8-K

UNITED STATES
SECURITIES AND EXCHANGE COMMISSION

Washington, D. C. 20549

FORM 8-K

CURRENT REPORT

Pursuant to Section 13 or 15(d) of the
Securities Exchange Act of 1934

Date of Report (Date of earliest event reported): April 21, 2005

SOLEXA, INC.

(Exact name of registrant as specified in its charter)

Delaware
(State or other jurisdiction of incorporation)

000-22570
(Commission File No.) 94-3161073
(IRS Employer Identification No.)

25861 Industrial Blvd.
Hayward, California 94545
(Address of principal executive offices and zip code)

Registrant’s telephone number, including area code: (510) 670-9300

Check the appropriate box below if the Form 8-K filing is intended to simultaneously satisfy the filing obligation of the registrant under any of the following provisions (see General Instruction A.2. below):

o Written communications pursuant to Rule 425 under the Securities Act (17 CFR 230.425)

o Soliciting material pursuant to Rule 14a-12 under the Exchange Act (17 CFR 240.14a-12)

o Pre-commencement communications pursuant to Rule 14d-2(b) under the Exchange Act (17 CFR 240.14d-2(b))

o Pre-commencement communications pursuant to Rule 13e-4(c) under the Exchange Act (17 CFR 240.13e-4(c))

TABLE OF CONTENTS

	Item 1.01 Entry into a Material Definitive Agreement.
	Item 3.02 Unregistered Sales of Equity Securities.
	Item 5.02. Departure of Directors or Principal Officers; Election of Directors; Appointment of Principal Officers.
	Item 9.01. Financial Statements and Exhibits.
SIGNATURE
EXHIBITS
EXHIBIT 10.58
EXHIBIT 10.59
EXHIBIT 10.60
EXHIBIT 10.61
EXHIBIT 99.1
EXHIBIT 99.2

Item 1.01 Entry into a Material Definitive Agreement.

On April 21, 2005, Solexa, Inc., a Delaware corporation, (the “Company”) entered into a definitive agreement for a private placement of common stock and warrants to purchase common stock (the “Financing”). Under the terms of the Financing, the Company will sell approximately 8,125,000 shares of common stock at $4.00 per share and will issue warrants to purchase approximately 4,063,000 shares of common stock at an exercise price of $5.00 per share in two closings. Approximately 2,160,000 shares of common stock and warrants to purchase up to approximately 1,060,000 shares of common stock were issued at the first closing on April 25, 2005 (the “First Closing”) and the balance of approximately 6,005,000 shares of common stock and warrants to purchase approximately 3,002,000 shares of common stock will be issued on the same terms in a second closing (the “Second Closing”) subject to stockholder approval at the Company’s 2005 annual meeting of stockholders. Certain of the Company’s current stockholders, including funds affiliated with Abingworth Management Limited, Amadeus Capital Partners Limited, Oxford Bioscience Partners and SV Life Sciences are expected to invest a total of approximately $10,800,000 in the Financing at the Second Closing and have entered into agreements with the Company to vote in favor of the Financing at the 2005 annual meeting of stockholders. The Company has agreed to file with the Securities and Exchange Commission a resale registration statement relating to the common stock and the common stock issuable upon exercise of the warrants issued or issuable in connection with the Financing.

The warrants are exercisable 180 days after issuance and remain exercisable until the 5 year anniversary of issuance. The price of the warrants is subject to certain adjustments as set forth in the form of warrants attached hereto as Exhibits 10.59 and 10.60. The Purchase Agreement and related documents for the Financing are attached as Exhibits 10.58, 10.59, 10.60 and 99.1 and are incorporated herein by reference. A press release announcing the Financing is attached as Exhibit 99.2 hereto and is incorporated herein by reference.

The Company also entered into a letter agreement, dated April 21, 2005 with ValueAct Capital Master Fund, L.P. (“ValueAct”) (the “Letter Agreement”) pursuant to which ValueAct has the right to nominate one member of the Company’s Board of Directors under certain circumstances as described therein. The Letter Agreement is attached as Exhibit 10.61 hereto and is incorporated herein by reference.

Item 3.02 Unregistered Sales of Equity Securities.

See Item 1.01 above. The issuance and sale of the common stock and warrants at the First Closing and pursuant to the terms and conditions of the Purchase Agreement were exempt from registration in reliance upon Section 4(2) of the Securities Act of 1933, as amended (the “Securities Act”), and/or Regulation D of the Securities Act, for transactions by an issuer not involving a public offering.

Item 5.02. Departure of Directors or Principal Officers; Election of Directors; Appointment of Principal Officers.

(d) See Item 1.01 above. On April 19, 2005, the Board of Directors of the Company appointed G. Mason Morfit as a director of the Company effective and contingent upon the First Closing. Mr. Morfit is a partner of ValueAct.

Item 9.01. Financial Statements and Exhibits.

(c) Exhibits:

Exhibit
No.	Description
10.58	Securities Purchase Agreement, dated April 21, 2005, by and among the Company and the individuals and entities identified on the signature pages thereto.
10.59	Form of Warrant issued by the Company in favor of each investor except SF Capital Partners, Ltd.
10.60	Form of Warrant issued by the Company in favor of SF Capital Partners, Ltd.
10.61	Letter Agreement, dated April 21, 2005, between the Company and ValueAct Capital Master Fund, L.P.
99.1	Form of Amended and Restated Company Support Agreement between the Company and certain stockholders of the Company.
99.2	Press Release, dated April 22, 2005, entitled “Solexa Announces Agreement For $32.5 Million Private Equity Financing.”

SIGNATURE

     Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized.

	SOLEXA, INC.
Dated: April 26, 2005	By:	/s/ Kathy A. San Roman
		Name:	Kathy A. San Roman
		Title:	Vice President, Human Resources and Administration

EXHIBITS

Exhibit
No.	Description
10.58	Securities Purchase Agreement, dated April 21, 2005, by and among Solexa, Inc. and the individuals and entities identified on the signature pages thereto.
10.59	Form of Warrant issued by the Company in favor of each investor except SF Capital Partners, Ltd.
10.60	Form of Warrant issued by the Company in favor of SF Capital Partners, Ltd.
10.61	Letter Agreement, dated April 21, 2005, between the Company and ValueAct Capital Master Fund, L.P.
99.1	Form of Amended and Restated Company Support Agreement between the Company and certain stockholders of the Company.
99.2	Press Release, dated April 22, 2005, entitled “Solexa Announces Agreement For $32.5 Million Private Equity Financing.”

EX-10.58

EXHIBIT 10.58

SOLEXA, INC.

SECURITIES PURCHASE AGREEMENT

APRIL 21, 2005

Table Of Contents

		Page
ARTICLE 1	AUTHORIZATION AND SALE OF COMMON SHARES AND WARRANTS	1
1.1	Authorization	1
ARTICLE 2	CLOSING DATES; DELIVERY	2
2.1	Closing Dates. Delivery	2
ARTICLE 3	REPRESENTATIONS AND WARRANTIES OF THE COMPANY	3
3.1	Organization and Standing	3
3.2	Corporate Power; Authorization	3
3.3	Issuance and Delivery of the Shares	4
3.4	SEC Documents; Financial Statements	4
3.5	Governmental Consents	4
3.6	No Material Adverse Change	4
3.7	Authorized Capital Stock	5
3.8	Litigation	5
3.9	Eligibility to Use Form S-3	5
3.10	Company not an “Investment Company.”	5
3.11	NASDAQ Compliance	5
3.12	Use of Proceeds	5
3.13	Brokers and Finders	5
3.14	No Directed Selling Efforts or General Solicitation	6
3.15	No Integrated Offering	6
3.16	Private Placement	6
3.17	Internal Accounting Controls	6
3.18	Intellectual Property	6
3.19	Questionable Payments	7
3.20	Transactions with Affiliates	7
3.21	Disclosure	7
3.22	Dilution; Sales By Purchasers	7
ARTICLE 4	REPRESENTATIONS, WARRANTIES AND COVENANTS OF THE PURCHASERS	8
4.1	Authorization	8

-i-

Table Of Contents
(CONTINUED)

		Page
4.2	Investment Experience	8
4.3	Investment Intent	8
4.4	Registration or Exemption Requirements	9
4.5	Dispositions	9
4.6	No Legal, Tax or Investment Advice	9
4.7	Confidentiality	9
4.8	Residency	9
4.9	Governmental Review	9
4.10	Legend	10
4.11	Foreign Investors	11
ARTICLE 5	CONDITIONS TO CLOSING OBLIGATIONS OF PURCHASERS	11
5.1	Representations and Warranties	11
5.2	Covenants	11
5.3	Certificates	11
5.4	Legal Opinion	12
5.5	Amended and Restated Company Support Agreement	12
5.6	Listing	12
5.7	Officer’s Certificate	12
5.8	Judgments	12
5.9	Secretary’s Certificate	12
5.10	Stop Orders	12
5.11	Stockholder Approval	12
5.12	Minimum Investment	12
ARTICLE 6	CONDITIONS TO CLOSING OBLIGATIONS OF COMPANY	13
6.1	Receipt of Payment	13
6.2	Representations and Warranties	13
6.3	Covenants	13
6.4	Delivery of Purchaser Questionnaire	13
ARTICLE 7	COVENANTS	13
7.1	Definitions	13

-ii-

Table Of Contents
(CONTINUED)

		Page
7.2	Registration Procedures and Expenses	14
7.3	Indemnification	16
7.4	Prospectus Delivery	18
7.5	Termination of Obligations	19
7.6	Reporting Requirements	19
7.7	Blue Sky	19
7.8	Stockholder Approval	19
7.9	Publicity	20
ARTICLE 8	RESTRICTIONS ON TRANSFERABILITY OF SECURITIES; COMPLIANCE WITH SECURITIES ACT	20
8.1	Restrictions on Transferability	20
8.2	Instruction Sheet	20
8.3	Transfer of Securities	20
8.4	Purchaser Information	21
8.5	Material Non-Public Information	21
ARTICLE 9	MISCELLANEOUS	21
9.1	Termination	21
9.2	Waivers and Amendments	21
9.3	Broker’s Fee	22
9.4	Governing Law	22
9.5	Survival	22
9.6	Successors and Assigns	22
9.7	Entire Agreement	22
9.8	Notices, etc	22
9.9	Severability of this Agreement	22
9.10	Counterparts	23
9.11	Further Assurances	23
9.12	Currency	23
9.13	Waiver of Conflicts	23
A.	GENERAL INFORMATION	1

-iii-

Table Of Contents
(CONTINUED)

		Page
B.	SECURITIES HOLDINGS	1
C.	NASD QUESTIONS	5

Exhibit A – Form of Warrant

Exhibit B – Form of Purchaser’s Questionnaire

Exhibit C – Form of Company Counsel Opinion

Exhibit D – Instruction Sheet

Exhibit E – Form of Purchaser’s Certificate of Subsequent Sale

Exhibit F – Form of Amended and Restated Company Support Agreement

-iv-

SOLEXA, INC.

