Precigen (PGEN) 10-Q 10 Aug 15 2015 Q2 Quarterly report Financial data

Document and Entity Information

Document and Entity Information - shares	6 Months Ended
	Jun. 30, 2015	Jul. 31, 2015
Document And Entity Information [Abstract]
Document Type	10-Q
Amendment Flag	false
Document Period End Date	Jun. 30, 2015
Document Fiscal Year Focus	2,015
Document Fiscal Period Focus	Q2
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		109,757,902

Consolidated Balance Sheets

Consolidated Balance Sheets - USD ($) $ in Thousands	Jun. 30, 2015	Dec. 31, 2014
Current assets
Cash and cash equivalents	$ 98,899	$ 27,466
Short-term investments	67,431	88,495
Receivables
Trade, net	141,133	14,582
Related parties	17,406	12,622
Note	1,521	1,501
Other	670	559
Inventory	27,001	25,789
Prepaid expenses and other	5,477	3,759
Total current assets	359,538	174,773
Long-term investments	0	27,113
Equity securities	101,896	164,889
Property, plant and equipment, net	40,863	38,000
Intangible assets, net	162,234	65,947
Goodwill	118,965	101,059
Investments in affiliates	2,960	3,220
Other assets	6,483	1,271
Total assets	792,939	576,272
Current liabilities
Accounts payable	7,322	6,267
Accrued compensation and benefits	12,430	7,736
Other accrued liabilities	6,875	5,731
Deferred revenue	28,737	16,522
Lines of credit	873	2,273
Current portion of long term debt	1,427	1,675
Current portion of deferred consideration	7,559	7,064
Related party payables	57,584	214
Total current liabilities	122,807	47,482
Long term debt, net of current portion	8,040	8,694
Deferred consideration, net of current portion	13,396	13,421
Deferred revenue, net of current portion	151,273	96,687
Deferred tax liability	9,609	0
Other long term liabilities	887	699
Total liabilities	$ 306,012	$ 166,983
Commitments and contingencies (Note 16)
Total equity
Common stock, no par value, 200,000,000 shares authorized as of June 30, 2015 and December 31, 2014; 109,729,717 and 100,557,932 shares issued and outstanding as of June 30, 2015 and December 31, 2014, respectively	$ 0	$ 0
Additional paid-in capital	948,922	843,001
Accumulated deficit	(471,802)	(458,236)
Accumulated other comprehensive loss	(2,285)	(4)
Total Intrexon shareholders' equity	474,835	384,761
Noncontrolling interests	12,092	24,528
Total equity	486,927	409,289
Total liabilities and total equity	$ 792,939	$ 576,272

Consolidated Balance Sheets (Pa

Consolidated Balance Sheets (Parenthetical) - $ / shares None in scaling factor is -9223372036854775296	Jun. 30, 2015	Dec. 31, 2014
Statement of Financial Position [Abstract]
Common stock, no par value
Common stock, shares authorized	200,000,000	200,000,000
Common stock, shares issued	109,729,717	100,557,932
Common stock, shares outstanding	109,729,717	100,557,932

Consolidated Statements of Oper

Consolidated Statements of Operations - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014	Jun. 30, 2015	Jun. 30, 2014
Revenues
Collaboration and licensing revenues	$ 17,181	$ 11,764	$ 31,964	$ 19,601
Product revenues	14,266	9	23,199	9
Service revenues	13,255	0	23,212	0
Other revenues	189	14	365	31
Total revenues	44,891	11,787	78,740	19,641
Operating Expenses
Cost of products	11,764	53	20,439	86
Cost of services	6,503	0	11,865	0
Research and development	20,381	14,434	99,688	26,492
Selling, general and administrative	23,673	15,382	51,301	29,017
Total operating expenses	62,321	29,869	183,293	55,595
Operating loss	(17,430)	(18,082)	(104,553)	(35,954)
Other Income (Expense), Net
Unrealized and realized appreciation (depreciation) in fair value of equity securities	(20,609)	(33,777)	94,845	(11,855)
Interest expense	(359)	(40)	(702)	(79)
Interest income	344	110	644	198
Other expense, net	(326)	(74)	(59)	(82)
Total other income (expense), net	(20,950)	(33,781)	94,728	(11,818)
Equity in net loss of affiliates	(2,180)	(1,355)	(4,136)	(1,891)
Loss before income taxes	(40,560)	(53,218)	(13,961)	(49,663)
Income tax benefit (expense)	(934)	283	(1,729)	(23)
Net loss	(41,494)	(52,935)	(15,690)	(49,686)
Net loss attributable to the noncontrolling interests	831	892	2,124	1,758
Net loss attributable to Intrexon	$ (40,663)	$ (52,043)	$ (13,566)	$ (47,928)
Net loss attributable to Intrexon per share, basic and diluted (usd per share)	$ (0.37)	$ (0.53)	$ (0.13)	$ (0.49)
Weighted average shares outstanding, basic and diluted	109,318,471	98,892,601	107,720,040	98,113,493

Consolidated Statements of Comp

Consolidated Statements of Comprehensive Loss - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014	Jun. 30, 2015	Jun. 30, 2014
Statement of Comprehensive Income [Abstract]
Net loss	$ (41,494)	$ (52,935)	$ (15,690)	$ (49,686)
Other comprehensive income (loss):
Unrealized gain (loss) on investments	(8)	22	19	91
Foreign currency translation adjustments	848	(108)	(2,272)	(67)
Comprehensive loss	(40,654)	(53,021)	(17,943)	(49,662)
Comprehensive loss attributable to the noncontrolling interests	843	915	2,096	1,763
Comprehensive loss attributable to Intrexon	$ (39,811)	$ (52,106)	$ (15,847)	$ (47,899)

Consolidated Statements of Shar

Consolidated Statements of Shareholders' and Total Equity - 6 months ended Jun. 30, 2015 - USD ($) $ in Thousands	Total	Common Stock	Additional Paid-in Capital	Accumulated Other Comprehensive Loss	Accumulated Deficit	Total Intrexon Shareholders' Equity	Noncontrolling Interests
Balances at Dec. 31, 2014	$ 409,289		$ 843,001	$ (4)	$ (458,236)	$ 384,761	$ 24,528
Balances (in shares) at Dec. 31, 2014	100,557,932	100,557,932
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Stock-based compensation expense	$ 18,166		18,027			18,027	139
Exercises of stock options and warrants	10,382		10,382			10,382	0
Exercises of stock options and warrants, shares		768,790
Shares issued to nonemployee members of the Board of Directors	480		480			480
Shares issued to nonemployee members of the Board of Directors (in shares)		10,106
Shares issued in public offering, net of offering costs	110,041		110,041			110,041
Shares issued in public offering, net of offering costs (in shares)		4,312,500
Shares issued as consideration of license agreement	59,579		59,579			59,579
Shares issued as consideration of license agreement (in shares)		2,100,085
Shares issued in acquisitions	70,668		70,668			70,668
Shares issued in acquisitions (in shares)		1,673,230
Acquisition of noncontrolling interest	(1,566)		9,412			9,412	(10,978)
Acquisition of noncontrolling interest (in shares)		307,074
Adjustments for noncontrolling interests	250		(249)			(249)	499
Noncash dividend	(172,419)		(172,419)			(172,419)
Net loss	(15,690)				(13,566)	(13,566)	(2,124)
Other comprehensive income (loss)	(2,253)			(2,281)		(2,281)	28
Balances at Jun. 30, 2015	$ 486,927		$ 948,922	$ (2,285)	$ (471,802)	$ 474,835	$ 12,092
Balances (in shares) at Jun. 30, 2015	109,729,717	109,729,717

Consolidated Statements of Cash

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014
Cash flows from operating activities
Net loss	$ (15,690)	$ (49,686)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	7,358	3,773
Loss on disposal of property, plant and equipment	201	81
Unrealized and realized (appreciation) depreciation on equity securities	(94,845)	11,855
Amortization of discount/premium on investments	196	792
Equity in net loss of affiliates	4,136	1,891
Stock-based compensation expense	18,139	10,622
Contribution of services by shareholder	0	977
Shares issued to nonemployee members of the Board of Directors	480	486
Shares issued as consideration for license agreement	59,579	0
Provision for bad debts	984	0
Deferred income taxes	952	0
Other noncash items	542	71
Receivables:
Trade	(127,516)	(18)
Related parties	213	(3,019)
Note	(20)	0
Other	210	(121)
Inventory	(1,212)	0
Prepaid expenses and other	(1,669)	(235)
Other assets	(4,876)	71
Accounts payable	(125)	339
Accrued compensation and benefits	4,099	(1,147)
Other accrued liabilities	839	(1,422)
Deferred revenue	60,909	20,657
Related party payables	57,370	(10)
Other long term liabilities	188	(128)
Net cash used in operating activities	(29,558)	(4,171)
Cash flows from investing activities
Purchases of investments	0	(60,478)
Maturities of investments	48,000	73,747
Purchases of equity securities and warrants	(14,900)	0
Acquisitions of businesses, net of cash received	(39,501)	(4,912)
Acquisition of noncontrolling interest	(1,566)	0
Investments in affiliates	(3,334)	(1,500)
Purchases of property, plant and equipment	(6,740)	(3,751)
Proceeds from sale of property, plant and equipment	233	151
Net cash provided by (used in) investing activities	(17,808)	3,257
Cash flows from financing activities
Proceeds from issuance of shares in a private placement	0	25,000
Proceeds from issuance of shares in a public offering, net of issuance costs	110,041	0
Advances from lines of credit	11,680	0
Repayments of advances from lines of credit	(13,080)	0
Payments of capital lease obligations	(8)	(17)
Proceeds from long term debt	44	268
Payments of long term debt	(670)	0
Proceeds from stock option exercises	10,382	976
Payment of stock issuance costs	0	(256)
Net cash provided by financing activities	118,389	25,971
Effect of exchange rate changes on cash and cash equivalents	410	(61)
Net increase in cash and cash equivalents	71,433	24,996
Cash and cash equivalents
Beginning of period	27,466	49,509
End of period	98,899	74,505
Supplemental disclosure of cash flow information
Cash paid during the period for interest	99	14
Significant noncash financing and investing activities
Note receivable as consideration for upfront fee from collaborator	5,000	0
Stock received as consideration for collaboration agreements	0	5,225
Stock issued in acquisitions, net	70,668	18,880
Stock issued to acquire noncontrolling interest	9,412	0
Noncash dividend to shareholders	172,419	0
Purchases of equipment included in accounts payable and other accrued liabilities	$ 1,064	$ 0

Organization and Basis of Prese

Organization and Basis of Presentation	6 Months Ended
	Jun. 30, 2015
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Organization and Basis of Presentation	Organization and Basis of Presentation Intrexon Corporation ("Intrexon"), a Virginia corporation, forms collaborations to create biologically based products and processes using synthetic biology. Intrexon has domestic operations in California, Florida, Maryland, and Virginia, and foreign operations in Belgium and Hungary. There have been no commercialized products derived from Intrexon's collaborations to date. Trans Ova Genetics, L.C. and Subsidiaries ("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 (Note 3 ). ViaGen, L.C. ("ViaGen"), a provider of genetic preservation and cloning technologies, is a wholly owned subsidiary of Trans Ova. Exemplar Genetics, LLC ("Exemplar"), a provider of genetically engineered swine for medical and genetic research, is a wholly owned subsidiary through the combined investments of Intrexon, Trans Ova, and ViaGen. 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 (Note 3 ). Fruit Orchard Holdings, Inc. ("FOHI") is a wholly owned subsidiary of IPHI with primary operations in Washington. In June 2015, Intrexon purchased an additional 12,728,044 shares of AquaBounty Technologies, Inc. ("AquaBounty") common stock for $3,000 . As of June 30, 2015 , Intrexon owned approximately 63% of AquaBounty, a biotechnology company focused on improving productivity in commercial aquaculture. At June 30, 2015 , Intrexon owned approximately 51% of Biological & Popular Culture, Inc. ("BioPop"). Intrexon Corporation and its consolidated subsidiaries are hereinafter referred to as the "Company." These consolidated financial statements are presented in United States dollars and are prepared under accounting principles generally accepted in the United States of America ("U.S. GAAP").

Summary of Significant Accounti

Summary of Significant Accounting Policies	6 Months Ended
	Jun. 30, 2015
Accounting Policies [Abstract]
Summary of Significant Accounting Policies	Summary of Significant Accounting Policies Principles of Consolidation The accompanying consolidated financial statements reflect the operations of the Company and its subsidiaries. All intercompany accounts and transactions have been eliminated. Unaudited Financial Information The accompanying interim consolidated financial statements are unaudited and have been prepared in accordance with 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 June 30, 2015 and results of operations and cash flows for the interim periods ended June 30, 2015 and 2014 . These interim financial results are not necessarily indicative of the results to be expected for the year ending December 31, 2015 , 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, 2014 . Revenue Recognition 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 licensee 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. Generally, the terms of these agreements provide that the Company receives some or all of the following: (i) upfront payments upon consummation of the agreement, (ii) reimbursements for costs incurred by the Company for research and development and/or manufacturing efforts related to specific applications provided for in the agreement, (iii) milestone payments upon the achievement of specified development, regulatory and commercial activities, and (iv) royalties on sales of products arising from the collaboration or licensing agreement. The Company's collaboration and licensing agreements typically contain multiple elements, or deliverables, including technology licenses, research and development services, and in certain cases manufacturing services. The Company identifies the deliverables within the agreements and evaluates which deliverables represent separate units of accounting. Analyzing the agreements to identify deliverables requires the use of judgment. A deliverable is considered a separate unit of accounting when the deliverable has value to the collaborator or licensee on a standalone basis based on the consideration of the relevant facts and circumstances for each agreement. Consideration received is allocated at the inception of the agreement to all identified units of accounting based on their relative selling price. When available, the relative selling price for each deliverable is determined using vendor specific objective evidence ("VSOE") of the selling price or third-party evidence of the selling price, if VSOE does not exist. If neither VSOE nor third-party evidence of the selling price exists, the Company uses its best estimate of the selling price ("BESP") for the deliverable. The amount of allocable consideration is limited to amounts that are fixed or determinable. The consideration received is allocated among the separate units of accounting, and the applicable revenue recognition criteria are applied to each of the separate units. The Company recognizes the revenue allocated to each unit of accounting as the Company delivers the related goods or services. If the Company determines that certain deliverables should be treated as a single unit of accounting, then the revenue is recognized using either a proportional performance or straight-line method, depending on whether the Company can reasonably estimate the level of effort required to complete its performance obligations under an arrangement and whether such performance obligations are provided on a best-efforts basis. As the Company cannot reasonably estimate its performance obligations related to its collaborators or licensees, the Company recognizes revenue on a straight-line basis over the period it expects to complete its performance obligations. The terms of the Company's agreements may provide for milestone payments upon achievement of certain defined events. The Company applies the Milestone Method for recognizing milestone payments. Under the Milestone Method, the Company recognizes consideration that is contingent upon the achievement of a milestone in its entirety as revenue in the period in which the milestone is achieved only if the milestone is substantive in its entirety. A milestone is considered substantive when it meets all of the following criteria: (1) The consideration is commensurate with either the entity's performance to achieve the milestone or the enhancement of the value of the delivered item or items as a result of a specific outcome resulting from the entity's performance to achieve the milestone; (2) The consideration relates solely to past performance; and (3) The consideration is reasonable relative to all of the deliverables and payment terms within the arrangement. In the event that a milestone is not considered substantive, the Company recognizes the milestone consideration as revenue using the same method applied to upfront payments. Research and development services are a deliverable satisfied by the Company in accordance with the terms of the collaboration and licensing agreements and the Company considers these services to be inseparable from the license to the core technology; therefore, reimbursements of services performed are recognized as revenue. Because reimbursement (i) is contingent upon performance of the services by the Company, (ii) does not include a profit component, and (iii) does not relate to any future deliverable, the revenue is recognized during the period in which the related services are performed and collection of such amounts is reasonably assured. Payments received for manufacturing services will be recognized when the earnings process related to the manufactured materials has been completed. Royalties to be received under the agreements will be recognized as earned. The Company also generates revenue through sales of advanced reproductive technologies, including bovine embryos derived from the Company's embryo transfer and in vitro fertilization processes and from genetic preservation and sexed semen processes and applications of such processes to other livestock, as well as sales of livestock used in production. Revenue is recognized when (i) persuasive evidence of an arrangement exists, (ii) services have been rendered or delivery has occurred such that risk of loss has passed to the customer, (iii) the price is fixed or determinable, and (iv) collection from the customer is reasonably assured. Research and Development The Company considers that regulatory and other uncertainties inherent in the research and development of new products preclude it from capitalizing such costs. Research and development expenses include salaries and related costs of research and development personnel, and the costs of consultants, certain in-licensed technology rights, facilities, materials and supplies associated with research and development projects as well as various laboratory studies. Indirect research and development costs include depreciation, amortization and other indirect overhead expenses. The Company has research and development arrangements with third parties that include upfront and milestone payments and primarily relate to collaborations. At June 30, 2015 and December 31, 2014 , the Company had research and development commitments with third parties that had not yet been incurred totaling $6,025 and $2,183 , respectively. The commitments are generally cancellable by the Company at any time upon written notice. Cash and Cash Equivalents All highly liquid investments with an original maturity of three months or less at the date of purchase are considered to be cash equivalents. Cash balances at a limited number of banks may periodically exceed insurable amounts. The Company believes that it mitigates its risk by investing in or through major financial institutions with high quality credit ratings. Recoverability of investments is dependent upon the performance of the issuer. At June 30, 2015 and December 31, 2014 , the Company had cash equivalent investments in highly liquid money market accounts at major financial institutions of $87,472 and $16,598 , respectively. Short-term and Long-term Investments At June 30, 2015 , investments include short-term investments in U.S. government debt securities and certificates of deposit. The Company determines the appropriate classification as short-term or long-term at the time of purchase based on original maturities and management's reasonable expectation of sales and redemption. The Company reevaluates such classification at each balance sheet date. The Company's written investment policy requires investments to be explicitly rated by two of the three following rating services: Standard & Poor's, Moody's and/or Fitch and to have a minimum rating of A1, P1 and/or F-1, respectively, from those agencies. In addition, the investment policy limits the amount of credit exposure to any one issuer. Equity Securities The Company holds equity securities received and/or purchased from certain collaborators. Other than investments accounted for using the equity method, the Company elected the fair value option to account for its equity securities held in these collaborators. These equity securities are recorded at fair value at each reporting date and are subject to market price volatility. Unrealized gains and losses resulting from fair value adjustments are reported in the consolidated statement of operations. The fair value of these equity securities is subject to fluctuation in the future due to the volatility of the stock market, changes in general economic conditions and changes in the financial conditions of these collaborators. These equity securities are classified as noncurrent in the consolidated balance sheet since the Company does not intend to sell these equity securities within one year. The Company records the fair value of securities received on the date the collaboration is consummated or the milestone is achieved using the closing, quoted price of the collaborator's security on that date, assuming the transfer of consideration is considered perfunctory. If the transfer of the consideration is not considered perfunctory, the Company considers the specific facts and circumstances to determine the appropriate date on which to evaluate fair value. The Company also evaluates whether any discounts for trading restrictions or other basis for lack of marketability should be applied to the fair value of the securities at inception of the collaboration. In the event the Company concludes that a discount should be applied, the fair value of the securities is adjusted at inception of the collaboration and re-evaluated at each reporting period thereafter. Fair Value of Financial Instruments Fair value is the price that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants at the measurement date. As such, fair value is a market-based measurement that should be determined based on assumptions that market participants would use in pricing an asset and liability. As a basis for considering such assumptions, the Company uses a three-tier fair value hierarchy that prioritizes the inputs used in its fair value measurements. The hierarchy gives the highest priority to unadjusted quoted prices in active markets for identical assets or liabilities (Level 1 measurements) and the lowest priority to unobservable inputs (Level 3 measurements). The three levels of the fair value hierarchy are as follows: Level 1: Quoted prices in active markets for identical assets and liabilities; Level 2: Other than quoted prices included in Level 1 inputs that are observable for the asset or liability, either directly or indirectly; and Level 3: Unobservable inputs for the asset or liability used to measure fair value to the extent that observable inputs are not available. Concentrations of Risk Due to the Company's mix of fixed and variable rate securities holdings, the Company's investment portfolio is susceptible to changes in interest rates. As of June 30, 2015 , there were no gross unrealized losses on the Company's investments. From time to time, the Company may liquidate some or all of its investments to fund operational needs or other activities, such as capital expenditures or business acquisitions. Depending on which investments the Company liquidates to fund these activities, the Company could recognize a portion, or all, of the gross unrealized losses. Financial instruments which potentially subject the Company to concentrations of credit risk consist primarily of trade receivables. The Company controls credit risk through credit approvals, credit limits and monitoring procedures. The Company performs ongoing credit evaluations of its customers, but generally does not require collateral to support accounts receivable. Equity Method Investments The Company is party to three strategic joint ventures (Note 4 ). The Company accounts for its investments in these joint ventures using the equity method of accounting since the Company has the ability to exercise significant influence, but not control, over the operating activities of these entities. The Company determined that it has significant influence over one of its collaborators, Oragenics, Inc. ("Oragenics"), as of June 30, 2015 , and over two of its collaborators, Oragenics and ZIOPHARM Oncology, Inc. ("ZIOPHARM"), as of December 31, 2014 , based on its ownership interests, representation on the board of directors of the collaborators and other qualitative factors. The Company accounts for its investments in Oragenics and ZIOPHARM using the fair value option. The fair value of the Company's equity securities of Oragenics was $11,071 and $7,192 as of June 30, 2015 and December 31, 2014 , respectively, and is included as equity securities in the respective consolidated balance sheets. The Company's ownership percentage of Oragenics was 24.3% and 24.4% at June 30, 2015 and December 31, 2014 , respectively. Unrealized appreciation (depreciation) in the fair value of the Company's equity securities held in Oragenics was $2,943 and $(7,113) for the three months ended June 30, 2015 and 2014 , respectively, and was $3,879 and $(6,403) for the six months ended June 30, 2015 and 2014 , respectively. In June 2015, the Company distributed all of its holdings in ZIOPHARM to the Company's shareholders in the form of a special stock dividend (Note 13 ). Upon disposition, the Company realized a gain of $81,401 for the three months ended June 30, 2015. As of December 31, 2014 , the Company's ownership percentage of ZIOPHARM was 15.7% and the fair value of the Company's equity securities of ZIOPHARM was $83,099 and is included as equity securities in the December 31, 2014 consolidated balance sheet. Unrealized depreciation in the fair value of the Company's equity securities held in ZIOPHARM was $9,015 and $5,081 for the three and six months ended June 30, 2014 , respectively. Summarized unaudited financial data as of June 30, 2015 and December 31, 2014 and for the three and six months ended June 30, 2015 and 2014 , for the Company's equity method investments are as follows: June 30, 2015 December 31, 2014 Current assets $ 15,259 $ 63,627 Non-current assets 209 1,259 Total assets 15,468 64,886 Current liabilities 9,181 15,346 Non-current liabilities — 570 Total liabilities 9,181 15,916 Net assets $ 6,287 $ 48,970 Three Months Ended Six Months Ended 2015 2014 2015 2014 Revenues $ 423 $ 504 $ 1,059 $ 919 Operating expenses 22,845 16,294 106,914 29,214 Loss from operations (22,422 ) (15,790 ) (105,855 ) (28,295 ) Other 2 5,608 1 5,689 Net loss $ (22,420 ) $ (10,182 ) $ (105,854 ) $ (22,606 ) Variable Interest Entities The Company identifies entities that (i) do not have sufficient equity investment at risk to permit the entity to finance its activities without additional subordinated financial support or (ii) in which the equity investors lack an essential characteristic of a controlling financial interest as variable interest entities ("VIE" or "VIEs"). The Company performs an initial and on-going evaluation of the entities with which the Company has variable interests to determine if any of these entities are VIEs. If an entity is identified as a VIE, the Company performs an assessment to determine whether the Company has both (i) the power to direct activities that most significantly impact the VIE's economic performance and (ii) have the obligation to absorb losses from or the right to receive benefits of the VIE that could potentially be significant to the VIE. If both of these criteria are satisfied, the Company is identified as the primary beneficiary of the VIE. As of June 30, 2015 , the Company determined that Genopaver, LLC ("Genopaver"); Intrexon Energy Partners, LLC ("Intrexon Energy Partners"); OvaXon, LLC ("OvaXon"); Persea Bio, LLC ("Persea Bio"); and ZIOPHARM were VIEs. As of December 31, 2014 , the Company determined that Genopaver, Intrexon Energy Partners, OvaXon, and Persea Bio were 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 June 30, 2015 was $557 , which represents the Company's maximum risk of loss related to the identified VIEs. As of December 31, 2014 , the Company did not hold any investment balances in the identified VIEs and therefore had no risk of loss as of that date. Trade Receivables Trade receivables consist of credit extended to the Company's customers and collaborators in the normal course of business and are reported net of an allowance for doubtful accounts. The Company reviews its customer accounts on a periodic basis and records bad debt expense for specific amounts the Company evaluates as uncollectible. Past due status is determined based upon contractual terms. Amounts are written off at the point when collection attempts have been exhausted. Management estimates uncollectible amounts considering such factors as current economic conditions and historic and anticipated customer performance. This estimate can fluctuate due to changes in economic, industry or specific customer conditions which may require adjustment to the allowance recorded by the Company. Management has included amounts believed to be uncollectible in the allowance for doubtful accounts. The following table shows the activity in the allowance for doubtful accounts for the six months ended June 30, 2015 : Six Months Ended June 30, 2015 Beginning balance $ 565 Charged to operating expenses 984 Write offs of accounts receivable (112 ) Ending balance $ 1,437 Inventory The Company's inventory primarily includes adult female cows which are used in certain production processes and are recorded at acquisition cost using the first-in, first-out method or at market, whichever is lower. Work-in-process inventory includes allocations of production costs and facility costs for products currently in production and is recorded at the lower of cost or market. Significant declines in the price of cows could result in unfavorable adjustments to inventory balances. Property, Plant and Equipment Property, plant and equipment are stated at cost, less accumulated depreciation and amortization. Major additions or betterments are capitalized and repairs and maintenance are generally expensed as incurred. Depreciation and amortization is calculated using the straight-line method over the estimated useful lives of the assets. The estimated useful lives of these assets are as follows: Years Land improvements 4–15 Buildings and building improvements 3–23 Furniture and fixtures 1–7 Equipment 1–10 Computer hardware and software 1–7 Leasehold improvements are amortized over the shorter of the useful life of the asset or the applicable lease term, generally one to fourteen years . Goodwill Goodwill represents the future economic benefits arising from other assets acquired in a business combination that are not individually identified and separately recognized (Note 3 ). Goodwill is reviewed for impairment at least annually. The Company performs a qualitative assessment to determine whether it is more-likely-than-not that the fair value of a reporting unit is less than its carrying amount prior to performing the two-step goodwill impairment test. If this is the case, the two-step goodwill impairment test is required. If it is more-likely-than-not that the fair value of a reporting unit is greater than the carrying amount, the two-step goodwill impairment test is not required. If the two-step goodwill impairment test is required, first, the fair value of the reporting unit is compared with its carrying amount (including goodwill). If the fair value of the reporting unit is less than its carrying amount, an indication of goodwill impairment exists for the reporting unit and the entity must perform step two of the impairment test. Under step two, an impairment loss is recognized for any excess of the carrying amount of the reporting unit's goodwill over the implied fair value of that goodwill. The implied fair value of goodwill is determined by allocating the fair value of the reporting unit in a manner similar to a purchase price allocation and the residual fair value after this allocation is the implied fair value of the reporting unit goodwill. Fair value of the reporting unit is determined using a discounted cash flow analysis. If the fair value of the reporting unit exceeds its carrying amount, step two does not need to be performed. The Company performs its annual impairment review of goodwill in the fourth quarter, or sooner if a triggering event occurs prior to the annual impairment review. Intangible Assets Intangible assets subject to amortization consist of patents, related technologies and know-how; customer relationships; trademarks; and a covenant not to compete acquired as a result of mergers and acquisitions (Note 3 ). These intangible assets are subject to amortization, were recorded at fair value at the date of acquisition and are stated net of accumulated amortization. Indefinite-lived intangible assets consist of in-process research and development acquired in mergers and acquisitions (Note 3 ) and were recorded at fair value at the dates of the respective acquisitions. The Company amortizes long-lived intangible assets to reflect the pattern in which the economic benefits of the intangible assets are expected to be realized. The intangible assets are amortized over their remaining estimated useful lives, ranging from two to fourteen years for the patents, related technologies and know-how; customer relationships; trademarks; and the covenant not to compete. Impairment of Long-Lived Assets Long-lived assets to be held and used, including property, plant and equipment and intangible assets subject to amortization, are reviewed for impairment whenever events or changes in circumstances indicate that the carrying amount of the assets may not be recoverable. Conditions that would necessitate an impairment assessment include a significant decline in the observable market value of an asset, a significant change in the extent or manner in which an asset is used, or a significant adverse change that would indicate that the carrying amount of an asset or group of assets is not recoverable. Indefinite-lived intangible assets, including in-process research and development, are tested for impairment annually, or more frequently if events or circumstances between annual tests indicate that the asset may be impaired. Impairment losses on indefinite-lived intangible assets are recognized based solely on a comparison of their fair value to carrying value, without consideration of any recoverability test. The Company monitors the progression of its in-process research and development, as the likelihood of success is contingent upon commercial development or regulatory approval. Foreign Currency Translation The assets and liabilities of foreign subsidiaries, where the local currency is the functional currency, are translated from their respective functional currencies into United States dollars at the exchange rates in effect at the balance sheet date, with resulting foreign currency translation adjustments recorded in the consolidated statement of comprehensive income. Revenue and expense amounts are translated at average rates during the period. Income Taxes Income taxes are accounted for under the asset and liability method. Deferred tax assets and liabilities are recognized for the future tax consequences attributable to both differences between the financial statement carrying amounts of existing assets and liabilities and their respective tax bases as well as operating loss and tax credit carryforwards. Deferred tax assets and liabilities are measured using enacted tax rates expected to apply to taxable income in the years in which those temporary differences are expected to be recovered or settled. The effect on deferred tax assets and liabilities of a change in tax rates is recognized in income in the period that includes the enactment date of the change. Valuation allowances are established when necessary to reduce deferred tax assets to the amount expected to be realized. The Company identifies any uncertain income tax positions and recognizes the effect of income tax positions only if those positions are more likely than not of being sustained. Recognized income tax positions are measured at the largest amount that is greater than 50% likely of being realized. Changes in recognition or measurement are reflected in the period in which the change in judgment occurs. The Company records interest, if any, related to unrecognized tax benefits as a component of interest expense. Penalties, if any, are recorded in selling, general and administrative expenses. Net Loss per Share Basic net loss per share is calculated by dividing net loss attributable to common shareholders by the weighted average shares outstanding during the period, without consideration of common stock equivalents. Diluted net loss per share is calculated by adjusting weighted average shares outstanding for the dilutive effect of common stock equivalents outstanding for the period, using the treasury-stock method. For purposes of the diluted net loss per share calculation, stock options and warrants are considered to be common stock equivalents but are excluded from the calculation of diluted net loss per share because their effect would be anti-dilutive and, therefore, basic and diluted net loss per share were the same for all periods presented.. Segment Information The Company has determined that it operates in one segment. The Company applies its technologies to create products and services which may be either sold directly to customers or developed through collaboration with third parties. As of June 30, 2015 and December 31, 2014 , the Company had $116,523 and $17,100 , respectively, of long-lived assets in foreign countries. For the three and six months ended June 30, 2015 , the Company recognized $925 and $2,263 of revenues derived in foreign countries, respectively. There were $369 of revenues derived in foreign countries for the three and six months ended June 30, 2014 . Recently Issued Accounting Pronouncements In July 2015, the Financial Accounting Standards Board ("FASB") issued Accounting Standards Update ("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 guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2016, and is effective for the Company for the year ending December 31, 2017. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. In February 2015, the FASB issued ASU 2015-02, Consolidation (Topic 810) - Amendments to the Consolidation Analysis ("ASU 2015-02"). The provisions of ASU 2015-02 provide guidance which changes the analysis that a reporting entity must perform to determine whether it should consolidate certain types of legal entities. This guidance is effective for annual periods and interim periods within those annual periods, beginning after December 15, 2015, and is effective for the Company for the year ending December 31, 2016, with early adoption permitted. 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 2014-9, Revenue from Contracts with Customers ("ASU 2014-9"). The FASB issued ASU 2014-9 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 July 2015, the FASB voted to defer the effective date 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. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. Reclassifications Certain insignificant reclassifications have been made to the prior interim period consolidated financial statements to conform to the current interim period presentation. 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.

