, December 31, Notes payable $ 5,122 $ 5,453 Royalty-based financing 2,108 1,896 Other 882 599 Long term debt 8,112 7,948 Less current portion 439 386 Long term debt, less current portion $ 7,673 $ 7,562 Trans Ova has a note payable to American State Bank which matures in April 2033 and has an outstanding principal balance of $4,967 as of September 30, 2017 . Trans Ova pays monthly installments of $39 , which includes interest at 3.95% . The note payable is collateralized by certain of Trans Ova's real estate and non-real estate assets. AquaBounty has a royalty-based financing grant from the Atlantic Canada Opportunities Agency, a Canadian government agency, to provide funding of a research and development project. The total amount available under the award was $2,302 , which AquaBounty claimed over a five year period. All amounts claimed by AquaBounty must be repaid in the form of a 10% royalty on any products commercialized out of this research and development project until fully paid. Because the timing of commercialization is subject to additional regulatory considerations, the timing of repayment is uncertain. As of the date of the acquisition by Intrexon in March 2013, AquaBounty had claimed $1,952 of the available funds and this amount was recorded at its acquisition date fair value of $1,107 . The Company accretes the difference of $845 between the face value of amounts drawn and the acquisition date fair value over the expected period of repayment. Subsequent to the acquisition date, AquaBounty claimed the remaining balance available under the grant, resulting in total long term debt of $2,108 as of September 30, 2017 . Future maturities of long term debt are as follows: 2017 $ 107 2018 462 2019 400 2020 371 2021 834 2022 360 Thereafter 3,470 Total $ 6,004 The AquaBounty royalty-based financing grant is not included in the table above due to the uncertainty of the timing of repayment.

Income Taxes

Income Taxes	9 Months Ended
	Sep. 30, 2017
Income Tax Disclosure [Abstract]
Income Taxes	Income Taxes Tax provisions for interim periods are calculated using an estimate of actual taxable income or loss for the respective period, rather than estimating the Company's annual effective income tax rate, as the Company is currently unable to reliably estimate its income for the full year. For the three and nine months ended September 30, 2017 , the Company had U.S. taxable income of approximately $3,930 and $23,680 , respectively, for which $78 and $473 , respectively, in current income tax expense was recognized due to the alternative minimum tax. For the three and nine months ended September 30, 2017 , the Company recognized $121 and $343 , respectively, of current foreign income tax benefit. For the three and nine months ended September 30, 2016 , the Company had U.S. taxable income (loss) of approximately $8,334 and $(9,346) , respectively, for which no current income tax benefit was recognized. For the three and nine months ended September 30, 2016 , the Company recognized $110 and $323 , respectively, of current foreign income tax benefit. For the three and nine months ended September 30, 2017 , the Company recorded deferred tax benefit of $775 and $2,294 , respectively. For the three and nine months ended September 30, 2016 , the Company recorded deferred tax benefit of $308 and $2,967 , respectively. The Company's net deferred tax assets, excluding certain deferred tax liabilities totaling $15,868 , are offset by a valuation allowance due to the Company's history of net losses combined with an inability to confirm recovery of the tax benefits of the Company's losses and other net deferred tax assets. In assessing the realizability of deferred tax assets, management considers whether it is more likely than not that some portion or all of the deferred tax assets will not be realized. The ultimate realization of deferred tax assets is dependent upon the generation of future taxable income during the periods in which those temporary differences become deductible. Management considers the scheduled reversal of deferred tax liabilities, projected future taxable income and tax planning strategies in making this assessment. As of September 30, 2017 , the Company has loss carryforwards for U.S. federal income tax purposes of approximately $243,700 available to offset future taxable income, including approximately $13,400 acquired in our acquisition of GenVec, and federal and state research and development tax credits of approximately $7,800 , prior to consideration of annual limitations that may be imposed under Section 382 of the Internal Revenue Code of 1986, as amended. These carryforwards will begin to expire in 2022. As of September 30, 2017 , the Company's direct foreign subsidiaries have foreign loss carryforwards of approximately $146,800 , most of which do not expire.

Shareholders' Equity

Shareholders' Equity	9 Months Ended
	Sep. 30, 2017
Equity [Abstract]
Shareholders' Equity	Shareholders' Equity Dividend to Shareholders In January 2017, the Company distributed to its shareholders 1,776,557 shares of AquaBounty common stock valued at $22,385 . The distribution constituted a dividend to shareholders of record as of January 9, 2017. In connection with the distribution and pursuant to the terms of the Company's equity incentive plans, the conversion terms of all outstanding options for shares of the Company's common stock as of January 9, 2017 were adjusted to reflect the value of the distribution with respect to shares of the Company's common stock by decreasing the exercise prices and increasing the number outstanding options. This adjustment resulted in 46,766 additional outstanding options at a weighted average exercise price of $31.11 . Components of Accumulated Other Comprehensive Loss The components of accumulated other comprehensive loss are as follows: September 30, December 31, Unrealized loss on investments $ (15 ) $ (89 ) Loss on foreign currency translation adjustments (16,735 ) (36,113 ) Total accumulated other comprehensive loss $ (16,750 ) $ (36,202 )

Share-Based Payments

Share-Based Payments	9 Months Ended
	Sep. 30, 2017
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Share-Based Payments	Share-Based Payments The Company records the fair value of stock options issued to employees and non-employees as of the grant date as stock-based compensation expense. Stock-based compensation expense for employees and non-employees is recognized over the requisite service period, which is typically the vesting period. Stock-based compensation costs included in the consolidated statements of operations are presented below: Three Months Ended Nine Months Ended 2017 2016 2017 2016 Cost of products $ 30 $ 21 $ 86 $ 61 Cost of services 82 68 242 206 Research and development 2,383 2,236 7,018 6,979 Selling, general and administrative 9,562 8,467 24,603 23,385 Total $ 12,057 $ 10,792 $ 31,949 $ 30,631 Intrexon Stock Option Plans In April 2008, Intrexon adopted the 2008 Equity Incentive Plan (the "2008 Plan") for employees and nonemployees pursuant to which Intrexon's board of directors granted share based awards, including stock options, to officers, key employees and nonemployees. Upon the effectiveness of the 2013 Omnibus Incentive Plan (the "2013 Plan"), no new awards may be granted under the 2008 Plan. As of September 30, 2017 , there were 492,414 stock options outstanding under the 2008 Plan. Intrexon adopted the 2013 Plan for employees and nonemployees pursuant to which Intrexon's board of directors may grant share based awards, including stock options and shares of common stock, to employees, officers, consultants, advisors, and nonemployee directors. The 2013 Plan became effective upon the closing of the Company's initial public offering in August 2013, and as of September 30, 2017 , there were 18,000,000 shares authorized for issuance under the 2013 Plan, of which 12,149,356 stock options were outstanding and 3,743,187 shares were available for grant. Stock option activity was as follows: Number of Shares Weighted Average Exercise Price Weighted Average Remaining Contractual Term (Years) Balances at December 31, 2016 11,640,383 $ 31.25 8.21 Granted 3,880,950 21.51 Adjustment due to dividend (Note 14) 46,766 31.11 Exercised (109,971 ) (7.63 ) Forfeited (2,610,431 ) (29.93 ) Expired (205,927 ) (33.17 ) Balances at September 30, 2017 12,641,770 28.59 7.86 Exercisable at September 30, 2017 5,313,100 29.85 6.77 Intrexon currently uses authorized and unissued shares to satisfy share award exercises. In October 2015, the compensation committee and the independent members of Intrexon's board of directors approved a compensation arrangement whereby the Company's Chief Executive Officer ("CEO") would receive a monthly salary. Previously, the CEO did not receive compensation for his services as an employee of the Company other than through his participation in the Company's Annual Executive Incentive Plan which became effective January 1, 2015. Pursuant to the compensation agreement, the CEO receives a base salary of $200 per month payable in fully vested shares of Intrexon common stock with such shares subject to a three -year lock-up on resale. The monthly number of shares of common stock is calculated based on the closing price on the last trading day of each month and the shares are issued pursuant to the terms of a Restricted Stock Unit Agreement ("RSU Agreement") which was executed between Intrexon and the CEO pursuant to the terms of the 2013 Plan. The RSU Agreement became effective in November 2015, and had an initial term of 12 months . In October 2016, the independent members of Intrexon's board of directors, with the recommendation of the compensation committee of the board of directors, approved an extension of the RSU Agreement through December 31, 2016, and in December 2016 further approved an extension of the RSU Agreement to expire on March 31, 2017, both of which were on the same terms as the original RSU Agreement. In March 2017, the independent members of Intrexon's board of directors, with the recommendation of the compensation committee of the board of directors, approved a renewal of the RSU Agreement through March 31, 2018 on the same terms as the original RSU Agreement. The fair value of the shares issued as compensation for services is included in selling, general and administrative expenses in the Company's consolidated statements of operations and totaled $480 and $463 for the three months ended September 30, 2017 and 2016 , respectively, and $1,428 and $1,397 for the nine months ended September 30, 2017 and 2016 , respectively. AquaBounty Stock Option Plans In March 2016, AquaBounty's board of directors adopted the AquaBounty 2016 Equity Incentive Plan ("AquaBounty 2016 Plan") to replace the AquaBounty 2006 Equity Incentive Plan ("AquaBounty 2006 Plan"). The AquaBounty 2016 Plan provides for the issuance of incentive stock options, non-qualified stock options and awards of restricted and direct stock purchases to directors, officers, employees, and consultants of AquaBounty. The AquaBounty 2016 Plan was approved by AquaBounty's shareholders at its annual meeting in April 2016. Upon the effectiveness of the AquaBounty 2016 Plan, no new awards may be granted under the AquaBounty 2006 Plan. As of September 30, 2017 , there were 227,203 options outstanding under both AquaBounty plans, of which 183,373 were exercisable, at a weighted average exercise price of $9.39 per share. As of December 31, 2016 , there were 185,591 options outstanding under these plans, of which 181,766 were exercisable, at a weighted average exercise price of $7.89 per share. The AquaBounty stock option data reflect a 1-for-30 reverse stock split of AquaBounty's common stock effective January 5, 2017.