SECURITIES PURCHASE AGREEMENT

     This Securities Purchase Agreement (this “Agreement”) is made as of April 21, 2005, by and among Solexa, Inc. , a Delaware corporation (the “Company”) with its principal office at 25861 Industrial Boulevard, Hayward, California 94545, and the individuals and entities identified on the signature pages hereto (the “Purchasers”).

RECITALS

     Whereas, the Company has authorized the sale and issuance of the Common Shares and the Warrants (each as defined herein);

     Whereas, the Company and the Purchasers are executing and delivering this Agreement in reliance upon the exemption from securities registration afforded by the provisions of Regulation D, as promulgated by the SEC (as defined herein) under the Securities Act (as defined herein);

     Whereas, at the First Closing (as defined herein), the Company desires to sell, and each Purchaser desires severally, and not jointly, to purchase, the Shares and the Warrants, each as indicated below such Purchaser’s name on the applicable signature page of this Agreement upon the terms and conditions stated in this Agreement and at the Second Closing (as defined herein), if Stockholder Approval (as defined herein) is obtained, each Purchaser hereto desires severally, and not jointly, to purchase, the Shares and the Warrants, each as indicated below such Purchaser’s name on the applicable signature page of this Agreement upon the terms and conditions stated in this Agreement;

     Whereas, concurrent with the execution and delivery of this Agreement, as a material inducement to the Purchasers to enter into this Agreement, certain principal stockholders of the Company are entering into Amended and Restated Company Support Agreements, in the form attached hereto as Exhibit G; and

     Now, Therefore, in consideration of the foregoing recitals and the mutual promises, representations, warranties and covenants hereinafter set forth and for other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the parties hereto agree as follows:

ARTICLE 1

Authorization and Sale of Common Shares and Warrants

     1.1 Authorization. The Company has authorized (a) the sale and issuance of up to eight million one hundred twenty five thousand (8,125,000) shares (the “Common Shares”) of Company’s common stock, par value $0.01 per share (the “Common Stock”) at a price per shares of four dollars ($4.00) and (b) the sale and issuance of warrants, in the form attached hereto as Exhibit A, and in the case of SF Capital Partners Ltd., Exhibit A-1 (the “Warrants”),

1.

to purchase up to four million sixty two thousand five hundred two (4,062,502) shares of the Common Stock, at a price per share of five dollars ($5.00) (the “Warrant Price”) pursuant to this Agreement. The shares of Common Stock issuable upon exercise of or otherwise pursuant to the Warrants are referred to herein as the “Warrant Shares.” The Common Shares and the Warrant Shares are collectively referred to herein as the “Shares.” The Shares and the Warrants are collectively referred to herein as the “Securities.”

               (a) First Closing. Subject to the terms and conditions of this Agreement, including without limitation, the conditions set forth in Article 5 and Article 6 of this Agreement (excluding Stockholder Approval in Section 7.8), there shall be a closing at which the Company shall issue and sell, and each Purchaser, shall severally, and not jointly, purchase, the number of shares of Common Stock and the number of Warrants, in each case, in the respective amounts indicated below such Purchaser’s name on the applicable signature page of this Agreement, in exchange for the cash consideration set forth as the “First Closing Purchase Price” indicated below such Purchaser’s name on the signature page of this Agreement (the “First Closing”).

               (b) Second Closing. Subject to the terms and conditions of this Agreement, including without limitation, the conditions set forth in Article 5 and Article 6 of this Agreement (including Stockholder Approval in Section 7.8), at the Second Closing, there shall be a closing at which the Company shall issue and sell, and each Purchaser, shall severally, and not jointly, purchase, the number of shares of Common Stock and the number of Warrants, in each case, in the respective amounts indicated below such Purchaser’s name on the signature page of this Agreement, in exchange for the cash consideration set forth as the “Second Closing Purchase Price” indicated below such Purchaser’s name on the applicable signature page of this Agreement (the “Second Closing”).

ARTICLE 2

Closing Dates; Delivery

     2.1 Closing Dates. Delivery.

               (a) Location. The First Closing and Second Closing of the purchase and sale of the Common Shares and Warrants hereunder (together, the “Closings”) shall be held at the offices of Cooley Godward llp (“Cooley Godward”), 3175 Hanover Street, Palo Alto, California 94304, or at such other location upon which the Company and the Purchasers purchasing a majority of the Common Shares at the applicable Closing shall agree, on the applicable Closing Date.

               (b) First Closing. Subject to the satisfaction (or waiver) of the conditions thereto set forth in Article 5 and Article 6 of this Agreement, on the date hereof or at such other time and place upon which the Company and the Purchasers purchasing a majority of the Common Shares at the First Closing shall agree, the Company will deliver or cause to be delivered to each Purchaser, a duly executed Warrant and a certificate representing the number of Common Shares purchased by such Purchaser, registered in the Purchaser’s name as indicated

2.

on the Stock Certificate Questionnaire in the form attached hereto as Exhibit B-1. Such delivery shall be against payment of the purchase price therefor by each such Purchaser as set forth as the “First Closing Purchase Price” below their respective names on the signature page attached hereto by wire transfer of immediately available funds to the Company in accordance with the Company’s written wiring instructions. The date of the First Closing is hereinafter referred to as the “First Closing Date.”

               (b) Second Closing. Subject to the satisfaction (or waiver) of the conditions thereto set forth in Article 5 and Article 6 of this Agreement, on the date one (1) business day following the Company’s receipt of the Stockholder Approval (as defined herein), or at such other time and place upon which the Company and the Purchasers purchasing a majority of the Common Shares at the Second Closing shall agree, the Company will deliver or cause to be delivered to each Purchaser, a duly executed Warrant and a certificate representing the number of Common Shares purchased by such Purchaser, registered in the Purchaser’s name as indicated on the Stock Certificate Questionnaire in the form attached hereto as Exhibit B-1. Such delivery shall be against payment of the purchase price therefor by each such Purchaser as set forth as the “Second Closing Purchase Price” below their names on the signature page attached hereto by wire transfer of immediately available funds to the Company in accordance with the Company’s written wiring instructions. The date of the Second Closing is hereinafter referred to as the “Second Closing Date.”

ARTICLE 3

Representations and Warranties of the Company

     Except as set forth on the Disclosure Schedule delivered by the Company to the Purchasers herewith, the Company represents and warrants to the Purchasers on and as of the date hereof and on the applicable Closing Date:

     3.1 Organization and Standing. The Company is a corporation duly organized and validly existing under, and by virtue of, the laws of the State of Delaware and is in good standing as a domestic corporation under the laws of said state. The Company does not own or control any equity security or other interest of any corporation, limited partnership or other business entity.

     3.2 Corporate Power; Authorization. The Company has all requisite legal and corporate power and has taken all requisite corporate action to execute and deliver this Agreement, to sell and issue the Common Shares and Warrants, to issue the Warrant Shares upon exercise of the Warrants in accordance with the terms of such Warrants, and to carry out and perform all of its obligations under this Agreement. This Agreement constitutes, and upon execution and delivery by the Company of the Warrants, the Warrants will constitute, legal, valid and binding obligations of the Company, enforceable in accordance with their respective terms, except (a) as limited by applicable bankruptcy, insolvency, reorganization or similar laws relating to or affecting the enforcement of creditors’ rights generally and (b) as limited by equitable principles generally. The execution and delivery of this Agreement does not, and the

3.

performance of this Agreement and the compliance with the provisions hereof, the issuance, sale and delivery of the Common Shares and the Warrants by the Company will not materially conflict with, or result in a material breach or violation of the terms, conditions or provisions of, or constitute a material default under, or result in the creation or imposition of any material lien pursuant to the terms of, the Amended and Restated Certificate of Incorporation, as amended (the “Restated Certificate”) or Bylaws of the Company or any statute, law, rule or regulation or any state or federal order, judgment or decree or any indenture, mortgage, lease or other material agreement or instrument to which the Company or any of its properties is subject.

     3.3 Issuance and Delivery of the Shares. When issued in compliance with the provisions of this Agreement and the Restated Certificate, the Common Shares will be validly issued, fully paid and nonassessable. Upon exercise of the Warrants in accordance with the terms thereof, the Warrant Shares will be validly issued, fully paid and nonassessable. The issuance and delivery of the Common Shares and the Warrants is not subject to preemptive or any other similar rights of the stockholders of the Company or any liens or encumbrances.