Mergers and Acquisitions

Mergers and Acquisitions	6 Months Ended
	Jun. 30, 2015
Business Combinations [Abstract]
Mergers and Acquisitions	Mergers and Acquisitions Okanagan Acquisition In April 2015, pursuant to a Stock Purchase Agreement (the “Okanagan Purchase Agreement”), the Company acquired 100% of the outstanding shares of Okanagan, the pioneering agricultural company behind the world's first non-browning apple. In addition to supporting Okanagan's further commercialization and exploitation of its apple products, the Company expects to utilize its proprietary technologies to assist Okanagan in the development of further novel beneficial plant traits. Pursuant to the Okanagan Purchase Agreement, the former shareholders of Okanagan received an aggregate of 707,853 shares of the Company’s common stock, and $10,000 cash in exchange for all shares in Okanagan. The results of Okanagan's operations subsequent to the acquisition date have been included in the consolidated financial statements. The fair value of the total consideration transferred was $40,933 . The acquisition date fair value of each class of consideration transferred is presented below: Cash $ 10,000 Common shares 30,933 $ 40,933 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 as of the date of the acquisition. The preliminary estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown below: Cash $ 58 Trade receivables 16 Other receivables 49 Property, plant, and equipment 32 Intangible assets 33,800 Total assets acquired 33,955 Accounts payable 181 Deferred revenue 181 Deferred tax liability 8,145 Total liabilities assumed 8,507 Net assets acquired 25,448 Goodwill 15,485 Total consideration $ 40,933 The fair value of assets acquired and liabilities assumed at the acquisition date are considered preliminary and are subject to revision when the valuation of intangible assets is finalized. The acquired intangible assets primarily include developed technology, patents and know-how and the fair values of the acquired assets were determined using the with and without method, which is a variation of the income approach that utilizes estimated cash flows with all assets in place at the valuation date and estimated cash flows with all assets in place except the intangible assets at the valuation date. The intangible assets are being amortized over a useful life of fourteen years . Goodwill, which is not expected to be deductible for tax purposes, represents potential future applications of Okanagan's technology to other fruits, including additional apple varietals, and anticipated buyer-specific synergies arising from the combination of the Company's and Okanagan's technologies. As of June 30, 2015 the Company had incurred $341 of acquisition-related costs, of which $104 and $267 is included in selling, general and administrative expenses in the accompanying consolidated statements of operations for the three and six months ended June 30, 2015 , respectively. ActoGeniX Acquisition In February 2015, the Company acquired 100% of the membership interests of ActoGeniX NV ("ActoGeniX"), a European clinical stage biopharmaceutical company, pursuant to a Stock Purchase Agreement (the "ActoGeniX Purchase Agreement"). ActoGeniX's platform technology complements our broad collection of technologies available for current and future collaborators. Pursuant to the ActoGeniX Purchase Agreement, the former members of ActoGeniX received an aggregate of 965,377 shares of the Company's common stock and $32,739 in cash in exchange for all membership interests of ActoGeniX. The results of ActoGeniX's operations subsequent to the acquisition date have been included in the consolidated financial statements. The fair value of the total consideration transferred was $72,474 . The acquisition date fair value of each class of consideration transferred is presented below: Cash $ 32,739 Common shares 39,735 $ 72,474 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 as of the date of the acquisition. The estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown below along with subsequent adjustments during the measurement period to the fair value of assets acquired and liabilities assumed. The adjustments resulted from the difference between estimated and actual accrued expenses. Initial Estimated Fair Value Adjustments Adjusted Fair Value Cash $ 3,180 $ — $ 3,180 Other receivables 305 — 305 Prepaid expenses and other 31 — 31 Property, plant and equipment 209 — 209 Intangible assets 68,100 — 68,100 Other assets 23 — 23 Total assets acquired 71,848 — 71,848 Accounts payable 230 — 230 Accrued compensation and benefits 624 (428 ) 196 Other accrued liabilities 307 (54 ) 253 Deferred revenue 732 — 732 Deferred tax liability 612 — 612 Total liabilities assumed 2,505 (482 ) 2,023 Net assets acquired 69,343 482 69,825 Goodwill 3,131 (482 ) 2,649 Total consideration $ 72,474 $ — $ 72,474 The acquired intangible assets primarily include in-process research and development, and the fair values of the acquired assets were determined using the multi-period excess earnings and with-and-without methods, which are both variations of the income approach that convert future cash flows to single discounted present value amounts. The in-process research and development is currently an indefinite-lived intangible asset. Goodwill, which is not expected to be deductible for tax purposes, represents the assembled workforce and anticipated buyer-specific synergies arising from the combination of the Company's and ActoGeniX's technologies. As of June 30, 2015 , the Company had incurred $418 of acquisition-related costs, of which $381 is included in selling, general and administrative expenses in the accompanying consolidated statements of operations for the six months ended June 30, 2015 . Trans Ova Acquisition In August 2014, the Company acquired 100% of the membership interests of Trans Ova, a provider of bovine reproductive technologies, pursuant to an Amended and Restated Membership Interest Purchase Agreement (the "Trans Ova Purchase Agreement"). The Company and Trans Ova intend to build upon Trans Ova's current platform with new capabilities with a goal of achieving higher levels of delivered value to dairy and beef cattle producers. Pursuant to the Trans Ova Purchase Agreement, the former members of Trans Ova received an aggregate of 1,444,388 shares of the Company's common stock and $63,625 in cash, and will receive deferred cash consideration valued at $20,115 in exchange for all membership interests of Trans Ova. The deferred cash consideration is payable in three equal installments upon the first, second, and third anniversaries of the transaction date. The Trans Ova Purchase Agreement also provides for payment to the former members of Trans Ova a portion of certain cash proceeds in the event there is an award under certain litigation matters pending as of the transaction date to which Trans Ova is a party. The results of Trans Ova's operations subsequent to the acquisition date have been included in the consolidated financial statements, including revenues of $27,534 and $46,460 , and net income of $4,422 and $4,185 for the three and six months ended June 30, 2015 , respectively. The fair value of the total consideration transferred, including the noncontrolling interest in a majority-owned subsidiary of Trans Ova, was $127,875 . The acquisition date fair value of each class of consideration transferred and noncontrolling interest is presented below: Cash $ 63,625 Common shares 32,802 Deferred cash consideration 20,115 Total consideration transferred 116,542 Fair value of noncontrolling interest 11,333 Total $ 127,875 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 as of the date of the acquisition. The estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown in the table below. Cash $ 960 Trade receivables 18,693 Related party receivables 1,219 Inventory 18,476 Prepaid expenses and other 590 Property, plant and equipment 21,164 Intangible assets 23,700 Other assets 147 Total assets acquired 84,949 Accounts payable 3,317 Accrued compensation and benefits 913 Other accrued liabilities 271 Deferred revenue 4,458 Lines of credit 4,091 Related party payables 1,246 Long term debt 9,090 Total liabilities assumed 23,386 Net assets acquired 61,563 Goodwill 66,312 Total consideration and fair value of noncontrolling interest $ 127,875 The fair value of acquired inventory was determined using the cost approach, which establishes value based on the cost of reproducing or replacing the asset. The fair value of acquired property, plant and equipment was determined using the cost approach and the market approach. The market approach uses prices and other relevant information generated by market transactions involving identical or comparable assets. The acquired intangible assets include various developed technologies and know-how, customer relationships, and trademarks, and the fair values of these assets were determined using the relief-from-royalty, multi-period excess earnings, and with-and-without methods, which are all variations of the income approach. The acquired intangible assets are being amortized over useful lives ranging from three to nine years. Goodwill, which will be deductible for tax purposes, represents the assembled workforce, potential future expansion of Trans Ova business lines and anticipated buyer-specific synergies arising from the combination of the Company's and Trans Ova's technologies. In conjunction with a prior transaction associated with Trans Ova's subsidiary, ViaGen, in September 2012, the Company may be obligated to make certain future contingent payments to the former equity holders of ViaGen, up to a total of $6,000 if certain revenue targets, as defined in the share purchase agreement, are met. The Company does not expect these revenue targets to be met and accordingly has assigned no value to this liability. The Company incurred $713 of costs primarily for legal and due diligence services related to this acquisition, which were all recorded in 2014, of which $312 is included in selling, general and administrative expenses in the accompanying consolidated statements of operations for the three and six months ended June 30, 2014 . In February 2015, the Company acquired, through an exchange offer, the remaining outstanding membership interests of Trans Ova's majority-owned subsidiary, Exemplar, for $1,566 in cash and 307,074 shares of Company common stock. Medistem Acquisition In March 2014, the Company acquired 100% of the outstanding common stock and securities convertible into common stock of Medistem, Inc. ("Medistem"), an entity engaged in the development of Endometrial Regenerative Cells ("ERCs"), for a combination of cash and Company common stock. The acquisition allows the Company to employ its synthetic biology platforms to engineer a diverse array of cell-based therapeutic candidates using Medistem's multipotent ERCs. Pursuant to the terms of the merger agreement, Medistem equity holders received 714,144 shares of the Company's common stock and $4,920 in cash in exchange for the outstanding Medistem common stock and securities convertible into common stock. Additionally, Medistem had issued the Company two promissory notes in the amount of $707 , including accrued interest, both of which were settled upon closing of the merger. Certain members of Medistem's management surrendered a total of 17,695 shares of their merger consideration to reimburse the Company for required payroll tax withholdings. The results of Medistem's operations subsequent to the acquisition date have been included in the consolidated financial statements. The fair value of the total consideration transferred was $24,995 . The acquisition date fair value of each class of consideration transferred is presented below: Cash $ 4,920 Common shares 19,368 Settlement of promissory notes 707 $ 24,995 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 as of the date of the acquisition. The estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown in the table below. Cash $ 8 Intangible assets 4,824 Total assets acquired 4,832 Accounts payable 644 Accrued compensation and benefits 67 Other accrued expenses 50 Total liabilities assumed 761 Net assets acquired 4,071 Goodwill 20,924 Total consideration $ 24,995 The fair value of acquired intangible assets was determined using the cost approach. The acquired intangible assets consist of in-process research and development, which is an indefinite-lived intangible asset. The goodwill consists of buyer-specific synergies between the Company's and Medistem's technologies present. The goodwill is not expected to be deductible for tax purposes. The Company incurred $680 of acquisition-related costs, all of which was recorded in 2014 and $19 and $310 is included in selling, general and administrative expenses in the accompanying consolidated statements of operations for the three and six months ended June 30, 2014 , respectively. Unaudited Condensed Pro Forma Financial Information The results of operations of the 2015 acquisitions discussed above are included in the consolidated statements of operations beginning on the day after the acquisition date. The following unaudited condensed pro forma financial information for the three and six months ended June 30, 2015 and 2014 is presented as if the acquisitions had been consummated on January 1, 2014: Three Months Ended Six Months Ended 2015 2014 2015 2014 Pro forma Revenues $ 44,891 $ 11,851 $ 78,929 $ 19,759 Loss before income taxes (40,734 ) (56,161 ) (18,411 ) (55,295 ) Net loss (41,668 ) (55,673 ) (19,891 ) (55,067 ) Net loss attributable to the noncontrolling interests 831 892 2,124 1,758 Net loss attributable to Intrexon (40,837 ) (54,781 ) (17,767 ) (53,309 ) The results of operations of the 2014 acquisitions discussed above are included in the consolidated statements of operations beginning on the day after their respective acquisition dates. The following unaudited condensed pro forma financial information for the three and six months ended June 30, 2014 is presented as if the acquisitions had been consummated on January 1, 2013: Three Months Ended Six Months Ended Pro forma Revenues $ 34,911 $ 57,122 Loss before income taxes (48,265 ) (46,953 ) Net loss (47,982 ) (46,976 ) Net loss attributable to the noncontrolling interests 1,085 2,031 Net loss attributable to Intrexon (46,897 ) (44,945 )

Investments in Joint Ventures

Investments in Joint Ventures	6 Months Ended
	Jun. 30, 2015
Equity Method Investments and Joint Ventures [Abstract]
Investments in Joint Ventures	Investments in Joint Ventures Intrexon Energy Partners In March 2014, the Company and certain investors (the "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, 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 our 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 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 additional capital contributions of up to $25,000 , and the 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 June 30, 2015 , the Company's remaining commitment was $21,791 . The Company and the Investors have the right, but not the obligation, to make additional capital contributions above these limits when and if solicited by the Intrexon Energy Partners Board. Intrexon Energy Partners is governed by a board of managers which has five members. Two members of the Intrexon Energy Partners Board are designated by the Company and three members of the Intrexon Energy Partners Board are designated by a majority of the Investors. See further discussion of the ECC at Note 5 . See discussion of a concurrent private placement securities purchase made by the Investors at Note 13 . The Company's investment in Intrexon Energy Partners was $(1,364) and $(740) as of June 30, 2015 and December 31, 2014 , respectively, and is included in other accrued liabilities 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 have the right, but not the obligation, to make additional capital contributions to OvaXon subject to the OvaXon LLC Agreement. Contemporaneously with the formation of the joint venture, the Company entered into an ECC with OvaXon (see Note 5 ). The Company's investment in OvaXon was $557 and $(83) as of June 30, 2015 and December 31, 2014 , respectively, and is included in investments in affiliates and other accrued liabilities, respectively, in the accompanying consolidated balance sheets. 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 have committed to making additional capital contributions to S & I Ophthalmic subject to certain limits defined in the 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. 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. Contemporaneously with the formation of the joint venture, the Company entered into an ECC with S & I Ophthalmic (see Note 5 ). The Company's investment in S & I Ophthalmic was $2,403 and $3,220 as of June 30, 2015 and December 31, 2014 , respectively, and is included in investments in affiliates in the accompanying consolidated balance sheets.