Commitments and Contingencies

Commitments and Contingencies	9 Months Ended
	Sep. 30, 2017
Commitments and Contingencies Disclosure [Abstract]
Commitments and Contingencies	Commitments and Contingencies Operating Leases The Company leases certain facilities and equipment under noncancelable operating leases. The equipment leases are renewable at the option of the Company. At September 30, 2017 , future minimum lease payments under operating leases having initial or remaining noncancelable lease terms in excess of one year are as follows: 2017 $ 1,252 2018 8,083 2019 8,042 2020 8,063 2021 7,132 2022 6,085 Thereafter 25,695 Total $ 64,352 Rent expense, including other facility expenses, was $3,165 and $2,075 for the three months ended September 30, 2017 and 2016 , respectively, and $7,772 and $6,410 for the nine months ended September 30, 2017 and 2016 , respectively. The Company maintains subleases for certain of its facilities. Rental income under sublease agreements was $32 and $184 for the three months ended September 30, 2017 and 2016 , respectively, and $105 and $854 for the nine months ended September 30, 2017 and 2016 , respectively. Future rental income is expected to be $20 for 2017 , $80 for 2018 , and $67 for 2019. Purchase Commitments As of September 30, 2017 , the Company had outstanding contractual purchase commitments of $10,618 , which primarily relate to amounts that will be paid in 2018 and 2019 upon delivery of commercial non-browning apple trees. Contingencies In March 2012, Trans Ova was named as a defendant in a licensing and patent infringement suit brought by XY, LLC ("XY") alleging that certain of Trans Ova's activities breached a 2004 licensing agreement and infringed on patents that XY allegedly owned. Trans Ova filed a number of counterclaims in the case. In Colorado District Court, the matter proceeded to a jury trial in January 2016. The jury determined that XY and Trans Ova had each breached the licensing agreement and that Trans Ova had infringed XY's patents. In April 2016, the court issued its post-trial order, awarding $528 in damages to Trans Ova and $6,066 in damages to XY. The order also provided Trans Ova with a compulsory license to XY's technology, subject to an ongoing royalty obligation. Both parties appealed the court's order, which appeal is pending before the Court of Appeals for the Federal Circuit. Since the inception of the 2004 agreement, Trans Ova has remitted payments to XY pursuant to the terms of that agreement and has recorded these payments in cost of services in the consolidated statements of operations for the respective periods. For the period from inception of the 2004 agreement through the court's April 2016 order, aggregate royalty and license payments were $3,170 , of which $2,759 had not yet been deposited by XY. For the nine months ended September 30, 2016 , the Company recorded litigation expense of $4,228 , which is included in selling, general and administrative expenses on the accompanying consolidated statement of operations and represents the excess of the net damages awarded to XY, including prejudgment interest, over the liability previously recorded by Trans Ova for uncashed checks previously remitted to XY. In August 2016, Trans Ova deposited the net damages amount, including prejudgment interest, into the court's treasury, to be held until the appeals process is complete and final judgment amounts are determined. As of September 30, 2017 , this amount is included in restricted cash on the accompanying consolidated balance sheet. In December 2016, Trans Ova elected to void the outstanding checks discussed above, and these amounts have been reclassified to other accrued liabilities on the accompanying consolidated balance sheets as of September 30, 2017 and December 31, 2016 . Depending on the outcome of an appeal decision, the damages awarded to either party could decrease, increase, or be eliminated. The appeal decision may also remand to the Colorado District Court all, or a portion, of the issues being appealed. In December 2016, XY filed a complaint for patent infringement and trade secret misappropriation against Trans Ova in the District Court of Waco, Texas. Since the claims in this 2016 complaint directly relate to the 2012 licensing dispute and patent issues, Trans Ova filed and was granted a motion for change of venue to Colorado District Court. Trans Ova also filed a motion to dismiss, which is now pending before the Colorado court. Trans Ova and the Company could elect to enter into a settlement agreement in order to avoid the further costs and uncertainties of litigation, to modify the court-ordered license to XY's technologies, or to recover monetary damages stemming from Trans Ova's counterclaims for antitrust violations by XY and its parent company, Inguran. In May 2016, two putative shareholder class action lawsuits, captioned Hoffman v. Intrexon Corporation et al. and Gibrall v. Intrexon Corporation et al. , were filed in the U.S. District Court for the Northern District of California on behalf of purchasers of Intrexon's common stock between May 12, 2015 and April 20, 2016 (the "Class Period"). In July 2016, the court consolidated the lawsuits and appointed a lead plaintiff. The consolidated amended complaint names as defendants Intrexon and certain of Intrexon's current and former officers (the "Defendants"). It alleges, among other things, that the Defendants made materially false and/or misleading statements during the Class Period with respect to the Company's business, operations, and prospects in violation of Sections 10(b) and 20(a) of the Securities Exchange Act of 1934, as amended. The plaintiffs' claims are based in part upon allegations in a report published in April 2016 on the Seeking Alpha financial blog. The plaintiffs seek compensatory damages, interest and an award of reasonable attorneys' fees and costs. The Defendants moved to dismiss the case. On February 24, 2017, the court granted the Company's motion to dismiss the lawsuit on the grounds that the plaintiff failed to state a claim, while granting the plaintiff leave to amend. The plaintiff subsequently notified the court that it would seek to appeal the court's ruling rather than amend its complaint. On April 26, 2017, the court entered final judgment in the case. Notice of appeal was filed by the plaintiff on May 26, 2017. On October 26, 2017, the plaintiff filed a voluntary motion to dismiss the case, which the court of appeals granted on November 1, 2017. In July 2016, a putative shareholder derivative action captioned Basile v. Kirk et al. was filed in the Circuit Court of Fairfax County, Virginia, against certain of the Company's directors, the Company's CEO, and Third Security, and naming the Company as a nominal defendant. The complaint alleges causes of action for breaches of fiduciary duty and unjust enrichment relating to the entry by the Company into the Services Agreement with Third Security. The plaintiff seeks, among other things, damages in an unspecified amount, disgorgement of improper benefits, appropriate equitable relief, and an award of attorney fees and other costs and expenses. The complaint is substantially similar to two separate demands made by shareholders concerning the Services Agreement and Mr. Kirk's compensation. The board of directors of the Company appointed a Special Litigation Committee ("SLC") consisting of independent directors to investigate the claims and allegations made in the derivative action and in the two shareholder demands and to decide on behalf of the Company whether the claims and allegations should be pursued. The Basile case was stayed pending the report of the SLC. In November 2016, the SLC completed its review and evaluation and unanimously determined that the claims were without merit because the compensation arrangements were the result of an informed and disinterested decision-making process and were fair to the Company, and that prosecution of the asserted claims was not in the best interest of Intrexon or its shareholders. Based upon the determination of the SLC, on February 24, 2017, the Company moved to dismiss the court action pursuant to Virginia statute. On June 8, 2017, the court granted the Company's motion to dismiss while granting the plaintiff leave to amend. On August 30, 2017, the plaintiff filed a consent motion for leave to amend along with the amended shareholder derivative complaint. The Company moved to dismiss the amended complaint on October 6, 2017. The Company intends to continue to defend the lawsuit vigorously. There can be no assurance, however, regarding the ultimate outcome of the case. In addition to the shareholder demands above, in June and July 2016, two shareholders made separate demands under Virginia law demanding that the Company file suit against certain of its current officers and directors for alleged breaches of fiduciary duty and other claims. The demands were based upon and asserted the allegations previously published in April 2016 in the Seeking Alpha financial blog. In July 2016, the Company's board of directors authorized the SLC to expand its review to include all such allegations. In February 2017, the SLC completed its review and evaluation and unanimously determined that there was no basis for any of the allegations, that the Company's officers and directors did not breach their fiduciary duties or any other applicable law, and that prosecution of the asserted claims was not in the best interest of Intrexon or its shareholders. Following the SLC's determination, in March 2017, one of the putative shareholders filed a derivative complaint captioned Luger v. Kirk et al. in the Circuit Court of Fairfax County, Virginia. The Company is a nominal defendant in this action, and other defendants include certain of the Company's directors, the Company's CEO, and Third Security. The complaint alleges causes of action for breaches of fiduciary duty and unjust enrichment relating to the entry by the Company into the Services Agreement with Third Security, Mr. Kirk's compensation, and certain allegations contained in the April 2016 Seeking Alpha financial blog piece. Based on the determination of the SLC and a review of applicable law, the Company intends to defend the lawsuit vigorously; however, there can be no assurance regarding the ultimate outcome of this case. The Division of Enforcement of the U.S. Securities and Exchange Commission ("SEC") is conducting an investigation which the Company believes concerns certain issues raised by the foregoing matters. The Company has met with the SEC staff and is voluntarily cooperating with their investigation. The Company's board of directors has authorized the SLC to monitor the Company's interaction with the SEC staff. The Company may become subject to other claims and assessments from time to time in the ordinary course of business. Such matters are subject to many uncertainties and outcomes are not predictable with assurance. The Company accrues liabilities for such matters when it is probable that future expenditures will be made and such expenditures can be reasonably estimated. As of September 30, 2017 and December 31, 2016 , the Company does not believe that any such matters, individually or in the aggregate, will have a material adverse effect on the Company's business, financial condition, results of operations, or cash flows.

Related Party Transactions

Related Party Transactions	9 Months Ended
	Sep. 30, 2017
Related Party Transactions [Abstract]
Related Party Transactions	Related Party Transactions Third Security and Affiliates The Company's CEO and Chairman of the board of directors of the Company is also the Senior Managing Director and CEO of Third Security and owns 100% of the equity interests of Third Security. In November 2015, the independent members of Intrexon's board of directors, with the recommendation of the audit committee of the board of directors, approved the execution of a Services Agreement ("Services Agreement") with Third Security pursuant to which Third Security provides the Company with certain professional, legal, financial, administrative, and other support services necessary to support the Company and its CEO. As consideration for providing these services, Third Security is entitled to a fee of $800 per month to be paid in the form of fully-vested shares of the Company's common stock. The number of shares of common stock is calculated based on the closing price of the Company's common stock on the 15th day of each month. The payments made by the Company under the Services Agreement constitute, in the aggregate, an award under the 2013 Plan and are subject to the terms of the 2013 Plan (Note 15 ). The Services Agreement had a term of one year , can be terminated by the Company at any time, and may be extended only by agreement of the parties, including approval of a majority of the independent members of Intrexon's board of directors. In October 2016, the independent members of Intrexon's board of directors, with the recommendation of the audit committee of the board of directors, approved an extension of the Services Agreement through December 31, 2016. In December 2016, the independent members of Intrexon's board of directors, with the recommendation of the audit committee of the board of directors, approved an extension of the Services Agreement through December 31, 2017. For the three months ended September 30, 2017 and 2016 , the Company issued 118,828 shares and 89,326 shares, respectively, with values of $2,251 and $2,132 , respectively, to Third Security as payment for services pursuant to the Services Agreement. For the nine months ended September 30, 2017 and 2016 , the Company issued 329,649 shares and 254,496 shares, respectively, with values of $6,506 and $6,542 , respectively, to Third Security as payment for services pursuant to the Services Agreement. In addition to the foregoing Services Agreement, the Company reimburses Third Security for certain out-of-pocket expenses incurred on the Company's behalf, and the total expenses incurred by the Company under this arrangement were $4 and $156 for the three months ended September 30, 2017 and 2016 , respectively, and $428 and $301 for the nine months ended September 30, 2017 and 2016 , respectively. See also Note 15 regarding compensation arrangements between the Company and its CEO. Transactions with ECC Parties In addition to entities controlled by Third Security, any entity in which the Company holds equity securities, including securities received as upfront or milestone consideration, and which also are party to a collaboration with the Company are considered to be related parties. The Company holds promissory notes convertible into shares of Fibrocell common stock ("convertible note") and warrants to purchase shares of Fibrocell common stock. As of September 30, 2017 and December 31, 2016 , the value of the convertible note and warrants totaled $4,172 and $1,642 , respectively, and is included in other assets on the accompanying consolidated balance sheets. See Note 7 for additional discussion of the Company's investments in Fibrocell. In May 2017, the Company purchased a promissory note from Oragenics ("Oragenics' Promissory Note") with a principal value of $2,400 which matures in May 2019 and accrues interest at a rate of 12% per annum. This note is included in other assets on the accompanying consolidated balance sheet as of September 30, 2017 . See Note 19 for additional discussion regarding the Oragenics Promissory Note. Other Related Parties In June 2015, the Company entered into an agreement with Harvest, an investment fund sponsored by Harvest Capital Strategies, LLC, and a related party based on ownership in the fund by affiliates of Third Security. Harvest was established to invest in life science research and development start-up opportunities that the Company offered to Harvest with exclusive rights of first-look and first negotiation. Based on this agreement, Harvest established six new collaboration entities, each of which entered into an ECC with the Company in a designated field. The terms of such ECCs were negotiated between the Company and Harvest. As consideration for providing exclusive rights of first-look and first negotiation for start-up opportunities, the Company received a portion of the management fee collected by the fund sponsor of Harvest. These fees are included in other income in the accompanying consolidated statements of operations and totaled $613 for the three months ended September 30, 2017 and 2016 , and $1,839 and $1,871 for the nine months ended September 30, 2017 and 2016 , respectively. In September 2017, the commitment period for Harvest was terminated and, as a result, our agreement with Harvest terminated. The termination of the agreement had no effect on the already-established collaborations with Harvest-sponsored entities.

Net Loss per Share

Net Loss per Share	9 Months Ended
	Sep. 30, 2017
Earnings Per Share [Abstract]
Net Loss per Share	Net Loss per Share The following table presents the computation of basic and diluted net loss per share: Three Months Ended Nine Months Ended 2017 2016 2017 2016 Historical net loss per share: Numerator: Net loss attributable to Intrexon $ (39,689 ) $ (28,982 ) $ (89,752 ) $ (142,475 ) Denominator: Weighted average shares outstanding, basic and diluted 120,518,885 118,346,782 119,741,291 117,785,160 Net loss attributable to Intrexon per share, basic and diluted $ (0.33 ) $ (0.24 ) $ (0.75 ) $ (1.21 ) The following potentially dilutive securities as of September 30, 2017 and 2016 , have been excluded from the above computations of diluted weighted average shares outstanding for the three and nine months then ended as they would have been anti-dilutive: September 30, 2017 2016 Options 12,641,770 12,103,407 Warrants 133,264 30,191 Total 12,775,034 12,133,598

Subsequent Events

Subsequent Events	9 Months Ended
	Sep. 30, 2017
Subsequent Events [Abstract]
Subsequent Events	Subsequent Events In November 2017, concurrent with the closing of Oragenics' preferred stock financing, the Company exchanged its Oragenics' Promissory Note and receivables due from Oragenics, as well as accrued interest, totaling $3,376 for Oragenics Series C preferred stock ("Series C Preferred Stock"). The Series C Preferred Stock is non-voting and non-convertible and is redeemable in whole or part at any time by Oragenics in cash. The Series C Preferred Stock accrues an annual 12% dividend payable in additional Series C Preferred Stock through May 10, 2019, and after such date, the annual dividend increases to 20% . Additionally, the Company and Oragenics amended certain future payment terms under its ECCs. In October 2017, the Company entered into a Preferred Stock Equity Facility ("Preferred Stock Facility") with an affiliate of Third Security ("Third Security Affiliate"). Under the Preferred Stock Facility, the Company may, from time to time at its sole and exclusive option, issue and sell to the Third Security Affiliate, up to $100,000 of newly issued Series A Redeemable Preferred Stock ("Series A Preferred Stock"). Any issued Series A Preferred Stock is non-voting, accrues dividends of 8% per annum and, subject to limited exceptions, is senior to Intrexon's common stock with respect to the rights to the payment of dividends and on parity with the common stock with respect to the distribution of assets in the event of any liquidation, dissolution or winding up or change of control of Intrexon. Any issued Series A Preferred Stock is convertible into common stock only following receipt of shareholder approval by the Company, including a majority of the shares voted by those shareholders unaffiliated with Mr. Kirk (the "Shareholder Approval"), subject to any necessary regulatory approvals. Following receipt of the Shareholder Approval and receipt of any necessary regulatory approvals, any issued Series A Preferred Stock is convertible into Intrexon common stock based on a conversion price using the 20 -day volume-weighted average market price as of market closing on the fifth business day prior to the mailing of the proxy statement soliciting the Shareholder Approval, subject to adjustment for certain stock splits and similar events. The Company has agreed to take all reasonable steps necessary to seek Shareholder Approval on or before the date of its annual meeting of shareholders in 2019. Any issued Series A Preferred Stock is redeemable at the election of the Company at any time, or at the election of the Third Security Affiliate after December 31, 2020. The Preferred Stock Facility will expire on the earliest to occur of: (i) the date on which the Third Security Affiliate has purchased shares of Series A Preferred Stock in the aggregate amount of $100,000 , (ii) April 30, 2019, (iii) the date of the Shareholder Approval, and (iv) the mutual agreement of the parties. Also, in November 2017, the Company filed with the State Corporation Commission of the Commonwealth of Virginia (the "SCC") Articles of Amendment to the Company's Amended and Restated Articles of Incorporation (the "Amendment"), which amended Article III thereof to set the designations of the Series A Preferred Stock (described above) to be issued pursuant to the Preferred Stock Facility. The Amendment became effective upon the issuance by the SCC in November 2017 of a certificate of amendment.