     3.4 SEC Documents; Financial Statements. The Company has filed in a timely manner all documents that the Company was required to file with the Securities and Exchange Commission (the “SEC”) under Sections 13, 14(a) and 15(d) of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), during the twelve (12) months preceding the date of this Agreement. As of their respective filing dates, all documents filed by the Company with the SEC (the “SEC Documents”) complied in all material respects with the requirements of the Exchange Act or the Securities Act of 1933, as amended (the “Securities Act”), as applicable. None of the SEC Documents as of their respective dates contained any untrue statement of material fact or omitted to state a material fact required to be stated therein or necessary to make the statements made therein, in light of the circumstances under which they were made, not misleading. The financial statements of the Company included in the SEC Documents (the “Financial Statements”) comply as to form in all material respects with applicable accounting requirements and with the published rules and regulations of the SEC with respect thereto. The Financial Statements have been prepared in accordance with generally accepted accounting principles consistently applied and fairly present the consolidated financial position of the Company and any subsidiaries at the dates thereof and the consolidated results of their operations and consolidated cash flows for the periods then ended (subject, in the case of unaudited statements, to normal, recurring adjustments or to the extent that such unaudited statements do not include footnotes).

     3.5 Governmental Consents. No consent, approval, order or authorization of, or registration, qualification, designation, declaration or filing with, any federal, state, or local governmental authority on the part of the Company is required in connection with the consummation of the transactions contemplated by this Agreement except for (a) compliance with the securities and blue sky laws in the states in which the Common Shares and Warrants are offered and/or sold, which compliance will be effected in accordance with such laws, (b) the filing of the Registration Statement (as defined herein) and all amendments thereto with the SEC as contemplated by Section 7.2 of this Agreement and (c) the filing of the Nasdaq Market Notification Form with the Nasdaq SmallCap Market.

4.

     3.6 No Material Adverse Change. Except as otherwise disclosed herein or in the SEC Documents, since December 31, 2004, there have not been any changes in the assets, liabilities, financial condition, business prospects or operations of the Company from that reflected in the Financial Statements except changes in the ordinary course of business which have not been, either individually or in the aggregate, materially adverse.

     3.7 Authorized Capital Stock. The authorized capital stock of the Company consists of (a) sixty million (60,000,0000) shares of Common Stock, $0.01 par value, of which, as of April 19, 2005, seventeen million six hundred six thousand four hundred seventy one (17,606,471) shares were outstanding, and (b) two million (2,000,000) shares of Preferred Stock, $0.01 par value, none of which shares is currently outstanding. Except as described on Schedule 3.7 of the Disclosure Schedule, there are no outstanding warrants, options, convertible securities or other rights, agreements or arrangements of any character under which the Company is or may be obligated to issue any equity securities of any kind and except as contemplated by this Agreement.

     3.8 Litigation. Except as disclosed in the SEC Documents, there are no actions, suits proceedings or investigations pending or, to the best of the Company’s knowledge, threatened against the Company or any of its properties before or by any court or arbitrator or any governmental body, agency or official in which there is a reasonable likelihood (in the judgment of the Company) of an adverse decision that as the case may be, could have or reasonably be expected to result in (i) a material adverse effect on the legality, validity or enforceability of this Agreement or the Warrants, (ii) a material adverse effect on the results of operations, assets, business, prospects or financial condition of the Company and any subsidiaries, taken as a whole, or (iii) a material adverse effect on the Company’s ability to perform in any material respect on a timely basis its obligations under this Agreement or the Warrants.

     3.9 Eligibility to Use Form S-3. The Company is eligible to use Form S-3 for the registration of its securities under the Securities Act which are offered in transactions involving secondary offerings.

     3.10 Company not an “Investment Company.” The Company has been advised of the rules and requirements under the Investment Company Act of 1940, as amended (the “Investment Company Act”). The Company is not, and immediately after receipt of payment for the Shares will not be, an “investment company” or an entity “controlled” by an “investment company” within the meaning of the Investment Company Act and shall conduct its business in a manner so that it will not become subject to the Investment Company Act.

     3.11 NASDAQ Compliance. The Common Stock is registered pursuant to Section 12(g) of the Exchange Act and is listed on The Nasdaq Stock Market, Inc. SmallCap Market (the “Nasdaq SmallCap Market”), and the Company has taken no action designed to, or likely to have the effect of, terminating the registration of the Common Stock under the Exchange Act or de-listing the Common Stock from the Nasdaq SmallCap Market, nor has the Company received any notification that the SEC or the National Association of Securities Dealers, Inc. (the “NASD”) is contemplating terminating such registration or listing.

5.

     3.12 Use of Proceeds. The proceeds of the sale of the Common Shares and the Warrants hereunder shall be used by the Company for the repayment of that certain promissory note in the aggregate principal amount of three million dollars ($3,000,000) issued in favor of Silicon Valley Bank, working capital and general corporate purposes.

     3.13 Brokers and Finders. No person or entity will have, as a result of the transactions contemplated by this Agreement, any valid right, interest or claim against or upon the Company or a Purchaser for any commission, fee or other compensation pursuant to any agreement, arrangement or understanding entered into by or on behalf of the Company, other than SG Cowen & Co., LLC as lead agent.

     3.14 No Directed Selling Efforts or General Solicitation. Neither the Company nor any person or entity acting on its behalf has conducted any general solicitation or general advertising (as those terms are used in Regulation D) in connection with the offer or sale of any of the Securities.

     3.15 No Integrated Offering. Neither the Company nor any of its Affiliates, nor any person or entity acting on its or their behalf has, directly or indirectly, made any offers or sales of any Company security or solicited any offers to buy any security, under circumstances that would adversely affect reliance by the Company on Section 4(2) for the exemption from registration for the transactions contemplated hereby or would require registration of the Securities under the Securities Act.

     3.16 Private Placement. The offer and sale of the Securities to the Purchasers as contemplated hereby is exempt from the registration requirements of the Securities Act

     3.17 Internal Accounting Controls. Except as described in the SEC Document, the Company maintains a system of internal accounting controls sufficient to provide reasonable assurance that (i) transactions are executed in accordance with management’s general or specific authorizations, (ii) transactions are recorded as necessary to permit preparation of financial statements in conformity with generally accepted accounting principles, (iii) access to assets is permitted only in accordance with management’s general or specific authorization, and (iv) the recorded accountability for assets is compared with the existing assets at reasonable intervals and appropriate action is taken with respect to any differences.

     3.18 Intellectual Property.

               (a) “Intellectual Property” shall mean patents, trademarks, service marks, trade names, copyrights, trade secrets, licenses, information and other proprietary rights and processes.

               (b) Except as disclosed in the SEC Documents and to the knowledge of the Company, the Company owns or has the valid right to use all of the Intellectual Property that is necessary for the conduct of the Company’s business as currently conducted or as currently

6.

proposed to be conducted as described in the SEC Documents, free and clear of all material liens and encumbrances.

               (c) Except as disclosed in the SEC Documents, the conduct of the Company’s business as currently conducted does not infringe or otherwise conflict with (collectively, “Infringe”) any Intellectual Property rights of any third party or any confidentiality obligation owed by the Company to a third party, and, to the knowledge of the Company, the Intellectual Property and confidential information of the Company are not being Infringed by any third party.

               (d) Each employee, consultant and contractor of the Company who has had access to confidential information of the Company that is necessary for the conduct of Company’s business as currently conducted or as currently proposed to be conducted has executed an agreement to maintain the confidentiality of such confidential information and has executed appropriate agreements that are substantially consistent with the Company’s standard forms thereof.

     3.19 Questionable Payments. Neither the Company nor, to the knowledge of the Company, any of its current or former stockholders, directors, officers, employees, agents or other persons acting on behalf of the Company, has on behalf of the Company or in connection with its business: (a) used any corporate funds for unlawful contributions, gifts, entertainment or other unlawful expenses relating to political activity; (b) made any direct or indirect unlawful payments to any governmental officials or employees from corporate funds; (c) established or maintained any unlawful or unrecorded fund of corporate monies or other assets; (d) made any false or fictitious entries on the books and records of the Company; or (e) made any unlawful bribe, rebate, payoff, influence payment, kickback or other unlawful payment of any nature.

     3.20 Transactions with Affiliates. Except as disclosed in the SEC Documents and as contemplated pursuant to this Agreement, none of the officers or directors of the Company and, to the knowledge of the Company, none of the employees of the Company is presently a party to any transaction with the Company or to a presently contemplated transaction (other than for services as employees, officers and directors) that would be required to be disclosed pursuant to Item 404 of Regulation S-K promulgated under the Securities Act.

     3.21 Disclosure. Except as disclosed on Schedule 3.21 of the Disclosure Schedule, the information contained in the Exchange Act Documents as of the date hereof and as of the applicable Closing Date, did not and shall not contain an untrue statement of a material fact or omit to state a material fact required to be stated therein or necessary to make the statements therein, in light of the circumstances under which they were made, not misleading. For purposes herein, “Exchange Act Documents” are the documents filed by the Company under the Exchange Act, since the end of its most recently completed fiscal year through the date hereof, including, without limitation, its most recent report on Form 10-K. The Company confirms that, neither the Company nor, to the Company’s knowledge, any other person acting on its behalf has provided any of the Purchasers or their agents or counsel with any information that constitutes or would reasonably be expected to constitute material, non-public information other than to those Purchasers listed on Schedule 5.5 or Purchasers who have executed a written agreement

7.

regarding the confidentiality and use of such information. The Company acknowledges and agrees that no Purchaser makes or has made any representations or warranties with respect to the transactions contemplated hereby other than those specifically set forth in Article IV hereof.