Collaboration and Licensing Rev

Collaboration and Licensing Revenue	6 Months Ended
	Jun. 30, 2015
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Collaboration and Licensing Revenue	Collaboration and Licensing Revenue The Company's collaborations and licensing agreements provide for multiple deliverables to be delivered by the Company and typically include a license to the Company's technology platforms, participation in collaboration committees, performance of certain research and development services and may include obligations for certain manufacturing services. The Company typically groups these deliverables into two units of accounting based on the nature of the deliverables and the separation criteria. The first deliverable ("Unit of Accounting 1") includes the license to the Company's technology platform, the Company's participation on the collaboration committees and any research and development services associated with its technology platforms. The deliverables for Unit of Accounting 1 are combined because they cannot be individually separated. If applicable, the second deliverable ("Unit of Accounting 2") includes manufacturing services to be provided for any Company materials in an approved product. These services have standalone value and are contingent due to uncertainties on whether an approved product will ever be developed thereby requiring manufacture by the Company at that time. All upfront consideration is allocated to Unit of Accounting 1. Unit of Accounting 2 is determined to be a contingent deliverable at the inception of the collaboration due to the uncertainties surrounding whether an approved product will ever be developed and require manufacturing by the Company. The upfront consideration allocated to Unit of Accounting 1 is 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 when the services are performed and collection is reasonably assured. At the inception of each collaboration and licensing agreement, the Company determines whether any milestone payments are substantive and can be recognized when earned. The milestone payments are typically not considered substantive. Royalties related to product sales will be recognized when earned since payments relate directly to products that have been fully developed and for which the Company has satisfied all of its obligations. The Company determines whether collaborations and licensing agreements are individually significant for disclosure based on a number of factors, including total revenue recorded by the Company pursuant to the collaboration or licensing agreement, collaborators or licensees either consolidated or accounted for using the equity method, or other qualitative factors. Collaboration and licensing revenues generated from consolidated subsidiaries are eliminated in consolidation. The following table summarizes the amounts recorded in the consolidated statements of operations for each significant collaboration and licensing agreement for the three and six months ended June 30, 2015 and 2014 . Three Months Ended June 30, 2015 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 644 $ 4,606 $ 5,250 Oragenics, Inc. 307 68 375 Fibrocell Science, Inc. 448 1,470 1,918 Genopaver, LLC 68 867 935 S & I Ophthalmic, LLC — 890 890 OvaXon, LLC — 662 662 Intrexon Energy Partners, LLC 625 2,731 3,356 Persea Bio, LLC 125 141 266 Ares Trading S.A. 739 — 739 Other 747 2,043 2,790 Total $ 3,703 $ 13,478 $ 17,181 Three Months Ended June 30, 2014 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 644 $ 3,697 $ 4,341 Oragenics, Inc. 261 52 313 Fibrocell Science, Inc. 448 883 1,331 Genopaver, LLC 68 423 491 S & I Ophthalmic, LLC — 607 607 OvaXon, LLC — 579 579 Intrexon Energy Partners, LLC 625 1,210 1,835 Other 471 1,796 2,267 Total $ 2,517 $ 9,247 $ 11,764 Six Months Ended June 30, 2015 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 1,288 $ 7,763 $ 9,051 Oragenics, Inc. 569 76 645 Fibrocell Science, Inc. 896 3,183 4,079 Genopaver, LLC 137 1,467 1,604 S & I Ophthalmic, LLC — 1,645 1,645 OvaXon, LLC — 1,306 1,306 Intrexon Energy Partners, LLC 1,250 4,916 6,166 Persea Bio, LLC 250 256 506 Ares Trading S.A. 739 — 739 Other 1,605 4,618 6,223 Total $ 6,734 $ 25,230 $ 31,964 Six Months Ended June 30, 2014 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 1,288 $ 5,733 $ 7,021 Oragenics, Inc. 523 585 1,108 Fibrocell Science, Inc. 896 1,745 2,641 Genopaver, LLC 137 844 981 S & I Ophthalmic, LLC — 1,486 1,486 OvaXon, LLC — 748 748 Intrexon Energy Partners, LLC 625 1,210 1,835 Other 930 2,851 3,781 Total $ 4,399 $ 15,202 $ 19,601 The following is a summary of the terms of the Company's significant collaborations and licensing agreements. Merck Licensing Agreement In March 2015, the Company signed a worldwide License and Collaboration Agreement ("Merck Agreement") with Ares Trading S.A. ("Ares Trading"), a subsidiary of the biopharmaceutical business of Merck KGaA, and ZIOPHARM through which the parties established a collaboration for the research and development and commercialization of certain products for the prophylactic, therapeutic, palliative or diagnostic use for cancer in humans. Pursuant to the Merck Agreement, the Company is entitled to receive an upfront fee of $115,000 which is included in trade receivables on the consolidated balance sheet as of June 30, 2015 . Within 30 days of receipt of the upfront fee, the Company must pay 50% to ZIOPHARM and, accordingly, has included $57,500 as a related party payable on the consolidated balance sheet as of June 30, 2015 . Upon the selection of the first two targets by Ares Trading, the Company is entitled to receive $10,000 payable in equal quarterly installments over two years, of which $5,000 is included in trade receivables and $5,000 in other long term assets on the consolidated balance sheet as of June 30, 2015 . The Company will be entitled to receive a further $5,000 for each additional target selected by Ares Trading. The Company is also entitled to up to $413,000 of potential payments for substantive and non-substantive development and commercial milestones for each product, and royalties ranging from the lower-single digits to the low-teens of the net sales derived from the sale of products developed under the Merck Agreement. The Company may also receive up to $50,000 of further cash fees upon certain technical milestones as provided for in the agreement. The term of the Merck Agreement commenced in May 2015 and may be terminated by either party in the event of a material breach as defined in the agreement and may be terminated voluntarily by Ares Trading upon 90 days written notice to the Company. The Company will pay to ZIOPHARM 50% of all payments received for upfront fees, milestones, and royalties under the Merck Agreement. The remaining balance of deferred revenue associated with the upfront payment was $56,761 at June 30, 2015 . ZIOPHARM Collaboration In January 2011, the Company entered into an ECC with ZIOPHARM, a related party. Pursuant to the ECC, ZIOPHARM received a license to the Company's technology platform within the field of oncology as defined more specifically in the agreement. Upon execution of the ECC, the Company received 3,636,926 shares of ZIOPHARM's common stock valued at $17,457 as upfront consideration. In addition to the deliverables discussed above, the Company transferred two clinical product candidates to ZIOPHARM that resulted in a separate unit of accounting for which $1,115 of the upfront consideration was allocated and recognized as collaboration revenue in 2011. The remaining $16,342 of upfront consideration was allocated to Unit of Accounting 1 discussed above. The Company is entitled to additional shares of common stock representing the lesser of (i) the original shares received or (ii) the number of shares representing 7.495% of ZIOPHARM's outstanding shares at the date of the dosing of the first patient in a Phase II clinical trial of a product candidate created, produced or developed by ZIOPHARM using the Company's technology ("ZIOPHARM Milestone"). In October 2012, the ZIOPHARM Milestone was achieved and the Company received 3,636,926 shares of ZIOPHARM's common stock valued at $18,330 as milestone consideration. Since the ZIOPHARM Milestone was not substantive, the Company allocated the ZIOPHARM Milestone to the applicable units of accounting and is recognizing it in a manner similar to these units of accounting. The remaining balance of deferred revenue associated with upfront and milestone payments was $21,905 and $23,193 at June 30, 2015 and December 31, 2014 , respectively. The Company receives reimbursement payments for research and development services provided and manufacturing services for Company materials provided to ZIOPHARM during the ECC. Subject to certain expense allocations, ZIOPHARM will pay the Company 50% of the quarterly net profits derived from the sale of products developed from the ECC, as defined in the agreement. ZIOPHARM is responsible for conducting preclinical and clinical development of product candidates, as well as for other aspects of commercialization or manufacturing of product candidates. The term of the ECC commenced in January 2011 and continues until terminated pursuant to the ECC agreement. The ECC may be terminated by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by ZIOPHARM upon 90 days written notice to the Company. In March 2015, in conjunction with the Merck Agreement, the Company and ZIOPHARM amended their existing ECC. The amendment modifies the scope of the ECC in connection with the Merck Agreement and provides that the Company will pay to ZIOPHARM 50% of all payments received for upfront fees, milestones and royalties under the Merck Agreement. See Notes 13 and 17 for further discussion related to ZIOPHARM. Oragenics Collaborations In June 2012, the Company entered into an ECC with Oragenics, a publicly traded company focused on becoming the world leader in novel antibiotics against infectious disease and probiotics for oral health for humans and pets and a related party. Pursuant to the ECC, at the transaction effective date, Oragenics received a license to the Company's technology platform within the field of lantibiotics for the treatment of infectious diseases in humans and companion animals as defined more specifically in the agreement. Upon execution of the ECC, the Company received a technology access fee of 4,392,425 shares of Oragenics' common stock valued at $6,588 as upfront consideration. The Company is entitled to receive additional shares of common stock, or at Oragenics' option, receive a cash payment based upon the fair market value of the shares, upon the separate achievement of certain regulatory milestones of the first product candidate developed from the ECC ("Oragenics ECC 1 Milestones"). The Oragenics ECC 1 Milestones include: (i) 1% of Oragenics' outstanding shares as defined in the ECC agreement at the date of the filing of the first Investigative New Drug Application with the U.S. FDA for a product candidate created, produced or developed using the Company's technology ("Oragenics ECC 1 Product"); (ii) 1.5% of Oragenics' outstanding shares as defined in the ECC agreement at the date of the dosing of the first patient in the first Phase II clinical trial of an Oragenics ECC 1 Product; (iii) 2% of Oragenics' outstanding shares as defined in the ECC agreement at the date of the dosing of the first patient in the first Phase III clinical trial of an Oragenics ECC 1 Product; (iv) 2.5% of Oragenics' outstanding shares as defined in the ECC agreement at the date of the first New Drug Application or Biologics License Application with the U.S. FDA for an Oragenics ECC 1 Product, or alternatively the first equivalent regulatory filing with a foreign agency; and (v) 3% of Oragenics' outstanding shares as defined in the ECC agreement at the date of the granting of the first regulatory approval of an Oragenics ECC 1 Product. The remaining balance of deferred revenue associated with the upfront payment was $4,896 and $5,171 at June 30, 2015 and December 31, 2014 , respectively. The Company receives reimbursement payments for research and development services provided pursuant to the agreement during the ECC and manufacturing services for Company materials provided to Oragenics during the ECC. Oragenics will pay the Company 25% of the quarterly profits derived from the sale of products developed from the ECC, as defined in the agreement. Oragenics is responsible for funding the further development of lantibiotics toward the goal of commercialization, conducting preclinical and clinical development of product candidates, as well as for other aspects of commercialization or manufacturing of the product candidates. The term of the ECC commenced in June 2012 and continues until terminated pursuant to the ECC agreement. The ECC may be terminated by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by Oragenics upon 90 days written notice to the Company. In September 2013, the Company entered into its second ECC with Oragenics ("ECC 2"). Pursuant to ECC 2, at the transaction effective date, Oragenics received a license to the Company's technology platform to develop and commercialize probiotics, specifically the direct administration to humans of genetically modified probiotics for the treatment of diseases of the oral cavity, throat, sinus and esophagus as defined more specifically in the agreement. Upon execution of ECC 2, the Company received a technology access fee of 1,348,000 shares of Oragenics' common stock valued at $3,503 and a $1,956 convertible promissory note maturing on or before December 31, 2013 as upfront consideration. Prior to the maturity date, Oragenics had the right to convert the promissory note into shares of Oragenics' common stock subject to its shareholders' approval. The conversion price is equal to the closing price of Oragenics' common stock on the last trading day immediately prior to the date of conversion. In December 2013, Oragenics converted the promissory note into 698,241 shares of Oragenics' common stock. The Company is entitled to receive additional shares of common stock, or at Oragenics' option, receive a cash payment based upon the fair market value of the shares, upon the first instance of attainment of certain commercialization milestones of a product candidate developed from ECC 2 ("Oragenics ECC 2 Milestones"). The Oragenics ECC 2 Milestones include: (i) $2,000 within thirty days of the first instance of the achievement of the first dosing of a patient in a phase II clinical trial for an Oragenics product developed from ECC 2 ("Oragenics ECC 2 Product"); (ii) $5,000 within thirty days of the first instance of the achievement of the meeting of the primary endpoint in a phase III clinical trial for an Oragenics ECC 2 Product; and (iii) $10,000 within thirty days of the first instance of the achievement of the first to occur of (a) the first commercial sale of an Oragenics ECC 2 Product anywhere in the world, or (b) the regulatory approval for an Oragenics ECC 2 Product. The remaining balance of deferred revenue associated with the upfront payment was $4,591 and $4,839 at June 30, 2015 and December 31, 2014 , respectively. The Company receives reimbursement payments for research and development services provided pursuant to the agreement during the ECC and manufacturing services for Company materials provided to Oragenics during ECC 2. Oragenics will pay the Company 10% of the net sales derived from the sale of products developed from ECC 2, as defined in the agreement. Oragenics is responsible for funding the further development of probiotics toward the goal of commercialization, conducting preclinical and clinical development of product candidates, as well as for other aspects of commercialization or manufacturing of the product candidates. The term of ECC 2 commenced in September 2013 and continues until terminated pursuant to ECC 2. ECC 2 may be terminated by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by Oragenics upon 90 days written notice to the Company. In June 2015, the Company entered into its third ECC with Oragenics ("ECC 3"). Pursuant to ECC 3, at the transaction effective date, Oragenics received a license to the Company's technology platform within the field of biotherapeutics for use in certain treatments of oral mucositis and other diseases and conditions of the oral cavity, throat, and esophagus. Upon execution of ECC 3, the Company received a technology access fee of a $5,000 convertible promissory note, which approximates fair value, maturing on or before December 31, 2015 as upfront consideration. Prior to the maturity date, Oragenics has the right to convert the promissory note into shares of Oragenics' common stock, subject to its shareholders' approval. The Company is also entitled to up to $22,000 of potential payments for development and commercial milestones for each Oragenics product developed from ECC 3 and up to $10,000 of potential one-time payments for certain regulatory milestones under ECC 3. The remaining balance of deferred revenue associated with the upfront payment was $4,954 at June 30, 2015 . The Company receives reimbursement payments for research and development services provided pursuant to the agreement during the ECC and manufacturing services for Company materials provided to Oragenics during ECC 3. Oragenics will pay the Company a royalty as a percentage in the low-teens of net sales derived from the sale of products developed from ECC 3, as defined in the agreement. Oragenics is responsible for funding the further development of ECC 3 products towards the goal of commercialization, conducting preclinical and clinical development of product candidates, as well as for other aspects of commercialization or manufacturing of the product candidates. The term of ECC 3 commenced in June 2015 and may be terminated by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by Oragenics upon 90 days written notice to the Company. See Note 17 for a discussion of additional arrangements with Oragenics. Fibrocell Science, Inc. Collaboration In October 2012, the Company entered into an ECC with Fibrocell Science, Inc. ("Fibrocell"), a publicly traded, autologous cellular therapeutic company focused on the development of innovative products for aesthetic, medical and scientific applications and a related party. Pursuant to the ECC, at the transaction effective date, Fibrocell received a license to the Company's technology platform to develop and commercialize genetically modified and non-genetically modified autologous fibroblasts and autologous dermal cells in the United States of America. Upon execution of the ECC, the Company received a technology access fee of 1,317,520 shares of Fibrocell's common stock valued at $7,576 as upfront consideration. The number of shares received reflects a 1-for-25 reverse stock split of Fibrocell's common stock effective April 30, 2013. The Company receives reimbursement payments for research and development services provided pursuant to the agreement during the ECC and manufacturing services for Company materials provided to Fibrocell during the ECC. On a quarterly basis, Fibrocell will pay the Company royalties of 7% of net sales up to $25,000 and 14% of net sales above $25,000 on each product developed from the ECC, as defined in the agreement. If Fibrocell uses the Company's technology platform to improve the production of a current or new Fibrocell product not developed from the ECC, Fibrocell will pay the Company a quarterly royalty equal to 33% of the cost of goods sold savings generated by the improvement, as defined in the agreement. Fibrocell is responsible for conducting preclinical and clinical development of product candidates, as well as for other aspects of commercialization and manufacturing of the product candidates. The term of the ECC commenced in October 2012 and continues until terminated pursuant to the ECC agreement. The ECC may be terminated by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by Fibrocell upon 90 days written notice to the Company. In June 2013, the Company entered into an amendment to the ECC with Fibrocell. The amendment expands the field of use defined in the ECC agreement. Under the terms of the amendment to the ECC, the Company received 1,243,781 shares of Fibrocell's common stock valued at $7,612 as a supplemental technology access fee. The Company allocated this additional consideration to the appropriate unit of accounting and is recognizing it consistent with the unit of accounting. In January 2014, the Company entered into a second amendment to the ECC with Fibrocell. The second amendment further expanded the field of use defined in the ECC agreement. Under the terms of the second amendment to the ECC, the Company received 1,024,590 shares of Fibrocell's common stock valued at $5,225 as a technology access fee. The Company allocated this additional consideration to the appropriate unit of accounting and is recognizing it consistent with the unit of accounting. The remaining balance of deferred revenue associated with the upfront payments was $16,595 and $17,491 at June 30, 2015 and December 31, 2014 , respectively. See Note 17 for further discussion related to Fibrocell. Genopaver Collaboration In March 2013, the Company entered into an ECC with Genopaver, an affiliate of Third Security (Note 17 ) and a related party. Genopaver was formed for the purpose of entering into the ECC and developing and commercializing products in the field of the fermentative production of alkaloids through genetically modified cell-lines and substrate feeds for use as active pharmaceutical ingredients or as commercially sold intermediates in the manufacture of active pharmaceutical ingredients. Upon execution of the ECC, the Company received a technology access fee of $3,000 as upfront consideration. The remaining balance of deferred revenue associated with the upfront payment was $2,386 and $2,523 at June 30, 2015 and December 31, 2014 , respectively. The Company receives reimbursement payments for research and development services provided pursuant to the agreement during the ECC. Genopaver will pay the Company a royalty as a percentage in the lower-double digits on the quarterly gross profits of product sales from products developed under the ECC, as defined in the agreement. Genopaver is responsible for the development and commercialization of the product candidates. The term of the ECC commenced in March 2013 and continues until terminated pursuant to the ECC agreement. The ECC may be terminated by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by Genopaver upon 90 days days written notice to the Company. AquaBounty Collaboration In February 2013, the Company entered into an ECC with AquaBounty, a majority-owned consolidated subsidiary. The Company will be reimbursed for research and development services as provided for in the ECC agreement. In the event of product sales from a product developed from the ECC, the Company will receive 16.66% of quarterly gross profits for each product, as defined in the agreement. All revenues and expenses related to this ECC are eliminated in consolidation. S & I Ophthalmic Collaboration In September 2013, the Company entered into an ECC with S & I Ophthalmic, a joint venture between the Company and Sun Pharmaceutical Subsidiary, an indirect subsidiary of Sun Pharmaceutical, an international specialty pharmaceutical company focused on chronic diseases (Note 4 ). The ECC grants S & I Ophthalmic an exclusive license to the Company's technology platform to develop and commercialize therapies in humans for the treatment of ocular diseases defined more specifically in the agreement. The Company will be reimbursed for research and development services pursuant to the agreement and manufacturing services for Company materials provided to S & I Ophthalmic during the ECC. Subject to certain expense allocations, S & I Ophthalmic will pay the Company royalties with percentages ranging from mid-single digits and above of the net sales derived from the sale of products developed under the ECC, as defined in the agreement. The term of the ECC commenced in September 2013 and continues until terminated by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by S & I Ophthalmic upon 90 days written notice to the Company. BioPop Collaboration In October 2013, the Company entered into an ECC with BioPop, a majority-owned consolidated subsidiary. The ECC grants BioPop an exclusive license to the Company's technology platform to develop and commercialize artwork, children's toys and novelty goods that are derived from living organisms or are enabled by synthetic biology. The Company will be reimbursed for research and development services and manufacturing services as provided for in the ECC agreement. The Company is entitled to royalties in the mid-single digits as a percentage of the net product sales of a product developed under the ECC, as defined in the agreement. All revenues and expenses related to this ECC are eliminated in consolidation. OvaXon Collaboration In December 2013, the Company entered into an ECC with OvaXon, a joint venture between the Company and OvaScience, a life sciences company focused on infertility treatments (Note 4 ) and a related party. The ECC grants OvaXon an exclusive license to the Company's technology platform to create new applications for improving human and animal health. OvaScience also licensed certain technology to OvaXon pursuant to a separate license agreement. The Company will be reimbursed for research and development services and manufacturing services as provided for in the ECC agreement. The term of the ECC commenced in December 2013 and continues until terminated by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by OvaXon upon 90 days written notice to the Company. Intrexon Energy Partners Collaboration In March 2014, the Company entered into an ECC with Intrexon Energy Partners, a joint venture between the Company and certain investors, including an affiliate of Third Security (Note 4 ), and a related party. The ECC grants Intrexon Energy Partners an exclusive license to the Company's technology platform to optimize and scale-up the Company's gas-to-liquid bioconversion platform for the production of certain fuels and lubricants. Upon execution of the ECC, the Company received a technology access fee of $25,000 as upfront consideration. The remaining balance of deferred revenue associated with the upfront payment was $21,875 and $23,125 at June 30, 2015 and December 31, 2014 , respectively. The Company will be reimbursed for research and development services as provided for in the ECC agreement. The term of the ECC commenced in March 2014 and continues until March 2034 unless terminated prior to that date by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by Intrexon Energy Partners upon 90 days written notice to the Company. Persea Bio Collaboration In December 2014, the Company entered into an ECC with Persea Bio, an affiliate of Third Security (Note 17 ) and a related party. Persea Bio was formed for the purpose of entering into the ECC and developing and commercializing a food program, as defined in the agreement. Upon execution of the ECC, the Company received a technology access fee of $5,000 as upfront consideration. The remaining balance of deferred revenue associated with the upfront payment was $4,750 and $5,000 at June 30, 2015 and December 31, 2014 , respectively. The Company receives reimbursement payments for research and development services provided pursuant to the agreement during the ECC. Persea Bio will pay the Company royalties as a percentage in the lower-double digits on the quarterly gross profits of product sales from products derived from the ECC, as defined in the agreement. Persea Bio is responsible for the development and commercialization of the product candidates. The term of the ECC commenced in December 2014 and continues until terminated by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by Persea Bio upon 90 days written notice to the Company. 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: June 30, December 31, Upfront and milestone payments $ 163,094 $ 107,228 Prepaid research and development services 11,496 1,045 Prepaid product and service revenues 4,679 4,365 Other 741 571 Total $ 180,010 $ 113,209 Current portion of deferred revenue $ 28,737 $ 16,522 Long-term portion of deferred revenue 151,273 96,687 Total $ 180,010 $ 113,209

Short-term and Long-term Invest

Short-term and Long-term Investments	6 Months Ended
	Jun. 30, 2015
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 June 30, 2015 : Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Aggregate Fair Value U.S. government debt securities $ 67,097 $ 61 $ — $ 67,158 Certificates of deposit 273 — — 273 Total $ 67,370 $ 61 $ — $ 67,431 The following table summarizes the amortized cost, gross unrealized gains and losses and fair value of available-for-sale investments as of December 31, 2014 : Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Aggregate Fair Value U.S. government debt securities $ 115,293 $ 54 $ (12 ) $ 115,335 Certificates of deposit 273 — — 273 Total $ 115,566 $ 54 $ (12 ) $ 115,608 For more information on our method for determining the fair value of our assets, see Note 2 – "Fair Value of Financial Instruments". 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 have been in a loss position for less than 12 months. As of June 30, 2015 and December 31, 2014 , 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.