Summary of Significant Accoun28

Summary of Significant Accounting Policies (Policies)	9 Months Ended
	Sep. 30, 2017
Accounting Policies [Abstract]
Basis of Presentation	Basis of Presentation The accompanying interim consolidated financial statements are unaudited and have been prepared in accordance with accounting principles generally accepted in the United States of America ("U.S. GAAP"). Certain information and footnote disclosures normally included in the Company's annual financial statements have been condensed or omitted. These interim consolidated financial statements, in the opinion of management, reflect all normal recurring adjustments necessary for fair statement of the Company's financial position as of September 30, 2017 and results of operations and cash flows for the interim periods ended September 30, 2017 and 2016 . The year-end consolidated balance sheet data was derived from the Company's audited financial statements but does not include all disclosures required by U.S. GAAP. These interim financial results are not necessarily indicative of the results to be expected for the year ending December 31, 2017 , or for any other future annual or interim period. The accompanying interim unaudited consolidated financial statements should be read in conjunction with the audited consolidated financial statements and related notes thereto included in the Company's Annual Report on Form 10-K for the year ended December 31, 2016 .
Consolidation	The accompanying consolidated financial statements reflect the operations of the Company and its subsidiaries. All intercompany accounts and transactions have been eliminated.
Investments in Preferred Stock	Investments in Preferred Stock The Company holds preferred stock in certain of its collaborators which may be converted to common stock as described in Note 7 . The Company elected the fair value option to account for its investments in preferred stock whereby the value of preferred stock is adjusted to fair value as of each reporting date and unrealized gains and losses are reported in the consolidated statement of operations. These investments are subject to fluctuation in the future due to, among other things, the likelihood and timing of conversion of the preferred stock into common stock, the volatility of each collaborator's common stock, and changes in general economic and financial conditions of the collaborators. The investments are classified as noncurrent in the consolidated balance sheet since the Company does not intend to sell the investments nor expect them to be converted into shares of common stock within one year. Until such time as the Company converts the preferred stock into common stock, the Company is entitled to monthly dividends and records dividend income as described in Note 7 .
Equity Method Investments	Equity Method Investments The Company accounts for its investments in each of its joint ventures and for its investments in start-up entities backed by the Harvest Intrexon Enterprise Fund I, LP ("Harvest"), a related party, (Note 17 ) using the equity method of accounting based upon relative ownership interest. The Company's investments in these entities are included in investments in affiliates in the accompanying consolidated balance sheets.
Self-insurance Reserves	Self-insurance Reserves Effective January 1, 2017, the Company commenced a self-insurance program for a significant portion of its employee health benefit programs. The Company maintains stop-loss coverage with third party insurers to limit its individual claims and total exposure under those programs. The Company estimates its accrued liability for the ultimate costs to close known claims, including claims incurred but not yet reported to the Company, as of the balance sheet date. The Company's recorded estimated liability for self-insurance is based on the insurance company's incurred loss estimates and management's judgment, including assumptions and factors related to the frequency and severity of claims and the Company's claims development history. The assessment of self-insurance reserves is a highly subjective process that requires judgments about future events. Self-insurance reserves are reviewed at least quarterly to determine the adequacy of the accruals and related financial statement disclosure. The ultimate settlement of self-insurance reserves may differ significantly from amounts the Company has accrued in its consolidated financial statements.
Segment Information	Segment Information While the Company generates revenues from multiple sources, including collaboration agreements, licensing, and products and services associated with bovine reproduction, management is organized around a singular research and development focus to further the development of the Company's underlying synthetic biology technologies. Accordingly, the Company has determined that it operates in one segment.
Use of Estimates	Use of Estimates The preparation of financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, the disclosure of contingent assets and liabilities at the date of the financial statements, and the reported amounts of revenues and expenses during the reporting periods. Actual results could differ from those estimates.
Recently Issued and Adopted Accounting Pronouncements	Recently Adopted Accounting Pronouncements In January 2017, the Financial Accounting Standards Board ("FASB") issued Accounting Standards Update ("ASU") 2017-01, Business Combinations (Topic 805) - Clarifying the Definition of a Business ("ASU 2017-01"). The provisions of ASU 2017-01 clarify the definition of a business to assist entities with evaluating whether transactions should be accounted for as acquisitions (or disposals) of assets or businesses. The Company adopted this standard in the second quarter of 2017, and the implementation of this standard did not have a material impact on the Company's consolidated financial statements. In October 2016, the FASB issued ASU 2016-17, Consolidation (Topic 810) - Interests Held through Related Parties That Are under Common Control ("ASU 2016-17"). The provisions of ASU 2016-17 amend the consolidation guidance on how a reporting entity that is the single decision maker of a VIE should treat indirect interests in the entity held through related parties that are under common control with the reporting entity when determining whether it is the primary beneficiary of that VIE. The Company adopted this standard effective January 1, 2017, and the implementation of this standard did not have a material impact on the Company's consolidated financial statements. In March 2016, the FASB issued ASU 2016-09, Stock Compensation (Topic 718) - Improvements to Employee Share-Based Payment Accounting ("ASU 2016-09"). The provisions of ASU 2016-09 simplify various aspects of the accounting for employee share-based payment transactions, including the income tax consequences, classification of awards as either equity or liabilities, and classification on the statement of cash flows. The Company adopted this standard effective January 1, 2017. Upon adoption in the first quarter of 2017, the Company elected to recognize forfeitures as they occur and recorded an opening adjustment to additional paid-in capital and accumulated deficit for previously unrecognized stock-based compensation costs due to estimating forfeitures on unvested shares totaling $1,461 . The Company also recognized deferred tax assets of approximately $17,900 related to the excess tax benefits that previously arose directly from tax deductions related to equity compensation greater than stock-based compensation costs recognized in the consolidated financial statements and the cumulative adjustment for forfeitures. These deferred tax assets were fully offset by a valuation allowance (Note 13 ). The adoption was on a modified retrospective basis and had no impact on prior periods. In March 2016, the FASB issued ASU 2016-07, Investments-Equity Method and Joint Ventures (Topic 323) - Simplifying the Transition to the Equity Method of Accounting ("ASU 2016-07"). The provisions of ASU 2016-07 eliminate the requirement that when an investment qualifies for use of the equity method as a result of an increase in the level of ownership interest or degree of influence, an adjustment must be made to the investment, results of operations, and retained earnings retroactively on a step-by-step basis as if the equity method had been in effect during all previous periods that the investment had been held. The Company adopted this standard effective January 1, 2017, and the implementation of this standard did not have a material impact on the Company's consolidated financial statements. In July 2015, the FASB issued ASU 2015-11, Inventory (Topic 330) - Simplifying the Measurement of Inventory ("ASU 2015-11"). The provisions of ASU 2015-11 provide guidance for simplifying the calculation for subsequent measurement of inventory measured using the first-in-first-out or average cost methods. The Company adopted this standard effective January 1, 2017, and the implementation of this standard did not have a material impact on the Company's consolidated financial statements. Recently Issued Accounting Pronouncements In July 2017, the FASB issued ASU 2017-11, Earnings Per Share (Topic 260), Distinguishing Liabilities from Equity (Topic 480) and Derivatives and Hedging (Topic 815): I. Accounting for Certain Financial Instruments with Down Round Features; II. Replacement of the Indefinite Deferral for Mandatorily Redeemable Financial Instruments of Certain Nonpublic Entities and Certain Mandatorily Redeemable Noncontrolling Interests with a Scope Exception ("ASU 2017-11"). The amendments in Part I of ASU 2017-11 change the classification analysis of certain equity-linked financial instruments (or embedded features) with down round features. When determining whether certain financial instruments should be classified as liabilities or equity instruments, a down round feature no longer precludes equity classification when assessing whether the instrument is indexed to an entity's own stock. The amendments also clarify existing disclosure requirements for equity-classified instruments. As a result, a freestanding equity-linked financial instrument (or embedded conversion option) no longer would be accounted for as a derivative liability at fair value as a result of the existence of a down round feature. For freestanding equity-classified financial instruments, the amendments require entities that present earnings per share ("EPS") in accordance with Topic 260 to recognize the effect of the down round feature when it is triggered. That effect is treated as a dividend and as a reduction of income available to common shareholders in basic EPS. Convertible instruments with embedded conversion options that have down round features are now subject to the specialized guidance for contingent beneficial conversion features (in Subtopic 470-20, Debt-Debt with Conversion and Other Options ), including related EPS guidance (in Topic 260). The amendments in Part II of ASU 2017-11 re-characterize the indefinite deferral of certain provisions of Topic 480 that now are presented as pending content in the FASB codification, to a scope exception. Those amendments do not have an accounting effect. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2018, with early adoption permitted, and is effective for the Company for the year ended December 31, 2019. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. In May 2017, the FASB issued ASU 2017-09, Compensation-Stock Compensation (Topic 718) – Scope of Modification Accounting ("ASU 2017-09") . The provisions of ASU 2017-09 provide guidance about which changes to the terms or conditions of a share-based payment award require an entity to apply modification accounting in Topic 718. An entity should account for the effects of a modification unless (a) the fair value of the modified award is the same as the fair value of the original award, (b) the vesting conditions of the modified award are the same as the vesting conditions of the original award and (c) the classification of the modified award as an equity instrument or a liability instrument is the same as the classification of the original award immediately before the original award is modified. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2017, with early adoption permitted, and is effective for the Company for the year ending December 31, 2018. The amendments in ASU 2017-09 should be applied prospectively to an award modified on or after the adoption date. As this standard is prospective in nature, the impact to the Company's consolidated financial statements will depend on the nature of any future award modifications. The Company does not intend to early adopt this standard. In January 2017, the FASB issued ASU 2017-04, Intangibles-Goodwill and Other (Topic 350): Simplifying the Test for Goodwill Impairment ("ASU 2017-04"). The provisions of ASU 2017-04 simplify how an entity is required to test goodwill for impairment by eliminating Step 2 from the goodwill impairment test. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2019, with early adoption permitted, and is effective for the Company for the year ending December 31, 2020. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. In November 2016, the FASB issued ASU 2016-18, Statement of Cash Flows (Topic 230) - Restricted Cash (A Consensus of the FASB Emerging Issues Task Force) ("ASU 2016-18"). The provisions of ASU 2016-18 require amounts generally described as restricted cash and restricted cash equivalents to be included with cash and cash equivalents when reconciling the total beginning and ending balances for the periods presented on the statement of cash flows. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2017, with early adoption permitted, and is effective for the Company for the year ending December 31, 2018. The implementation of this standard is not expected to have a material impact on the Company's consolidated financial statements. In August 2016, the FASB issued ASU 2016-15, Statement of Cash Flows (Topic 230) - Classification of Certain Cash Receipts and Cash Payments ("ASU 2016-15"). The provisions of ASU 2016-15 address eight specific cash flow issues and how those certain cash receipts and cash payments are presented and classified in the statement of cash flows under Topic 230, Statement of Cash Flows , and other Topics. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2017, with early adoption permitted, and is effective for the Company for the year ending December 31, 2018. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. In February 2016, the FASB issued ASU 2016-02, Leases (Topic 842) ("ASU 2016-02"). The provisions of ASU 2016-02 set out the principles for the recognition, measurement, presentation and disclosure of leases for both parties to a contract (i.e. lessees and lessors). The new standard requires lessees to apply a dual approach, classifying leases as either finance or operating leases based on the principle of whether or not the lease is effectively a financed purchase by the lessee. This classification will determine whether lease expense is recognized based on an effective interest method or on a straight-line basis over the term of the lease, respectively. A lessee is also required to record a right-of-use asset and a lease liability for all leases with a term of greater than 12 months regardless of their classification. Leases with a term of 12 months or less will be accounted for in a similar manner as under existing guidance for operating leases today. ASU 2016-02 supersedes the previous lease standard, Topic 840, Leases . The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2018, and is effective for the Company for the year ending December 31, 2019. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. In January 2016, the FASB issued ASU 2016-01, Financial Instruments - Overall (Subtopic 825-10) - Recognition and Measurement of Financial Assets and Financial Liabilities ("ASU 2016-01"). The provisions of ASU 2016-01 make targeted improvements to enhance the reporting model for financial instruments to provide users of financial statements with more decision-useful information, including certain aspects of recognition, measurement, presentation, and disclosure of financial instruments. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2017, and is effective for the Company for the year ending December 31, 2018. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. In May 2014, the FASB issued ASU 2014-09, Revenue from Contracts with Customers ("ASU 2014-09"). The FASB issued ASU 2014-09 to clarify the principles for recognizing revenue and to develop a common revenue standard for U.S. GAAP. The standard outlines a single comprehensive model for entities to use in accounting for revenue arising from contracts with customers and supersedes the most current revenue recognition guidance. This guidance was originally effective for annual periods and interim periods within those annual periods beginning after December 15, 2016 and early adoption was not permitted. In August 2015, the FASB issued ASU 2015-14, Revenue from Contracts with Customers (Topic 606) - Deferral of the Effective Date , which deferred the effective date of the guidance in ASU 2014-09 by one year to December 15, 2017 for interim and annual reporting periods beginning after that date and permitted early adoption of the standard, but not before the original effective date of December 15, 2016, and is effective for the Company for the year ending December 31, 2018. In 2016 and 2017, the FASB clarified the implementation guidance on principal versus agent, identifying performance obligations, licensing, narrow-scope improvements, practical expedients, and to expedite improvements to ASU 2014-09 by issuing ASU 2016-08, Revenue from Contracts with Customers (Topic 606) - Principal versus Agent Considerations , ASU 2016-10, Revenue from Contracts with Customers (Topic 606) - Identifying Performance Obligations and Licensing , and ASU 2016-12, Revenue from Contracts with Customers (Topic 606) - Narrow-Scope Improvements and Practical Expedients , ASU 2016-20, Technical Corrections and Improvements to Topic 606, Revenue from Contracts with Customers , and ASU 2017-13, Revenue Recognition (Topic 605), Revenue from Contracts with Customers (Topic 606), Leases (Topic 840), and Leases (Topic 842) . The Company continues to progress in the evaluation of its collaborations and licensing agreements and product and service revenue arrangements to determine the impact, if any, that the implementation of this standard will have on the Company's consolidated financial statements. The Company has completed its review of collaboration and licensing agreements and product and service revenue arrangements and plans to finalize its analysis in the fourth quarter of 2017 to determine the impact, if any, this standard may have on its financial position, results of operations and disclosures. Additionally, any revenue arrangements entered into subsequent to December 31, 2017 with financial or other significant terms which differ from the financial or other significant terms of the Company's existing revenue arrangements will be evaluated under this new standard.