     3.22 Dilution; Sales By Purchasers. The Company acknowledges that the issuance of the Securities may result in dilution of the outstanding shares of Common Stock, which dilution may be substantial under certain market conditions. The Company further acknowledges that its obligations under this Agreement and the Warrant, including without limitation its obligation to issue the Warrant, are unconditional and absolute and not subject to any right of set off, counterclaim, delay or reduction, regardless of the effect of any such dilution or any claim the Company may have against any Purchaser and regardless of the dilutive effect that such issuance may have on the ownership of the other stockholders of the Company. Anything in this Agreement or elsewhere herein to the contrary notwithstanding (except for Section 4.5 hereof and pursuant to those certain Amended and Restated Support Agreements, dated as of the date hereof), it is understood and agreed by the Company (i) that none of the Purchasers have been asked by the Company to agree, nor has any Purchaser agreed, to desist from purchasing or selling, long and/or short, securities of the Company, or “derivative” securities based on securities issued by the Company or to hold the Securities for any specified term; (ii) that future open market or other transactions by any Purchaser, including short sales, and specifically including, without limitation, short sales or “derivative” transactions, before or after the closing of this or future private placement transactions, may negatively impact the market price of the Company’s publicly-traded securities; (iii) that any Purchaser, and counter parties in “derivative” transactions to which any such Investor is a party, directly or indirectly, presently may have a “short” position in the Common Stock, and (iv) that each Purchaser shall not be deemed to have any affiliation with or control over any arm’s length counter-party in any “derivative” transaction.

ARTICLE 4

Representations, Warranties and Covenants of the Purchasers

     Each Purchaser hereby severally, and not jointly, represents and warrants to the Company on and as of the date hereof and on the applicable Closing Date:

     4.1 Authorization. Purchaser represents and warrants to the Company that: (a) Purchaser has all requisite legal and corporate or other power and capacity and has taken all requisite corporate or other action to execute and deliver this Agreement, to purchase the Common Shares and the Warrants to be purchased by it and to carry out and perform all of its obligations under this Agreement; and (b) this Agreement constitutes the legal, valid and binding obligation of such Purchaser, enforceable in accordance with its terms, except (i) as limited by applicable bankruptcy, insolvency, reorganization or similar laws relating to or affecting the enforcement of creditors’ rights generally and (ii) as limited by equitable principles generally.

8.

     4.2 Investment Experience. Purchaser is an “accredited investor” as defined in Rule 501(a) under the Securities Act. Purchaser is aware of the Company’s business affairs and financial condition and has had access to and has acquired sufficient information about the Company to reach an informed and knowledgeable decision to acquire the Common Shares and the Warrants. Purchaser has such business and financial experience as is required to give it the capacity to protect its own interests in connection with the purchase of the Common Shares and Warrants.

     4.3 Investment Intent. Purchaser is purchasing the Common Shares and the Warrants for its own account as principal, for investment purposes only, and not with a present view to, or for, resale, distribution or fractionalization thereof, in whole or in part, within the meaning of the Securities Act, other than as contemplated by Article 7. Purchaser understands that its acquisition of the Common Shares and the Warrants has not been registered under the Securities Act or registered or qualified under any state securities law in reliance on specific exemptions therefrom, which exemptions may depend upon, among other things, the bona fide nature of Purchaser’s investment intent as expressed herein. Purchaser has completed or caused to be completed the Purchaser Questionnaire attached hereto as Exhibit C for use in preparation of the Registration Statement, and the responses provided therein shall be true and correct as of the applicable Closing Date and will be true and correct as of the effective date of the Registration Statement. Purchaser, in connection with its decision to purchase the Common Shares and the Warrants, has relied solely upon the SEC Documents and the representations and warranties of the Company contained herein. Purchaser will not, directly or indirectly, offer, sell, pledge, transfer or otherwise dispose of (or solicit any offers to buy, purchase or otherwise acquire or take a pledge of) any of the Securities except in compliance with the Securities Act, and the rules and regulations promulgated thereunder.

     4.4 Registration or Exemption Requirements. Purchaser further acknowledges and understands that the Securities may not be resold or otherwise transferred except in a transaction registered under the Securities Act or unless an exemption from such registration is available.

     4.5 Dispositions. Purchaser will not, prior to the effectiveness of the Registration Statement (as defined below), if then prohibited by law or regulation: (a) sell, offer to sell, solicit offers to buy, dispose of, loan, pledge or grant any right with respect to (collectively, a “Disposition”) the Securities; or (b) engage in any hedging or other transaction which is designed or could reasonably be expected to lead to or result in a Disposition of Securities by such Purchaser or an affiliate. In addition, Purchaser agrees that for so long as it owns any Common Shares, it will not enter into any short sale of Shares executed at a time when the Purchaser has no equivalent offsetting long position in the Common Shares. For purposes of determining whether the Purchaser has an equivalent offsetting long position in the Common Shares, shares that the Purchaser is entitled to receive within sixty (60) days (whether pursuant to contract or upon conversion or exercise of convertible securities) will be included as if held long by the Purchaser.

     4.6 No Legal, Tax or Investment Advice. Purchaser understands that nothing in this Agreement or any other materials presented to Purchaser in connection with the purchase and

9.

sale of the Common Shares and the Warrants constitutes legal, tax or investment advice. Purchaser has consulted such legal, tax and investment advisors as it, in its sole discretion, has deemed necessary or appropriate in connection with its purchase of the Common Shares and the Warrants.

     4.7 Confidentiality. Purchaser will hold in confidence all information concerning this Agreement and the placement of the Securities hereunder until the earlier of such time as (a) the Company has made a public announcement concerning the Agreement and the placement of the Securities hereunder or (b) this Agreement is terminated.

     4.8 Residency. Purchaser’s principal executive offices are in the jurisdiction set forth immediately below Purchaser’s name on the applicable signature page attached hereto.

     4.9 Governmental Review. Purchaser understands that no United States federal or state agency or any other government or governmental agency has passed upon or made any recommendation or endorsement of the Shares or the Warrants.

     4.10 Legend. Purchaser understands that, until such time as the Registration Statement has been declared effective or the Securities may be sold pursuant to Rule 144 under the Securities Act without any restriction as to the number of securities as of a particular date that can then be immediately sold, the Securities may bear a restrictive legend in substantially the following form (and a stop transfer order may be placed against transfer of the certificates for the Shares):

     “THE SECURITIES REPRESENTED BY THIS CERTIFICATE HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED, OR THE SECURITIES LAWS OF ANY STATE OF THE UNITED STATES OR IN ANY OTHER JURISDICTION. THE SECURITIES REPRESENTED HEREBY MAY NOT BE OFFERED, SOLD OR TRANSFERRED IN THE ABSENCE OF AN EFFECTIVE REGISTRATION STATEMENT FOR THE SECURITIES UNDER APPLICABLE SECURITIES LAWS UNLESS OFFERED, SOLD OR TRANSFERRED PURSUANT TO AN AVAILABLE EXEMPTION FROM THE REGISTRATION REQUIREMENTS OF THOSE LAWS.”

               (a) The Company agrees that following the effectiveness of the Registration Statement or at such time as such legend is no longer required under this Section 4.10, it will, no later than three business days following the delivery by an Purchaser to the Company or the Company’s transfer agent of a certificate representing Common Shares or Warrant Shares, as applicable, issued with a restrictive legend and a signed and completed notice of sale in substantially the form of Exhibit E attached hereto (such third Trading Day, the “Legend Removal Date”), deliver or cause to be delivered to such Purchaser a certificate representing such shares that is free from any legend referring to the Securities Act. The Company may not make any notation on its records or give instructions to any transfer agent of the Company that

10.

enlarge the restrictions on transfer set forth in this Section. Certificates for Securities subject to legend removal hereunder shall be transmitted by the transfer agent of the Company to the Purchasers by crediting the account of the Purchaser’s prime broker with the Depository Trust Company System. All costs and expenses related to the removal of the legends and the reissuance of any Securities shall be borne by the Company.

               (b) In addition to such Purchaser’s other available remedies, the Company shall pay to a Purchaser, in cash, as partial liquidated damages and not as a penalty, for each $1,000 of Common Shares (or Warrant Shares underlying a Warrant tendered for legend removal) (based on the VWAP of the Common Stock on the date such Securities are submitted to the Company’s transfer agent) delivered for removal of the restrictive legend together with a signed and completed notice of sale in substantially the form of Exhibit E attached hereto and subject to Section 4.10(a), $10 per Trading Day (increasing to $15 per Trading Day 5 Trading Days after such damages have begun to accrue) for each Trading Day after the Legend Removal Date until such certificate is delivered without a legend referring to the Securities Act. Nothing herein shall limit such Purchaser’s right to pursue actual damages for the Company’s failure to deliver certificates representing any Securities as required by the Agreement, and such Purchaser shall have the right to pursue all remedies available to it at law or in equity including, without limitation, a decree of specific performance and/or injunctive relief, without the necessity of showing economic loss and without any bond or other security being required..

               (c) Each Purchaser, severally and not jointly with the other Purchasers, agrees that the removal of the restrictive legend from certificates representing Securities as set forth in this Section 4.10 is predicated upon the Company’s reliance that the Purchaser will sell any Securities pursuant to either the registration requirements of the Securities Act, including any applicable prospectus delivery requirements, or an exemption therefrom.

     4.11 Foreign Investors. If Purchaser is not a United States person (as defined by Section 7701(a)(30) of the Internal Revenue Code of 1986, as amended), Purchaser hereby represents that it has satisfied itself as to the full observance of the laws of its jurisdiction in connection with any invitation to subscribe for the Common Shares and the Warrants or any use of this Agreement, including (a) the legal requirements within its jurisdiction for the purchase of the Common Shares and the Warrants, (b) any foreign exchange restrictions applicable to such purchase or acquisition, (c) any government or other consents that may need to be obtained, and (d) the income tax and other tax consequences, if any, that may be relevant to the purchase, holding, redemption, sale or transfer of the Securities. Purchaser’s subscription and payment for and continued beneficial ownership of the Securities will not violate any applicable securities or other laws of Purchaser’s jurisdiction.

11.

ARTICLE 5

Conditions to Closing Obligations of Purchasers

     Each Purchaser’s obligation to purchase the Common Shares and the Warrants at the relevant Closing is, at the option of such Purchaser, subject to the fulfillment or waiver as of the relevant Closing Date of the following conditions:

     5.1 Representations and Warranties. The representations and warranties made by the Company in Article 3 hereof qualified as to materiality shall be true and correct at all times prior to and on the applicable Closing Date, except to the extent any such representation or warranty expressly speaks as of an earlier date, in which case such representation or warranty shall be true and correct as of such earlier date, and the representations and warranties made by the Company in Article 3 hereof not qualified as to materiality shall be true and correct in all material respects at all times prior to and on the applicable Closing Date, except to the extent any such representation or warranty expressly speaks as of an earlier date, in which case such representation or warranty shall be true and correct in all material respects as of such earlier date.

