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	Jun. 30, 2013	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013 AstraZeneca Collaborations and Licensing Agreements	Sep. 30, 2013 AstraZeneca Collaborations and Licensing Agreements	Dec. 31, 2012 AstraZeneca Collaborations and Licensing Agreements	Jun. 30, 2013 AstraZeneca Agreement entered into in December 2012	Dec. 31, 2012 AstraZeneca Agreement entered into in December 2012 target program drug	Jun. 30, 2013 AstraZeneca Agreement entered into in December 2012	Sep. 30, 2013 AstraZeneca Agreement entered into in December 2012	Sep. 30, 2013 AstraZeneca Agreement entered into in December 2012 Pre-specified events	Sep. 30, 2013 AstraZeneca Agreement entered into in December 2012 Development milestones	Sep. 30, 2013 AstraZeneca Agreement entered into in December 2012 Regulatory milestones	Aug. 31, 2013 AstraZeneca Agreement entered into in August 2013	Sep. 30, 2013 AstraZeneca Agreement entered into in August 2013	Jun. 30, 2013 AstraZeneca Agreement entered into in August 2013	Sep. 30, 2013 AstraZeneca Agreement entered into in August 2013 Pre-specified events	Sep. 30, 2013 AstraZeneca Agreement entered into in August 2013 Development milestones	Sep. 30, 2013 AstraZeneca Agreement entered into in August 2013 Regulatory milestones	Sep. 30, 2013 Biogen Idec Collaborations and Licensing Agreements	Sep. 30, 2012 Biogen Idec Collaborations and Licensing Agreements	Sep. 30, 2013 Biogen Idec Collaborations and Licensing Agreements agreement	Sep. 30, 2012 Biogen Idec Collaborations and Licensing Agreements	Dec. 31, 2012 Biogen Idec Collaborations and Licensing Agreements	Mar. 31, 2013 Biogen Idec Agreement entered into in January 2012 payment	Jan. 31, 2012 Biogen Idec Agreement entered into in January 2012	Sep. 30, 2013 Biogen Idec Agreement entered into in January 2012	Oct. 31, 2013 Biogen Idec Agreement entered into in January 2012 payment	Sep. 30, 2013 Biogen Idec Agreement entered into in January 2012 Development milestones	Sep. 30, 2013 Biogen Idec Agreement entered into in January 2012 Regulatory milestones	Sep. 30, 2013 Biogen Idec Agreement entered into in January 2012 License fee and substantive milestones	Oct. 31, 2013 Biogen Idec Agreement entered into in June 2012	Jun. 30, 2012 Biogen Idec Agreement entered into in June 2012	Sep. 30, 2013 Biogen Idec Agreement entered into in June 2012	Sep. 30, 2013 Biogen Idec Agreement entered into in June 2012 Development milestones	Sep. 30, 2013 Biogen Idec Agreement entered into in June 2012 Regulatory milestones	Sep. 30, 2013 Biogen Idec Agreement entered into in June 2012 License fee and substantive milestones	Dec. 31, 2012 Biogen Idec Agreement entered into in December 2012 target	Sep. 30, 2013 Biogen Idec Agreement entered into in December 2012	Sep. 30, 2013 Biogen Idec Agreement entered into in December 2012 Development milestones	Sep. 30, 2013 Biogen Idec Agreement entered into in December 2012 Development milestones - new development candidate	Sep. 30, 2013 Biogen Idec Agreement entered into in December 2012 Regulatory milestones	Sep. 30, 2013 Biogen Idec Agreement entered into in December 2012 License fee and substantive milestones	Sep. 30, 2013 Biogen Idec Agreement entered into in September 2013	Sep. 30, 2013 Biogen Idec Agreement entered into in September 2013 Maximum	Sep. 30, 2013 Biogen Idec Agreement entered into in September 2013 Antisense drug for neurological disease Pre-specified events	Sep. 30, 2013 Biogen Idec Agreement entered into in September 2013 Antisense drug for neurological disease Development milestones	Sep. 30, 2013 Biogen Idec Agreement entered into in September 2013 Antisense drug for neurological disease Regulatory milestones	Sep. 30, 2013 Biogen Idec Agreement entered into in September 2013 Other modalities Pre-specified events	Sep. 30, 2013 Biogen Idec Agreement entered into in September 2013 Other modalities Development milestones	Sep. 30, 2013 Biogen Idec Agreement entered into in September 2013 Other modalities Regulatory milestones	Jan. 31, 2013 Genzyme Corporation Collaborations and Licensing Agreements	May 31, 2012 Genzyme Corporation Collaborations and Licensing Agreements	Jan. 31, 2008 Genzyme Corporation Collaborations and Licensing Agreements	Mar. 31, 2013 Genzyme Corporation Collaborations and Licensing Agreements	Sep. 30, 2012 Genzyme Corporation Collaborations and Licensing Agreements	Sep. 30, 2013 Genzyme Corporation Collaborations and Licensing Agreements	Sep. 30, 2012 Genzyme Corporation Collaborations and Licensing Agreements	Dec. 31, 2012 Genzyme Corporation Collaborations and Licensing Agreements	Sep. 30, 2013 Genzyme Corporation Collaborations and Licensing Agreements Minimum	Sep. 30, 2013 Genzyme