Summary of Significant Accoun29

Summary of Significant Accounting Policies (Tables)	9 Months Ended
	Sep. 30, 2017
Accounting Policies [Abstract]
Summarized Financial Information for the Equity Method Investments	Summarized financial data as of September 30, 2017 and December 31, 2016 and for the three and nine months ended September 30, 2017 and 2016 , for the Company's equity method investments are shown in the following tables. September 30, December 31, Current assets $ 68,021 $ 77,761 Non-current assets 12,856 11,040 Total assets 80,877 88,801 Current liabilities 9,032 11,588 Non-current liabilities 2,400 — Total liabilities 11,432 11,588 Net assets $ 69,445 $ 77,213 Three Months Ended Nine Months Ended 2017 2016 2017 2016 Revenues $ 58 $ 65 $ 175 $ 394 Operating expenses 9,693 18,363 33,128 50,406 Operating loss (9,635 ) (18,298 ) (32,953 ) (50,012 ) Other (145 ) 75 37 1,502 Net loss $ (9,780 ) $ (18,223 ) $ (32,916 ) $ (48,510 )

Mergers and Acquisitions (Table

Mergers and Acquisitions (Tables)	9 Months Ended
	Sep. 30, 2017
Business Acquisition [Line Items]
Condensed Pro forma Financial Information	The following condensed pro forma financial information for the three months ended September 30, 2016 and the nine months ended September 30, 2017 and 2016 is presented as if the acquisition had been consummated on January 1, 2016: Three Months Ended Nine Months Ended 2016 2017 2016 Pro forma Revenues $ 49,158 $ 154,185 $ 145,413 Loss before income taxes (31,954 ) (102,305 ) (153,868 ) Net loss (31,536 ) (100,330 ) (150,389 ) Net loss attributable to the noncontrolling interests 1,029 3,123 2,887 Net loss attributable to Intrexon (30,507 ) (97,207 ) (147,502 )
GenVec, Inc.
Business Acquisition [Line Items]
Fair Value of Consideration Transferred	The fair value of the total consideration transferred was $17,582 . The acquisition date fair value of each class of consideration transferred is presented below: Common shares $ 15,616 Warrants 1,381 Contingent consideration 585 $ 17,582
Fair Value of Assets Acquired and Liabilities Assumed	The estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown below: Cash and cash equivalents $ 2,054 Short term investments 542 Trade receivables 75 Other receivables 97 Prepaid expenses and other 227 Property and equipment 250 Intangible assets 14,000 Other non-current assets 58 Total assets acquired 17,303 Accounts payable 2,158 Accrued compensation and benefits 1,226 Other accrued expenses 856 Other long term liabilities 92 Deferred tax liabilities 239 Total liabilities assumed 4,571 Net assets acquired 12,732 Goodwill 4,850 Total consideration $ 17,582

Collaboration and Licensing R31

Collaboration and Licensing Revenue (Tables)	9 Months Ended
	Sep. 30, 2017
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Summarized Collaboration and Licensing Revenues	The following tables summarize the amounts recorded as revenue in the consolidated statements of operations for each significant counterparty to a collaboration or licensing agreement for the three and nine months ended September 30, 2017 and 2016 . Three Months Ended September 30, 2017 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 4,843 $ 5,530 $ 10,373 Oragenics, Inc. 262 213 475 Fibrocell Science, Inc. 604 1,079 1,683 Genopaver, LLC 68 1,354 1,422 S & I Ophthalmic, LLC — 376 376 OvaXon, LLC — 262 262 Intrexon Energy Partners, LLC 625 1,278 1,903 Persea Bio, LLC 125 141 266 Ares Trading S.A. 1,597 759 2,356 Intrexon Energy Partners II, LLC 500 316 816 Intrexon T1D Partners, LLC 287 1,175 1,462 Harvest start-up entities (1) 616 3,404 4,020 Other 979 1,762 2,741 Total $ 10,506 $ 17,649 $ 28,155 (1) For the three months ended September 30, 2017 , revenue recognized from collaborations with Harvest start-up entities include Thrive Agrobiotics, Inc.; Exotech Bio, Inc.; Relieve Genetics, Inc.; AD Skincare, Inc.; Genten Therapeutics, Inc.; and CRS Bio, Inc. Three Months Ended September 30, 2016 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 4,843 $ 5,586 $ 10,429 Oragenics, Inc. 262 294 556 Fibrocell Science, Inc. 604 563 1,167 Genopaver, LLC 68 1,625 1,693 S & I Ophthalmic, LLC — 2,782 2,782 OvaXon, LLC — 709 709 Intrexon Energy Partners, LLC 625 4,230 4,855 Persea Bio, LLC 125 208 333 Ares Trading S.A. 1,597 719 2,316 Intrexon Energy Partners II, LLC 500 372 872 Intrexon T1D Partners, LLC 276 511 787 Harvest start-up entities (1) 425 868 1,293 Other 895 1,903 2,798 Total $ 10,220 $ 20,370 $ 30,590 (1) For the three months ended September 30, 2016 , revenue recognized from collaborations with Harvest start-up entities include Thrive Agrobiotics, Inc.; Exotech Bio, Inc.; Relieve Genetics, Inc.; and AD Skincare, Inc. Nine Months Ended September 30, 2017 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 14,527 $ 16,795 $ 31,322 Oragenics, Inc. 786 733 1,519 Fibrocell Science, Inc. 1,814 3,561 5,375 Genopaver, LLC 205 4,410 4,615 S & I Ophthalmic, LLC — 751 751 OvaXon, LLC — 1,966 1,966 Intrexon Energy Partners, LLC 1,875 7,034 8,909 Persea Bio, LLC 375 446 821 Ares Trading S.A. 4,791 3,683 8,474 Intrexon Energy Partners II, LLC 1,500 1,421 2,921 Intrexon T1D Partners, LLC 823 3,059 3,882 Harvest start-up entities (1) 1,823 10,012 11,835 Other 3,735 3,259 6,994 Total $ 32,254 $ 57,130 $ 89,384 (1) For the nine months ended September 30, 2017 , revenue recognized from collaborations with Harvest start-up entities include Thrive Agrobiotics, Inc.; Exotech Bio, Inc.; Relieve Genetics, Inc.; AD Skincare, Inc.; Genten Therapeutics, Inc.; and CRS Bio, Inc. Nine Months Ended September 30, 2016 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 6,687 $ 17,693 $ 24,380 Oragenics, Inc. 786 1,083 1,869 Fibrocell Science, Inc. 1,814 2,604 4,418 Genopaver, LLC 205 4,703 4,908 S & I Ophthalmic, LLC — 6,326 6,326 OvaXon, LLC — 2,211 2,211 Intrexon Energy Partners, LLC 1,875 11,180 13,055 Persea Bio, LLC 375 613 988 Ares Trading S.A. 4,791 2,148 6,939 Intrexon Energy Partners II, LLC 1,500 816 2,316 Intrexon T1D Partners, LLC 554 543 1,097 Harvest start-up entities (1) 776 1,890 2,666 Other 4,684 6,287 10,971 Total $ 24,047 $ 58,097 $ 82,144 (1) For the nine months ended September 30, 2016 , revenue recognized from collaborations with Harvest start-up entities include Thrive Agrobiotics, Inc.; Exotech Bio, Inc.; Relieve Genetics, Inc.; and AD Skincare, Inc.
Summary of Deferred Revenue	Deferred revenue consists of the following: September 30, December 31, Upfront and milestone payments $ 269,649 $ 297,867 Prepaid research and development services 1,718 6,015 Prepaid product and service revenues 4,869 5,554 Other 51 706 Total $ 276,287 $ 310,142 Current portion of deferred revenue $ 48,289 $ 53,364 Long-term portion of deferred revenue 227,998 256,778 Total $ 276,287 $ 310,142
Summary of Deferred Revenue by Collaborator	The following table summarizes the remaining balance of deferred revenue associated with upfront and milestone payments for each significant collaboration and licensing agreement. September 30, December 31, ZIOPHARM Oncology, Inc. $ 124,282 $ 138,809 Oragenics, Inc. 6,980 7,766 Fibrocell Science, Inc. 17,212 19,026 Genopaver, LLC 1,772 1,977 Intrexon Energy Partners, LLC 16,250 18,125 Persea Bio, LLC 3,625 4,000 Ares Trading S.A. 42,387 47,178 Intrexon Energy Partners II, LLC 14,333 15,833 Intrexon T1D Partners, LLC 8,628 8,653 Harvest start-up entities (1) 18,953 20,208 Other 15,227 16,292 Total $ 269,649 $ 297,867 (1) As of September 30, 2017 and December 31, 2016 , the balance of deferred revenue for collaborations with Harvest start-up entities includes Thrive Agrobiotics, Inc.; Exotech Bio, Inc.; Relieve Genetics, Inc.; AD Skincare, Inc.; Genten Therapeutics, Inc.; and CRS Bio, Inc.

Short-term and Long-term Inve32

Short-term and Long-term Investments (Tables)	9 Months Ended
	Sep. 30, 2017
Investments, Debt and Equity Securities [Abstract]
Summary of Amortized Cost, Gross Unrealized Gains and Losses, and Fair Value of Short-term and Long-term Investments	The following table summarizes the amortized cost, gross unrealized gains and losses, and fair value of available-for-sale investments as of September 30, 2017 : Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Aggregate Fair Value U.S. government debt securities $ 44,000 $ 2 $ (17 ) $ 43,985 Corporate notes and bonds 242 — — 242 Certificates of deposit 275 — — 275 Total $ 44,517 $ 2 $ (17 ) $ 44,502 The following table summarizes the amortized cost, gross unrealized gains and losses, and fair value of available-for-sale investments as of December 31, 2016 : Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Aggregate Fair Value U.S. government debt securities $ 180,412 $ 5 $ (94 ) $ 180,323 Certificates of deposit 272 — — 272 Total $ 180,684 $ 5 $ (94 ) $ 180,595

Investments in Preferred Stock

Investments in Preferred Stock (Tables)	9 Months Ended
	Sep. 30, 2017
Investment in Preferred Stock [Abstract]
Schedule of Changes in Level 3 Investments	The following table summarizes the changes in the Level 3 investments in preferred stock during the nine months ended September 30, 2017 . Nine Months Ended Beginning balance $ 129,545 Purchase of preferred stock 766 Dividend income from investments in preferred stock 12,303 Unrealized appreciation in the fair value of the investments in preferred stock 5,885 Ending balance $ 148,499

Fair Value Measurements (Tables

Fair Value Measurements (Tables)	9 Months Ended
	Sep. 30, 2017
Fair Value Disclosures [Abstract]
Summary of Placement in the Fair Value Hierarchy of Financial Assets that are Measured at Fair Value on a Recurring Basis	The following table presents the placement in the fair value hierarchy of financial assets that are measured at fair value on a recurring basis, including the items for which the fair value option has been elected, at September 30, 2017 : Quoted Prices in Active Markets (Level 1) Significant Other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) September 30, Assets U.S. government debt securities $ — $ 43,985 $ — $ 43,985 Equity securities 19,830 6,812 — 26,642 Preferred stock — — 148,499 148,499 Other — 7,089 — 7,089 Total $ 19,830 $ 57,886 $ 148,499 $ 226,215 The following table presents the placement in the fair value hierarchy of financial assets that are measured at fair value on a recurring basis, including the items for which the fair value option has been elected, at December 31, 2016 : Quoted Prices in Active Markets Significant Other Observable Inputs Significant Unobservable Inputs December 31, Assets U.S. government debt securities $ — $ 180,323 $ — $ 180,323 Equity securities 15,544 7,978 — 23,522 Preferred stock — — 129,545 129,545 Other — 1,917 — 1,917 Total $ 15,544 $ 190,218 $ 129,545 $ 335,307
Schedule of Changes in Level 3 Liabilities	The changes in the fair value of the Level 3 liabilities during the nine months ended September 30, 2017 were as follows: Nine Months Ended Beginning balance $ 2,081 Acquisition date fair value of contingent consideration liability (Note 3) 585 Change in fair value of contingent consideration recognized in selling, general and administrative expenses 245 Ending balance $ 2,911

Inventory (Tables)

Inventory (Tables)	9 Months Ended
	Sep. 30, 2017
Inventory Disclosure [Abstract]
Schedule of Inventory	Inventory consists of the following: September 30, December 31, Supplies, embryos and other production materials $ 2,185 $ 1,835 Work in process 4,618 5,466 Livestock 8,738 11,752 Feed 2,189 2,086 Total inventory $ 17,730 $ 21,139

Property, Plant and Equipment36

Property, Plant and Equipment, Net (Tables)	9 Months Ended
	Sep. 30, 2017
Property, Plant and Equipment [Abstract]
Schedule of Property, Plant and Equipment	Property, plant and equipment consist of the following: September 30, December 31, Land and land improvements $ 11,642 $ 10,904 Buildings and building improvements 15,216 8,123 Furniture and fixtures 2,220 2,176 Equipment 58,851 44,392 Leasehold improvements 22,974 15,105 Breeding stock 3,822 3,893 Computer hardware and software 9,817 6,844 Trees 5,719 2,772 Construction and other assets in progress 15,138 4,513 145,399 98,722 Less: Accumulated depreciation and amortization (42,523 ) (34,050 ) Property, plant and equipment, net $ 102,876 $ 64,672