     5.2 Covenants. All covenants, agreements and conditions contained in this Agreement to be performed by the Company on or prior to the applicable Closing Date shall have been performed or complied with in all material respects.

     5.3 Certificates. The Company shall have delivered to the Purchasers duly executed certificates for the Common Shares and the Warrants (in such denominations as set forth below each Purchaser’s name on the applicable signature page attached hereto.

     5.4 Legal Opinion. The Purchasers shall have received on the applicable Closing Date an opinion of Cooley Godward, counsel for the Company, dated the applicable Closing Date, in substantially the form of Exhibit C.

     5.5 Amended and Restated Company Support Agreement. An Amended and Restated Company Support Agreement, in the form of Exhibit F shall have been executed by the Company and each of the entities set forth on Schedule 5.5.

     5.6 Listing. The Company shall have complied with all requirements with respect to the listing of the Shares on the Nasdaq SmallCap Market, except for such requirements not required until after the issuance of the Shares, such requirements to be complied with promptly after the applicable Closing.

     5.7 Officer’s Certificate. The Company shall have delivered a Certificate, executed on behalf of the Company by its Chief Executive Officer or its Chief Financial Officer, dated as of the applicable Closing Date, certifying to the fulfillment of the conditions specified in Sections 5.1 and 5.2.

     5.8 Judgments. No judgment, writ, order, injunction, award or decree of or by any court, or judge, justice or magistrate, including any bankruptcy court or judge, or any order of or

12.

by any governmental authority, shall have been issued, and no action or proceeding shall have been instituted by any governmental authority, enjoining or preventing the consummation of the transactions contemplated hereby.

     5.9 Secretary’s Certificate. The Company shall have delivered a Certificate, executed on behalf of the Company by its Secretary or Chief Financial Officer, dated as of the applicable Closing Date, certifying the resolutions adopted by the Board of Directors of the Company approving the transactions contemplated by this Agreement and the issuance of the Securities, certifying the current versions of the Restated Certificate and Bylaws of the Company and certifying as to the signatures and authority of persons signing this Agreement and related documents on behalf of the Company.

     5.10 Stop Orders. No stop order or suspension of trading shall have been imposed by the Nasdaq SmallCap Market, the SEC or any other governmental regulatory body with respect to public trading in the Common Stock.

     5.11 Stockholder Approval. In the case of the Second Closing, the Company shall have obtained Stockholder Consent prior to the 120^th day following the date hereof.

     5.12 Minimum Investment. In the case of the Second Closing, the Company shall have received an aggregate gross proceeds of at least thirty million dollars ($30,000,000) from the Purchasers at the First Closing and Second Closing.

ARTICLE 6

Conditions to Closing Obligations of Company

     The Company’s obligation to sell and issue the Common Shares and the Warrants at the relevant Closing is, at the option of the Company, subject to the fulfillment or waiver of the following conditions:

     6.1 Receipt of Payment. The Purchasers shall have delivered payment of the purchase price to the Company for the Common Shares and the Warrants being issued at the applicable Closing.

     6.2 Representations and Warranties. The representations and warranties made by the Purchasers in Article 4 hereof qualified as to materiality shall be true and correct at all times prior to and on the applicable Closing Date, except to the extent any such representation or warranty expressly speaks as of an earlier date, in which case such representation or warranty shall be true and correct as of such earlier date, and, the representations and warranties made by the Purchasers in Article 4 hereof not qualified as to materiality shall be true and correct in all material respects at all times prior to and on the applicable Closing Date, except to the extent any such representation or warranty expressly speaks as of an earlier date, in which case such representation or warranty shall be true and correct in all material respects as of such earlier date.

13.

     6.3 Covenants. All covenants, agreements and conditions contained in this Agreement to be performed by the Purchasers on or prior to the applicable Closing Date shall have been performed or complied with in all material respects.

     6.4 Delivery of Purchaser Questionnaire. The Company shall have received from each Purchaser a fully completed Purchaser Questionnaire in the form attached hereto as Exhibit B prior to the Second Closing for the Company’s use in preparing the Registration Statement pursuant to Article 7 below; provided, however, in the event that the Second Closing does not take place, such Purchaser Questionnaire shall have been received from each Purchaser within ten (10) days following notification by the Company of the filing of such Registration Statement.

ARTICLE 7

Covenants

     7.1 Definitions. For the purpose of this Article 7:

               (a) the term “Registration Statement” shall mean any registration statement required to be filed by Section 7.2 below, and shall include any preliminary prospectus, final prospectus, exhibit or amendment included in or relating to such registration statements; and

               (b) the term “Registrable Shares” shall mean all of the Common Shares issued pursuant to this Agreement and the Warrant Shares issuable upon exercise of the Warrants issued pursuant to this Agreement.

     7.2 Registration Procedures and Expenses. The Company shall:

               (a) use its best efforts to file a Registration Statement with the SEC within ten (10) days following the Second Closing Date, but in no event after the date that is eighty (80) days after the First Closing Date (the “Filing Date”), to register the Registrable Shares and shares of the Common Stock listed on Schedule 7.2 attached hereto on Form S-3 under the Securities Act (providing for shelf registration of such Registrable Shares and shares of the Common Stock listed on Schedule 7.2 under SEC Rule 415) or on such other form which is appropriate to register such Registrable Shares for resale from time to time by the Purchasers; provided, however, if a Registration Statement covering the Registrable Shares is not filed with the SEC on or prior to the Filing Date, the Company will make payments to each Holder, as liquidated damages and not as a penalty, in an amount equal to one percent (1%) of the aggregate amount invested by such Holder (the amount invested by a Holder shall include the purchase price of the Common Shares acquired by such Holder and shall exclude any amount attributable to the Warrants acquired by such Holder pursuant to the Agreement) for each 30 day period (or a portion thereof) following the date by which such Registration Statement should have been filed for which no Registration Statement is filed with respect to the Registrable Securities;

14.

               (b) use its best efforts, subject to receipt of necessary information from the Purchasers, to cause any such Registration Statement filed pursuant to Section 7.2(a) above to become effective as promptly after filing of such Registration Statement as practicable but in any event by the date that is one hundred (100) days following the First Closing Date; provided, however, that in the event that a Registration Statement is reviewed by the SEC, then such date shall be the date that is one hundred fifty (150) days following the First Closing Date. If (i) the Company fails to file with the SEC a request for acceleration in accordance with Rule 461 promulgated under the Securities Act, within five business days of the date that the Company is notified (orally or in writing, whichever is earlier) by the SEC that a Registration Statement will not be “reviewed,” or is not subject to further review, or (ii) the Registration Statement has not been declared effective by the appropriate date in the preceding sentence, then the Company will make payments to each Holder, as liquidated damages and not as a penalty, in an amount equal to one percent (1%) of the aggregate amount invested by such Holder (the amount invested by a Holder shall include the purchase price of the Shares acquired by such Holder and shall exclude any amount attributable to the Warrants acquired by such Holder pursuant to the Purchase Agreement) for each thirty (30) day period (or a portion thereof) following the date by which such Registration Statement should have been effective as described above had the Company used its best efforts to have the Registration Statement declared effective;

               (c) prepare and file with the SEC such amendments and supplements to such Registration Statement and the prospectus used in connection therewith as may be necessary to keep such Registration Statement continuously effective until termination of such obligation as provided in Section 7.6 below, subject to the Company’s right to suspend pursuant to Section 7.5;

               (d) furnish to each Purchaser (and to each underwriter, if any, of such Registrable Shares) such number of copies of prospectuses in conformity with the requirements of the Securities Act and such other documents as the Purchasers may reasonably request, in order to facilitate the public sale or other disposition of all or any of the Registrable Shares by the Purchasers, including a copy of the prospectus to be furnished to each Purchaser pursuant to Section 7.2(g);

               (e) file such documents as may be required of the Company for normal securities law clearance for the resale of the Registrable Shares in such states of the United States as may be reasonably requested by each Purchaser; provided, however, that the Company shall not be required in connection with this paragraph (e) to qualify as a foreign corporation or execute a general consent to service of process in any jurisdiction;

               (f) upon notification by the SEC that that the Registration Statement will not be reviewed or is no longer subject to further review and comments by the SEC, the Company shall within five business days request acceleration of such Registration Statement such that it becomes effective at 5:00 p.m. New York Time on the date that effectiveness is requested (the “Effective Date”);

15.

     (g) deliver to each Purchaser, by 9:00 a.m. New York time on the day following the Effective Date, without charge, an electronic copy of each prospectus or prospectuses (including each form of prospectus) and each amendment or supplement thereto. The Company hereby consents to the use of such prospectus and each amendment or supplement thereto by each of the selling Holders in connection with the offering and sale of the Registrable Securities covered by such prospectus and any amendment or supplement thereto;

     (h) advise each Purchaser promptly:

                         (i) of the effectiveness of the Registration Statement or any post-effective amendments thereto;

                         (ii) of any request by the SEC for amendments to the Registration Statement or amendments to the prospectus or for additional information relating thereto;

                         (iii) of the issuance by the SEC of any stop order suspending the effectiveness of the Registration Statement under the Securities Act or of the suspension by any state securities commission of the qualification of the Registrable Shares for offering or sale in any jurisdiction, or the initiation of any proceeding for any of the preceding purposes; and

                         (iv) of the existence of any fact and the happening of any event that makes any statement of a material fact made in the Registration Statement, the prospectus and amendment or supplement thereto, or any document incorporated by reference therein, untrue, or that requires the making of any additions to or changes in the Registration Statement or the prospectus in order to make the statements therein not misleading;

               (i) use its best efforts to cause all Registrable Shares to be listed on each securities exchange, if any, on which equity securities by the Company are then listed;

               (j) bear all expenses in connection with the procedures in paragraphs (a) through (g) of this Section 7.2 and the registration of the Registrable Shares on such Registration Statement and the satisfaction of the blue sky laws of such states; and

               (k) otherwise use commercially reasonable efforts to make available to its security holders no later than the Availability Date (as defined below), an earnings statement covering a period of at least twelve (12) months, beginning after the effective date of each Registration Statement, which earnings statement shall satisfy the provisions of Section 11(a) of the Securities Act, including Rule 158 promulgated thereunder (for the purpose of this subsection 7.2(i), “Availability Date” means the 45th day following the end of the fourth fiscal quarter after the fiscal quarter that includes the effective date of such Registration Statement, except that, if such fourth fiscal quarter is the last quarter of the Company’s fiscal year, “Availability Date” means the 90th day after the end of such fourth fiscal quarter).