Fair Value Measurements

Fair Value Measurements	6 Months Ended
	Jun. 30, 2015
Fair Value Disclosures [Abstract]
Fair Value Measurements	Fair Value Measurements The carrying amount of cash and cash equivalents, 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 June 30, 2015 : Quoted Prices in Active Markets (Level 1) Significant Other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) June 30, Assets U.S. government debt securities (Note 6) $ — $ 67,158 $ — $ 67,158 Equity securities (Note 5) 84,547 17,349 — 101,896 Other — 709 — 709 Total $ 84,547 $ 85,216 $ — $ 169,763 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, 2014 : Quoted Prices in Active Markets Significant Other Observable Inputs Significant Unobservable Inputs December 31, Assets U.S. government debt securities (Note 6) $ — $ 115,335 $ — $ 115,335 Equity securities (Note 5) 143,927 20,962 — 164,889 Other — 273 — 273 Total $ 143,927 $ 136,570 $ — $ 280,497 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. Financial liabilities measured on a recurring basis were not significant at June 30, 2015 and December 31, 2014 . 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. At March 31, 2015, $7,200 of certain equity securities have been transferred from Level 2 to Level 1 as a result of no longer needing to apply a discount for lack of marketability to these transferred equity securities. There have been no additional transfers through June 30, 2015 .

Inventory

Inventory	6 Months Ended
	Jun. 30, 2015
Inventory Disclosure [Abstract]
Inventory	Inventory Inventory consists of the following: June 30, December 31, Supplies, semen and embryos $ 1,587 $ 1,184 Work in process 6,844 5,637 Livestock 17,682 16,996 Feed 888 1,972 Total inventory $ 27,001 $ 25,789

Property, Plant and Equipment,

Property, Plant and Equipment, net	6 Months Ended
	Jun. 30, 2015
Property, Plant and Equipment [Abstract]
Property, Plant and Equipment, net	Property, Plant and Equipment, net Property, plant and equipment consist of the following: June 30, December 31, Land and land improvements $ 8,975 $ 7,565 Buildings and building improvements 7,208 7,265 Furniture and fixtures 1,309 1,236 Equipment 34,495 31,983 Leasehold improvements 6,572 6,382 Computer hardware and software 5,514 5,060 Construction in progress 1,851 1,002 65,924 60,493 Less: Accumulated depreciation and amortization (25,061 ) (22,493 ) Property, plant and equipment, net $ 40,863 $ 38,000 Depreciation expense was $1,828 and $1,281 for the three months ended June 30, 2015 and 2014 , respectively, and $3,781 and $2,399 for the six months ended June 30, 2015 and 2014 , respectively.

Goodwill and Intangible Assets,

Goodwill and Intangible Assets, net	6 Months Ended
	Jun. 30, 2015
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 six months ended June 30, 2015 and 2014 are as follows: Six Months Ended 2015 2014 Beginning balance $ 101,059 $ 13,823 Acquisitions 18,134 21,042 Foreign currency translation adjustment (228 ) — Ending balance $ 118,965 $ 34,865 No goodwill or accumulated impairment losses existed as of June 30, 2015 and December 31, 2014 . Intangible assets consist of the following at June 30, 2015 : Weighted Average Useful Life (Years) Gross Carrying Amount Accumulated Amortization Net Patents, related technologies and know-how 12.6 $ 75,318 $ (13,038 ) $ 62,280 Customer relationships 6.5 10,700 (1,772 ) 8,928 Trademarks 8.4 5,900 (655 ) 5,245 Covenant not to compete 2.0 390 (65 ) 325 In-process research and development 85,456 — 85,456 Total $ 177,764 $ (15,530 ) $ 162,234 Intangible assets consist of the following at December 31, 2014 : Gross Carrying Amount Accumulated Amortization Net Patents, related technologies and know-how $ 41,872 $ (10,849 ) $ 31,023 Customer relationships 10,700 (806 ) 9,894 Trademarks 5,900 (298 ) 5,602 In-process research and development 19,428 — 19,428 Total $ 77,900 $ (11,953 ) $ 65,947 Amortization expense was $1,981 and $687 for the three months ended June 30, 2015 and 2014 , respectively and $3,577 and $1,374 for the six months ended June 30, 2015 and 2014 , respectively.

Lines of Credit and Long Term D

Lines of Credit and Long Term Debt	6 Months Ended
	Jun. 30, 2015
Debt Disclosure [Abstract]
Lines of Credit and Long Term Debt	Lines of Credit and Long Term Debt Lines of Credit Trans Ova has a $6,000 revolving line of credit with First National Bank of Omaha which matures on May 1, 2016. The line of credit bears interest at the greater of 2.95% above the London Interbank Offered Rate or 3.00% and was 3.14% at June 30, 2015 . As of June 30, 2015 , there was an outstanding balance of $208 . The amount available under the line of credit is based on eligible accounts receivable and inventory or the maximum line of credit amount. As of June 30, 2015 , the amount available under the line of credit was $5,792 . Trans Ova's revolving line of credit is collateralized by certain of its assets and contain certain restricted covenants that include maintaining minimum tangible net worth, maximum allowable annual capital expenditures and working capital. Trans Ova was in compliance with these covenants as of June 30, 2015 . Exemplar has a $700 revolving line of credit with American State Bank which matures on November 1, 2015. The line of credit bears interest at 4.50% per annum. As of June 30, 2015 , there was an outstanding balance of $665 . As of June 30, 2015 , the amount available under the line of credit was $35 . Long Term Debt Long term debt consists of the following: June 30, December 31, Notes payable $ 7,066 $ 7,653 Royalty-based financing 1,944 1,926 Other 457 790 Long term debt 9,467 10,369 Less current portion 1,427 1,675 Long term debt, less current portion $ 8,040 $ 8,694 Trans Ova has a note payable to American State Bank which matures in April 2033 and has an outstanding principal balance of $5,780 as of June 30, 2015 . Trans Ova pays monthly installments of $39 , which includes interest at 3.95% . The note payable is collateralized by all of Trans Ova's assets. Trans Ova has a note payable to the Iowa Economic Development Authority which matures in July 2016 and has an outstanding principal balance of $733 as of June 30, 2015 . Trans Ova pays quarterly installments of $183 . The note payable in collateralized by certain of Trans Ova's real estate. Exemplar has notes payable with outstanding principal balances totaling $553 as of June 30, 2015 . Exemplar pays monthly installments ranging from $1 to $4 with interest rates ranging from 0% to 3.00% . These notes mature from September 2018 to May 2020 and are collateralized by certain of Exemplar's real estate or letters of credit of certain of its members. AquaBounty has a royalty-based financing grant from the Atlantic Canada Opportunities Agency ("ACOA"), a Canadian government agency, to provide funding of a research and development project. The total amount available under the award was $2,324 , 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 regulatory approval, the timing of repayment is uncertain. As of the acquisition date, 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. Since the acquisition date, AquaBounty has claimed the remaining balance available under the grant, resulting in total long term debt of $1,944 as of June 30, 2015 . Future maturities of long term debt are as follows: 2015 $ 809 2016 897 2017 365 2018 512 2019 339 2020 308 Thereafter 4,293 Total $ 7,523 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	6 Months Ended
	Jun. 30, 2015
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 six months ended June 30, 2015 , the Company had taxable income of approximately $65,400 and $38,800 , respectively, which, after offset by available loss carryforwards, resulted in $777 of current income tax expense due to the corporate alternative minimum tax. For the three months ended June 30, 2014 , the Company had taxable loss of approximately $14,100 , which resulted in an income tax benefit of $283 that was recognized to offset income tax expense recognized for the three months ended March 31, 2014. For the six months ended June 30, 2014 , the Company had taxable income of approximately $1,200 , which, after offset by available loss carryforwards, resulted in $23 of current income tax expense due to the corporate alternative minimum tax. For the three and six months ended June 30, 2015 , the Company recorded deferred tax expense of $157 and $952 , respectively. There was no deferred tax expense for the three and six months ended June 30, 2014 . The Company's net deferred tax assets, excluding certain deferred tax liabilities totaling $9,609 , 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. At June 30, 2015 , the Company has loss carryforwards for federal income tax purposes of approximately $215,700 available to offset future taxable income and federal and state research and development tax credits of approximately $6,800 , prior to consideration of annual limitations that may be imposed under Section 382. These carryforwards will begin to expire in 2022 . Of these loss carryforwards, approximately $25,800 relate to benefits from stock compensation deductions that will be recorded as a component of paid-in capital when realized. The Company's direct foreign subsidiaries have foreign loss carryforwards of approximately $80,600 , most of which do not expire.

Shareholders' Equity

Shareholders' Equity	6 Months Ended
	Jun. 30, 2015
Equity [Abstract]
Shareholders' Equity	Shareholders' Equity Issuances of Common Stock In January 2015, the Company closed a public offering of 4,312,500 shares of its common stock, inclusive of 562,500 shares of common stock sold by the Company pursuant to the full exercise of an overallotment option granted to the underwriters in connection with the offering and 555,556 shares of common stock purchased by affiliates of Third Security (Note 17 ), at a public offering price of $27.00 per share. The aggregate proceeds of the offering were $110,041 , net of underwriting discounts and commissions of $6,086 and offering expenses paid by the Company of approximately $311 , all of which were capitalized. In March 2014 and concurrent with the formation of Intrexon Energy Partners, the Company entered into securities purchase agreements with each of the Investors in Intrexon Energy Partners for the private placement of 972,004 shares of the Company's common stock at a price per share of $25.72 for gross proceeds of $25,000 . Each Investor purchased an amount proportionate to its investment in Intrexon Energy Partners, including 243,001 shares, or $6,250 , purchased by an affiliate of Third Security (Note 17 ). Dividend to Shareholders In June 2015, the Company distributed to its shareholders 17,830,305 shares of ZIOPHARM common stock, representing all of the equity interests of ZIOPHARM held by the Company and resulting in a realized gain of $81,401 . The distribution constituted a dividend to shareholders of record as of June 4, 2015. In connection with the distribution, pursuant to the terms of the Company's equity incentive plans, the conversion terms of all outstanding options for shares of the Company's stock as of June 4, 2015 were adjusted to reflect the value of the distribution with respect to shares of the Company's common stock. Components of Accumulated Other Comprehensive Loss The components of accumulated other comprehensive loss were as follows: June 30, December 31, Unrealized gain on investments $ 61 $ 42 Foreign currency translation adjustments (2,346 ) (46 ) Total accumulated other comprehensive loss $ (2,285 ) $ (4 )

Stock Option Plans

Stock Option Plans	6 Months Ended
	Jun. 30, 2015
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Stock Option Plans	Stock Option Plans 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 Six Months Ended 2015 2014 2015 2014 Cost of products $ 21 $ — $ 55 $ — Cost of services 105 — 203 — Research and development 2,138 1,364 3,907 1,712 Selling, general and administrative 5,616 5,484 13,974 8,910 Total $ 7,880 $ 6,848 $ 18,139 $ 10,622 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 may grant 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 June 30, 2015 , there are 1,477,951 stock options outstanding under the 2008 Plan. In July 2013, the Company 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 June 30, 2015 , there were 13,000,000 shares authorized for issuance under the 2013 Plan, of which 8,025,778 stock options were outstanding and 4,534,088 shares were available. Stock option activity under Intrexon's award plans was as follows: Number of Shares Weighted Average Exercise Price Weighted Average Remaining Contractual Term (Years) Balances at December 31, 2014 8,323,544 $ 22.59 8.64 Granted 1,849,000 43.15 Adjustment due to dividend (Note 13) 312,795 25.40 Exercised (638,790 ) (16.25 ) Forfeited (342,678 ) (27.77 ) Expired (142 ) (7.12 ) Balances at June 30, 2015 9,503,729 26.08 8.38 Exercisable at June 30, 2015 2,322,052 18.06 7.03 Vested and Expected to Vest at June 30, 2015(1) 7,930,652 25.25 8.28 (1) The number of stock options expected to vest takes into account an estimate of expected forfeitures. Total unrecognized compensation costs related to nonvested awards at June 30, 2015 and December 31, 2014 were $79,699 and $62,281 , respectively, and are expected to be recognized over a weighted-average period of approximately three years . Intrexon currently uses authorized and unissued shares to satisfy share award exercises. Other Plans As of June 30, 2015 , there were 5,382,000 options outstanding under the AquaBounty 2006 Equity Incentive Plan ("AquaBounty Plan") at a weighted average exercise price of $0.26 per share of which 4,320,333 were exercisable. As of December 31, 2014 , there were 7,347,000 options outstanding under the AquaBounty Plan at a weighted average exercise price of $0.31 per share of which 6,171,520 were exercisable.

License Agreement

License Agreement	6 Months Ended
	Jun. 30, 2015
License Agreement [Abstract]
License Agreement	License Agreement In January 2015, the Company and ZIOPHARM jointly entered into a license agreement with the University of Texas System Board of Regents on behalf of the University of Texas MD Anderson Cancer Center ("MD Anderson") whereby the Company received an exclusive license to certain research and development technologies owned and licensed by MD Anderson, including technologies relating to novel chimeric antigen receptor (CAR) T-cell therapies, as well as co-licenses and non-exclusive licenses to certain other related technologies. ZIOPHARM shall receive access to these technologies pursuant to the terms of the Company's ECC with ZIOPHARM. The Company issued 2,100,085 shares of its common stock valued at $59,579 to MD Anderson as consideration, which is included in research and development expenses in the accompanying consolidated statement of operations for the six months ended June 30, 2015 . Subject to certain exceptions, the license agreement expires on the last to occur of (i) the expiration of all patents licensed thereunder, or (ii) the twentieth anniversary of the date of the license agreement. In connection with the license agreement, the Company, ZIOPHARM, and MD Anderson agreed to enter into a research and development agreement which will govern certain operational activities between the parties and pursuant to which ZIOPHARM will provide funding for certain research and development activities of MD Anderson for a period of three years , in an amount between $15,000 and $20,000 per year. The Company and ZIOPHARM are obligated to reimburse MD Anderson for out of pocket expenses for maintaining patents covering the licensed technologies.

Commitments and Contingencies

Commitments and Contingencies	6 Months Ended
	Jun. 30, 2015
Commitments and Contingencies Disclosure [Abstract]
Commitments and Contingencies	Commitments and Contingencies Operating Leases The Company leases facilities and certain equipment under noncancelable operating leases. The equipment leases are renewable at the option of the Company. At June 30, 2015 , future minimum lease payments under operating leases having initial or remaining noncancelable lease terms in excess of one year are as follows: 2015 $ 1,656 2016 4,013 2017 2,714 2018 1,362 2019 1,276 2020 1,311 Thereafter 1,120 Total $ 13,452 Rent expense, including other facility expenses, was $2,247 and $1,361 for the three months ended June 30, 2015 and 2014 , respectively, and $4,381 and $2,731 for the six months ended June 30, 2015 and 2014 , respectively. The Company maintains subleases for certain of its facilities. Rental income under sublease agreements was $394 and $171 for the three months ended June 30, 2015 and 2014 , respectively, and $819 and $262 for the six months ended June 30, 2015 and 2014 , respectively. Future rental income approximates $362 for 2015 , $741 for 2016 , and $96 for 2017 . Contingencies In March 2012, Trans Ova was named as a defendant in a licensing and patent infringement suit brought by XY, Inc. alleging that certain of Trans Ova's activities breach a licensing agreement and infringe on patents that XY, Inc. allegedly owns. Trans Ova is reviewing, defending and filing counter claims in the case. The matter may go to trial in 2015. Based on advice from legal counsel, Trans Ova believes that XY, Inc.'s complaints are without merit; however, no assurances can be given that this matter will be resolved in Trans Ova's favor. Furthermore, no assurances can be made that the legal proceedings will be concluded in accordance with the present schedule. The Company may become subject to 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 June 30, 2015 and December 31, 2014 , 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	6 Months Ended
	Jun. 30, 2015
Related Party Transactions [Abstract]
Related Party Transactions	Related Party Transactions Third Security and Affiliates The Company reimburses Third Security for certain administrative services and out-of-pocket expenses incurred on the Company's behalf. The total amount of expenses incurred by the Company for the three months ended June 30, 2015 and 2014 was $111 and $64 , respectively and $152 and $88 for the six months ended June 30, 2015 and 2014 , respectively. The Manager of Third Security is also the Chief Executive Officer ("CEO") and Chairman of the Board of Directors of the Company. Prior to 2015, the CEO did not receive compensation for his services as CEO, and as a result, the Company recorded $507 and $977 in compensation expense for the three and six months ended June 30, 2014 , respectively, based on the estimated salary and benefits appropriate for the role. The Company anticipates that the CEO will participate in the Company's executive annual incentive compensation plan beginning in 2015. 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. In March 2015, the Company purchased 13,939,392 shares of common stock of AmpliPhi Biosciences Corporation ("AmpliPhi"), a collaborator, and 3,484,848 warrants for $2,300 . Of the total purchase price, $1,979 was allocated to the value of the shares of common stock and $321 was allocated to the value of the warrants. The AmpliPhi warrants have been included in other assets on the consolidated balance sheet with a value of $436 as of June 30, 2015 . Between February 2011 and February 2015, the Company purchased $43,582 of ZIOPHARM securities. See Note 13 for additional discussion related to the Company's investment in ZIOPHARM. The Company entered into an ECC with Histogenics Corporation ("Histogenics") in September 2014 and received a $10,000 convertible promissory note as upfront consideration. The note originally matured in September 2015 and accrued interest at 6.0% per annum. Upon the closing of Histogenics' IPO in December 2014, the note, with accrued interest, was converted to Histogenics common stock. Additionally, the Company purchased 1,772,364 shares of Histogenics common stock at $11.00 per share in the IPO. In conjunction with the ECC with Oragenics (Note 5 ), the Company is entitled to, at its election, purchase up to 30% of securities offerings that may be conducted by Oragenics in the future, subject to certain conditions and limitations. In November 2013, the Company purchased 1,100,000 shares of Oragenics common stock at $2.50 per share. In September 2013, the Company purchased 1,300,000 shares of Oragenics common stock at $3.00 per share in a private transaction. In connection with Oragenics ECC 3 (Note 5 ), the Company agreed to purchase additional common stock in a qualified financing, as defined in the agreement, during the sixteen months following the effective date of the Oragenics ECC 3 in an amount up to the lesser of (i) the amount that is the proportion of such financing equal to the Company's pro rata equity holdings in Oragenics as of the effective date and (ii) $10,000 , subject to certain conditions. The Company recognized $15,239 and $10,920 of collaboration revenues from related parties in the three months ended June 30, 2015 and 2014 , respectively, and $28,035 and $18,318 for the six months ended June 30, 2015 and 2014 , respectively.

Net Loss per Share

Net Loss per Share	6 Months Ended
	Jun. 30, 2015
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 for the three and six months ended June 30, 2015 and 2014 : Three Months Ended Six Months Ended 2015 2014 2015 2014 Historical net loss per share: Numerator: Net loss attributable to Intrexon $ (40,663 ) $ (52,043 ) $ (13,566 ) $ (47,928 ) Denominator: Weighted average shares outstanding, basic and diluted 109,318,471 98,892,601 107,720,040 98,113,493 Net loss attributable to Intrexon per share, basic and diluted $ (0.37 ) $ (0.53 ) $ (0.13 ) $ (0.49 ) The following potentially dilutive securities have been excluded from the above computations of diluted weighted average shares outstanding for the three and six months ended June 30, 2015 and 2014 , as they would have been anti-dilutive: June 30, 2015 2014 Options 9,503,729 8,622,579 Warrants 220,021 373,102 Total 9,723,750 8,995,681

Subsequent Events Subsequent Ev

Subsequent Events Subsequent Events	6 Months Ended
	Jun. 30, 2015
Subsequent Events [Abstract]
Subsequent Events	19 . Subsequent Events In August 2015, the Company entered into a definitive purchase agreement to acquire 100% of Oxitec Limited for approximately $80,000 in Company common stock and approximately $80,000 in cash, subject to certain adjustments as defined in the agreement. Consummation of the transaction, anticipated in the second half of 2015, is subject to customary closing conditions.