Corporation Collaborations and Licensing Agreements Maximum	Sep. 30, 2013 Genzyme Corporation Collaborations and Licensing Agreements Pre-specified events	Sep. 30, 2013 Genzyme Corporation Collaborations and Licensing Agreements Regulatory milestones	Sep. 30, 2013 Genzyme Corporation Collaborations and Licensing Agreements Commercialization milestones	Sep. 30, 2013 Glaxo Smith Kline Collaborations and Licensing Agreements	Sep. 30, 2012 Glaxo Smith Kline Collaborations and Licensing Agreements	Sep. 30, 2013 Glaxo Smith Kline Collaborations and Licensing Agreements	Sep. 30, 2012 Glaxo Smith Kline Collaborations and Licensing Agreements	Dec. 31, 2012 Glaxo Smith Kline Collaborations and Licensing Agreements	Mar. 31, 2010 Glaxo Smith Kline Collaborations and Licensing Agreements Maximum program	Sep. 30, 2013 Glaxo Smith Kline Collaborations and Licensing Agreements Maximum program	Sep. 30, 2013 Glaxo Smith Kline Collaborations and Licensing Agreements Pre-specified events	Sep. 30, 2013 Glaxo Smith Kline Collaborations and Licensing Agreements Development milestones	Sep. 30, 2013 Glaxo Smith Kline Collaborations and Licensing Agreements Development milestones up to Phase 2 proof-of-concept	Sep. 30, 2013 Glaxo Smith Kline Collaborations and Licensing Agreements Regulatory milestones	Sep. 30, 2013 Glaxo Smith Kline Collaborations and Licensing Agreements Commercialization milestones	Dec. 31, 2012 Glaxo Smith Kline Collaborations and Licensing Agreements ISIS-TTR	Sep. 30, 2013 Glaxo Smith Kline Collaborations and Licensing Agreements ISIS-TTR	Jul. 31, 2013 Glaxo Smith Kline Collaborations and Licensing Agreements ISIS-TTR Development milestones	Feb. 28, 2013 Glaxo Smith Kline Collaborations and Licensing Agreements ISIS-TTR Development milestones	Sep. 30, 2013 Glaxo Smith Kline Collaborations and Licensing Agreements ISIS-TTR Development milestones	Sep. 30, 2013 Glaxo Smith Kline Collaborations and Licensing Agreements ISIS-GSK3 Development milestones	Apr. 30, 2013 Roche Collaborations and Licensing Agreements	Sep. 30, 2013 Roche Collaborations and Licensing Agreements	Sep. 30, 2013 Roche Collaborations and Licensing Agreements	Sep. 30, 2013 Roche Collaborations and Licensing Agreements Drug targeting HTT protein	Sep. 30, 2013 Roche Collaborations and Licensing Agreements Drug targeting HTT protein Pre-specified events	Sep. 30, 2013 Roche Collaborations and Licensing Agreements Drug targeting HTT protein Development milestones	Sep. 30, 2013 Roche Collaborations and Licensing Agreements Drug targeting HTT protein Regulatory milestones	Sep. 30, 2013 Roche Collaborations and Licensing Agreements Drug targeting HTT protein Commercialization milestones	Sep. 30, 2013 Roche Collaborations and Licensing Agreements Additional drugs Development milestones	Sep. 30, 2013 Roche Collaborations and Licensing Agreements Drug using Roche's proprietary brain shuttle technology Commercialization milestones	Sep. 30, 2013 Xenon Pharmaceuticals Inc. Collaborations and Licensing Agreements	Jun. 30, 2013 Xenon Pharmaceuticals Inc. Agreement entered into in November 2010	Jun. 30, 2013 Xenon Pharmaceuticals Inc. Agreement entered into in November 2010	Sep. 30, 2013 Xenon Pharmaceuticals Inc. Agreement entered into in November 2010	Sep. 30, 2013 Xenon Pharmaceuticals Inc. Agreement entered into in November 2010 Pre-specified events drug	Sep. 30, 2013 Xenon Pharmaceuticals Inc. Agreement entered into in November 2010 Development milestones	Sep. 30, 2013 Xenon Pharmaceuticals Inc. Agreement entered into in November 2010 Regulatory milestones	Sep. 30, 2013 Xenon Pharmaceuticals Inc. Agreement entered into in November 2010 Commercialization milestones	Oct. 31, 2013 CHDI Foundation, Inc. Collaborations and Licensing Agreements	Apr. 30, 2013 CHDI Foundation, Inc. Collaborations and Licensing Agreements	Sep. 30, 2013 CHDI Foundation, Inc. Collaborations and Licensing Agreements
Collaborative Arrangements and Licensing Agreements
Number of targets										5																														4
Upfront and near-term payments										$ 31,000,000
Upfront fee received									6,000,000	25,000,000	31,000,000					750,000												29,000,000							12,000,000					30,000,000						100,000,000										175,000,000																							2,500,000						30,000,000
Number of drugs the collaborative partner may license under a separate research program										3
Number of collaborations																								4
Period of exclusive rights to use antisense technology																																														6 years
Period during which a change in control could result in requirement to refund upfront payment																																														6 years	6 years