16.

     7.3 Indemnification.

               (a) The Company agrees to indemnify and hold harmless each Purchaser, the partners, members, officers and directors of each Purchaser and each person, if any, who controls such Purchaser within the meaning of the Securities Act or the Exchange Act, from and against any losses, claims, damages or liabilities to which they may become subject (under the Securities Act or otherwise) insofar as such losses, claims, damages or liabilities (or actions or proceedings in respect thereof) arise out of, or are based upon, any untrue statement or alleged untrue statement of a material fact contained in the Registration Statement or any omission or alleged omission to state therein a material fact required to be stated therein or necessary to make the statements therein, in light of the circumstances under which they were made, not misleading or arise out of any failure by the Company to fulfill any undertaking included in the Registration Statement and the Company will, as incurred, reimburse such Purchaser, partner, member, officer, director or controlling person for any legal or other expenses reasonably incurred in investigating, defending or preparing to defend any such action, proceeding or claim; provided, however, that the Company shall not be liable in any such case to the extent that such loss, claim, damage or liability (collectively, “Loss”) arises out of, or is based upon, an untrue statement or omission or alleged untrue statement or omission made in such Registration Statement in reliance upon and in conformity with written information furnished to the Company by or on behalf of such Purchaser, partner, member, officer, director or controlling person specifically for use in preparation of the Registration Statement or any breach of this Agreement by such Purchaser; and provided further, however, that the Company shall not be liable to any Purchaser of Registrable Shares (or any partner, member, officer, director or controlling person of such Purchaser) to the extent that any such Loss is caused by an untrue statement or omission or alleged untrue statement or omission made in any preliminary prospectus if either (i)(A) such Purchaser failed to send or deliver a copy of the final prospectus with or prior to the delivery of written confirmation of the sale by such Purchaser to the person asserting the claim from which such Loss resulted and (B) the final prospectus corrected such untrue statement or omission, (ii) (X) such untrue statement or omission is corrected in an amendment or supplement to the prospectus and (Y) having previously been furnished by or on behalf of the Company with copies of the prospectus as so amended or supplemented, such Purchaser thereafter fails to deliver such prospectus as so amended or supplemented, with or prior to the delivery of written confirmation of the sale of a Registrable Share to the person asserting the claim from which such Loss resulted or (iii) such Purchaser sold Registrable Shares in violation of such Purchaser’s covenant contained in Section 7.5 of this Agreement.

     (b) Each Purchaser, severally and not jointly, agrees to indemnify and hold harmless the Company (and each person, if any, who controls the Company within the meaning of Section 15 of the Securities Act or Section 20 of the Exchange Act, each officer of the Company who signs the Registration Statement and each director of the Company), from and against any losses, claims, damages or liabilities to which the Company (or any such officer, director or controlling person) may become subject (under the Securities Act or otherwise), insofar as such losses, claims, damages or liabilities (or actions or proceedings in respect thereof) arise out of, or are based upon, any breach of this Agreement by such Purchaser or any untrue statement or alleged untrue statement of a material fact contained in the Registration Statement

17.

or any omission or alleged omission to state therein a material fact required to be stated therein or necessary to make the statements therein, in light of the circumstances under which they were made, not misleading in each case, on the effective date thereof, if, and to the extent, such untrue statement or omission or alleged untrue statement or omission was made in reliance upon and in conformity with written information furnished by or on behalf of such Purchaser specifically for use in preparation of the Registration Statement, and such Purchaser will reimburse the Company (and each of its officers, directors or controlling persons) for any legal or other expenses reasonably incurred in investigating, defending or preparing to defend any such action, proceeding or claim; provided, however, that in no event shall any indemnity under this Section 7.4(b) be greater in amount than the dollar amount of the proceeds (net of the amount of any damages such Purchaser has otherwise been required to pay by reason of such untrue statement or omission or alleged untrue statement or omission) received by such Purchaser upon the sale of the Registrable Securities included in the Registration Statement giving rise to such indemnification obligation.

               (c) Promptly after receipt by any indemnified person of a notice of a claim or the beginning of any action in respect of which indemnity is to be sought against an indemnifying person pursuant to this Section 7.4, such indemnified person shall notify the indemnifying person in writing of such claim or of the commencement of such action, and, subject to the provisions hereinafter stated, in case any such action shall be brought against an indemnified person and such indemnifying person shall have been notified thereof, such indemnifying person shall be entitled to participate therein, and, to the extent that it shall wish, to assume the defense thereof, with counsel reasonably satisfactory to such indemnified person. After notice from the indemnifying person to such indemnified person of its election to assume the defense thereof, such indemnifying person shall not be liable to such indemnified person for any legal expenses subsequently incurred by such indemnified person in connection with the defense thereof; provided, however, that if there exists or shall exist a conflict of interest that would make it inappropriate in the reasonable judgment of the indemnified person for the same counsel to represent both the indemnified person and such indemnifying person or any affiliate or associate thereof, the indemnified person shall be entitled to retain its own counsel at the expense of such indemnifying person; provided, further, that no indemnifying person shall be responsible for the fees and expense of more than one separate counsel for all indemnified parties. The indemnifying party shall not settle an action without the consent of the indemnified party, which consent shall not be unreasonably withheld.

               (d) If after proper notice of a claim or the commencement of any action against the indemnified party, the indemnifying party does not choose to participate, then the indemnified party shall assume the defense thereof and upon written notice by the indemnified party requesting advance payment of a stated amount for its reasonable defense costs and expenses, the indemnifying party shall advance payment for such reasonable defense costs and expenses (the “Advance Indemnification Payment”) to the indemnified party. In the event that the indemnified party’s actual defense costs and expenses exceed the amount of the Advance Indemnification Payment, then upon written request by the indemnified party, the indemnifying party shall reimburse the indemnified party for such difference; in the event that the Advance

18.

Indemnification Payment exceeds the indemnified party’s actual costs and expenses, the indemnified party shall promptly remit payment of such difference to the indemnifying party.

               (e) If the indemnification provided for in this Section 7.4 is held by a court of competent jurisdiction to be unavailable to an indemnified party with respect to any losses, claims, damages or liabilities referred to herein, the indemnifying party, in lieu of indemnifying such indemnified party thereunder, shall to the extent permitted by applicable law contribute to the amount paid or payable by such indemnified party as a result of such loss, claim, damage or liability in such proportion as is appropriate to reflect the relative fault of the indemnifying party on the one hand and of the indemnified party on the other, as well as any other relevant equitable considerations; provided, that in no event shall any contribution by an indemnifying party hereunder be greater in amount than the dollar amount of the proceeds (net of the amount of any damages such indemnifying party has otherwise been required to pay by reason of such untrue statement or omission or alleged untrue statement or omission) received by such indemnifying party upon the sale of the Registrable Securities included in the Registration Statement giving rise to such indemnification obligation.

     7.4 Prospectus Delivery. Each Purchaser hereby covenants with the Company not to make any sale of the Registrable Shares without complying with Section 8.3. The Purchaser acknowledges that there may be times when the Company must suspend the use of the prospectus forming a part of the Registration Statement until such time as an amendment to the Registration Statement has been filed by the Company and declared effective by the SEC, or until such time as the Company has filed an appropriate report with the SEC pursuant to the Exchange Act. The Purchaser hereby covenants that it will not sell any Registrable Shares pursuant to said prospectus during the period commencing at the time at which the Company gives the Purchaser notice of the suspension of the use of said prospectus and ending at the time the Company gives the Purchaser notice that the Purchaser may thereafter effect sales pursuant to said prospectus; provided that such suspension periods shall in no event exceed thirty (30) days in any twelve (12) month period and that, in the good faith judgment of the Company’s Board of Directors, the Company would, in the absence of such delay or suspension hereunder, be required under state or federal securities laws to disclose any corporate development, a potentially significant transaction or event involving the Company, or any negotiations, discussions, or proposals directly relating thereto, in either case the disclosure of which would reasonably be expected to have a material adverse effect upon the Company or its stockholders; provided further, that the Company may suspend the use of the prospectus forming a part of the Registration Statement to the extent necessary to file any post-effective amendment to the Registration Statement in order to amend the table of selling stockholders within the Registration Statement to reflect transfers of the Securities pursuant to Sections 8.3(a) and 8.3(b). If, after the Registration Statement has been declared effective by the SEC, sales cannot be made pursuant to such Registration Statement, except as excused pursuant to this Section 7.4, then the Company will make pro rata payments to each Holder, as liquidated damages and not as a penalty, in an amount equal to one (1%) of the aggregate amount invested by such Holder (the amount invested by a Holder shall include the purchase price of the Shares acquired by such Holder and shall exclude any amount attributable to the Warrants acquired by such Holder pursuant to the

19.

Purchase Agreement) for each thirty (30) day period following the date sales cannot be made pursuant to such Registration Statement after it has been declared effective.