Goodwill and Intangible Asset37

Goodwill and Intangible Assets, Net (Tables)	9 Months Ended
	Sep. 30, 2017
Goodwill and Intangible Assets Disclosure [Abstract]
Schedule of Changes in Carrying Amount of Goodwill	The changes in the carrying amount of goodwill for the nine months ended September 30, 2017 are as follows: Balance at December 31, 2016 $ 157,175 Acquisitions 4,850 Foreign currency translation adjustments 4,796 Balance at September 30, 2017 $ 166,821
Schedule of Intangible Assets	Intangible assets consist of the following as of September 30, 2017 : Weighted Average Useful Life (Years) Gross Carrying Amount Accumulated Amortization Net Patents, developed technologies and know-how 15.7 $ 266,697 $ (43,465 ) $ 223,232 Customer relationships 6.5 10,700 (6,033 ) 4,667 Trademarks 9.3 6,800 (2,373 ) 4,427 In-process research and development 8,571 — 8,571 Total $ 292,768 $ (51,871 ) $ 240,897 Intangible assets consist of the following as of December 31, 2016 : Gross Carrying Amount Accumulated Amortization Net Patents, developed technologies and know-how $ 236,401 $ (29,748 ) $ 206,653 Customer relationships 10,700 (4,672 ) 6,028 Trademarks 6,800 (1,792 ) 5,008 Covenant not to compete 370 (339 ) 31 In-process research and development 7,895 — 7,895 Total $ 262,166 $ (36,551 ) $ 225,615

Lines of Credit and Long Term38

Lines of Credit and Long Term Debt (Tables)	9 Months Ended
	Sep. 30, 2017
Debt Disclosure [Abstract]
Schedule of Long Term Debt Instruments	Long term debt consists of the following: September 30, December 31, Notes payable $ 5,122 $ 5,453 Royalty-based financing 2,108 1,896 Other 882 599 Long term debt 8,112 7,948 Less current portion 439 386 Long term debt, less current portion $ 7,673 $ 7,562
Schedule of Future Maturities of Long Term Debt	Future maturities of long term debt are as follows: 2017 $ 107 2018 462 2019 400 2020 371 2021 834 2022 360 Thereafter 3,470 Total $ 6,004

Shareholders' Equity (Tables)

Shareholders' Equity (Tables)	9 Months Ended
	Sep. 30, 2017
Equity [Abstract]
Components of Accumulated Other Comprehensive Loss	The components of accumulated other comprehensive loss are as follows: September 30, December 31, Unrealized loss on investments $ (15 ) $ (89 ) Loss on foreign currency translation adjustments (16,735 ) (36,113 ) Total accumulated other comprehensive loss $ (16,750 ) $ (36,202 )

Share-Based Payments (Tables)

Share-Based Payments (Tables)	9 Months Ended
	Sep. 30, 2017
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Schedule of Stock-Based Compensation Costs	Stock-based compensation costs included in the consolidated statements of operations are presented below: Three Months Ended Nine Months Ended 2017 2016 2017 2016 Cost of products $ 30 $ 21 $ 86 $ 61 Cost of services 82 68 242 206 Research and development 2,383 2,236 7,018 6,979 Selling, general and administrative 9,562 8,467 24,603 23,385 Total $ 12,057 $ 10,792 $ 31,949 $ 30,631
Schedule of Stock Option Activity	Stock option activity was as follows: Number of Shares Weighted Average Exercise Price Weighted Average Remaining Contractual Term (Years) Balances at December 31, 2016 11,640,383 $ 31.25 8.21 Granted 3,880,950 21.51 Adjustment due to dividend (Note 14) 46,766 31.11 Exercised (109,971 ) (7.63 ) Forfeited (2,610,431 ) (29.93 ) Expired (205,927 ) (33.17 ) Balances at September 30, 2017 12,641,770 28.59 7.86 Exercisable at September 30, 2017 5,313,100 29.85 6.77

Commitments and Contingencies (

Commitments and Contingencies (Tables)	9 Months Ended
	Sep. 30, 2017
Commitments and Contingencies Disclosure [Abstract]
Future Minimum Lease Payments Under Noncancelable Operating Leases	At September 30, 2017 , future minimum lease payments under operating leases having initial or remaining noncancelable lease terms in excess of one year are as follows: 2017 $ 1,252 2018 8,083 2019 8,042 2020 8,063 2021 7,132 2022 6,085 Thereafter 25,695 Total $ 64,352

Net Loss per Share (Tables)

Net Loss per Share (Tables)	9 Months Ended
	Sep. 30, 2017
Earnings Per Share [Abstract]
Computation of Basic and Diluted Net Loss per Share	The following table presents the computation of basic and diluted net loss per share: Three Months Ended Nine Months Ended 2017 2016 2017 2016 Historical net loss per share: Numerator: Net loss attributable to Intrexon $ (39,689 ) $ (28,982 ) $ (89,752 ) $ (142,475 ) Denominator: Weighted average shares outstanding, basic and diluted 120,518,885 118,346,782 119,741,291 117,785,160 Net loss attributable to Intrexon per share, basic and diluted $ (0.33 ) $ (0.24 ) $ (0.75 ) $ (1.21 )
Schedule of Antidilutive Securities Excluded from Computation of Net Loss per Share	The following potentially dilutive securities as of September 30, 2017 and 2016 , have been excluded from the above computations of diluted weighted average shares outstanding for the three and nine months then ended as they would have been anti-dilutive: September 30, 2017 2016 Options 12,641,770 12,103,407 Warrants 133,264 30,191 Total 12,775,034 12,133,598

Organization (Details)

Organization (Details) $ in Thousands	1 Months Ended		9 Months Ended
	Mar. 31, 2017USD ($)shares	Jan. 31, 2017USD ($)	Sep. 30, 2017USD ($)
Noncontrolling Interest [Line Items]
Purchase of noncontrolling interest by parent, parent equity issued			$ 913
Biological & Popular Culture, Inc.
Noncontrolling Interest [Line Items]
Purchase of noncontrolling interest by parent, percentage	0.49
Purchase of noncontrolling interest by parent, cash paid	$ 900
Purchase of noncontrolling interest by parent, parent equity issued (in shares) | shares	221,743
Purchase of noncontrolling interest by parent, parent equity issued	$ 5,082
AquaBounty Technologies, Inc.
Noncontrolling Interest [Line Items]
Parent ownership interest			58.00%
Purchase of additional equity of majority-owned subsidiary		$ 25,000

Summary of Significant Accoun44

Summary of Significant Accounting Policies - Equity Method Investments - Additional Information (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2017	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016	Dec. 31, 2016
Schedule of Equity Method Investments [Line Items]
Fair value of financial assets measured at fair value on a recurring basis	$ 226,215		$ 226,215		$ 335,307
Oragenics, Inc.
Schedule of Equity Method Investments [Line Items]
Company's ownership percentage	29.40%		29.40%		29.50%
Equity securities
Schedule of Equity Method Investments [Line Items]
Fair value of financial assets measured at fair value on a recurring basis	$ 26,642		$ 26,642		$ 23,522
Equity securities | Oragenics, Inc.
Schedule of Equity Method Investments [Line Items]
Fair value of financial assets measured at fair value on a recurring basis	5,634		5,634		$ 7,244
Unrealized appreciation/(depreciation) in fair value of equity securities	$ 827	$ (455)	$ (1,610)	$ (11,597)

Summary of Significant Accoun45

Summary of Significant Accounting Policies - Summarized Unaudited Financial Information for the Equity Method Investments (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2017	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016	Dec. 31, 2016
Schedule of Equity Method Investments [Line Items]
Operating expenses	$ 90,763	$ 77,806	$ 265,351	$ 237,500
Operating loss	(44,747)	(28,821)	(111,398)	(92,576)
Other	6,086	4,647	27,632	(39,125)
Equity Method Investments
Schedule of Equity Method Investments [Line Items]
Current assets	68,021		68,021		$ 77,761
Non-current assets	12,856		12,856		11,040
Total assets	80,877		80,877		88,801
Current liabilities	9,032		9,032		11,588
Non-current liabilities	2,400		2,400		0
Total liabilities	11,432		11,432		11,588
Net assets	69,445		69,445		$ 77,213
Revenues	58	65	175	394
Operating expenses	9,693	18,363	33,128	50,406
Operating loss	(9,635)	(18,298)	(32,953)	(50,012)
Other	(145)	75	37	1,502
Net loss	$ (9,780)	$ (18,223)	$ (32,916)	$ (48,510)

Summary of Significant Accoun46

Summary of Significant Accounting Policies - Variable Interest Entities - Additional Information (Details) - USD ($) $ in Thousands	Sep. 30, 2017	Dec. 31, 2016
Accounting Policies [Abstract]
Maximum risk of loss related to the identified VIEs	$ 187,555	$ 159,115

Summary of Significant Accoun47

Summary of Significant Accounting Policies - Segment Information - Additional Information (Details) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2017USD ($)	Sep. 30, 2016USD ($)	Sep. 30, 2017USD ($)segment	Sep. 30, 2016USD ($)	Dec. 31, 2016USD ($)
Segment Reporting Information [Line Items]
Number of segments | segment			1
Property, plant and equipment, net	$ 102,876		$ 102,876		$ 64,672
Revenues	46,016	$ 48,985	153,953	$ 144,924
Foreign Countries
Segment Reporting Information [Line Items]
Property, plant and equipment, net	19,335		19,335		$ 13,265
Revenues	$ 4,448	$ 3,502	$ 11,773	$ 8,678

Summary of Significant Accoun48

Summary of Significant Accounting Policies - Recently Issued and Adopted Accounting Pronouncements (Details) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2017	Jan. 01, 2017
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Cumulative effect of adoption of ASU 2016-09	$ 0
Accounting Standards Update 2016-09
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Deferred tax assets related to stock-based compensation costs		$ 17,900
Additional Paid-in Capital
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Cumulative effect of adoption of ASU 2016-09	$ 1,461

Mergers and Acquisitions - GenV

Mergers and Acquisitions - GenVec - Additional Information (Details) - GenVec, Inc. - USD ($) $ in Thousands	1 Months Ended	3 Months Ended	9 Months Ended
	Jun. 30, 2017	Sep. 30, 2017	Sep. 30, 2017
Business Acquisition [Line Items]
Percentage of outstanding common stock acquired	100.00%
Business combination, consideration paid, shares issued	684,240
Percent of collaboration payments	50.00%
Expected useful life of intangible asset	11 years
Period subsequent to acquisition during which a portion of collaboration payments received will be paid to former stockholders of acquired entity	3 years
Business combination, acquisition related costs			$ 519
Selling, general and administrative
Business Acquisition [Line Items]
Business combination, acquisition related costs		$ 9	$ 507

Mergers and Acquisitions - Ge50

Mergers and Acquisitions - GenVec - Fair Value of Consideration Transferred (Details) - GenVec, Inc. $ in Thousands	1 Months Ended
	Jun. 30, 2017USD ($)
Business Acquisition [Line Items]
Common shares	$ 15,616
Warrants	1,381
Contingent consideration	585
Total consideration transferred	$ 17,582

Mergers and Acquisitions - Ge51

Mergers and Acquisitions - GenVec - Fair Value of Assets Acquired and Liabilities Assumed (Details) - USD ($) $ in Thousands	Sep. 30, 2017	Jun. 30, 2017	Dec. 31, 2016
Business Acquisition [Line Items]
Goodwill	$ 166,821		$ 157,175
GenVec, Inc.
Business Acquisition [Line Items]
Cash and cash equivalents		$ 2,054
Short term investments		542
Trade receivables		75
Other receivables		97
Prepaid expenses and other		227
Property and equipment		250
Intangible assets		14,000
Other non-current assets		58
Total assets acquired		17,303
Accounts payable		2,158
Accrued compensation and benefits		1,226
Other accrued expenses		856
Other long term liabilities		92
Deferred tax liabilities		239
Total liabilities assumed		4,571
Net assets acquired		12,732
Goodwill		4,850
Total consideration		$ 17,582

Mergers and Acquisitions - Cond

Mergers and Acquisitions - Condensed Pro forma Financial Information (Details) - USD ($) $ in Thousands	3 Months Ended	9 Months Ended
	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016
Business Combinations [Abstract]
Revenues	$ 49,158	$ 154,185	$ 145,413
Loss before income taxes	(31,954)	(102,305)	(153,868)
Net loss	(31,536)	(100,330)	(150,389)
Net loss attributable to the noncontrolling interests	1,029	3,123	2,887
Net loss attributable to Intrexon	$ (30,507)	$ (97,207)	$ (147,502)

Investments in Joint Ventures -

Investments in Joint Ventures - S & I Ophthalmic - Additional Information (Details) $ in Thousands	1 Months Ended	12 Months Ended
	Oct. 31, 2013USD ($)	Dec. 31, 2015USD ($)	Sep. 30, 2017USD ($)board_seat	Dec. 31, 2016USD ($)
Schedule of Equity Method Investments [Line Items]
Investment			$ 22,942	$ 23,655
S & I Ophthalmic, LLC
Schedule of Equity Method Investments [Line Items]
Capital contributions	$ 5,000	$ 5,000
Membership interest	50.00%
Total number of seats on the joint venture's governing board | board_seat			4
Total number of seats on the joint venture's governing board, internally selected | board_seat			2
Total number of seats on the joint venture's governing board, externally selected | board_seat			2
S & I Ophthalmic, LLC | Investors
Schedule of Equity Method Investments [Line Items]
Capital contributions	$ 5,000	$ 5,000
Membership interest	50.00%
S & I Ophthalmic, LLC | Investments In Affiliates
Schedule of Equity Method Investments [Line Items]
Investment			$ 2,621	$ 3,236

Investments in Joint Ventures54

Investments in Joint Ventures - OvaXon - Additional Information (Details) $ in Thousands	1 Months Ended	44 Months Ended
	Jan. 31, 2014USD ($)	Sep. 30, 2017USD ($)board_seat	Dec. 31, 2016USD ($)
Schedule of Equity Method Investments [Line Items]
Investment		$ 22,942	$ 23,655
OvaXon, LLC
Schedule of Equity Method Investments [Line Items]
Capital contributions	$ 1,500	$ 3,800
Membership interest	50.00%
Total number of seats on the joint venture's governing board | board_seat		4
Total number of seats on the joint venture's governing board, internally selected | board_seat		2
Total number of seats on the joint venture's governing board, externally selected | board_seat		2
OvaXon, LLC | Other Accrued Liabilities
Schedule of Equity Method Investments [Line Items]
Investment		$ (401)
OvaXon, LLC | Investments In Affiliates
Schedule of Equity Method Investments [Line Items]
Investment			$ 65
Investors | OvaXon, LLC
Schedule of Equity Method Investments [Line Items]
Capital contributions	$ 1,500	$ 3,800
Membership interest	50.00%