Summary of Significant Accoun27

Summary of Significant Accounting Policies (Policies)	6 Months Ended
	Jun. 30, 2015
Accounting Policies [Abstract]
Principles of Consolidation	Principles of Consolidation The accompanying consolidated financial statements reflect the operations of the Company and its subsidiaries. All intercompany accounts and transactions have been eliminated.
Unaudited Financial Information	Unaudited Financial Information The accompanying interim consolidated financial statements are unaudited and have been prepared in accordance with 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 June 30, 2015 and results of operations and cash flows for the interim periods ended June 30, 2015 and 2014 . These interim financial results are not necessarily indicative of the results to be expected for the year ending December 31, 2015 , 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, 2014 .
Revenue Recognition	Revenue Recognition 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 licensee 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. Generally, the terms of these agreements provide that the Company receives some or all of the following: (i) upfront payments upon consummation of the agreement, (ii) reimbursements for costs incurred by the Company for research and development and/or manufacturing efforts related to specific applications provided for in the agreement, (iii) milestone payments upon the achievement of specified development, regulatory and commercial activities, and (iv) royalties on sales of products arising from the collaboration or licensing agreement. The Company's collaboration and licensing agreements typically contain multiple elements, or deliverables, including technology licenses, research and development services, and in certain cases manufacturing services. The Company identifies the deliverables within the agreements and evaluates which deliverables represent separate units of accounting. Analyzing the agreements to identify deliverables requires the use of judgment. A deliverable is considered a separate unit of accounting when the deliverable has value to the collaborator or licensee on a standalone basis based on the consideration of the relevant facts and circumstances for each agreement. Consideration received is allocated at the inception of the agreement to all identified units of accounting based on their relative selling price. When available, the relative selling price for each deliverable is determined using vendor specific objective evidence ("VSOE") of the selling price or third-party evidence of the selling price, if VSOE does not exist. If neither VSOE nor third-party evidence of the selling price exists, the Company uses its best estimate of the selling price ("BESP") for the deliverable. The amount of allocable consideration is limited to amounts that are fixed or determinable. The consideration received is allocated among the separate units of accounting, and the applicable revenue recognition criteria are applied to each of the separate units. The Company recognizes the revenue allocated to each unit of accounting as the Company delivers the related goods or services. If the Company determines that certain deliverables should be treated as a single unit of accounting, then the revenue is recognized using either a proportional performance or straight-line method, depending on whether the Company can reasonably estimate the level of effort required to complete its performance obligations under an arrangement and whether such performance obligations are provided on a best-efforts basis. As the Company cannot reasonably estimate its performance obligations related to its collaborators or licensees, the Company recognizes revenue on a straight-line basis over the period it expects to complete its performance obligations. The terms of the Company's agreements may provide for milestone payments upon achievement of certain defined events. The Company applies the Milestone Method for recognizing milestone payments. Under the Milestone Method, the Company recognizes consideration that is contingent upon the achievement of a milestone in its entirety as revenue in the period in which the milestone is achieved only if the milestone is substantive in its entirety. A milestone is considered substantive when it meets all of the following criteria: (1) The consideration is commensurate with either the entity's performance to achieve the milestone or the enhancement of the value of the delivered item or items as a result of a specific outcome resulting from the entity's performance to achieve the milestone; (2) The consideration relates solely to past performance; and (3) The consideration is reasonable relative to all of the deliverables and payment terms within the arrangement. In the event that a milestone is not considered substantive, the Company recognizes the milestone consideration as revenue using the same method applied to upfront payments. Research and development services are a deliverable satisfied by the Company in accordance with the terms of the collaboration and licensing agreements and the Company considers these services to be inseparable from the license to the core technology; therefore, reimbursements of services performed are recognized as revenue. Because reimbursement (i) is contingent upon performance of the services by the Company, (ii) does not include a profit component, and (iii) does not relate to any future deliverable, the revenue is recognized during the period in which the related services are performed and collection of such amounts is reasonably assured. Payments received for manufacturing services will be recognized when the earnings process related to the manufactured materials has been completed. Royalties to be received under the agreements will be recognized as earned. The Company also generates revenue through sales of advanced reproductive technologies, including bovine embryos derived from the Company's embryo transfer and in vitro fertilization processes and from genetic preservation and sexed semen processes and applications of such processes to other livestock, as well as sales of livestock used in production. Revenue is recognized when (i) persuasive evidence of an arrangement exists, (ii) services have been rendered or delivery has occurred such that risk of loss has passed to the customer, (iii) the price is fixed or determinable, and (iv) collection from the customer is reasonably assured.
Research and Development	Research and Development The Company considers that regulatory and other uncertainties inherent in the research and development of new products preclude it from capitalizing such costs. Research and development expenses include salaries and related costs of research and development personnel, and the costs of consultants, certain in-licensed technology rights, facilities, materials and supplies associated with research and development projects as well as various laboratory studies. Indirect research and development costs include depreciation, amortization and other indirect overhead expenses. The Company has research and development arrangements with third parties that include upfront and milestone payments and primarily relate to collaborations. At June 30, 2015 and December 31, 2014 , the Company had research and development commitments with third parties that had not yet been incurred totaling $6,025 and $2,183 , respectively. The commitments are generally cancellable by the Company at any time upon written notice.
Cash and Cash Equivalents	Cash and Cash Equivalents All highly liquid investments with an original maturity of three months or less at the date of purchase are considered to be cash equivalents. Cash balances at a limited number of banks may periodically exceed insurable amounts. The Company believes that it mitigates its risk by investing in or through major financial institutions with high quality credit ratings. Recoverability of investments is dependent upon the performance of the issuer.
Short-term and Long-term Investments	Short-term and Long-term Investments At June 30, 2015 , investments include short-term investments in U.S. government debt securities and certificates of deposit. The Company determines the appropriate classification as short-term or long-term at the time of purchase based on original maturities and management's reasonable expectation of sales and redemption. The Company reevaluates such classification at each balance sheet date. The Company's written investment policy requires investments to be explicitly rated by two of the three following rating services: Standard & Poor's, Moody's and/or Fitch and to have a minimum rating of A1, P1 and/or F-1, respectively, from those agencies. In addition, the investment policy limits the amount of credit exposure to any one issuer.
Equity Securities	Equity Securities The Company holds equity securities received and/or purchased from certain collaborators. Other than investments accounted for using the equity method, the Company elected the fair value option to account for its equity securities held in these collaborators. These equity securities are recorded at fair value at each reporting date and are subject to market price volatility. Unrealized gains and losses resulting from fair value adjustments are reported in the consolidated statement of operations. The fair value of these equity securities is subject to fluctuation in the future due to the volatility of the stock market, changes in general economic conditions and changes in the financial conditions of these collaborators. These equity securities are classified as noncurrent in the consolidated balance sheet since the Company does not intend to sell these equity securities within one year. The Company records the fair value of securities received on the date the collaboration is consummated or the milestone is achieved using the closing, quoted price of the collaborator's security on that date, assuming the transfer of consideration is considered perfunctory. If the transfer of the consideration is not considered perfunctory, the Company considers the specific facts and circumstances to determine the appropriate date on which to evaluate fair value. The Company also evaluates whether any discounts for trading restrictions or other basis for lack of marketability should be applied to the fair value of the securities at inception of the collaboration. In the event the Company concludes that a discount should be applied, the fair value of the securities is adjusted at inception of the collaboration and re-evaluated at each reporting period thereafter.
Fair Value of Financial Instruments	Fair Value of Financial Instruments Fair value is the price that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants at the measurement date. As such, fair value is a market-based measurement that should be determined based on assumptions that market participants would use in pricing an asset and liability. As a basis for considering such assumptions, the Company uses a three-tier fair value hierarchy that prioritizes the inputs used in its fair value measurements. The hierarchy gives the highest priority to unadjusted quoted prices in active markets for identical assets or liabilities (Level 1 measurements) and the lowest priority to unobservable inputs (Level 3 measurements). The three levels of the fair value hierarchy are as follows: Level 1: Quoted prices in active markets for identical assets and liabilities; Level 2: Other than quoted prices included in Level 1 inputs that are observable for the asset or liability, either directly or indirectly; and Level 3: Unobservable inputs for the asset or liability used to measure fair value to the extent that observable inputs are not available.
Concentrations of Risk	Concentrations of Risk Due to the Company's mix of fixed and variable rate securities holdings, the Company's investment portfolio is susceptible to changes in interest rates. As of June 30, 2015 , there were no gross unrealized losses on the Company's investments. From time to time, the Company may liquidate some or all of its investments to fund operational needs or other activities, such as capital expenditures or business acquisitions. Depending on which investments the Company liquidates to fund these activities, the Company could recognize a portion, or all, of the gross unrealized losses. Financial instruments which potentially subject the Company to concentrations of credit risk consist primarily of trade receivables. The Company controls credit risk through credit approvals, credit limits and monitoring procedures. The Company performs ongoing credit evaluations of its customers, but generally does not require collateral to support accounts receivable.
Equity Method Investments	Equity Method Investments The Company is party to three strategic joint ventures (Note 4 ). The Company accounts for its investments in these joint ventures using the equity method of accounting since the Company has the ability to exercise significant influence, but not control, over the operating activities of these entities.
Variable Interest Entities	Variable Interest Entities The Company identifies entities that (i) do not have sufficient equity investment at risk to permit the entity to finance its activities without additional subordinated financial support or (ii) in which the equity investors lack an essential characteristic of a controlling financial interest as variable interest entities ("VIE" or "VIEs"). The Company performs an initial and on-going evaluation of the entities with which the Company has variable interests to determine if any of these entities are VIEs. If an entity is identified as a VIE, the Company performs an assessment to determine whether the Company has both (i) the power to direct activities that most significantly impact the VIE's economic performance and (ii) have the obligation to absorb losses from or the right to receive benefits of the VIE that could potentially be significant to the VIE. If both of these criteria are satisfied, the Company is identified as the primary beneficiary of the VIE. As of June 30, 2015 , the Company determined that Genopaver, LLC ("Genopaver"); Intrexon Energy Partners, LLC ("Intrexon Energy Partners"); OvaXon, LLC ("OvaXon"); Persea Bio, LLC ("Persea Bio"); and ZIOPHARM were VIEs. As of December 31, 2014 , the Company determined that Genopaver, Intrexon Energy Partners, OvaXon, and Persea Bio were 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 June 30, 2015 was $557 , which represents the Company's maximum risk of loss related to the identified VIEs. As of December 31, 2014 , the Company did not hold any investment balances in the identified VIEs and therefore had no risk of loss as of that date.
Trade Receivables	Trade Receivables Trade receivables consist of credit extended to the Company's customers and collaborators in the normal course of business and are reported net of an allowance for doubtful accounts. The Company reviews its customer accounts on a periodic basis and records bad debt expense for specific amounts the Company evaluates as uncollectible. Past due status is determined based upon contractual terms. Amounts are written off at the point when collection attempts have been exhausted. Management estimates uncollectible amounts considering such factors as current economic conditions and historic and anticipated customer performance. This estimate can fluctuate due to changes in economic, industry or specific customer conditions which may require adjustment to the allowance recorded by the Company. Management has included amounts believed to be uncollectible in the allowance for doubtful accounts.
Inventory	Inventory The Company's inventory primarily includes adult female cows which are used in certain production processes and are recorded at acquisition cost using the first-in, first-out method or at market, whichever is lower. Work-in-process inventory includes allocations of production costs and facility costs for products currently in production and is recorded at the lower of cost or market. Significant declines in the price of cows could result in unfavorable adjustments to inventory balances.
Property, Plant and Equipment	Property, Plant and Equipment Property, plant and equipment are stated at cost, less accumulated depreciation and amortization. Major additions or betterments are capitalized and repairs and maintenance are generally expensed as incurred. Depreciation and amortization is calculated using the straight-line method over the estimated useful lives of the assets. The estimated useful lives of these assets are as follows: Years Land improvements 4–15 Buildings and building improvements 3–23 Furniture and fixtures 1–7 Equipment 1–10 Computer hardware and software 1–7 Leasehold improvements are amortized over the shorter of the useful life of the asset or the applicable lease term, generally one to fourteen years .
Goodwill	Goodwill Goodwill represents the future economic benefits arising from other assets acquired in a business combination that are not individually identified and separately recognized (Note 3 ). Goodwill is reviewed for impairment at least annually. The Company performs a qualitative assessment to determine whether it is more-likely-than-not that the fair value of a reporting unit is less than its carrying amount prior to performing the two-step goodwill impairment test. If this is the case, the two-step goodwill impairment test is required. If it is more-likely-than-not that the fair value of a reporting unit is greater than the carrying amount, the two-step goodwill impairment test is not required. If the two-step goodwill impairment test is required, first, the fair value of the reporting unit is compared with its carrying amount (including goodwill). If the fair value of the reporting unit is less than its carrying amount, an indication of goodwill impairment exists for the reporting unit and the entity must perform step two of the impairment test. Under step two, an impairment loss is recognized for any excess of the carrying amount of the reporting unit's goodwill over the implied fair value of that goodwill. The implied fair value of goodwill is determined by allocating the fair value of the reporting unit in a manner similar to a purchase price allocation and the residual fair value after this allocation is the implied fair value of the reporting unit goodwill. Fair value of the reporting unit is determined using a discounted cash flow analysis. If the fair value of the reporting unit exceeds its carrying amount, step two does not need to be performed. The Company performs its annual impairment review of goodwill in the fourth quarter, or sooner if a triggering event occurs prior to the annual impairment review.
Intangible Assets	Intangible Assets Intangible assets subject to amortization consist of patents, related technologies and know-how; customer relationships; trademarks; and a covenant not to compete acquired as a result of mergers and acquisitions (Note 3 ). These intangible assets are subject to amortization, were recorded at fair value at the date of acquisition and are stated net of accumulated amortization. Indefinite-lived intangible assets consist of in-process research and development acquired in mergers and acquisitions (Note 3 ) and were recorded at fair value at the dates of the respective acquisitions. The Company amortizes long-lived intangible assets to reflect the pattern in which the economic benefits of the intangible assets are expected to be realized. The intangible assets are amortized over their remaining estimated useful lives, ranging from two to fourteen years for the patents, related technologies and know-how; customer relationships; trademarks; and the covenant not to compete.
Impairment of Long-Lived Assets	Impairment of Long-Lived Assets Long-lived assets to be held and used, including property, plant and equipment and intangible assets subject to amortization, are reviewed for impairment whenever events or changes in circumstances indicate that the carrying amount of the assets may not be recoverable. Conditions that would necessitate an impairment assessment include a significant decline in the observable market value of an asset, a significant change in the extent or manner in which an asset is used, or a significant adverse change that would indicate that the carrying amount of an asset or group of assets is not recoverable. Indefinite-lived intangible assets, including in-process research and development, are tested for impairment annually, or more frequently if events or circumstances between annual tests indicate that the asset may be impaired. Impairment losses on indefinite-lived intangible assets are recognized based solely on a comparison of their fair value to carrying value, without consideration of any recoverability test. The Company monitors the progression of its in-process research and development, as the likelihood of success is contingent upon commercial development or regulatory approval.
Foreign Currency Translation	Foreign Currency Translation The assets and liabilities of foreign subsidiaries, where the local currency is the functional currency, are translated from their respective functional currencies into United States dollars at the exchange rates in effect at the balance sheet date, with resulting foreign currency translation adjustments recorded in the consolidated statement of comprehensive income. Revenue and expense amounts are translated at average rates during the period.
Income Taxes	Income Taxes Income taxes are accounted for under the asset and liability method. Deferred tax assets and liabilities are recognized for the future tax consequences attributable to both differences between the financial statement carrying amounts of existing assets and liabilities and their respective tax bases as well as operating loss and tax credit carryforwards. Deferred tax assets and liabilities are measured using enacted tax rates expected to apply to taxable income in the years in which those temporary differences are expected to be recovered or settled. The effect on deferred tax assets and liabilities of a change in tax rates is recognized in income in the period that includes the enactment date of the change. Valuation allowances are established when necessary to reduce deferred tax assets to the amount expected to be realized. The Company identifies any uncertain income tax positions and recognizes the effect of income tax positions only if those positions are more likely than not of being sustained. Recognized income tax positions are measured at the largest amount that is greater than 50% likely of being realized. Changes in recognition or measurement are reflected in the period in which the change in judgment occurs. The Company records interest, if any, related to unrecognized tax benefits as a component of interest expense. Penalties, if any, are recorded in selling, general and administrative expenses.
Net Loss per Share	Net Loss per Share Basic net loss per share is calculated by dividing net loss attributable to common shareholders by the weighted average shares outstanding during the period, without consideration of common stock equivalents. Diluted net loss per share is calculated by adjusting weighted average shares outstanding for the dilutive effect of common stock equivalents outstanding for the period, using the treasury-stock method. For purposes of the diluted net loss per share calculation, stock options and warrants are considered to be common stock equivalents but are excluded from the calculation of diluted net loss per share because their effect would be anti-dilutive and, therefore, basic and diluted net loss per share were the same for all periods presented..
Segment Information	Segment Information The Company has determined that it operates in one segment. The Company applies its technologies to create products and services which may be either sold directly to customers or developed through collaboration with third parties.
Recently Issued Accounting Pronouncements	Recently Issued Accounting Pronouncements In July 2015, the Financial Accounting Standards Board ("FASB") issued Accounting Standards Update ("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 guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2016, and is effective for the Company for the year ending December 31, 2017. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. In February 2015, the FASB issued ASU 2015-02, Consolidation (Topic 810) - Amendments to the Consolidation Analysis ("ASU 2015-02"). The provisions of ASU 2015-02 provide guidance which changes the analysis that a reporting entity must perform to determine whether it should consolidate certain types of legal entities. This guidance is effective for annual periods and interim periods within those annual periods, beginning after December 15, 2015, and is effective for the Company for the year ending December 31, 2016, with early adoption permitted. 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 2014-9, Revenue from Contracts with Customers ("ASU 2014-9"). The FASB issued ASU 2014-9 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 July 2015, the FASB voted to defer the effective date 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. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements.
Reclassifications	Reclassifications Certain insignificant reclassifications have been made to the prior interim period consolidated financial statements to conform to the current interim period presentation.
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.

Summary of Significant Accoun28

Summary of Significant Accounting Policies (Tables)	6 Months Ended
	Jun. 30, 2015
Accounting Policies [Abstract]
Summarized Unaudited Financial Information	Summarized unaudited financial data as of June 30, 2015 and December 31, 2014 and for the three and six months ended June 30, 2015 and 2014 , for the Company's equity method investments are as follows: June 30, 2015 December 31, 2014 Current assets $ 15,259 $ 63,627 Non-current assets 209 1,259 Total assets 15,468 64,886 Current liabilities 9,181 15,346 Non-current liabilities — 570 Total liabilities 9,181 15,916 Net assets $ 6,287 $ 48,970 Three Months Ended Six Months Ended 2015 2014 2015 2014 Revenues $ 423 $ 504 $ 1,059 $ 919 Operating expenses 22,845 16,294 106,914 29,214 Loss from operations (22,422 ) (15,790 ) (105,855 ) (28,295 ) Other 2 5,608 1 5,689 Net loss $ (22,420 ) $ (10,182 ) $ (105,854 ) $ (22,606 )
Allowance for Doubtful Accounts	The following table shows the activity in the allowance for doubtful accounts for the six months ended June 30, 2015 : Six Months Ended June 30, 2015 Beginning balance $ 565 Charged to operating expenses 984 Write offs of accounts receivable (112 ) Ending balance $ 1,437
Estimated Useful Lives	The estimated useful lives of these assets are as follows: Years Land improvements 4–15 Buildings and building improvements 3–23 Furniture and fixtures 1–7 Equipment 1–10 Computer hardware and software 1–7

Mergers and Acquisitions (Table

Mergers and Acquisitions (Tables)	6 Months Ended
	Jun. 30, 2015
Okanagan Specialty Fruits Inc
Business Acquisition [Line Items]
Acquisition Date Fair Value Consideration Transferred	The fair value of the total consideration transferred was $40,933 . The acquisition date fair value of each class of consideration transferred is presented below: Cash $ 10,000 Common shares 30,933 $ 40,933
Estimated Fair Value of Assets Acquired and Liabilities Assumed at Acquisition Date	The preliminary estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown below: Cash $ 58 Trade receivables 16 Other receivables 49 Property, plant, and equipment 32 Intangible assets 33,800 Total assets acquired 33,955 Accounts payable 181 Deferred revenue 181 Deferred tax liability 8,145 Total liabilities assumed 8,507 Net assets acquired 25,448 Goodwill 15,485 Total consideration $ 40,933
ActoGeniX NV
Business Acquisition [Line Items]
Acquisition Date Fair Value Consideration Transferred	The fair value of the total consideration transferred was $72,474 . The acquisition date fair value of each class of consideration transferred is presented below: Cash $ 32,739 Common shares 39,735 $ 72,474
Estimated Fair Value of Assets Acquired and Liabilities Assumed at Acquisition Date	The estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown below along with subsequent adjustments during the measurement period to the fair value of assets acquired and liabilities assumed. The adjustments resulted from the difference between estimated and actual accrued expenses. Initial Estimated Fair Value Adjustments Adjusted Fair Value Cash $ 3,180 $ — $ 3,180 Other receivables 305 — 305 Prepaid expenses and other 31 — 31 Property, plant and equipment 209 — 209 Intangible assets 68,100 — 68,100 Other assets 23 — 23 Total assets acquired 71,848 — 71,848 Accounts payable 230 — 230 Accrued compensation and benefits 624 (428 ) 196 Other accrued liabilities 307 (54 ) 253 Deferred revenue 732 — 732 Deferred tax liability 612 — 612 Total liabilities assumed 2,505 (482 ) 2,023 Net assets acquired 69,343 482 69,825 Goodwill 3,131 (482 ) 2,649 Total consideration $ 72,474 $ — $ 72,474
Trans Ova Genetics, LC
Business Acquisition [Line Items]
Acquisition Date Fair Value Consideration Transferred	The fair value of the total consideration transferred, including the noncontrolling interest in a majority-owned subsidiary of Trans Ova, was $127,875 . The acquisition date fair value of each class of consideration transferred and noncontrolling interest is presented below: Cash $ 63,625 Common shares 32,802 Deferred cash consideration 20,115 Total consideration transferred 116,542 Fair value of noncontrolling interest 11,333 Total $ 127,875
Estimated Fair Value of Assets Acquired and Liabilities Assumed at Acquisition Date	The estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown in the table below. Cash $ 960 Trade receivables 18,693 Related party receivables 1,219 Inventory 18,476 Prepaid expenses and other 590 Property, plant and equipment 21,164 Intangible assets 23,700 Other assets 147 Total assets acquired 84,949 Accounts payable 3,317 Accrued compensation and benefits 913 Other accrued liabilities 271 Deferred revenue 4,458 Lines of credit 4,091 Related party payables 1,246 Long term debt 9,090 Total liabilities assumed 23,386 Net assets acquired 61,563 Goodwill 66,312 Total consideration and fair value of noncontrolling interest $ 127,875
Medistem, Inc.
Business Acquisition [Line Items]
Acquisition Date Fair Value Consideration Transferred	The fair value of the total consideration transferred was $24,995 . The acquisition date fair value of each class of consideration transferred is presented below: Cash $ 4,920 Common shares 19,368 Settlement of promissory notes 707 $ 24,995
Estimated Fair Value of Assets Acquired and Liabilities Assumed at Acquisition Date	The estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown in the table below. Cash $ 8 Intangible assets 4,824 Total assets acquired 4,832 Accounts payable 644 Accrued compensation and benefits 67 Other accrued expenses 50 Total liabilities assumed 761 Net assets acquired 4,071 Goodwill 20,924 Total consideration $ 24,995
2015 Business Acquisitions
Business Acquisition [Line Items]
Condensed Pro forma Financial Information	The following unaudited condensed pro forma financial information for the three and six months ended June 30, 2015 and 2014 is presented as if the acquisitions had been consummated on January 1, 2014: Three Months Ended Six Months Ended 2015 2014 2015 2014 Pro forma Revenues $ 44,891 $ 11,851 $ 78,929 $ 19,759 Loss before income taxes (40,734 ) (56,161 ) (18,411 ) (55,295 ) Net loss (41,668 ) (55,673 ) (19,891 ) (55,067 ) Net loss attributable to the noncontrolling interests 831 892 2,124 1,758 Net loss attributable to Intrexon (40,837 ) (54,781 ) (17,767 ) (53,309 )
2014 Business Acquisitions
Business Acquisition [Line Items]
Condensed Pro forma Financial Information	The following unaudited condensed pro forma financial information for the three and six months ended June 30, 2014 is presented as if the acquisitions had been consummated on January 1, 2013: Three Months Ended Six Months Ended Pro forma Revenues $ 34,911 $ 57,122 Loss before income taxes (48,265 ) (46,953 ) Net loss (47,982 ) (46,976 ) Net loss attributable to the noncontrolling interests 1,085 2,031 Net loss attributable to Intrexon (46,897 ) (44,945 )