     7.5 Termination of Obligations. The obligations of the Company pursuant to Section 7.2 hereof shall cease and terminate upon the earlier to occur of (a) such time as all of the Registrable Shares have been resold, (b) such time as all of the Registrable Shares may be resold in a three-month period pursuant to Rule 144(k), or (c) the fifth anniversary of later of the First Closing Date or Second Closing Date.

     7.6 Reporting Requirements.

               (a) With a view to making available the benefits of certain rules and regulations of the SEC that may at any time permit the sale of the Securities to the public without registration or pursuant to a registration statement on Form S-3, the Company agrees to use its best efforts to:

                         (i) make and keep public information available, as those terms are understood and defined in Rule 144 under the Securities Act;

                         (ii) file with the SEC in a timely manner all reports and other documents required of the Company under the Securities Act and the Exchange Act; and

                         (iii) so long as any of the Purchasers own Registrable Shares, to furnish to such Purchaser upon request (A) a written statement by the Company as to whether it is in compliance with the reporting requirements of Rule 144, the Securities Act and the Exchange Act, or whether it is qualified as a registrant whose securities may be resold pursuant to SEC Form S-3, and (B) a copy of the most recent annual or quarterly report of the Company and such other reports and documents so filed by the Company.

     7.7 Blue Sky. The Company shall obtain and maintain all necessary blue sky law permits and qualifications, or secured exemptions therefrom, required by any state for the offer and sale of Securities.

     7.8 Stockholder Approval. Promptly following the First Closing Date, the Company shall take all action necessary to call the annual meeting of its stockholders (the “Annual Stockholders Meeting”) and seek the approval of the Company’s stockholders for, among other matters, the authorization and issuance of the Common Shares and Warrants at the Second Closing and the issuance of the Warrant Shares upon exercise of such Warrants in compliance with Rule 4350(i) of the Marketplace Rules of the NASD (the “Stockholder Approval”), to the extent required by The Nasdaq Stockmarket, Inc. In connection therewith, the Company will promptly prepare and file with the SEC proxy materials (including a proxy statement and form of proxy) for use at the Annual Stockholders Meeting and, promptly after receiving clearance from the SEC, shall promptly mail such proxy materials to the stockholders of the Company.

20.

     7.9 Publicity. The Company shall, on or before 9:30 a.m. New York City time on the first business day following the date hereof, issue a press release disclosing the material terms of the transactions contemplated hereby.

ARTICLE 8

Restrictions on Transferability of Securities;
Compliance with Securities Act

     8.1 Restrictions on Transferability. The Securities shall not be transferable in the absence of a registration under the Securities Act or an exemption therefrom. The Company shall be entitled to give stop transfer instructions to its transfer agent with respect to the Securities in order to enforce the foregoing restrictions.

     8.2 Instruction Sheet. Each certificate representing Registrable Shares shall bear the Instruction Sheet attached hereto as Exhibit D (in addition to any legends required under applicable securities laws).

8.3 Transfer of Securities.

               (a) Each Purchaser hereby covenants with the Company not to make any sale of the Securities except:

                         (i) in accordance with the Registration Statement, in which case Purchaser covenants to comply with the requirement of delivering a current prospectus; or

                         (ii) in accordance with Rule 144, in which case Purchaser covenants to comply with Rule 144; or

                         (iii) (A) If the transferee has agreed in writing to be bound by the terms of this Agreement, (B) such Purchaser shall have notified the Company of the proposed disposition and shall have furnished the Company with a detailed statement of the circumstances surrounding the proposed disposition and (C) if reasonably requested by the Company, such Purchaser shall have furnished the Company with an opinion of counsel, reasonably satisfactory to the Company, that such disposition will not require registration of such shares under the Securities Act.

               (b) Notwithstanding the provisions of subsection (a) above, no such restriction shall apply to a transfer by a Purchaser that is (i) a partnership transferring to its partners or former partners in accordance with partnership interests, (ii) a corporation transferring to a wholly-owned subsidiary or a parent corporation that owns all of the capital stock of the Purchaser, (iii) a limited liability company transferring to its members or former members in accordance with their interest in the limited liability company or (iv) an individual transferring to the Purchaser’s family member or trust for the benefit of an individual Purchaser; provided that in each case the transferee will agree in writing to be subject to the terms of this Agreement to the same extent as if he were an original Purchaser hereunder.

21.

               (c) Purchaser further acknowledges and agrees that, if a Purchaser is selling the Securities using the prospectus forming a part of the Registration Statement, such Securities are not transferable on the books of the Company unless the certificate evidencing such Securities is submitted to the Company’s transfer agent and a separate certificate executed by an officer of, or other person duly authorized by, the Purchaser in the form attached hereto as Exhibit E is submitted to Cooley Godward.

     8.4 Purchaser Information. Each Purchaser covenants that it will promptly notify the Company of any changes in the information set forth in the Registration Statement regarding such Purchaser or such Purchaser’s “Plan of Distribution.

     8.5 Material Non-Public Information. Except with respect to those Purchasers listed on Schedule 5.5 hereof, the Company covenants and agrees that neither it nor any other person acting on its behalf will provide any Purchaser or its agents or counsel with any information that the Company believes constitutes material non-public information, unless either prior thereto such Purchaser shall have executed a written agreement regarding the confidentiality and use of such information. The Company understands and confirms that each Purchaser shall be relying on the foregoing representations in effecting transactions in securities of the Company.

ARTICLE 9

Miscellaneous

     9.1 Termination.

               (a) This Agreement may be terminated and the sale and purchase of the Common Shares and the Warrants abandoned at any time prior to the First Closing, by written notice of any individual Purchaser if the First Closing has not occurred within five (5) business days of the date hereof (other than as a result of the failure on the part of the party giving such notice of termination to perform its covenants and obligations under this Agreement in all material respects); provided, however, that the abandonment of the sale and purchase of the Common Shares and the Warrants shall be applicable only to such Purchaser providing such written notice.

               (b) If this Agreement is terminated pursuant to this Section 9.1 all further obligations of the parties shall terminate; provided, however, that (i) no party shall be relieved of any liability arising from any breach by such party of any provision of this Agreement and (ii) the parties shall, in all events, remain bound by and continue to be subject to the provisions set forth in this Article 9.

     9.2 Waivers and Amendments. With the exception of Article 7 hereof, the terms of this Agreement may be waived or amended with the written consent of the Company and each Purchaser. With respect to Article 7 hereof, with the written consent of the Company and the

22.

record holders of a majority in interest of the Registrable Shares issued or issuable hereunder, the terms of this Agreement may be waived or amended and any such amendment or waiver shall be binding upon the Company and all holders of Registrable Shares.

     9.3 Broker’s Fee. Each Purchaser acknowledges that the Company intends to pay a fee in respect of the sale of the Securities to SG Cowen & Co., LLC as sole agent. Each of the parties to this Agreement represents that, on the basis of any actions and agreements by it, there are no other brokers or finders entitled to compensation in connection with the sale of Securities to the Purchasers.

     9.4 Governing Law. This Agreement shall be governed in all respects by and construed in accordance with the laws of the State of California without any regard to conflicts of laws principles.

     9.5 Survival. The representations, warranties, covenants and agreements made in this Agreement shall survive any investigation made by the Company or the Purchasers and the Closing.

     9.6 Successors and Assigns. The provisions hereof shall inure to the benefit of, and be binding upon, the successors, assigns, heirs, executors and administrators of the parties to this Agreement. Upon a permitted transfer of a Purchaser’s Securities on the books of the Company in accordance with the terms of Sections 8.3(a)(iii) or 8.3(b), the Purchaser may assign this Agreement to the permitted transferee upon prior written notice to the Company. Except as set forth in the previous sentence, no Purchaser shall assign this Agreement without the prior written consent of the Company.

     9.7 Entire Agreement. This Agreement constitutes the full and entire understanding and agreement between the parties with regard to the subjects thereof.

     9.8 Notices, etc. All notices and other communications required or permitted under this Agreement shall be in writing and may be delivered in person, by telecopy, overnight delivery service or registered or certified United States mail, addressed to the Company or the Purchasers, as the case may be, at their respective addresses set forth on the applicable signature pages hereto, or at such other address as the Company or the Purchasers shall have furnished to the other party in writing. All notices and other communications shall be effective upon the earlier of actual receipt thereof by the person to whom notice is directed or (a) in the case of notices and communications sent by personal delivery or telecopy, one business day after such notice or communication arrives at the applicable address or was successfully sent to the applicable telecopy number, (b) in the case of notices and communications sent by overnight delivery service, at noon (local time) on the second business day following the day such notice or communication was sent, and (c) in the case of notices and communications sent by United States mail, seven days after such notice or communication shall have been deposited in the United States mail.

23.

     9.9 Severability of this Agreement. If any provision of this Agreement shall be judicially determined to be invalid, illegal or unenforceable, the validity, legality and enforceability of the remaining provisions shall not in any way be affected or impaired thereby.

     9.10 Counterparts. This Agreement may be executed in any number of counterparts, each of which shall be an original, but all of which together shall constitute one instrument.

     9.11 Further Assurances. Each party to this Agreement shall do and perform or cause to be done and performed all such further acts and things and shall execute and deliver all such other agreements, certificates, instruments and documents as the other party hereto may reasonably request in order to carry out the intent and accomplish the purposes of this Agreement and the consummation of the transactions contemplated hereby.

     9.12 Currency. All references to “dollars” or “$” in this Agreement shall be deemed to refer to United States dollars.

     9.13 Waiver of Conflicts. Each party to this Agreement acknowledges that legal counsel for the Company, Cooley Godward, has in the past and may continue in the future to perform legal services for one or more of the Purchasers or their affiliates in matters unrelated to the transactions contemplated by this Agreement, including, but not limited to, the representation of the Purchasers in matters of a similar nature to the transactions contemplated herein. Each party to this Agreement hereby: (a) acknowledges that they have had an opportunity to ask for and have obtained information relevant to such representation, including disclosure of the reasonably foreseeable adverse consequences of such representation; (b) acknowledges that with respect to the transactions contemplated herein, Cooley Godward has represented the Company and not any individual Purchaser or any individual stockholder, director or employee of the Company; and (c) gives its informed consent to Cooley Godward’s representation of the Company in the transactions contemplated by this Agreement.