Investments in Joint Ventures55

Investments in Joint Ventures - Intrexon Energy Partners - Additional Information (Details)	1 Months Ended
	Mar. 31, 2014USD ($)	Sep. 30, 2017USD ($)board_seat	Dec. 31, 2016USD ($)
Schedule of Equity Method Investments [Line Items]
Investment		$ 22,942,000	$ 23,655,000
Intrexon Energy Partners, LLC
Schedule of Equity Method Investments [Line Items]
Membership interest	50.00%
Maximum additional capital contribution committed	$ 25,000,000
Additional capital contributions committed, remaining commitment		$ 6,011,000
Total number of seats on the joint venture's governing board | board_seat		5
Total number of seats on the joint venture's governing board, internally selected | board_seat		2
Total number of seats on the joint venture's governing board, externally selected | board_seat		3
Intrexon Energy Partners, LLC | Other Accrued Liabilities
Schedule of Equity Method Investments [Line Items]
Investment			$ (477,000)
Intrexon Energy Partners, LLC | Investments In Affiliates
Schedule of Equity Method Investments [Line Items]
Investment		$ 144,000
Intrexon Energy Partners, LLC | Investors
Schedule of Equity Method Investments [Line Items]
Membership interest	50.00%
Capital contributions	$ 25,000,000
Maximum additional capital contribution committed	25,000,000
Upfront and Milestone Payments | Intrexon Energy Partners, LLC | Upfront
Schedule of Equity Method Investments [Line Items]
Collaborative arrangement consideration received, value	$ 25,000,000

Investments in Joint Ventures56

Investments in Joint Ventures - Intrexon Energy Partners II - Additional Information (Details)	1 Months Ended
	Dec. 31, 2015USD ($)	Sep. 30, 2017USD ($)board_seat	Dec. 31, 2016USD ($)
Schedule of Equity Method Investments [Line Items]
Investment		$ 22,942,000	$ 23,655,000
Intrexon Energy Partners II, LLC
Schedule of Equity Method Investments [Line Items]
Membership interest	50.00%
Maximum additional capital contribution committed	$ 10,000,000
Total number of seats on the joint venture's governing board | board_seat		5
Total number of seats on the joint venture's governing board, internally selected | board_seat		1
Total number of seats on the joint venture's governing board, externally selected | board_seat		4
Intrexon Energy Partners II, LLC | Investments In Affiliates
Schedule of Equity Method Investments [Line Items]
Investment		$ 698,000	$ 1,414,000
Intrexon Energy Partners II, LLC | Investors
Schedule of Equity Method Investments [Line Items]
Membership interest	50.00%
Capital contributions	$ 18,000,000
Maximum additional capital contribution committed	10,000,000
Intrexon Energy Partners II, LLC | All Investors
Schedule of Equity Method Investments [Line Items]
Capital contributions	4,000,000
Intrexon Energy Partners II, LLC | Upfront and Milestone Payments | Upfront
Schedule of Equity Method Investments [Line Items]
Collaborative arrangement consideration received, value	$ 18,000,000

Investments in Joint Ventures57

Investments in Joint Ventures - EnviroFlight - Additional Information (Details) - USD ($)	1 Months Ended		9 Months Ended
	Oct. 31, 2016	Feb. 29, 2016	Sep. 30, 2017	Sep. 30, 2016	Dec. 31, 2016
Schedule of Equity Method Investments [Line Items]
Cash paid in asset acquisition			$ 14,219,000	$ 7,244,000
Shares issued in asset acquisition			0	4,401,000
Contingent consideration assumed in asset acquisition			0	$ 3,660,000
Shares issued as payment of deferred consideration			0
Investment			22,942,000		$ 23,655,000
Significant Unobservable Inputs (Level 3)
Schedule of Equity Method Investments [Line Items]
Fair value of financial liabilities measured at fair value on a recurring basis			2,911,000		2,081,000
EnviroFlight, LLC
Schedule of Equity Method Investments [Line Items]
Cash paid in asset acquisition		$ 4,244,000
Shares issued in asset acquisition (in shares)		136,340
Shares issued in asset acquisition		$ 4,401,000
Contingent consideration assumed in asset acquisition		3,660,000
Capital contributions		$ 3,000,000
Membership interest		50.00%
Maximum additional capital contribution committed		$ 5,000,000
Additional capital contributions committed, remaining commitment			250,000
Estimated fair value of investment		5,425,000
Shares issued for contingent consideration (in shares)	59,337
Shares issued as payment of deferred consideration	$ 1,583,000
Contingent consideration for commercial milestones payable in common stock, maximum		4,000,000
EnviroFlight, LLC | Investments In Affiliates
Schedule of Equity Method Investments [Line Items]
Investment			7,687,000		$ 4,189,000
EnviroFlight, LLC | Significant Unobservable Inputs (Level 3)
Schedule of Equity Method Investments [Line Items]
Fair value of financial liabilities measured at fair value on a recurring basis			$ 2,326,000
EnviroFlight, LLC | Patents, developed technologies and know-how
Schedule of Equity Method Investments [Line Items]
Estimated fair value of developed technology acquired		$ 9,880,000
Expected useful life of intangible asset		21 years
EnviroFlight, LLC | Investors
Schedule of Equity Method Investments [Line Items]
Membership interest		50.00%
Maximum additional capital contribution committed		$ 5,000,000

Investments in Joint Ventures58

Investments in Joint Ventures - Intrexon T1D Partners - Additional Information (Details)	1 Months Ended
	Mar. 31, 2016USD ($)	Sep. 30, 2017USD ($)board_seat	Dec. 31, 2016USD ($)
Schedule of Equity Method Investments [Line Items]
Investment		$ 22,942,000	$ 23,655,000
Intrexon T1D Partners, LLC
Schedule of Equity Method Investments [Line Items]
Membership interest	50.00%
Maximum additional capital contribution committed	$ 5,000,000
Additional capital contributions committed, remaining commitment		$ 2,900,000
Total number of seats on the joint venture's governing board | board_seat		5
Total number of seats on the joint venture's governing board, internally selected | board_seat		2
Total number of seats on the joint venture's governing board, externally selected | board_seat		3
Intrexon T1D Partners, LLC | Investors
Schedule of Equity Method Investments [Line Items]
Membership interest	50.00%
Capital contributions	$ 10,000,000
Maximum additional capital contribution committed	5,000,000
Intrexon T1D Partners, LLC | Upfront | Upfront and Milestone Payments
Schedule of Equity Method Investments [Line Items]
Collaborative arrangement consideration received, value	$ 10,000,000
Intrexon T1D Partners, LLC | Investments In Affiliates
Schedule of Equity Method Investments [Line Items]
Investment		$ 51,000	$ 806,000

Collaboration and Licensing R59

Collaboration and Licensing Revenue - Summarized Collaboration and Licensing Revenues (Details) - USD ($) $ in Thousands	3 Months Ended				9 Months Ended
	Sep. 30, 2017		Sep. 30, 2016		Sep. 30, 2017		Sep. 30, 2016
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	$ 28,155		$ 30,590		$ 89,384		$ 82,144
Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	10,506		10,220		32,254		24,047
Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	17,649		20,370		57,130		58,097
ZIOPHARM Oncology, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	10,373		10,429		31,322		24,380
ZIOPHARM Oncology, Inc. | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	4,843		4,843		14,527		6,687
ZIOPHARM Oncology, Inc. | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	5,530		5,586		16,795		17,693
Oragenics, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	475		556		1,519		1,869
Oragenics, Inc. | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	262		262		786		786
Oragenics, Inc. | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	213		294		733		1,083
Fibrocell Science, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,683		1,167		5,375		4,418
Fibrocell Science, Inc. | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	604		604		1,814		1,814
Fibrocell Science, Inc. | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,079		563		3,561		2,604
Genopaver, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,422		1,693		4,615		4,908
Genopaver, LLC | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	68		68		205		205
Genopaver, LLC | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,354		1,625		4,410		4,703
S & I Ophthalmic, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	376		2,782		751		6,326
S & I Ophthalmic, LLC | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	0		0		0		0
S & I Ophthalmic, LLC | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	376		2,782		751		6,326
OvaXon, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	262		709		1,966		2,211
OvaXon, LLC | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	0		0		0		0
OvaXon, LLC | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	262		709		1,966		2,211
Intrexon Energy Partners, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,903		4,855		8,909		13,055
Intrexon Energy Partners, LLC | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	625		625		1,875		1,875
Intrexon Energy Partners, LLC | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,278		4,230		7,034		11,180
Persea Bio, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	266		333		821		988
Persea Bio, LLC | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	125		125		375		375
Persea Bio, LLC | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	141		208		446		613
Ares Trading S.A.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	2,356		2,316		8,474		6,939
Ares Trading S.A. | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,597		1,597		4,791		4,791
Ares Trading S.A. | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	759		719		3,683		2,148
Intrexon Energy Partners II, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	816		872		2,921		2,316
Intrexon Energy Partners II, LLC | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	500		500		1,500		1,500
Intrexon Energy Partners II, LLC | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	316		372		1,421		816
Intrexon T1D Partners, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,462		787		3,882		1,097
Intrexon T1D Partners, LLC | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	287		276		823		554
Intrexon T1D Partners, LLC | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,175		511		3,059		543
Harvest start-up entities
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	4,020	[1]	1,293	[2]	11,835	[3]	2,666	[4]
Harvest start-up entities | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	616	[1]	425	[2]	1,823	[3]	776	[4]
Harvest start-up entities | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	3,404	[1]	868	[2]	10,012	[3]	1,890	[4]
Other
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	2,741		2,798		6,994		10,971
Other | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	979		895		3,735		4,684
Other | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	$ 1,762		$ 1,903		$ 3,259		$ 6,287
[1]	For the three months ended September 30, 2017, revenue recognized from collaborations with Harvest start-up entities include Thrive Agrobiotics, Inc.; Exotech Bio, Inc.; Relieve Genetics, Inc.; AD Skincare, Inc.; Genten Therapeutics, Inc.; and CRS Bio, Inc.
[2]	For the three months ended September 30, 2016, revenue recognized from collaborations with Harvest start-up entities include Thrive Agrobiotics, Inc.; Exotech Bio, Inc.; Relieve Genetics, Inc.; and AD Skincare, Inc.
[3]	For the nine months ended September 30, 2017, revenue recognized from collaborations with Harvest start-up entities include Thrive Agrobiotics, Inc.; Exotech Bio, Inc.; Relieve Genetics, Inc.; AD Skincare, Inc.; Genten Therapeutics, Inc.; and CRS Bio, Inc.
[4]	For the nine months ended September 30, 2016, revenue recognized from collaborations with Harvest start-up entities include Thrive Agrobiotics, Inc.; Exotech Bio, Inc.; Relieve Genetics, Inc.; and AD Skincare, Inc.

Collaboration and Licensing R60

Collaboration and Licensing Revenue - Summary of Deferred Revenue (Details) - USD ($) $ in Thousands	Sep. 30, 2017	Dec. 31, 2016
Deferred Revenue Arrangement [Line Items]
Deferred revenue	$ 276,287	$ 310,142
Current portion of deferred revenue	48,289	53,364
Long-term portion of deferred revenue	227,998	256,778
Deferred revenue	276,287	310,142
Upfront and milestone payments
Deferred Revenue Arrangement [Line Items]
Deferred revenue	269,649	297,867
Deferred revenue	269,649	297,867
Prepaid research and development services
Deferred Revenue Arrangement [Line Items]
Deferred revenue	1,718	6,015
Deferred revenue	1,718	6,015
Prepaid product and service revenues
Deferred Revenue Arrangement [Line Items]
Deferred revenue	4,869	5,554
Deferred revenue	4,869	5,554
Other
Deferred Revenue Arrangement [Line Items]
Deferred revenue	51	706
Deferred revenue	$ 51	$ 706

Collaboration and Licensing R61

Collaboration and Licensing Revenue - Summary of Deferred Revenue by Collaborator (Details) - USD ($) $ in Thousands		Sep. 30, 2017	Dec. 31, 2016
Deferred Revenue Arrangement [Line Items]
Deferred revenue		$ 276,287	$ 310,142
Upfront and Milestone Payments
Deferred Revenue Arrangement [Line Items]
Deferred revenue		269,649	297,867
Upfront and Milestone Payments | ZIOPHARM Oncology, Inc.
Deferred Revenue Arrangement [Line Items]
Deferred revenue		124,282	138,809
Upfront and Milestone Payments | Oragenics, Inc.
Deferred Revenue Arrangement [Line Items]
Deferred revenue		6,980	7,766
Upfront and Milestone Payments | Fibrocell Science, Inc.
Deferred Revenue Arrangement [Line Items]
Deferred revenue		17,212	19,026
Upfront and Milestone Payments | Genopaver, LLC
Deferred Revenue Arrangement [Line Items]
Deferred revenue		1,772	1,977
Upfront and Milestone Payments | Intrexon Energy Partners, LLC
Deferred Revenue Arrangement [Line Items]
Deferred revenue		16,250	18,125
Upfront and Milestone Payments | Persea Bio, LLC
Deferred Revenue Arrangement [Line Items]
Deferred revenue		3,625	4,000
Upfront and Milestone Payments | Ares Trading S.A.
Deferred Revenue Arrangement [Line Items]
Deferred revenue		42,387	47,178
Upfront and Milestone Payments | Intrexon Energy Partners II, LLC
Deferred Revenue Arrangement [Line Items]
Deferred revenue		14,333	15,833
Upfront and Milestone Payments | Intrexon T1D Partners, LLC
Deferred Revenue Arrangement [Line Items]
Deferred revenue		8,628	8,653
Upfront and Milestone Payments | Harvest start-up entities
Deferred Revenue Arrangement [Line Items]
Deferred revenue	[1]	18,953	20,208
Upfront and Milestone Payments | Other
Deferred Revenue Arrangement [Line Items]
Deferred revenue		$ 15,227	$ 16,292
[1]	As of September 30, 2017 and December 31, 2016, the balance of deferred revenue for collaborations with Harvest start-up entities includes Thrive Agrobiotics, Inc.; Exotech Bio, Inc.; Relieve Genetics, Inc.; AD Skincare, Inc.; Genten Therapeutics, Inc.; and CRS Bio, Inc.