Collaboration and Licensing R30

Collaboration and Licensing Revenue (Tables)	6 Months Ended
	Jun. 30, 2015
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Summarized Collaboration and Licensing Revenue	The following table summarizes the amounts recorded in the consolidated statements of operations for each significant collaboration and licensing agreement for the three and six months ended June 30, 2015 and 2014 . Three Months Ended June 30, 2015 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 644 $ 4,606 $ 5,250 Oragenics, Inc. 307 68 375 Fibrocell Science, Inc. 448 1,470 1,918 Genopaver, LLC 68 867 935 S & I Ophthalmic, LLC — 890 890 OvaXon, LLC — 662 662 Intrexon Energy Partners, LLC 625 2,731 3,356 Persea Bio, LLC 125 141 266 Ares Trading S.A. 739 — 739 Other 747 2,043 2,790 Total $ 3,703 $ 13,478 $ 17,181 Three Months Ended June 30, 2014 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 644 $ 3,697 $ 4,341 Oragenics, Inc. 261 52 313 Fibrocell Science, Inc. 448 883 1,331 Genopaver, LLC 68 423 491 S & I Ophthalmic, LLC — 607 607 OvaXon, LLC — 579 579 Intrexon Energy Partners, LLC 625 1,210 1,835 Other 471 1,796 2,267 Total $ 2,517 $ 9,247 $ 11,764 Six Months Ended June 30, 2015 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 1,288 $ 7,763 $ 9,051 Oragenics, Inc. 569 76 645 Fibrocell Science, Inc. 896 3,183 4,079 Genopaver, LLC 137 1,467 1,604 S & I Ophthalmic, LLC — 1,645 1,645 OvaXon, LLC — 1,306 1,306 Intrexon Energy Partners, LLC 1,250 4,916 6,166 Persea Bio, LLC 250 256 506 Ares Trading S.A. 739 — 739 Other 1,605 4,618 6,223 Total $ 6,734 $ 25,230 $ 31,964 Six Months Ended June 30, 2014 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 1,288 $ 5,733 $ 7,021 Oragenics, Inc. 523 585 1,108 Fibrocell Science, Inc. 896 1,745 2,641 Genopaver, LLC 137 844 981 S & I Ophthalmic, LLC — 1,486 1,486 OvaXon, LLC — 748 748 Intrexon Energy Partners, LLC 625 1,210 1,835 Other 930 2,851 3,781 Total $ 4,399 $ 15,202 $ 19,601
Summary of Deferred Revenue	Deferred revenue consists of the following: June 30, December 31, Upfront and milestone payments $ 163,094 $ 107,228 Prepaid research and development services 11,496 1,045 Prepaid product and service revenues 4,679 4,365 Other 741 571 Total $ 180,010 $ 113,209 Current portion of deferred revenue $ 28,737 $ 16,522 Long-term portion of deferred revenue 151,273 96,687 Total $ 180,010 $ 113,209

Short-term and Long-term Inve31

Short-term and Long-term Investments (Tables)	6 Months Ended
	Jun. 30, 2015
Investments, Debt and Equity Securities [Abstract]
Summary of Amortized Cost, Gross Unrealized Gains and Losses and Fair Value of Investments	The following table summarizes the amortized cost, gross unrealized gains and losses and fair value of available-for-sale investments as of June 30, 2015 : Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Aggregate Fair Value U.S. government debt securities $ 67,097 $ 61 $ — $ 67,158 Certificates of deposit 273 — — 273 Total $ 67,370 $ 61 $ — $ 67,431 The following table summarizes the amortized cost, gross unrealized gains and losses and fair value of available-for-sale investments as of December 31, 2014 : Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Aggregate Fair Value U.S. government debt securities $ 115,293 $ 54 $ (12 ) $ 115,335 Certificates of deposit 273 — — 273 Total $ 115,566 $ 54 $ (12 ) $ 115,608

Fair Value Measurements (Tables

Fair Value Measurements (Tables)	6 Months Ended
	Jun. 30, 2015
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 June 30, 2015 : Quoted Prices in Active Markets (Level 1) Significant Other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) June 30, Assets U.S. government debt securities (Note 6) $ — $ 67,158 $ — $ 67,158 Equity securities (Note 5) 84,547 17,349 — 101,896 Other — 709 — 709 Total $ 84,547 $ 85,216 $ — $ 169,763 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, 2014 : Quoted Prices in Active Markets Significant Other Observable Inputs Significant Unobservable Inputs December 31, Assets U.S. government debt securities (Note 6) $ — $ 115,335 $ — $ 115,335 Equity securities (Note 5) 143,927 20,962 — 164,889 Other — 273 — 273 Total $ 143,927 $ 136,570 $ — $ 280,497

Inventory (Tables)

Inventory (Tables)	6 Months Ended
	Jun. 30, 2015
Inventory Disclosure [Abstract]
Schedule of Inventory	Inventory consists of the following: June 30, December 31, Supplies, semen and embryos $ 1,587 $ 1,184 Work in process 6,844 5,637 Livestock 17,682 16,996 Feed 888 1,972 Total inventory $ 27,001 $ 25,789

Property, Plant and Equipment34

Property, Plant and Equipment, net (Tables)	6 Months Ended
	Jun. 30, 2015
Property, Plant and Equipment [Abstract]
Schedule of Property, Plant and Equipment	Property, plant and equipment consist of the following: June 30, December 31, Land and land improvements $ 8,975 $ 7,565 Buildings and building improvements 7,208 7,265 Furniture and fixtures 1,309 1,236 Equipment 34,495 31,983 Leasehold improvements 6,572 6,382 Computer hardware and software 5,514 5,060 Construction in progress 1,851 1,002 65,924 60,493 Less: Accumulated depreciation and amortization (25,061 ) (22,493 ) Property, plant and equipment, net $ 40,863 $ 38,000

Goodwill and Intangible Asset35

Goodwill and Intangible Assets, net (Tables)	6 Months Ended
	Jun. 30, 2015
Goodwill and Intangible Assets Disclosure [Abstract]
Schedule of Changes in Carrying Amount of Goodwill	The changes in the carrying amount of goodwill for the six months ended June 30, 2015 and 2014 are as follows: Six Months Ended 2015 2014 Beginning balance $ 101,059 $ 13,823 Acquisitions 18,134 21,042 Foreign currency translation adjustment (228 ) — Ending balance $ 118,965 $ 34,865
Schedule of Intangible Assets	Intangible assets consist of the following at June 30, 2015 : Weighted Average Useful Life (Years) Gross Carrying Amount Accumulated Amortization Net Patents, related technologies and know-how 12.6 $ 75,318 $ (13,038 ) $ 62,280 Customer relationships 6.5 10,700 (1,772 ) 8,928 Trademarks 8.4 5,900 (655 ) 5,245 Covenant not to compete 2.0 390 (65 ) 325 In-process research and development 85,456 — 85,456 Total $ 177,764 $ (15,530 ) $ 162,234 Intangible assets consist of the following at December 31, 2014 : Gross Carrying Amount Accumulated Amortization Net Patents, related technologies and know-how $ 41,872 $ (10,849 ) $ 31,023 Customer relationships 10,700 (806 ) 9,894 Trademarks 5,900 (298 ) 5,602 In-process research and development 19,428 — 19,428 Total $ 77,900 $ (11,953 ) $ 65,947

Lines of Credit and Long Term36

Lines of Credit and Long Term Debt (Tables)	6 Months Ended
	Jun. 30, 2015
Debt Disclosure [Abstract]
Schedule of Long-term Debt Instruments	Long term debt consists of the following: June 30, December 31, Notes payable $ 7,066 $ 7,653 Royalty-based financing 1,944 1,926 Other 457 790 Long term debt 9,467 10,369 Less current portion 1,427 1,675 Long term debt, less current portion $ 8,040 $ 8,694
Schedule of Future Maturities of Long-term Debt	Future maturities of long term debt are as follows: 2015 $ 809 2016 897 2017 365 2018 512 2019 339 2020 308 Thereafter 4,293 Total $ 7,523

Shareholders' Equity (Tables)

Shareholders' Equity (Tables)	6 Months Ended
	Jun. 30, 2015
Equity [Abstract]
Components of Accumulated Other Comprehensive Loss	The components of accumulated other comprehensive loss were as follows: June 30, December 31, Unrealized gain on investments $ 61 $ 42 Foreign currency translation adjustments (2,346 ) (46 ) Total accumulated other comprehensive loss $ (2,285 ) $ (4 )

Stock Option Plans (Tables)

Stock Option Plans (Tables)	6 Months Ended
	Jun. 30, 2015
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Schedule of Employee Service Share-based Compensation Allocation	Stock-based compensation costs included in the consolidated statements of operations are presented below: Three Months Ended Six Months Ended 2015 2014 2015 2014 Cost of products $ 21 $ — $ 55 $ — Cost of services 105 — 203 — Research and development 2,138 1,364 3,907 1,712 Selling, general and administrative 5,616 5,484 13,974 8,910 Total $ 7,880 $ 6,848 $ 18,139 $ 10,622
Schedule of Stock Option Activity	Stock option activity under Intrexon's award plans was as follows: Number of Shares Weighted Average Exercise Price Weighted Average Remaining Contractual Term (Years) Balances at December 31, 2014 8,323,544 $ 22.59 8.64 Granted 1,849,000 43.15 Adjustment due to dividend (Note 13) 312,795 25.40 Exercised (638,790 ) (16.25 ) Forfeited (342,678 ) (27.77 ) Expired (142 ) (7.12 ) Balances at June 30, 2015 9,503,729 26.08 8.38 Exercisable at June 30, 2015 2,322,052 18.06 7.03 Vested and Expected to Vest at June 30, 2015(1) 7,930,652 25.25 8.28 (1) The number of stock options expected to vest takes into account an estimate of expected forfeitures.

Commitments and Contingencies (

Commitments and Contingencies (Tables)	6 Months Ended
	Jun. 30, 2015
Commitments and Contingencies Disclosure [Abstract]
Future Minimum Lease Payments Under Noncancelable Operating Leases	At June 30, 2015 , future minimum lease payments under operating leases having initial or remaining noncancelable lease terms in excess of one year are as follows: 2015 $ 1,656 2016 4,013 2017 2,714 2018 1,362 2019 1,276 2020 1,311 Thereafter 1,120 Total $ 13,452

Net Loss per Share (Tables)

Net Loss per Share (Tables)	6 Months Ended
	Jun. 30, 2015
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 for the three and six months ended June 30, 2015 and 2014 : Three Months Ended Six Months Ended 2015 2014 2015 2014 Historical net loss per share: Numerator: Net loss attributable to Intrexon $ (40,663 ) $ (52,043 ) $ (13,566 ) $ (47,928 ) Denominator: Weighted average shares outstanding, basic and diluted 109,318,471 98,892,601 107,720,040 98,113,493 Net loss attributable to Intrexon per share, basic and diluted $ (0.37 ) $ (0.53 ) $ (0.13 ) $ (0.49 )
Schedule of Antidilutive Securities Excluded from Computation of Earnings Per Share	The following potentially dilutive securities have been excluded from the above computations of diluted weighted average shares outstanding for the three and six months ended June 30, 2015 and 2014 , as they would have been anti-dilutive: June 30, 2015 2014 Options 9,503,729 8,622,579 Warrants 220,021 373,102 Total 9,723,750 8,995,681

Organization and Basis of Pre41

Organization and Basis of Presentation - Additional Information (Details) - Jun. 30, 2015 - USD ($) $ in Thousands	Total
AquaBounty Technologies, Inc.
Organization, Consolidation and Presentation of Financial Statements Disclosure [Line Items]
Shares issued by majority owned subsidiary to parent	12,728,044
Purchase of additional equity interest of majority owned subsidiary	$ 3,000
Parent ownership interest	63.00%
Biological & Popular Culture, Inc.
Organization, Consolidation and Presentation of Financial Statements Disclosure [Line Items]
Parent ownership interest	51.00%

Summary of Significant Accoun42

Summary of Significant Accounting Policies - Additional Information (Details)	3 Months Ended		6 Months Ended
	Jun. 30, 2015USD ($)joint_ventureEntity	Jun. 30, 2014USD ($)	Jun. 30, 2015USD ($)Segmentjoint_ventureEntity	Jun. 30, 2014USD ($)	Dec. 31, 2014USD ($)Entity
Organization And Significant Accounting Policies [Line Items]
Number Of Joint Ventures In Which The Company Participates | joint_venture	3		3
Research and development commitments with third parties not incurred	$ 6,025,000		$ 6,025,000		$ 2,183,000
Maturity period of liquid investment			3 months
Cash equivalent investments in highly liquid money market accounts	87,472,000		$ 87,472,000		$ 16,598,000
Unrealized losses on investments	$ 0		$ 0
Number of collaborators over which the Company has significant influence | Entity	1		1		2
Fair value of financial assets measured at fair value on a recurring basis	$ 169,763,000		$ 169,763,000		$ 280,497,000
Unrealized and realized appreciation (depreciation) in fair value of equity securities	(20,609,000)	$ (33,777,000)	94,845,000	$ (11,855,000)
Variable interest entities, risk of loss	557,000		$ 557,000		0
Number of segments | Segment			1
Revenues	44,891,000	11,787,000	$ 78,740,000	19,641,000
Foreign Countries
Organization And Significant Accounting Policies [Line Items]
Long-lived assets	116,523,000		116,523,000		17,100,000
Revenues	925,000	369,000	2,263,000	369,000
Equity Securities
Organization And Significant Accounting Policies [Line Items]
Fair value of financial assets measured at fair value on a recurring basis	$ 101,896,000		$ 101,896,000		$ 164,889,000
Oragenics, Inc.
Organization And Significant Accounting Policies [Line Items]
Company's ownership percentage	24.30%		24.30%		24.40%
Oragenics, Inc. | Equity Securities
Organization And Significant Accounting Policies [Line Items]
Fair value of financial assets measured at fair value on a recurring basis	$ 11,071,000		$ 11,071,000		$ 7,192,000
Unrealized and realized appreciation (depreciation) in fair value of equity securities	2,943,000	(7,113,000)	$ 3,879,000	(6,403,000)
ZIOPHARM Oncology, Inc.
Organization And Significant Accounting Policies [Line Items]
Company's ownership percentage					15.70%
Realized gain on equity securities	$ 81,401,000
ZIOPHARM Oncology, Inc. | Equity Securities
Organization And Significant Accounting Policies [Line Items]
Fair value of financial assets measured at fair value on a recurring basis					$ 83,099,000
Unrealized and realized appreciation (depreciation) in fair value of equity securities		$ (9,015,000)		$ (5,081,000)
Minimum
Organization And Significant Accounting Policies [Line Items]
Weighted average useful life (years)			2 years
Minimum | Leasehold Improvements
Organization And Significant Accounting Policies [Line Items]
Property plant and equipment, useful life			1 year
Maximum
Organization And Significant Accounting Policies [Line Items]
Weighted average useful life (years)			14 years
Maximum | Leasehold Improvements
Organization And Significant Accounting Policies [Line Items]
Property plant and equipment, useful life			14 years

Summary of Significant Accoun43

Summary of Significant Accounting Policies - Summarized Financial Data (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014	Jun. 30, 2015	Jun. 30, 2014	Dec. 31, 2014
Schedule of Equity Method Investments [Line Items]
Operating expenses	$ 62,321	$ 29,869	$ 183,293	$ 55,595
Equity Method Investments
Schedule of Equity Method Investments [Line Items]
Current assets	15,259		15,259		$ 63,627
Non-current assets	209		209		1,259
Total assets	15,468		15,468		64,886
Current liabilities	9,181		9,181		15,346
Non-current liabilities	0		0		570
Total liabilities	9,181		9,181		15,916
Net assets	6,287		6,287		$ 48,970
Revenues	423	504	1,059	919
Operating expenses	22,845	16,294	106,914	29,214
Loss from operations	(22,422)	(15,790)	(105,855)	(28,295)
Other	2	5,608	1	5,689
Net loss	$ (22,420)	$ (10,182)	$ (105,854)	$ (22,606)

Summary of Significant Accoun44

Summary of Significant Accounting Policies - Trade Receivables - Rollforward of Allowance for Doubtful Accounts (Details) - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014
Allowance for Doubtful Accounts Receivable [Roll Forward]
Beginning balance	$ 565
Charged to operating expenses	984	$ 0
Write offs of accounts receivable	(112)
Ending balance	$ 1,437

Summary of Significant Accoun45

Summary of Significant Accounting Policies - Estimated Useful Lives of Property, Plant and Equipment (Details)	6 Months Ended
	Jun. 30, 2015
Minimum | Land improvements
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	4 years
Minimum | Buildings and building improvements
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	3 years
Minimum | Furniture and fixtures
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	1 year
Minimum | Equipment
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	1 year
Minimum | Computer hardware and software
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	1 year
Maximum | Land improvements
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	15 years
Maximum | Buildings and building improvements
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	23 years
Maximum | Furniture and fixtures
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	7 years
Maximum | Equipment
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	10 years
Maximum | Computer hardware and software
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	7 years

Mergers and Acquisitions - Addi

Mergers and Acquisitions - Additional Information (Details)	Aug. 08, 2014USD ($)installmentshares	Mar. 06, 2014USD ($)Noteshares	Apr. 30, 2015USD ($)shares	Feb. 28, 2015USD ($)shares	Jun. 30, 2015USD ($)	Jun. 30, 2014USD ($)	Jun. 30, 2015USD ($)	Jun. 30, 2014USD ($)	Dec. 31, 2014USD ($)	Sep. 30, 2012USD ($)
Business Acquisition [Line Items]
Revenues					$ 44,891,000	$ 11,787,000	$ 78,740,000	$ 19,641,000
Net loss attributable to Intrexon					(40,663,000)	(52,043,000)	(13,566,000)	(47,928,000)
Okanagan Specialty Fruits Inc
Business Acquisition [Line Items]
Percentage of outstanding common stock acquired			100.00%
Business acquisition, consideration paid, shares issued | shares			707,853
Cash			$ 10,000,000
Total consideration transferred			$ 40,933,000
Weighted average useful life (years)			14 years
Business combination, acquisition related cost							341,000
Okanagan Specialty Fruits Inc | Selling, general and administrative
Business Acquisition [Line Items]
Business combination, acquisition related cost					104,000		267,000
ActoGeniX NV
Business Acquisition [Line Items]
Percentage of outstanding common stock acquired				100.00%
Business acquisition, consideration paid, shares issued | shares				965,377
Cash				$ 32,739,000
Total consideration transferred				72,474,000
Business combination, acquisition related cost							418,000
ActoGeniX NV | Selling, general and administrative
Business Acquisition [Line Items]
Business combination, acquisition related cost							381,000
Trans Ova Genetics, LC
Business Acquisition [Line Items]
Percentage of outstanding common stock acquired	100.00%
Business acquisition, consideration paid, shares issued | shares	1,444,388
Cash	$ 63,625,000
Total consideration transferred	116,542,000
Business combination, acquisition related cost									$ 713,000
Deferred cash consideration	$ 20,115,000
Deferred cash consideration, number of payment installments | installment	3
Revenues					27,534,000		46,460,000
Net loss attributable to Intrexon					4,422,000		4,185,000
Total	$ 127,875,000
Possible future contingent payments to former equity holders										$ 6,000,000
Possible future contingent payments to former equity holders, current valuation					$ 0		$ 0
Trans Ova Genetics, LC | Selling, general and administrative
Business Acquisition [Line Items]
Business combination, acquisition related cost						312,000		312,000
Exemplar Genetics, LLC
Business Acquisition [Line Items]
Cash paid to acquire noncontrolling interest				$ 1,566,000
Shares issued to acquire noncontrolling interest | shares				307,074
Medistem, Inc.
Business Acquisition [Line Items]
Percentage of outstanding common stock acquired		100.00%
Business acquisition, consideration paid, shares issued | shares		714,144
Cash		$ 4,920,000
Total consideration transferred		$ 24,995,000
Business combination, acquisition related cost									$ 680,000
Number of promissory notes settled upon the closing of the merger | Note		2
Shares of merger consideration surrendered by acquiree management to reimburse for required payroll tax withholdings | shares		17,695
Medistem, Inc. | Settlement of Promissory Notes
Business Acquisition [Line Items]
Total consideration transferred		$ 707,000
Medistem, Inc. | Selling, general and administrative
Business Acquisition [Line Items]
Business combination, acquisition related cost						$ 19,000		$ 310,000
Minimum
Business Acquisition [Line Items]
Weighted average useful life (years)							2 years
Minimum | Trans Ova Genetics, LC
Business Acquisition [Line Items]
Weighted average useful life (years)	3 years
Maximum
Business Acquisition [Line Items]
Weighted average useful life (years)							14 years
Maximum | Trans Ova Genetics, LC
Business Acquisition [Line Items]
Weighted average useful life (years)	9 years
Scenario, Plan | Okanagan Specialty Fruits Inc
Business Acquisition [Line Items]
Total consideration transferred			$ 40,933,000

