Exhibit
Number
Description of Document
10.12
Amended and Restated LicenseAgreement between the Registrant andAtlantic
Pharmaceuticals Limited dated November 30, 2009. Portions of this exhibit have been
omitted and separately filed with the SECwith a request for confidential treatment. (24)
10.13
Amended and Restated LicenseAgreement dated July 2, 2008 between the Registrant and
OncoGenex Technologies Inc. Portions of this exhibit have been omitted and separately filed
with the SECwith a request for confidential treatment. (17)
10.14
LeaseAgreement between the Registrant and BMR-Gazelle Court LLC datedMarch 30,
2010. Portions of this exhibit have been omitted and separately filed with the SECwith a
request for confidential treatment. (25)
10.15
SecondAmendment to LeaseAgreement datedMay 15, 2011 between the Registrant and
BMR-Gazelle Court LLC, with First Amendment to LeaseAgreement included. (10)
10.16
Registrant’s Amended and Restated Isis Pharmaceuticals, Inc. 10b5-1 Trading Plan dated
September 12, 2013. (34)
10.17*
Registrant’s Amended and Restated 2002 Non-Employee Directors’ Stock Option Plan, as
amended. (42)
10.18*
Registrant’s Form of 2002 Non-Employee Directors’ Stock OptionAgreement. (21)
10.19*
Form of Restricted Stock Unit Agreement for Restricted Stock Units granted under the Isis
Pharmaceuticals, Inc. 2002 Non-Employee Directors’ Stock Option Plan. (32)
10.20*
Amended and Restated SeveranceAgreement dated December 3, 2008 between the
Registrant and Stanley T. Crooke. (16)
10.21*
Amended and Restated SeveranceAgreement dated December 3, 2008 between the
Registrant and B. Lynne Parshall. (16)
10.22
Amended and Restated Strategic Collaboration and LicenseAgreement datedApril 28, 2009
between the Registrant andAlnylamPharmaceuticals, Inc. Portions of this exhibit have been
omitted and separately filed with the SECwith a request for confidential treatment. (20)
10.23*
Isis Pharmaceuticals, Inc. 2011 Equity Incentive Plan (19)
10.24
LoanAgreement dated October 15, 2008 between the Registrant and RBSAsset Finance,
Inc. (23)
10.25*
Form of OptionAgreement for Options granted under the 2011 Equity Incentive Plan. (29)
10.26*
Form of Restricted Stock Unit Agreement for Restricted Stock Units granted under the 2011
Equity Incentive Plan. (29)
10.27
SecondAmendment to LeaseAgreement between the Registrant and BMR-2282 Faraday
Avenue LLC datedMarch 30, 2010. Portions of this exhibit have been omitted and
separately filed with the SECwith a request for confidential treatment. (25)
10.28*
Form of OptionAgreement for Options Granted after March 8, 2005 under the 1989 Stock
Option Plan. (11)
10.29*
Form of OptionAgreement for Options Granted after March 8, 2005 under the 2000
Broad-Based Equity Incentive Plan. (11)
10.30*
Form of OptionAgreement for Options Granted after March 8, 2005 under the 2002
Non-Employee Director’s Stock Option Plan. (11)
129