Short-term and Long-term Inve62

Short-term and Long-term Investments - Summary of Amortized Cost, Gross Unrealized Gains and Losses, and Fair Value of Short-term and Long-term Investments (Details) - USD ($) $ in Thousands	Sep. 30, 2017	Dec. 31, 2016
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	$ 44,517	$ 180,684
Gross Unrealized Gains	2	5
Gross Unrealized Losses	(17)	(94)
Aggregate Fair Value	44,502	180,595
U.S. government debt securities
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	44,000	180,412
Gross Unrealized Gains	2	5
Gross Unrealized Losses	(17)	(94)
Aggregate Fair Value	43,985	180,323
Corporate notes and bonds
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	242
Gross Unrealized Gains	0
Gross Unrealized Losses	0
Aggregate Fair Value	242
Certificates of deposit
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	275	272
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Aggregate Fair Value	$ 275	$ 272

Investments in Preferred Stoc63

Investments in Preferred Stock - Additional Information (Details) $ / shares in Units, $ in Thousands	Mar. 10, 2017	Mar. 31, 2017USD ($)shares	Jun. 30, 2016$ / sharesshares	Sep. 30, 2017USD ($)shares	Sep. 30, 2016USD ($)shares	Sep. 30, 2017USD ($)$ / sharesshares	Sep. 30, 2016USD ($)shares	Dec. 31, 2016USD ($)
Schedule of Investments [Line Items]
Fair value of financial assets measured at fair value on a recurring basis				$ 226,215		$ 226,215		$ 335,307
Noncash Dividend Income						12,303	$ 3,676
Purchases of preferred stock and warrants						1,161	$ 2,308
Preferred stock
Schedule of Investments [Line Items]
Fair value of financial assets measured at fair value on a recurring basis				$ 148,499		$ 148,499		129,545
Fibrocell Science, Inc.
Schedule of Investments [Line Items]
Convertible preferred shares issued (in shares) | shares		1,161
Number of common shares into which warrants are convertible (in shares) | shares		498,843
Reverse stock split ratio	1-for-3
Reverse stock split, conversion ratio	0.3333
Convertible preferred shares, dividend rate						4.00%
ZIOPHARM Oncology, Inc.
Schedule of Investments [Line Items]
Preferred shares, stated value (in usd per share) | $ / shares			$ 1,200
Threshold consecutive trading days, conversion of shares						20 days
Preferred shares, dividend rate (in usd per share) | $ / shares						$ 12
Preferred shares, dividend rate, for unconverted shares after conversion event (in usd per share) | $ / shares						24
ZIOPHARM Oncology, Inc. | Minimum
Schedule of Investments [Line Items]
Preferred shares, conversion calculation, divisor (in usd per share) | $ / shares						$ 1
Other Contractual Payments | Upfront and Milestone Payments | ZIOPHARM Oncology, Inc.
Schedule of Investments [Line Items]
Collaborative arrangement consideration received, number of preferred shares (in shares) | shares			100,000
ZIOPHARM Oncology, Inc.
Schedule of Investments [Line Items]
Dividend income, number of preferred shares received (in shares) | shares				3,414	3,063	9,943	3,063
Noncash Dividend Income				$ 4,311	$ 3,676	$ 12,276	$ 3,676
ZIOPHARM Oncology, Inc. | Preferred stock
Schedule of Investments [Line Items]
Fair value of financial assets measured at fair value on a recurring basis				146,637		146,637		$ 129,545
Fibrocell Science, Inc.
Schedule of Investments [Line Items]
Purchases of preferred stock and warrants		$ 1,161
Fibrocell Science, Inc. | Preferred stock
Schedule of Investments [Line Items]
Fair value of financial assets measured at fair value on a recurring basis				$ 1,862		$ 1,862

Investments in Preferred Stoc64

Investments in Preferred Stock - Schedule of Changes in Level 3 Investments (Details) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2017	Sep. 30, 2016
Fair Value, Assets Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Purchase of preferred stock	$ 1,161	$ 2,308
Dividend income from investments in preferred stock	12,303	$ 3,676
Significant Unobservable Inputs (Level 3)
Fair Value, Assets Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Beginning balance	129,545
Purchase of preferred stock	766
Dividend income from investments in preferred stock	12,303
Unrealized appreciation in the fair value of the investments in preferred stock	5,885
Ending balance	$ 148,499

Fair Value Measurements - Summa

Fair Value Measurements - Summary of Placement in the Fair Value Hierarchy of Financial Assets that are Measured at Fair Value on a Recurring Basis (Details) - USD ($) $ in Thousands	Sep. 30, 2017	Dec. 31, 2016
Assets
Fair value of financial assets measured at fair value on a recurring basis	$ 226,215	$ 335,307
U.S. government debt securities
Assets
Fair value of financial assets measured at fair value on a recurring basis	43,985	180,323
Equity securities
Assets
Fair value of financial assets measured at fair value on a recurring basis	26,642	23,522
Preferred stock
Assets
Fair value of financial assets measured at fair value on a recurring basis	148,499	129,545
Other
Assets
Fair value of financial assets measured at fair value on a recurring basis	7,089	1,917
Quoted Prices in Active Markets (Level 1)
Assets
Fair value of financial assets measured at fair value on a recurring basis	19,830	15,544
Quoted Prices in Active Markets (Level 1) | U.S. government debt securities
Assets
Fair value of financial assets measured at fair value on a recurring basis	0	0
Quoted Prices in Active Markets (Level 1) | Equity securities
Assets
Fair value of financial assets measured at fair value on a recurring basis	19,830	15,544
Quoted Prices in Active Markets (Level 1) | Preferred stock
Assets
Fair value of financial assets measured at fair value on a recurring basis	0	0
Quoted Prices in Active Markets (Level 1) | Other
Assets
Fair value of financial assets measured at fair value on a recurring basis	0	0
Significant Other Observable Inputs (Level 2)
Assets
Fair value of financial assets measured at fair value on a recurring basis	57,886	190,218
Significant Other Observable Inputs (Level 2) | U.S. government debt securities
Assets
Fair value of financial assets measured at fair value on a recurring basis	43,985	180,323
Significant Other Observable Inputs (Level 2) | Equity securities
Assets
Fair value of financial assets measured at fair value on a recurring basis	6,812	7,978
Significant Other Observable Inputs (Level 2) | Preferred stock
Assets
Fair value of financial assets measured at fair value on a recurring basis	0	0
Significant Other Observable Inputs (Level 2) | Other
Assets
Fair value of financial assets measured at fair value on a recurring basis	7,089	1,917
Significant Unobservable Inputs (Level 3)
Assets
Fair value of financial assets measured at fair value on a recurring basis	148,499	129,545
Significant Unobservable Inputs (Level 3) | U.S. government debt securities
Assets
Fair value of financial assets measured at fair value on a recurring basis	0	0
Significant Unobservable Inputs (Level 3) | Equity securities
Assets
Fair value of financial assets measured at fair value on a recurring basis	0	0
Significant Unobservable Inputs (Level 3) | Preferred stock
Assets
Fair value of financial assets measured at fair value on a recurring basis	148,499	129,545
Significant Unobservable Inputs (Level 3) | Other
Assets
Fair value of financial assets measured at fair value on a recurring basis	$ 0	$ 0

Fair Value Measurements - Addit

Fair Value Measurements - Additional Information (Details) - USD ($) $ in Thousands	Sep. 30, 2017	Dec. 31, 2016
Significant Unobservable Inputs (Level 3)
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of financial liabilities measured at fair value on a recurring basis	$ 2,911	$ 2,081

Fair Value Measurements - Sched

Fair Value Measurements - Schedule of Changes in Level 3 Liabilities (Details) - Significant Unobservable Inputs (Level 3) $ in Thousands	9 Months Ended
	Sep. 30, 2017USD ($)
Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Beginning balance	$ 2,081
Acquisition date fair value of contingent consideration liability	585
Change in fair value of contingent consideration recognized in selling, general and administrative expenses	245
Ending balance	$ 2,911

Inventory (Details)

Inventory (Details) - USD ($) $ in Thousands	Sep. 30, 2017	Dec. 31, 2016
Inventory [Line Items]
Inventory	$ 17,730	$ 21,139
Supplies, embryos and other production materials
Inventory [Line Items]
Inventory	2,185	1,835
Work in process
Inventory [Line Items]
Inventory	4,618	5,466
Livestock
Inventory [Line Items]
Inventory	8,738	11,752
Feed
Inventory [Line Items]
Inventory	$ 2,189	$ 2,086

Property, Plant and Equipment69

Property, Plant and Equipment, Net - Schedule of Property, Plant and Equipment (Details) - USD ($) $ in Thousands	Sep. 30, 2017	Dec. 31, 2016
Property, Plant and Equipment [Abstract]
Land and land improvements	$ 11,642	$ 10,904
Buildings and building improvements	15,216	8,123
Furniture and fixtures	2,220	2,176
Equipment	58,851	44,392
Leasehold improvements	22,974	15,105
Breeding stock	3,822	3,893
Computer hardware and software	9,817	6,844
Trees	5,719	2,772
Construction and other assets in progress	15,138	4,513
Property, plant and equipment, gross	145,399	98,722
Less: Accumulated depreciation and amortization	(42,523)	(34,050)
Property, plant and equipment, net	$ 102,876	$ 64,672

Property, Plant and Equipment70

Property, Plant and Equipment, Net - Additional Information (Details) - USD ($) $ in Thousands	1 Months Ended	3 Months Ended		9 Months Ended
	Jun. 30, 2017	Sep. 30, 2017	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016
Property, Plant and Equipment [Line Items]
Depreciation expense		$ 2,989	$ 2,332	$ 8,623	$ 6,769
Cash paid in asset acquisition				$ 14,219	$ 7,244
AquaBounty Technologies, Inc.
Property, Plant and Equipment [Line Items]
Cash paid in asset acquisition	$ 14,219

Goodwill and Intangible Asset71

Goodwill and Intangible Assets, Net - Schedule of Changes in Carrying Amount of Goodwill (Details) $ in Thousands	9 Months Ended
	Sep. 30, 2017USD ($)
Goodwill
Beginning balance	$ 157,175
Goodwill, Acquired During Period	4,850
Foreign currency translation adjustments	4,796
Ending balance	$ 166,821

Goodwill and Intangible Asset72

Goodwill and Intangible Assets, Net - Additional Information (Details) - USD ($)	3 Months Ended		9 Months Ended
	Sep. 30, 2017	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016	Dec. 31, 2016
Goodwill and Intangible Assets Disclosure [Abstract]
Goodwill accumulated impairment losses	$ 0		$ 0		$ 0
Amortization expense	$ 5,001,000	$ 3,651,000	$ 14,258,000	$ 10,888,000

Goodwill and Intangible Asset73

Goodwill and Intangible Assets, Net - Schedule of Intangible Assets (Details) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2017	Dec. 31, 2016
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	$ 292,768	$ 262,166
Accumulated Amortization	(51,871)	(36,551)
Net	240,897	225,615
Patents, developed technologies and know-how
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	266,697	236,401
Accumulated Amortization	(43,465)	(29,748)
Net	223,232	206,653
Customer relationships
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	10,700	10,700
Accumulated Amortization	(6,033)	(4,672)
Net	4,667	6,028
Trademarks
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	6,800	6,800
Accumulated Amortization	(2,373)	(1,792)
Net	4,427	5,008
Covenant not to compete
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount		370
Accumulated Amortization		(339)
Net		31
In-process research and development
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	8,571	7,895
Accumulated Amortization	0	0
Net	$ 8,571	$ 7,895
Weighted Average | Patents, developed technologies and know-how
Finite-Lived Intangible Assets [Line Items]
Weighted Average Useful Life	15 years 8 months 12 days
Weighted Average | Customer relationships
Finite-Lived Intangible Assets [Line Items]
Weighted Average Useful Life	6 years 6 months
Weighted Average | Trademarks
Finite-Lived Intangible Assets [Line Items]
Weighted Average Useful Life	9 years 3 months 18 days

Lines of Credit and Long Term74

Lines of Credit and Long Term Debt - Lines of Credit - Additional Information (Details) - Revolving Line of Credit	9 Months Ended
	Sep. 30, 2017USD ($)
Trans Ova Genetics, LC | First National Bank of Omaha
Line of Credit Facility [Line Items]
Line of credit facility, maximum borrowing capacity	$ 5,000,000
Line of credit facility, interest rate at period end	4.19%
Line of credit facility, outstanding balance	$ 0
Trans Ova Genetics, LC | First National Bank of Omaha | Minimum
Line of Credit Facility [Line Items]
Debt instrument, interest rate, stated percentage	3.00%
Trans Ova Genetics, LC | First National Bank of Omaha | London Interbank Offered Rate (LIBOR)
Line of Credit Facility [Line Items]
Line of credit facility, basis spread on variable rate	2.95%
Exemplar Genetics, LLC | American State Bank
Line of Credit Facility [Line Items]
Line of credit facility, maximum borrowing capacity	$ 700,000
Debt instrument, interest rate, stated percentage	4.50%
Line of credit facility, outstanding balance	$ 234,000

Lines of Credit and Long Term75

Lines of Credit and Long Term Debt - Schedule of Long Term Debt Instruments (Details) - USD ($) $ in Thousands	Sep. 30, 2017	Dec. 31, 2016
Debt Instrument [Line Items]
Long term debt	$ 8,112	$ 7,948
Less current portion	439	386
Long term debt, net of current portion	7,673	7,562
Notes payable
Debt Instrument [Line Items]
Long term debt	5,122	5,453
Royalty-based financing
Debt Instrument [Line Items]
Long term debt	2,108	1,896
Other
Debt Instrument [Line Items]
Long term debt	$ 882	$ 599