Mergers and Acquisitions - Fair

Mergers and Acquisitions - Fair Value of Consideration Transferred (Details) - USD ($) $ in Thousands	Aug. 08, 2014	Mar. 06, 2014	Apr. 30, 2015	Feb. 28, 2015
Okanagan Specialty Fruits Inc
Business Acquisition [Line Items]
Cash			$ 10,000
Common shares			30,933
Total consideration transferred			$ 40,933
Trans Ova Genetics, LC
Business Acquisition [Line Items]
Cash	$ 63,625
Common shares	32,802
Deferred cash consideration	20,115
Total consideration transferred	116,542
Fair value of noncontrolling interest	11,333
Total	$ 127,875
ActoGeniX NV
Business Acquisition [Line Items]
Cash				$ 32,739
Common shares				39,735
Total consideration transferred				$ 72,474
Medistem, Inc.
Business Acquisition [Line Items]
Cash		$ 4,920
Common shares		19,368
Total consideration transferred		24,995
Medistem, Inc. | Settlement of Promissory Notes
Business Acquisition [Line Items]
Total consideration transferred		$ 707

Mergers and Acquisitions - Fa48

Mergers and Acquisitions - Fair Value of Assets Acquired and Liabilities Assumed (Details) - USD ($) $ in Thousands	Aug. 08, 2014	Mar. 06, 2014	Apr. 30, 2015	Feb. 28, 2015	Jun. 30, 2015	Dec. 31, 2014	Jun. 30, 2014	Dec. 31, 2013
Business Acquisition [Line Items]
Goodwill					$ 118,965	$ 101,059	$ 34,865	$ 13,823
ActoGeniX NV
Business Acquisition [Line Items]
Total consideration				$ 72,474
ActoGeniX NV | Scenario, Plan
Business Acquisition [Line Items]
Cash				3,180
Other receivables				305
Prepaid expenses and other				31
Property, plant and equipment				209
Intangible assets				68,100
Other assets				23
Total assets acquired				71,848
Accounts payable				230
Accrued compensation and benefits				624
Other accrued liabilities				307
Deferred revenue				732
Deferred tax liability				612
Total liabilities assumed				2,505
Net assets acquired				69,343
Goodwill				3,131
Total consideration and fair value of noncontrolling interest				72,474
ActoGeniX NV | Scenario, Adjustment
Business Acquisition [Line Items]
Cash				0
Other receivables				0
Prepaid expenses and other				0
Property, plant and equipment				0
Intangible assets				0
Other assets				0
Total assets acquired				0
Accounts payable				0
Accrued compensation and benefits				(428)
Other accrued liabilities				(54)
Deferred revenue				0
Deferred tax liability				0
Total liabilities assumed				(482)
Net assets acquired				482
Goodwill				(482)
Total consideration and fair value of noncontrolling interest				0
ActoGeniX NV | Scenario, Actual
Business Acquisition [Line Items]
Cash				3,180
Other receivables				305
Prepaid expenses and other				31
Property, plant and equipment				209
Intangible assets				68,100
Other assets				23
Total assets acquired				71,848
Accounts payable				230
Accrued compensation and benefits				196
Other accrued liabilities				253
Deferred revenue				732
Deferred tax liability				612
Total liabilities assumed				2,023
Net assets acquired				69,825
Goodwill				2,649
Total consideration and fair value of noncontrolling interest				$ 72,474
Okanagan Specialty Fruits Inc
Business Acquisition [Line Items]
Total consideration			$ 40,933
Okanagan Specialty Fruits Inc | Scenario, Plan
Business Acquisition [Line Items]
Cash			58
Trade receivables			16
Other receivables			49
Property, plant and equipment			32
Intangible assets			33,800
Total assets acquired			33,955
Accounts payable			181
Deferred revenue			181
Deferred tax liability			8,145
Total liabilities assumed			8,507
Net assets acquired			25,448
Goodwill			15,485
Total consideration			$ 40,933
Trans Ova Genetics, LC
Business Acquisition [Line Items]
Cash	$ 960
Trade receivables	18,693
Related party receivables	1,219
Inventory	18,476
Prepaid expenses and other	590
Property, plant and equipment	21,164
Intangible assets	23,700
Other assets	147
Total assets acquired	84,949
Accounts payable	3,317
Accrued compensation and benefits	913
Other accrued liabilities	271
Deferred revenue	4,458
Lines of credit	4,091
Related party payables	1,246
Long term debt	9,090
Total liabilities assumed	23,386
Net assets acquired	61,563
Goodwill	66,312
Total consideration and fair value of noncontrolling interest	127,875
Total consideration	$ 116,542
Medistem, Inc.
Business Acquisition [Line Items]
Cash		$ 8
Intangible assets		4,824
Total assets acquired		4,832
Accounts payable		644
Accrued compensation and benefits		67
Other accrued liabilities		50
Total liabilities assumed		761
Net assets acquired		4,071
Goodwill		20,924
Total consideration and fair value of noncontrolling interest		24,995
Total consideration		$ 24,995

Mergers and Acquisitions - Pro

Mergers and Acquisitions - Pro Forma Financial Information (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014	Jun. 30, 2015	Jun. 30, 2014
Business Acquisition, Pro Forma Information, Nonrecurring Adjustment [Line Items]
Loss before income taxes	$ (40,560)	$ (53,218)	$ (13,961)	$ (49,663)
Net loss	(41,494)	(52,935)	(15,690)	(49,686)
Net loss attributable to the noncontrolling interests	831	892	2,124	1,758
2015 Business Acquisitions | Pro Forma
Business Acquisition, Pro Forma Information, Nonrecurring Adjustment [Line Items]
Revenues	44,891	11,851	78,929	19,759
Loss before income taxes	(40,734)	(56,161)	(18,411)	(55,295)
Net loss	(41,668)	(55,673)	(19,891)	(55,067)
Net loss attributable to the noncontrolling interests	831	892	2,124	1,758
Net loss attributable to Intrexon	$ (40,837)	(54,781)	$ (17,767)	(53,309)
2014 Business Acquisitions | Pro Forma
Business Acquisition, Pro Forma Information, Nonrecurring Adjustment [Line Items]
Revenues		34,911		57,122
Loss before income taxes		(48,265)		(46,953)
Net loss		(47,982)		(46,976)
Net loss attributable to the noncontrolling interests		1,085		2,031
Net loss attributable to Intrexon		$ (46,897)		$ (44,945)

Investments in Joint Ventures -

Investments in Joint Ventures - Additional Information (Details)	1 Months Ended
	Mar. 31, 2014USD ($)	Jan. 31, 2014USD ($)	Oct. 31, 2013USD ($)	Jun. 30, 2015USD ($)board_seat	Dec. 31, 2014USD ($)
Schedule Of Investments In Joint Venture [Line Items]
Investment				$ 2,960,000	$ 3,220,000
Intrexon Energy Partners, LLC
Schedule Of Investments In Joint Venture [Line Items]
Membership interest	50.00%
Additional capital contribution				$ 21,791,000
Number of board members designated by the Company | board_seat				2
Number of board members not designated by the Company | board_seat				3
Investment				$ (1,364,000)	(740,000)
Intrexon Energy Partners, LLC | Investors
Schedule Of Investments In Joint Venture [Line Items]
Membership interest	50.00%
Initial capital contribution	$ 25,000,000
Intrexon Energy Partners, LLC | Maximum
Schedule Of Investments In Joint Venture [Line Items]
Additional capital contribution	25,000,000
Intrexon Energy Partners, LLC | Maximum | Investors
Schedule Of Investments In Joint Venture [Line Items]
Additional capital contribution	25,000,000
OvaXon, LLC
Schedule Of Investments In Joint Venture [Line Items]
Membership interest		50.00%
Initial capital contribution		$ 1,500,000
Number of board members designated by the Company | board_seat				2
Number of board members not designated by the Company | board_seat				2,000
Investment				$ 557,000	(83,000)
S & I Ophthalmic, LLC
Schedule Of Investments In Joint Venture [Line Items]
Membership interest			50.00%
Initial capital contribution			$ 5,000,000
Number of board members designated by the Company | board_seat				2
Number of board members not designated by the Company | board_seat				2,000
Investment				$ 2,403,000	$ 3,220,000
Upfront | Upfront and Milestone Payments | Intrexon Energy Partners, LLC
Schedule Of Investments In Joint Venture [Line Items]
Collaborative arrangement consideration received, value	$ 25,000,000

Collaboration and Licensing R51

Collaboration and Licensing Revenue - Summarized Amount of Collaboration Recorded in Consolidated Statements of Income (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014	Jun. 30, 2015	Jun. 30, 2014
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	$ 17,181	$ 11,764	$ 31,964	$ 19,601
ZIOPHARM Oncology, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	5,250	4,341	9,051	7,021
Oragenics, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	375	313	645	1,108
Fibrocell Science, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	1,918	1,331	4,079	2,641
Genopaver, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	935	491	1,604	981
S & I Ophthalmic, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	890	607	1,645	1,486
OvaXon, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	662	579	1,306	748
Intrexon Energy Partners, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	3,356	1,835	6,166	1,835
Persea Bio, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	266		506
Ares Trading S.A.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	739		739
Other Collaborations
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	2,790	2,267	6,223	3,781
Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	3,703	2,517	6,734	4,399
Upfront and Milestone Payments | ZIOPHARM Oncology, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	644	644	1,288	1,288
Upfront and Milestone Payments | Oragenics, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	307	261	569	523
Upfront and Milestone Payments | Fibrocell Science, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	448	448	896	896
Upfront and Milestone Payments | Genopaver, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	68	68	137	137
Upfront and Milestone Payments | S & I Ophthalmic, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	0	0	0	0
Upfront and Milestone Payments | OvaXon, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	0	0	0	0
Upfront and Milestone Payments | Intrexon Energy Partners, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	625	625	1,250	625
Upfront and Milestone Payments | Persea Bio, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	125		250
Upfront and Milestone Payments | Ares Trading S.A.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	739		739
Upfront and Milestone Payments | Other Collaborations
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	747	471	1,605	930
Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	13,478	9,247	25,230	15,202
Research and Development Services | ZIOPHARM Oncology, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	4,606	3,697	7,763	5,733
Research and Development Services | Oragenics, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	68	52	76	585
Research and Development Services | Fibrocell Science, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	1,470	883	3,183	1,745
Research and Development Services | Genopaver, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	867	423	1,467	844
Research and Development Services | S & I Ophthalmic, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	890	607	1,645	1,486
Research and Development Services | OvaXon, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	662	579	1,306	748
Research and Development Services | Intrexon Energy Partners, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	2,731	1,210	4,916	1,210
Research and Development Services | Persea Bio, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	141		256
Research and Development Services | Ares Trading S.A.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	0		0
Research and Development Services | Other Collaborations
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration And Licensing Revenue	$ 2,043	$ 1,796	$ 4,618	$ 2,851

Collaboration and Licensing R52

Collaboration and Licensing Revenue - Additional Information (Details)	Mar. 26, 2014USD ($)	Jan. 10, 2014USD ($)shares	Dec. 18, 2013shares	Sep. 30, 2013USD ($)shares	Jun. 28, 2013USD ($)shares	Apr. 30, 2013	Mar. 29, 2013USD ($)	Feb. 14, 2013	Oct. 24, 2012USD ($)shares	Oct. 05, 2012USD ($)shares	Jun. 05, 2012USD ($)shares	Jan. 06, 2011USD ($)shares	Jun. 30, 2015USD ($)	May. 31, 2015USD ($)	Dec. 31, 2014USD ($)	Jun. 30, 2015USD ($)	Jun. 30, 2014USD ($)	Jun. 30, 2015USD ($)	Jun. 30, 2014USD ($)
Collaboration and Licensing Agreements [Line Items]
Related party payables													$ 57,584,000		$ 214,000	$ 57,584,000		$ 57,584,000
Deferred revenue													180,010,000		113,209,000	180,010,000		180,010,000
Trade, net													141,133,000		14,582,000	141,133,000		141,133,000
Other assets													6,483,000		$ 1,271,000	6,483,000		6,483,000
Collaboration And Licensing Revenue																17,181,000	$ 11,764,000	31,964,000	$ 19,601,000
Ares Trading S.A.
Collaboration and Licensing Agreements [Line Items]
Trade, net													5,000,000			5,000,000		5,000,000
Other assets													5,000,000			5,000,000		5,000,000
Collaborative agreement additional target fee														$ 5,000,000
Maximum milestone payments required upon successful achievement, per product														413,000
Maximum milestone payments required upon successful achievement, one-time														$ 50,000,000
Required notice period for voluntary termination of collaborative agreement														90 days
Collaboration And Licensing Revenue																739,000		$ 739,000
Ares Trading S.A. | ZIOPHARM Oncology, Inc.
Collaboration and Licensing Agreements [Line Items]
Collaboration Arrangement, Percent Of Collaboration Payments																		50.00%
Related party payables													57,500,000			57,500,000		$ 57,500,000
ZIOPHARM Oncology, Inc.
Collaboration and Licensing Agreements [Line Items]
Required notice period for voluntary termination of collaborative agreement												90 days
Collaboration And Licensing Revenue																5,250,000	4,341,000	9,051,000	7,021,000
Percent of shares outstanding at the date of achievement of future milestone												7.495%
Royalty rate as a percentage of net profit												50.00%
Oragenics ECC 1
Collaboration and Licensing Agreements [Line Items]
Required notice period for voluntary termination of collaborative agreement											90 days
Percent of shares outstanding at the date of achievement of future milestone											1.00%
Royalty rate as a percentage of net profit											25.00%
Percentage of shares outstanding at the date of achievement of future milestone 2											1.50%
Percentage of shares outstanding at the date of achievement of future milestone 3											2.00%
Percentage of shares outstanding at the date of achievement of future milestone 4											2.50%
Percentage of shares outstanding at the date of achievement of future milestone 5											3.00%
Oragenics ECC 2
Collaboration and Licensing Agreements [Line Items]
Required notice period for voluntary termination of collaborative agreement				90 days
Consideration to be received upon achievement of future milestone 1																	2,000,000		2,000,000
Consideration to be received upon achievement of future milestone 2																	5,000,000		5,000,000
Consideration to be received upon achievement of future milestone 3																	10,000,000		10,000,000
Royalty rate as a percentage of net sales, tier 1				10.00%
Oragenics ECC 3
Collaboration and Licensing Agreements [Line Items]
Maximum milestone payments required upon successful achievement, per product													22,000
Maximum milestone payments required upon successful achievement, one-time													$ 10,000
Required notice period for voluntary termination of collaborative agreement													90 days
Fibrocell Science, Inc.
Collaboration and Licensing Agreements [Line Items]
Required notice period for voluntary termination of collaborative agreement										90 days
Collaboration And Licensing Revenue																1,918,000	1,331,000	4,079,000	2,641,000
Royalty rate as a percentage of net sales, tier 1										7.00%
Reverse stock split ratio						1-for-25
Reverse stock split, conversion ratio						0.04
Level of net sales at which royalty rate changes to tier 2										$ 25,000,000
Royalty rate as a percentage of net sales, tier 2										14.00%
Royalty rate of savings from improvement										33.00%
Genopaver, LLC
Collaboration and Licensing Agreements [Line Items]
Required notice period for voluntary termination of collaborative agreement							90 days
Collaboration And Licensing Revenue																935,000	491,000	1,604,000	981,000
AquaBounty Technologies, Inc.
Collaboration and Licensing Agreements [Line Items]
Royalty rate as a percentage of gross profit								16.66%
S & I Ophthalmic, LLC
Collaboration and Licensing Agreements [Line Items]
Required notice period for voluntary termination of collaborative agreement				90 days
Collaboration And Licensing Revenue																890,000	607,000	1,645,000	1,486,000
OvaXon, LLC
Collaboration and Licensing Agreements [Line Items]
Required notice period for voluntary termination of collaborative agreement			90 days
Collaboration And Licensing Revenue																662,000	579,000	1,306,000	748,000
Intrexon Energy Partners, LLC
Collaboration and Licensing Agreements [Line Items]
Required notice period for voluntary termination of collaborative agreement	90 days
Collaboration And Licensing Revenue																3,356,000	1,835,000	6,166,000	1,835,000
Persea Bio, LLC
Collaboration and Licensing Agreements [Line Items]
Required notice period for voluntary termination of collaborative agreement															90 days
Collaboration And Licensing Revenue																266,000		506,000
Upfront and Milestone Payments
Collaboration and Licensing Agreements [Line Items]
Deferred revenue													$ 163,094,000		$ 107,228,000	163,094,000		163,094,000
Collaboration And Licensing Revenue																3,703,000	2,517,000	6,734,000	4,399,000
Upfront and Milestone Payments | Ares Trading S.A.
Collaboration and Licensing Agreements [Line Items]
Deferred revenue													56,761,000			56,761,000		56,761,000
Collaboration And Licensing Revenue																739,000		739,000
Upfront and Milestone Payments | ZIOPHARM Oncology, Inc.
Collaboration and Licensing Agreements [Line Items]
Deferred revenue													21,905,000		23,193,000	21,905,000		21,905,000
Collaboration And Licensing Revenue																644,000	644,000	1,288,000	1,288,000
Upfront and Milestone Payments | ZIOPHARM Oncology, Inc. | Upfront
Collaboration and Licensing Agreements [Line Items]
Collaborative arrangement consideration received, value												$ 17,457,000
Collaborative arrangement consideration received, shares | shares												3,636,926
Upfront and Milestone Payments | ZIOPHARM Oncology, Inc. | Milestone One
Collaboration and Licensing Agreements [Line Items]
Collaborative arrangement consideration received, value									$ 18,330,000
Collaborative arrangement consideration received, shares | shares									3,636,926
Upfront and Milestone Payments | Ziopharm Oncology ECC Separate Unit of Accounting | Upfront
Collaboration and Licensing Agreements [Line Items]
Collaboration And Licensing Revenue												$ 1,115,000
Upfront and Milestone Payments | Ziopharm Oncology ECC Unit of Accounting One | Upfront
Collaboration and Licensing Agreements [Line Items]
Deferred revenue												$ 16,342,000
Upfront and Milestone Payments | Oragenics ECC 1
Collaboration and Licensing Agreements [Line Items]
Deferred revenue													4,896,000		5,171,000	4,896,000		4,896,000
Upfront and Milestone Payments | Oragenics ECC 1 | Upfront
Collaboration and Licensing Agreements [Line Items]
Collaborative arrangement consideration received, value											$ 6,588,000
Collaborative arrangement consideration received, shares | shares											4,392,425
Upfront and Milestone Payments | Oragenics ECC 2
Collaboration and Licensing Agreements [Line Items]
Deferred revenue													4,591,000		4,839,000	4,591,000		4,591,000
Upfront and Milestone Payments | Oragenics ECC 2 | Upfront
Collaboration and Licensing Agreements [Line Items]
Collaborative arrangement consideration received, value				$ 3,503,000
Collaborative arrangement consideration received, shares | shares				1,348,000
Collaborative arrangement consideration received, value of convertible promissory note				$ 1,956,000
Conversion of promissory note into Common stock | shares			698,241
Upfront and Milestone Payments | Oragenics ECC 3
Collaboration and Licensing Agreements [Line Items]
Deferred revenue													4,954,000			4,954,000		4,954,000
Upfront and Milestone Payments | Oragenics ECC 3 | Upfront
Collaboration and Licensing Agreements [Line Items]
Collaborative arrangement consideration received, value of convertible promissory note													5,000,000
Upfront and Milestone Payments | Fibrocell Science, Inc.
Collaboration and Licensing Agreements [Line Items]
Deferred revenue													16,595,000		17,491,000	16,595,000		16,595,000
Collaboration And Licensing Revenue																448,000	448,000	896,000	896,000
Upfront and Milestone Payments | Fibrocell Science, Inc. | Upfront
Collaboration and Licensing Agreements [Line Items]
Collaborative arrangement consideration received, value										$ 7,576,000
Collaborative arrangement consideration received, shares | shares										1,317,520
Upfront and Milestone Payments | Fibrocell Science, Inc. | Supplemental Upfront
Collaboration and Licensing Agreements [Line Items]
Collaborative arrangement consideration received, value		$ 5,225,000			$ 7,612,000
Collaborative arrangement consideration received, shares | shares		1,024,590			1,243,781
Upfront and Milestone Payments | Genopaver, LLC
Collaboration and Licensing Agreements [Line Items]
Deferred revenue													2,386,000		2,523,000	2,386,000		2,386,000
Collaboration And Licensing Revenue																68,000	68,000	137,000	137,000
Upfront and Milestone Payments | Genopaver, LLC | Upfront
Collaboration and Licensing Agreements [Line Items]
Collaborative arrangement consideration received, value							$ 3,000,000
Upfront and Milestone Payments | S & I Ophthalmic, LLC
Collaboration and Licensing Agreements [Line Items]
Collaboration And Licensing Revenue																0	0	0	0
Upfront and Milestone Payments | OvaXon, LLC
Collaboration and Licensing Agreements [Line Items]
Collaboration And Licensing Revenue																0	0	0	0
Upfront and Milestone Payments | Intrexon Energy Partners, LLC
Collaboration and Licensing Agreements [Line Items]
Deferred revenue													21,875,000		23,125,000	21,875,000		21,875,000
Collaboration And Licensing Revenue																625,000	$ 625,000	1,250,000	$ 625,000
Upfront and Milestone Payments | Intrexon Energy Partners, LLC | Upfront
Collaboration and Licensing Agreements [Line Items]
Collaborative arrangement consideration received, value	$ 25,000,000
Upfront and Milestone Payments | Persea Bio, LLC
Collaboration and Licensing Agreements [Line Items]
Deferred revenue													4,750,000		5,000,000	4,750,000		4,750,000
Collaboration And Licensing Revenue																125,000		250,000
Upfront and Milestone Payments | Persea Bio, LLC | Upfront
Collaboration and Licensing Agreements [Line Items]
Collaborative arrangement consideration received, value															5,000,000
Prepaid Research and Development Services
Collaboration and Licensing Agreements [Line Items]
Deferred revenue													11,496,000		$ 1,045,000	11,496,000		11,496,000
Prepaid Research and Development Services | Ares Trading S.A.
Collaboration and Licensing Agreements [Line Items]
Deferred revenue													$ 10,000,000			$ 10,000,000		$ 10,000,000
Accounts Receivable [Member] | Upfront and Milestone Payments | Ares Trading S.A. | Upfront
Collaboration and Licensing Agreements [Line Items]
Collaborative arrangement consideration received, value														$ 115,000,000

