0001047469-04-002335 Sample Contracts

AFFYMETRIX, INC. as Issuer and THE BANK OF NEW YORK as Trustee
Indenture • January 29th, 2004 • Affymetrix Inc • Laboratory analytical instruments • New York

INDENTURE, dated as of December 15, 2003, between Affymetrix, Inc., a corporation duly organized and existing under the laws of the State of Delaware, as Issuer (the “Company”), having its principal office at 3380 Central Expressway, Santa Clara, CA 95051 and The Bank of New York, a New York banking corporation, as Trustee (the “Trustee”).

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AFFYMETRIX, INC.
Registration Rights Agreement • January 29th, 2004 • Affymetrix Inc • Laboratory analytical instruments • New York

Affymetrix, Inc., a Delaware corporation (the “Company”), proposes to issue and sell (such issuance and sale, the “Initial Placement”) to the Initial Purchasers (as defined below), upon the terms set forth in a purchase agreement, dated December 10, 2003 (the “Purchase Agreement”), $100,000,000 aggregate principal amount, plus an option (the “Option”) to purchase up to an additional $20,000,000 aggregate principal amount, of its 0.75% Senior Convertible Notes due 2033 (the “Securities”). The Securities will be convertible into shares of Common Stock (as defined herein), at the conversion price set forth in the Offering Memorandum (as defined herein), as the same may be adjusted from time to time pursuant to the Indenture (as defined herein). As an inducement to you to enter into the Purchase Agreement and in satisfaction of a condition to your obligations thereunder, the Company agrees with you, (i) for your benefit and (ii) for the benefit of the Holders (as defined herein) from time

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