Lines of Credit and Long Term76

Lines of Credit and Long Term Debt - Long Term Debt - Additional Information (Details) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2017	Dec. 31, 2016	Mar. 31, 2013
Debt Instrument [Line Items]
Long term debt	$ 8,112	$ 7,948
Notes payable to banks | Trans Ova Genetics, LC | American State Bank
Debt Instrument [Line Items]
Long term debt	4,967
Debt instrument, periodic payment	$ 39
Debt instrument, interest rate, stated percentage	3.95%
Royalty-based financing
Debt Instrument [Line Items]
Long term debt	$ 2,108	$ 1,896
Royalty-based financing | AquaBounty Technologies, Inc. | Atlantic Canada Opportunities Agency
Debt Instrument [Line Items]
Long term debt	2,108
Amount available under the grant for research and development	$ 2,302
Claims period	5 years
Royalty on products, percentage	10.00%
Amount claimed			$ 1,952
Long term debt, fair value at date of business combination			1,107
Accreted difference between face value of amount drawn and acquisition date fair value			$ 845

Lines of Credit and Long Term77

Lines of Credit and Long Term Debt - Schedule of Future Maturities of Long Term Debt (Details) $ in Thousands	Sep. 30, 2017USD ($)
Debt Disclosure [Abstract]
2,017	$ 107
2,018	462
2,019	400
2,020	371
2,021	834
2,022	360
Thereafter	3,470
Total	$ 6,004

Income Taxes (Details)

Income Taxes (Details) - USD ($)	3 Months Ended		9 Months Ended
	Sep. 30, 2017	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016
Operating Loss Carryforwards [Line Items]
Deferred income tax benefit	$ (775,000)	$ (308,000)	$ (2,294,000)	$ (2,967,000)
Deferred tax liabilities	15,868,000		15,868,000
Domestic Tax Authority
Operating Loss Carryforwards [Line Items]
Taxable income (loss)	3,930,000	8,334,000	23,680,000	(9,346,000)
Current income tax expense (benefit)	78,000	0	473,000	0
Operating loss carryforwards	243,700,000		243,700,000
Operating loss carryforwards acquired in acquisition of business	13,400,000		13,400,000
Federal and state research and development tax credits	7,800,000		7,800,000
Foreign Tax Authority
Operating Loss Carryforwards [Line Items]
Current income tax expense (benefit)	(121,000)	$ (110,000)	(343,000)	$ (323,000)
Operating loss carryforwards	$ 146,800,000		$ 146,800,000

Shareholders' Equity - Dividend

Shareholders' Equity - Dividend to Shareholders (Details) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended	9 Months Ended
	Jan. 31, 2017	Sep. 30, 2017
Class of Stock [Line Items]
Noncash dividend to shareholders		$ 0
Intrexon Stock Option Plans
Class of Stock [Line Items]
Adjustment due to dividend (in shares)		46,766
Adjustment due to dividend (in usd per share)		$ 31.11
AquaBounty Technologies, Inc.
Class of Stock [Line Items]
Noncash dividend, shares	1,776,557
Noncash dividend to shareholders	$ 22,385

Shareholders' Equity - Componen

Shareholders' Equity - Components of Accumulated Other Comprehensive Loss (Details) - USD ($) $ in Thousands	Sep. 30, 2017	Dec. 31, 2016
Accumulated Other Comprehensive Income (Loss) [Line Items]
Intrexon shareholders' equity	$ 533,613	$ 560,237
Unrealized loss on investments
Accumulated Other Comprehensive Income (Loss) [Line Items]
Intrexon shareholders' equity	(15)	(89)
Loss on foreign currency translation adjustments
Accumulated Other Comprehensive Income (Loss) [Line Items]
Intrexon shareholders' equity	(16,735)	(36,113)
Total accumulated other comprehensive loss
Accumulated Other Comprehensive Income (Loss) [Line Items]
Intrexon shareholders' equity	$ (16,750)	$ (36,202)

Share-Based Payments - Schedule

Share-Based Payments - Schedule of Stock-Based Compensation Costs (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2017	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation costs	$ 12,057	$ 10,792	$ 31,949	$ 30,631
Cost of products
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation costs	30	21	86	61
Cost of services
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation costs	82	68	242	206
Research and development
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation costs	2,383	2,236	7,018	6,979
Selling, general and administrative
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation costs	$ 9,562	$ 8,467	$ 24,603	$ 23,385

Share-Based Payments - Addition

Share-Based Payments - Additional Information (Details) $ / shares in Units, $ in Thousands	Jan. 05, 2017	Nov. 30, 2015USD ($)	Sep. 30, 2017USD ($)$ / sharesshares	Sep. 30, 2016USD ($)	Sep. 30, 2017USD ($)$ / sharesshares	Sep. 30, 2016USD ($)	Dec. 31, 2016$ / sharesshares	Apr. 30, 2016shares	Aug. 31, 2013shares
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares issued as payment for services | $					$ 8,440	$ 8,284
Chief Executive Officer
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Monthly compensation, in the form of equity | $		$ 200
Lock-up period		3 years
Initial term of compensation arrangement		12 months
Chief Executive Officer | Selling, general and administrative
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares issued as payment for services | $			$ 480	$ 463	$ 1,428	$ 1,397
Intrexon Stock Option Plan - 2008 Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Remaining shares available to grant (in shares)									0
Options outstanding (in shares)			492,414		492,414
Intrexon Stock Option Plan - 2013 Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Remaining shares available to grant (in shares)			3,743,187		3,743,187
Options outstanding (in shares)			12,149,356		12,149,356
Number of shares authorized for issuance (in shares)			18,000,000		18,000,000
Intrexon Stock Option Plans
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Options outstanding (in shares)			12,641,770		12,641,770		11,640,383
Options exercisable (in shares)			5,313,100		5,313,100
Weighted average exercise price of option (in usd per share) | $ / shares			$ 28.59		$ 28.59		$ 31.25
AquaBounty Stock Option Plan - 2006 Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Remaining shares available to grant (in shares)								0
Aqua Bounty Stock Option Plans
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Options outstanding (in shares)			227,203		227,203		185,591
Options exercisable (in shares)			183,373		183,373		181,766
Weighted average exercise price of option (in usd per share) | $ / shares			$ 9.39		$ 9.39		$ 7.89
AquaBounty Technologies, Inc.
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Reverse stock split ratio	1-for-30
Reverse stock split, conversion ratio	0.0333

Share-Based Payments - Schedu83

Share-Based Payments - Schedule of Stock Option Activity (Details) - Intrexon Stock Option Plans - $ / shares	9 Months Ended	12 Months Ended
	Sep. 30, 2017	Dec. 31, 2016
Number of Shares
Balances at beginning of period (in shares)	11,640,383
Granted (in shares)	3,880,950
Adjustment due to dividend (in shares)	46,766
Exercised (in shares)	(109,971)
Forfeited (in shares)	(2,610,431)
Expired (in shares)	(205,927)
Balances at end of period (in shares)	12,641,770	11,640,383
Exercisable at end of period (in shares)	5,313,100
Weighted Average Exercise Price
Balances at beginning of period (in usd per share)	$ 31.25
Granted (in usd per share)	21.51
Adjustment due to dividend (in usd per share)	31.11
Exercised (in usd per share)	(7.63)
Forfeited (in usd per share)	(29.93)
Expired (in usd per share)	(33.17)
Balances at period end (in usd per share)	28.59	$ 31.25
Exercisable, weighted average exercise price, at end of period (in usd per share)	$ 29.85
Weighted Average Remaining Contractual Term (Years)
Balances, weighted average remaining contractual period	7 years 10 months 8 days	8 years 2 months 15 days
Exercisable at period end, weighted average remaining contractual period	6 years 9 months 7 days

Commitments and Contingencies -

Commitments and Contingencies - Future Minimum Lease Payments Under Noncancelable Operating Leases (Details) $ in Thousands	Sep. 30, 2017USD ($)
Commitments and Contingencies Disclosure [Abstract]
2,017	$ 1,252
2,018	8,083
2,019	8,042
2,020	8,063
2,021	7,132
2,022	6,085
Thereafter	25,695
Total	$ 64,352

Commitments and Contingencies85

Commitments and Contingencies - Operating Leases - Additional Information (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2017	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016
Commitments and Contingencies Disclosure [Abstract]
Rent expense	$ 3,165	$ 2,075	$ 7,772	$ 6,410
Rental income under sublease agreement	32	$ 184	105	$ 854
Future rental income under sublease agreements, 2017	20		20
Future rental income under sublease agreements, 2018	80		80
Future rental income under sublease agreements, 2019	$ 67		$ 67

Commitments and Contingencies86

Commitments and Contingencies - Purchase Commitments - Additional Information (Details) $ in Thousands	Sep. 30, 2017USD ($)
Commitments and Contingencies Disclosure [Abstract]
Outstanding contractual purchase commitments	$ 10,618

Commitments and Contingencies87

Commitments and Contingencies - Contingencies - Additional Information (Details) $ in Thousands	1 Months Ended				2 Months Ended	9 Months Ended	50 Months Ended
	Mar. 31, 2017claim	Jul. 31, 2016claim	May 31, 2016claim	Apr. 30, 2016USD ($)	Jul. 31, 2016claim	Sep. 30, 2016USD ($)	Apr. 30, 2016USD ($)
Licensing and patent infringement suit
Loss Contingencies [Line Items]
Damages awarded to Trans Ova				$ 528
Cumulative payments for royalties and licenses							$ 3,170
Royalty payments not yet deposited				2,759			$ 2,759
Licensing and patent infringement suit | Selling, general and administrative
Loss Contingencies [Line Items]
Litigation settlement expense						$ 4,228
Licensing and patent infringement suit | XY, LLC
Loss Contingencies [Line Items]
Damages awarded against Trans Ova				$ 6,066
Hoffman v. Intrexon Corporation et al. and Gibrall v. Intrexon Corporation et al.
Loss Contingencies [Line Items]
Number of lawsuits | claim			2
Shareholder demand regarding Third Security Services Agreement and CEO Compensation
Loss Contingencies [Line Items]
Number of similar lawsuits | claim		2
Shareholder demand regarding allegations made by Seeking Alpha financial blog
Loss Contingencies [Line Items]
Number of lawsuits | claim	1				2

Related Party Transactions (Det

Related Party Transactions (Details) - USD ($) $ in Thousands	1 Months Ended		3 Months Ended		9 Months Ended
	May 31, 2017	Nov. 30, 2015	Sep. 30, 2017	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016	Dec. 31, 2016
Related Party Transaction [Line Items]
Shares issued as payment for services					$ 8,440
Fair value of financial assets measured at fair value on a recurring basis			$ 226,215		226,215		$ 335,307
Other nonoperating income			(1,021)	$ (32)	4,453	$ 1,205
Third Security, LLC
Related Party Transaction [Line Items]
Expense for services			$ 4	$ 156	$ 428	$ 301
Initial term of services agreement		1 year
Shares issued as payment for services (in shares)			118,828	89,326	329,649	254,496
Shares issued as payment for services			$ 2,251	$ 2,132	$ 6,506	$ 6,542
Third Security, LLC | Common Stock
Related Party Transaction [Line Items]
Expense for services		$ 800
Oragenics, Inc.
Related Party Transaction [Line Items]
Promissory note, interest rate, stated percentage	12.00%
Harvest Intrexon Enterprise Fund I, LP
Related Party Transaction [Line Items]
Other nonoperating income			613	$ 613	1,839	$ 1,871
Other Assets | Oragenics, Inc.
Related Party Transaction [Line Items]
Promissory note receivable	$ 2,400
Convertible Note and Warrants | Other Assets | Fibrocell Science, Inc.
Related Party Transaction [Line Items]
Fair value of financial assets measured at fair value on a recurring basis			$ 4,172		$ 4,172		$ 1,642
Third Security, LLC | Chief Executive Officer
Related Party Transaction [Line Items]
Ownership interest			100.00%		100.00%

Net Loss per Share - Computatio

Net Loss per Share - Computation of Basic and Diluted Net Loss Per Share (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2017	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016
Numerator:
Net loss attributable to Intrexon	$ (39,689)	$ (28,982)	$ (89,752)	$ (142,475)
Denominator:
Weighted average shares outstanding, basic and diluted (in shares)	120,518,885	118,346,782	119,741,291	117,785,160
Net loss attributable to Intrexon per share, basic and diluted (in usd per share)	$ (0.33)	$ (0.24)	$ (0.75)	$ (1.21)

Net Loss per Share - Schedule o

Net Loss per Share - Schedule of Antidilutive Securities Excluded from Calculation of Net Loss per Share (Details) - shares	3 Months Ended		9 Months Ended
	Sep. 30, 2017	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of net loss per share (in shares)	12,775,034	12,133,598	12,775,034	12,133,598
Options
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of net loss per share (in shares)	12,641,770	12,103,407	12,641,770	12,103,407
Warrants
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of net loss per share (in shares)	133,264	30,191	133,264	30,191

Subsequent Events (Details)

Subsequent Events (Details) - Subsequent Event - USD ($)	Nov. 09, 2017	Oct. 31, 2017
Series C preferred shares | Oragenics, Inc.
Subsequent Event [Line Items]
Preferred shares stated value	$ 3,376,000
Preferred shares, initial dividend rate	12.00%
Preferred shares, subsequent dividend rate	20.00%
Series A preferred shares
Subsequent Event [Line Items]
Convertible preferred shares, conversion price, number of days used to calculate volume-weighted average market price		20 days
Series A preferred shares | Affiliate of Third Security, LLC
Subsequent Event [Line Items]
Value of convertible preferred shares authorized for issuance		$ 100,000,000
Convertible preferred shares, dividend rate		8.00%