Collaboration and Licensing R53

Collaboration and Licensing Revenue - Summary of Deferred Revenue (Details) - USD ($) $ in Thousands	Jun. 30, 2015	Dec. 31, 2014
Deferred Revenue Arrangement [Line Items]
Current portion of deferred revenue	$ 28,737	$ 16,522
Long-term portion of deferred revenue	151,273	96,687
Deferred revenue	180,010	113,209
Upfront and Milestone Payments
Deferred Revenue Arrangement [Line Items]
Deferred revenue	163,094	107,228
Prepaid Research and Development Services
Deferred Revenue Arrangement [Line Items]
Deferred revenue	11,496	1,045
Prepaid Product and Service Revenues
Deferred Revenue Arrangement [Line Items]
Deferred revenue	4,679	4,365
Other
Deferred Revenue Arrangement [Line Items]
Deferred revenue	$ 741	$ 571

Short-term and Long-term Inve54

Short-term and Long-term Investments - Summary of Amortized Cost, Gross Unrealized Gains and Losses and Fair Value of Short-term Investments (Details) - USD ($) $ in Thousands	Jun. 30, 2015	Dec. 31, 2014
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	$ 67,370	$ 115,566
Gross Unrealized Gains	61	54
Gross Unrealized Losses	0	(12)
Aggregate Fair Value	67,431	115,608
U.S. government debt securities
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	67,097	115,293
Gross Unrealized Gains	61	54
Gross Unrealized Losses	0	(12)
Aggregate Fair Value	67,158	115,335
Certificates of deposit
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	273	273
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Aggregate Fair Value	$ 273	$ 273

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	Jun. 30, 2015	Dec. 31, 2014
Assets
Fair value of financial assets measured at fair value on a recurring basis	$ 169,763	$ 280,497
U.S. government debt securities
Assets
Fair value of financial assets measured at fair value on a recurring basis	67,158	115,335
Equity Securities
Assets
Fair value of financial assets measured at fair value on a recurring basis	101,896	164,889
Other
Assets
Fair value of financial assets measured at fair value on a recurring basis	709	273
Quoted Prices in Active Markets (Level 1)
Assets
Fair value of financial assets measured at fair value on a recurring basis	84,547	143,927
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	84,547	143,927
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	85,216	136,570
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	67,158	115,335
Significant Other Observable Inputs (Level 2) | Equity Securities
Assets
Fair value of financial assets measured at fair value on a recurring basis	17,349	20,962
Significant Other Observable Inputs (Level 2) | Other
Assets
Fair value of financial assets measured at fair value on a recurring basis	709	273
Significant Unobservable Inputs (Level 3)
Assets
Fair value of financial assets measured at fair value on a recurring basis	0	0
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) | 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 ($)	Jun. 30, 2015	Mar. 31, 2015
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of assets transferred from Level 2 to Level 1	$ 0
Equity Securities
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of assets transferred from Level 2 to Level 1		$ 7,200,000

Inventory - Schedule of Invento

Inventory - Schedule of Inventory (Details) - USD ($) $ in Thousands	Jun. 30, 2015	Dec. 31, 2014
Inventory [Line Items]
Inventory	$ 27,001	$ 25,789
Supplies, semen and embryos
Inventory [Line Items]
Inventory	1,587	1,184
Work in process
Inventory [Line Items]
Inventory	6,844	5,637
Livestock
Inventory [Line Items]
Inventory	17,682	16,996
Feed
Inventory [Line Items]
Inventory	$ 888	$ 1,972

Property, Plant and Equipment58

Property, Plant and Equipment, net - Schedule of Property Plant and Equipment (Details) - USD ($) $ in Thousands	Jun. 30, 2015	Dec. 31, 2014
Property, Plant and Equipment [Abstract]
Land and land improvements	$ 8,975	$ 7,565
Buildings and building improvements	7,208	7,265
Furniture and fixtures	1,309	1,236
Equipment	34,495	31,983
Leasehold improvements	6,572	6,382
Computer hardware and software	5,514	5,060
Construction in progress	1,851	1,002
Property, plant and equipment, gross	65,924	60,493
Less: Accumulated depreciation and amortization	(25,061)	(22,493)
Property, plant and equipment, net	$ 40,863	$ 38,000

Property, Plant and Equipment59

Property, Plant and Equipment, net - Additional Information (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014	Jun. 30, 2015	Jun. 30, 2014
Property, Plant and Equipment [Abstract]
Depreciation expense	$ 1,828	$ 1,281	$ 3,781	$ 2,399

Goodwill and Intangible Asset60

Goodwill and Intangible Assets, net - Schedule of Changes in Carrying Amount of Goodwill (Details) - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014
Goodwill [Roll Forward]
Beginning balance	$ 101,059	$ 13,823
Acquisitions	18,134	21,042
Foreign currency translation adjustment	(228)	0
Ending balance	$ 118,965	$ 34,865

Goodwill and Intangible Asset61

Goodwill and Intangible Assets, net - Additional Information (Details) - USD ($)	3 Months Ended		6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014	Jun. 30, 2015	Jun. 30, 2014	Dec. 31, 2014
Goodwill and Intangible Assets Disclosure [Abstract]
Goodwill accumulated impairment losses	$ 0		$ 0		$ 0
Amortization expense	$ 1,981,000	$ 687,000	$ 3,577,000	$ 1,374,000

Goodwill and Intangible Asset62

Goodwill and Intangible Assets, net - Schedule of Intangible Assets (Details) - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2015	Dec. 31, 2014
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	$ 177,764	$ 77,900
Accumulated Amortization	(15,530)	(11,953)
Net	162,234	65,947
Patents, related technologies and know-how
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	75,318	41,872
Accumulated Amortization	(13,038)	(10,849)
Net	62,280	31,023
Customer relationships
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	10,700	10,700
Accumulated Amortization	(1,772)	(806)
Net	8,928	9,894
Trademarks
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	5,900	5,900
Accumulated Amortization	(655)	(298)
Net	5,245	5,602
Covenant not to compete
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	390
Accumulated Amortization	(65)
Net	325
In-process research and development
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	85,456	19,428
Accumulated Amortization	0	0
Net	$ 85,456	$ 19,428
Weighted Average | Patents, related technologies and know-how
Finite-Lived Intangible Assets [Line Items]
Weighted Average Useful Life (Years)	12 years 7 months 6 days
Weighted Average | Customer relationships
Finite-Lived Intangible Assets [Line Items]
Weighted Average Useful Life (Years)	6 years 6 months
Weighted Average | Trademarks
Finite-Lived Intangible Assets [Line Items]
Weighted Average Useful Life (Years)	8 years 4 months 24 days
Weighted Average | Covenant not to compete
Finite-Lived Intangible Assets [Line Items]
Weighted Average Useful Life (Years)	2 years

Lines of Credit and Long Term63

Lines of Credit and Long Term Debt - Lines of Credit - Additional Information (Details) - Jun. 30, 2015 - Revolving Line of Credit - USD ($)	Total
First National Bank of Omaha | Trans Ova Genetics, LC
Line of Credit Facility [Line Items]
Line of credit, maximum borrowing capacity	$ 6,000,000
Stated fixed interest rate	3.00%
Actual interest rate at period end	3.14%
Line of credit, outstanding balance	$ 208,000
Line of credit, available borrowing capacity	$ 5,792,000
First National Bank of Omaha | Trans Ova Genetics, LC | London Interbank Offered Rate (LIBOR)
Line of Credit Facility [Line Items]
Basis spread on variable rate	2.95%
American State Bank | Exemplar Genetics, LLC
Line of Credit Facility [Line Items]
Line of credit, maximum borrowing capacity	$ 700,000
Line of credit, outstanding balance	665,000
Line of credit, available borrowing capacity	$ 35,000
Interest rate	4.50%

Lines of Credit and Long Term64

Lines of Credit and Long Term Debt - Components of Long Term Debt (Details) - USD ($) $ in Thousands	Jun. 30, 2015	Dec. 31, 2014
Debt Instrument [Line Items]
Long-term debt	$ 9,467	$ 10,369
Current portion of long term debt	1,427	1,675
Long term debt, net of current portion	8,040	8,694
Notes payable
Debt Instrument [Line Items]
Long-term debt	7,066	7,653
Royalty-based financing
Debt Instrument [Line Items]
Long-term debt	1,944	1,926
Other
Debt Instrument [Line Items]
Long-term debt	$ 457	$ 790

Lines of Credit and Long Term65

Lines of Credit and Long Term Debt - Long Term Debt - Additional Information (Details) - USD ($)	6 Months Ended
	Jun. 30, 2015	Dec. 31, 2014	Mar. 15, 2013
Debt Instrument [Line Items]
Outstanding principal balance	$ 9,467,000	$ 10,369,000
Notes payable to banks | Trans Ova Genetics, LC | American State Bank
Debt Instrument [Line Items]
Outstanding principal balance	5,780,000
Periodic payment amount	$ 39,000
Interest rate	3.95%
Notes payable
Debt Instrument [Line Items]
Outstanding principal balance	$ 7,066,000	7,653,000
Notes payable | Trans Ova Genetics, LC | Iowa Economic Development Authority
Debt Instrument [Line Items]
Outstanding principal balance	733,000
Periodic principal payment amount	183,000
Notes payable | Exemplar Genetics, LLC
Debt Instrument [Line Items]
Outstanding principal balance	553,000
Notes payable | Exemplar Genetics, LLC | Minimum
Debt Instrument [Line Items]
Periodic payment amount	$ 1,000
Interest rate	0.00%
Notes payable | Exemplar Genetics, LLC | Maximum
Debt Instrument [Line Items]
Periodic payment amount	$ 4,000
Interest rate	3.00%
Royalty-based financing
Debt Instrument [Line Items]
Outstanding principal balance	$ 1,944,000	$ 1,926,000
Royalty-based financing | AquaBounty Technologies, Inc. | Atlantic Canada Opportunities Agency
Debt Instrument [Line Items]
Outstanding principal balance	1,944,000
Amount available under financial grant for research and development	$ 2,324,000
Period to claim funding from government award	5 years
Royalty rate to be paid	10.00%
Amount claimed under financial grant			$ 1,952,000
Long term debt			1,107,000
Accreted difference between face value of amount drawn and acquisition date fair value			$ 845,000

Lines of Credit and Long Term66

Lines of Credit and Long Term Debt - Schedule of Future Maturities of Long Term Debt (Details) $ in Thousands	Jun. 30, 2015USD ($)
Maturities of Long-term Debt [Abstract]
2,015	$ 809
2,016	897
2,017	365
2,018	512
2,019	339
2,020	308
Thereafter	4,293
Long-term Debt	$ 7,523

Income Taxes - Additional Infor

Income Taxes - Additional Information (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014	Jun. 30, 2015	Jun. 30, 2014
Operating Loss Carryforwards [Line Items]
Taxable income (loss)	$ 65,400	$ (14,100)	$ 38,800	$ 1,200
Current income tax expense (benefit)	777	(283)	777	23
Deferred income tax expense (benefit)	157	$ 0	952	$ 0
Deferred tax liabilities	9,609		9,609
Domestic Tax Authority
Operating Loss Carryforwards [Line Items]
Operating loss carryforwards	215,700		215,700
Federal and state research and development tax credits	6,800		$ 6,800
Expiration date of Federal income tax loss carryforwards			2,022
Domestic Tax Authority | Stock Compensation Deductions
Operating Loss Carryforwards [Line Items]
Operating loss carryforwards	25,800		$ 25,800
Foreign Tax Authority
Operating Loss Carryforwards [Line Items]
Operating loss carryforwards	$ 80,600		$ 80,600

Shareholders' Equity - Addition

Shareholders' Equity - Additional Information (Details) - USD ($) $ / shares in Units, $ in Thousands	Mar. 26, 2014	Jun. 30, 2015	Jan. 31, 2015	Jun. 30, 2015	Jun. 30, 2015	Jun. 30, 2014
Schedule of Capitalization, Equity [Line Items]
Securities purchase agreements, shares	972,004		4,312,500
Price per share of common stock	$ 25.72		$ 27
Proceeds from issuance of shares in a public offering, net of issuance costs			$ 110,041		$ 110,041	$ 0
Underwriting discounts and commissions			6,086
Offering expenses capitalized by the Company			$ 311
Securities purchase agreements gross proceed	$ 25,000				0	$ 25,000
Securities purchase agreements, value					$ 110,041
Affiliates of Third Security
Schedule of Capitalization, Equity [Line Items]
Securities purchase agreements, shares	243,001		555,556
Securities purchase agreements, value	$ 6,250
Overallotment Option Exercise By Underwriters
Schedule of Capitalization, Equity [Line Items]
Securities purchase agreements, shares			562,500
ZIOPHARM Oncology, Inc.
Schedule of Capitalization, Equity [Line Items]
Noncash dividend, shares		17,830,305
Realized gain on equity securities				$ 81,401

Shareholders' Equity - Componen

Shareholders' Equity - Components of Accumulated Other Comprehensive Income (Loss) (Details) - USD ($) $ in Thousands	Jun. 30, 2015	Dec. 31, 2014
Accumulated Other Comprehensive Income (Loss) [Line Items]
Accumulated other comprehensive loss	$ (2,285)	$ (4)
Unrealized gain on investments
Accumulated Other Comprehensive Income (Loss) [Line Items]
Accumulated other comprehensive loss	61	42
Foreign currency translation adjustments
Accumulated Other Comprehensive Income (Loss) [Line Items]
Accumulated other comprehensive loss	$ (2,346)	$ (46)

Stock Option Plans - Additional

Stock Option Plans - Additional Information (Details) - USD ($) $ / shares in Units, $ in Thousands	6 Months Ended	12 Months Ended
	Jun. 30, 2015	Dec. 31, 2014
Intrexon Stock Option Plan - 2008 Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Options outstanding	1,477,951
Intrexon Stock Option Plan 2013 Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Options outstanding	8,025,778
Number of authorized awards	13,000,000
Remaining shares available to grant	4,534,088
Intrexon Stock Option Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Options outstanding	9,503,729	8,323,544
Unrecognized compensation costs related to nonvested awards	$ 79,699	$ 62,281
Recognized over weighted-average period	3 years	3 years
Weighted average price of option	$ 26.08	$ 22.59
Exercisable at end of period	2,322,052
Aqua Bounty Stock Option Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Options outstanding	5,382,000	7,347,000
Weighted average price of option	$ 0.26	$ 0.31
Exercisable at end of period	4,320,333	6,171,520

Stock Option Plans - Stock Comp

Stock Option Plans - Stock Compensation Expense (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014	Jun. 30, 2015	Jun. 30, 2014
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock based compensation cost	$ 7,880	$ 6,848	$ 18,139	$ 10,622
Cost of products
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock based compensation cost	21	0	55	0
Cost of services
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock based compensation cost	105	0	203	0
Research and development
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock based compensation cost	2,138	1,364	3,907	1,712
Selling, general and administrative
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock based compensation cost	$ 5,616	$ 5,484	$ 13,974	$ 8,910

Stock Option Plans - Schedule o

Stock Option Plans - Schedule of Stock Option Activity (Details) - Intrexon Stock Option Plan - $ / shares		6 Months Ended	12 Months Ended
		Jun. 30, 2015	Dec. 31, 2014
Number of shares
Balances at beginning of period		8,323,544
Granted		1,849,000
Adjustment due to dividend		312,795
Exercised		(638,790)
Forfeited		(342,678)
Expired		(142)
Balances at end of period		9,503,729	8,323,544
Exercisable at end of period		2,322,052
Vested and Expected to Vest at end of period	[1]	7,930,652
Weighted average exercise price (usd per share)
Balances at beginning of period		$ 22.59
Granted		43.15
Adjustment due to dividend		25.40
Exercised		(16.25)
Forfeited		(27.77)
Expired		(7.12)
Balances at period end		26.08	$ 22.59
Exercisable, weighted average exercise price, at end of period		18.06
Vested and Expected to Vest, weighted average exercise price at end of period	[1]	$ 25.25
Weighted average remaining contractual term
Balances at period end, weighted average remaining contractual period		8 years 4 months 17 days	8 years 7 months 21 days
Exercisable at period end, weighted average remaining contractual period		7 years 11 days
Vested and Expected to Vest at period end, weighted average remaining contractual period	[1]	8 years 3 months 11 days
[1]	The number of stock options expected to vest takes into account an estimate of expected forfeitures.

License Agreement - Additional

License Agreement - Additional Information (Details) - USD ($)	1 Months Ended	6 Months Ended
	Jan. 31, 2015	Jun. 30, 2015
Other Commitments [Line Items]
Shares issued as consideration of license agreement (in shares)	2,100,085
Research and development
Other Commitments [Line Items]
Payment of license fees		$ 59,579,000
ZIOPHARM Oncology, Inc.
Other Commitments [Line Items]
Annual funding commitment, term	3 years
Minimum | ZIOPHARM Oncology, Inc.
Other Commitments [Line Items]
Annual funding commitment, amount	$ 15,000,000
Maximum | ZIOPHARM Oncology, Inc.
Other Commitments [Line Items]
Annual funding commitment, amount	$ 20,000,000

Commitments and Contingencies -

Commitments and Contingencies - Future Minimum Lease Payments Under Noncancelable Operating Leases (Details) $ in Thousands	Jun. 30, 2015USD ($)
Future Minimum Lease Payments
2,015	$ 1,656
2,016	4,013
2,017	2,714
2,018	1,362
2,019	1,276
2,020	1,311
Thereafter	1,120
Operating Leases, Future Minimum Payments Due, Total	$ 13,452

Commitments and Contingencies75

Commitments and Contingencies - Additional Information (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014	Jun. 30, 2015	Jun. 30, 2014
Commitments and Contingencies Disclosure [Abstract]
Rent expense	$ 2,247	$ 1,361	$ 4,381	$ 2,731
Rental income under sublease agreement	394	$ 171	819	$ 262
Future Rental Income
2,015	362		362
2,016	741		741
2,017	$ 96		$ 96

Related Party Transactions - Ad

Related Party Transactions - Additional Information (Details) - USD ($)	Dec. 07, 2014	Sep. 30, 2014	Nov. 20, 2013	Sep. 30, 2013	Mar. 31, 2015	Jun. 30, 2015	Jun. 30, 2014	Jun. 30, 2015	Jun. 30, 2014	Feb. 28, 2015	Dec. 31, 2014
Related Party Transaction [Line Items]
Compensation expense								$ 0	$ 977,000
Payments to acquire other investments								14,900,000	0
Value of warrants included in other assets						$ 169,763,000		169,763,000			$ 280,497,000
Third Security
Related Party Transaction [Line Items]
Total amount of expenses reimbursed						$ 111,000	$ 64,000	$ 152,000	88,000
Chief Executive Officer
Related Party Transaction [Line Items]
Compensation expense							507,000		977,000
AmpliPhi Biosciences Corp
Related Party Transaction [Line Items]
Common stock purchased from collaborative partners, shares					13,939,392
Warrants purchased from collaborative partners					3,484,848
Payments to acquire other investments					$ 2,300,000
ZIOPHARM Oncology, Inc.
Related Party Transaction [Line Items]
Common stock purchased from collaborative partners, value										$ 43,582,000
Histogenics Corporation
Related Party Transaction [Line Items]
Common stock purchased from collaborative partners, shares	1,772,364
Note receivable, stated interest rate		6.00%
Price per share of common shares	$ 11
Oragenics, Inc.
Related Party Transaction [Line Items]
Common stock purchased from collaborative partners, shares				1,300,000
Price per share of common shares				$ 3
Maximum percentage of shares of future securities offerings of collaborative partners to which the entity is entitled to purchase						30.00%		30.00%
Oragenics, Inc. | Share Purchase Rights Plan
Related Party Transaction [Line Items]
Common stock purchased from collaborative partners, shares			1,100,000
Price per share of common shares			$ 2.50
Related Parties, Aggregated
Related Party Transaction [Line Items]
Collaboration revenue						$ 15,239,000	$ 10,920,000	$ 28,035,000	$ 18,318,000
Common Stock | AmpliPhi Biosciences Corp
Related Party Transaction [Line Items]
Payments to acquire other investments					1,979,000
Warrants | AmpliPhi Biosciences Corp
Related Party Transaction [Line Items]
Payments to acquire other investments					$ 321,000
Value of warrants included in other assets						436,000		436,000
Upfront and Milestone Payments | Upfront | Histogenics Corporation
Related Party Transaction [Line Items]
Collaborative arrangement consideration received, value of convertible promissory note		$ 10,000,000
Maximum | Oragenics, Inc.
Related Party Transaction [Line Items]
Common stock purchase commitment						$ 10,000		$ 10,000

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		6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014	Jun. 30, 2015	Jun. 30, 2014
Numerator:
Net loss attributable to Intrexon	$ (40,663)	$ (52,043)	$ (13,566)	$ (47,928)
Denominator:
Weighted average shares outstanding, basic and diluted	109,318,471	98,892,601	107,720,040	98,113,493
Net loss attributable to Intrexon per share, basic and diluted (usd per share)	$ (0.37)	$ (0.53)	$ (0.13)	$ (0.49)

Net Loss per Share - Potentiall

Net Loss per Share - Potentially Dilutive Securities Excluded from Calculation of Net Loss per Share (Details) - shares	6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	9,723,750	8,995,681
Options
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	9,503,729	8,622,579
Warrants
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	220,021	373,102

Subsequent Events - Additional

Subsequent Events - Additional Information (Details) - Aug. 10, 2015 - Oxitec Limited - Subsequent Event - USD ($) $ in Thousands	Total
Subsequent Event [Line Items]
Percentage of outstanding common stock acquired	100.00%
Common shares	$ 80,000
Cash	$ 80,000