Equity investment in entity	173,200,000			173,292,000																																																				150,000,000
Equity investment in entity (in shares)	9,617,869																																																							5,000,000
Profit share as percentage of commercial sales																																																														30.00%	50.00%
Milestone payment earned				60,500,000																														10,000,000																				25,000,000			25,000,000																								2,000,000	7,500,000		7,000,000
Cumulative milestone payments earned under collaborative arrangement at period end																		10,000,000											5,500,000																																																				19,500,000
Number of milestone payments earned																														2
Number of programs under which drugs are to be developed										3																																																														6	5
Average maximum milestone payments receivable per program																																																																												20,000,000
Maximum amount of payments receivable													970,000,000	315,500,000	655,000,000				153,200,000	35,200,000	105,000,000										45,000,000	150,000,000	270,000,000				49,000,000	130,000,000	259,000,000			59,000,000						260,000,000	60,000,000	130,000,000	90,000,000	35,000,000	55,000,000											1,500,000,000	700,000,000	825,000,000								1,200,000,000	195,500,000		526,500,000	445,000,000					48,000,000						362,000,000	67,000,000	170,000,000	80,000,000		50,000,000					296,000,000	26,000,000	150,000,000	120,000,000
Number of milestone payments																											4
Next prospective milestone payment before amendment																											18,000,000
Next prospective milestone												50,000,000					3,200,000												1,500,000							14,000,000					10,000,000					10,000,000													25,000,000																					2,000,000								22,000,000										3,000,000
Maximum amount of payments receivable per drug under strategic alliance																																											10,000,000	130,000,000																																																	136,500,000
Maximum amount of payments receivable per program																																													259,000,000
Minimum annual net revenues to earn next milestone payment																																																											250,000,000
Number of independent products required to achieve pre-specified milestone events																																																																																																			2
Initial development cost contributed																																																											125,000,000
Period following an acquisition within which collaborator may purchase rights to receive payments																																																											180 days
Period for which additional shares of Isis common stock will not be purchased without consent																																																								10 years
Ownership percentage of Isis stock below which strategic partner may acquire additional shares without prior consent																																																											2.00%
Premium for which amortization was completed during the period																																																							100,000,000
License fee for which amortization was completed during the period																																																							175,000,000
Research and development revenue recognized		23,383,000	11,127,000	102,918,000	80,085,000																																																																																												1,500,000
License fee recognized		202,000	474,000	2,118,000	2,091,000																																																																																											2,000,000	2,000,000
Convertible promissory note repaid by Xenon																																																																																																1,500,000
Revenue earned		23,585,000	11,601,000	105,036,000	82,176,000	4,200,000	22,000,000															5,900,000	2,400,000	17,100,000	6,000,000																																	4,700,000	32,500,000	63,900,000							11,300,000	2,100,000	23,500,000	6,000,000																1,900,000	3,100,000								3,500,000										414,000
Percent of total revenue						18.00%	21.00%															25.00%		16.00%																																			31.00%								48.00%		22.00%
Deferred revenue						14,300,000	14,300,000	15,700,000														152,500,000		152,500,000		62,600,000																																			3,800,000						13,200,000		13,200,000		19,900,000															26,900,000	26,900,000
Expense reimbursement paid																																																																																																							$ 1,500,000	$ 1,500,000