24.

     The foregoing agreement is hereby executed as of the date first above written.

Solexa, Inc. , a Delaware corporation
By:	/s/ John West
Name:		John West
Title:		CEO

Signature Page To Securities Purchase Agreement

     IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
(Signature)	Prothro Family Limited Partnership, Ltd.
	Print name of entity
(Printed Name)	By:	/s/ J.H. Cullum Clark
		Name:	J.H. Cullum Clark
		Title:	Managing General Partner
	Texas/USA
	Print jurisdiction of organization of entity
Address:	Address:
	Prothro Family Limited Partnership, Ltd.
	2626 Cole Avenue, Suite 200
	Dallas, TX 75204

Signature Page to Securities Purchase Agreement

     IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
(Signature)	Cimarron Biomedical Equity Master Fund, L.P.
	Print name of entity
(Printed Name)	By:	/s/ J.H. Cullum Clark
		Name:	J.H. Cullum Clark
		Title:	General Partner for GP, Cimarron
			Biomedical Equity Fund, L.P.
	Cayman Islands
	Print jurisdiction of organization of entity
Address:	Address:
	c/o Cimarron Biomedical Investors, L.P.
	2626 Cole Avenue, Suite 200
	Dallas, TX 75204

Signature Page to Securities Purchase Agreement

     IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
(Signature)	UBS O’Connor LLC F/B/O
	O’Connor PIPES Corporate Strategies Master
	Limited
	Print name of entity
(Printed Name)	By:	/s/ George Locasto
		Name:	George Locasto
		Title:	Managing director
	Cayman Islands
	Print jurisdiction of organization of entity
Address:	Address:
	UBS O’Connor LLC
	One North Wacker Drive - 32nd Floor
	Chicago, IL 60606

Signature Page to Securities Purchase Agreement

     IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
(Signature)	Nite Capital LP
	Print name of entity
(Printed Name)	By:	/s/ Keith A Goodman
		Name:	Keith A. Goodman
		Title:	Manager of the General Partner
	Delaware
	Print jurisdiction of organization of entity
Address:	Address:
	Nite Capital LP
	100 E. Cook Avenue #201
	Libertyville, IL 60048

Signature Page to Securities Purchase Agreement

     IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
(Signature)	SRB Greenway Capital (QP), L.P.
	By: SRB Management, L.P., General Partner
	By: BC Advisors, L.L.C., General Partner
	Print name of entity
(Printed Name)	By:	/s/ Steven R. Becker
		Name:	Steven R. Becker
		Title:	Member
	Print jurisdiction of organization of entity
Address:	Address:
	SRB Greenway Capital (QP), L.P.
	3000 Crescent Court, Suite 1111
	Dallas, TX 75201

Signature Page to Securities Purchase Agreement

     IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
(Signature)	SRB Greenway Capital, L.P.
	By: SRB Management, L.P., General Partner
	By: BC Advisors, L.L.C., General Partner
	Print name of entity
(Printed Name)	By:	/s/ Steven R. Becker
		Name:	Steven R. Becker
		Title:	Member
	Print jurisdiction of organization of entity
Address:	Address:
	SRB Greenway Capital, L.P.
	3000 Crescent Court, Suite 1111
	Dallas, TX 75201

Signature Page to Securities Purchase Agreement

     IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
(Signature)	SRB Greenway Offshore Operating Fund, L.P.
	By: SRB Management, L.P., General Partner
	By: BC Advisors, L.L.C., General Partner
	Print name of entity
(Printed Name)	By:	/s/ Steven R. Becker
		Name:	Steven R. Becker
		Title:	Member
	Print jurisdiction of organization of entity
Address:	Address:
	SRB Greenway Offshore Operating Fund, L.P.
	3000 Crescent Court, Suite 1111
	Dallas, TX 75201

Signature Page to Securities Purchase Agreement

     IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
(Signature)	Omnicron Master Trust
	Print name of entity
(Printed Name)	By:	/s/ Bruce Bernstein
		Name:	Bruce Bernstein
		Title:	Managing Partner
	Print jurisdiction of organization of entity
Address:	Address:
	Omnicron Capital, L.P.
	650 Fifth Avenue, 24th Floor
	New York, NY 10019

Signature Page to Securities Purchase Agreement

     IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
(Signature)	Special Situations Private Equity Fund, L.P.
	Print name of entity
(Printed Name)	By:	/s/ Austin Mance
		Name:	Austin Mance
		Title:	Managing Director
	Print jurisdiction of organization of entity
Address:	Address:
	Special Situations Private Equity Fund, L.P.
	153 East 53rd Street, 55th Floor
	New York, NY 10022

Signature Page to Securities Purchase Agreement

     IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
/s/ Paul M. Bruckman
(Signature)
	Print name of entity
Paul M. Bruckman
(Printed Name)	By:
		Name:
		Title:
	Print jurisdiction of organization of entity
Address:	Address:
P.O. Box 998
Mobile, AL 36601

Signature Page to Securities Purchase Agreement

     IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
/s/ Anthony Montagu
(Signature)
	Print name of entity
Anthony Montagu
(Printed Name)	By:
		Name:
		Title:
	Print jurisdiction of organization of entity
Address:	Address:
c/o Indian Rock Corporation
P.O. box 2606
Greenwich, CT 06836

Signature Page to Securities Purchase Agreement

     IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
/s/ Andrew Rockefeller
(Signature)
	Print name of entity
Andrew Rockefeller
(Printed Name)	By:
		Name:
		Title:
	Print jurisdiction of organization of entity
Address:	Address:
c/o Indian Rock Corporation
P.O. Box 2606
Greenwich, CT 06836

Signature Page to Securities Purchase Agreement

     IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
/s/ Charles Murphy
(Signature)
	Print name of entity
Charles Murphy
(Printed Name)	By:
		Name:
		Title:
	Print jurisdiction of organization of entity
Address:	Address	:
27 Taylor Road
Mount Kisco, NY 10549

Signature Page to Securities Purchase Agreement

     IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
(Signature)	Enable Growth Partners
	Print name of entity
(Printed Name)	By:	/s/ Mitch Levine
		Name:	Mitch Levine
		Title:	Managing Partner
	Delaware
	Print jurisdiction of organization of entity
Address:	Address:
	Enable Growth Partners
	One Ferry Building, Suite 255
	San Francisco, CA 94111

Signature Page to Securities Purchase Agreement

     IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
(Signature)	Enable Opportunity Partners
	Print name of entity
(Printed Name)	By:	/s/ Mitch Levine
		Name:	Mitch Levine
		Title:	Managing Partner
	Delaware
	Print jurisdiction of organization of entity
Address:	Address:
	Enable Opportunity Partners
	One Ferry Building, Suite 255
	San Francisco, CA 94111

Signature Page to Securities Purchase Agreement

15

     IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,  TRUST, ESTATE OR OTHER ENTITY:
(Signature)	ValueAct Capital Master Fund, L.P.
	Print name of entity
(Printed Name)	By:	/s/ George F. Hamel, Jr.
		Name:	George F. Hamel, Jr.
		Title:	Managing Member of General
			Partner, VA Partners, LLC
	British Virgin Islands
	Print jurisdiction of organization of entity
Address:	Address:
	ValueAct Capital Master Fund, L.P.
	435 Pacific Avenue, 4th Floor
	San Francisco, CA 94133

Signature Page to Securities Purchase Agreement

     IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP, TRUST, ESTATE OR OTHER ENTITY:
(Signature)	Capital Ventures International
	By:	Heights Capital Management, Inc.
		its Authorizing Agent
	Print name of entity
(Printed Name)	By:	/s/ Martin Kobinger
		Name:	Martin Kobinger
		Title:	Investment Manager
	Print jurisdiction of organization of entity
Address:	Address:
	Capital Ventures International
	101 California Street, Suite 3250
	San Francisco, CA 94111

Signature Page to Securities Purchase Agreement

     IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP, TRUST, ESTATE OR OTHER ENTITY:
(Signature)	SF Capital Partners LTD.
	Print name of entity
(Printed Name)	By:	/s/ Brian H. Davidson
		Name:	Brian H. Davidson
		Title:	Authorized Signatory
	British Virgin Islands
	Print jurisdiction of organization of entity
Address:	Address:
	SF Capital Partners, LTD
	c/o Stark Offshore Management, LLC
	3600 South Lake Drive
	St. Francis, Wisconsin 53235

Signature Page to Securities Purchase Agreement

      IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
(Signature)	Oxford Bioscience Partners IV L.P.
	By:	OBP Management IV L.P.
		its General Partner
	Print name of entity
(Printed Name)	By:	/s/ Jonathan J. Fleming
		Name:	Jonathan J. Fleming
		Title:	General Partner
	Delaware
	Print jurisdiction of organization of entity
Address:	Address:
	Oxford Biosciences Partners
	222 Berkeley Street, Suite 1650
	Boston, MA 02116

      IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
(Signature)	MRNA Fund II L.P.
	By:	OBP Management IV L.P.
		its General Partner
	Print name of entity
(Printed Name)	By:	/s/ Jonathan J. Fleming
		Name:	Jonathan J. Fleming
		Title:	General Partner
	Delaware
	Print jurisdiction of organization of entity
Address:	Address:
	Oxford Biosciences Partners
	222 Berkeley Street, Suite 1650
	Boston, MA 02116

      IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
(Signature)	Schroder Ventures International
	Life Sciences Fund II L.P.1
	Print name of entity
(Printed Name)	By:	/s/ Gary Carr
		Name:	Gary Carr
		Title:	Director and Vice President
	By:	/s/ Douglas Mello
		Name:	Douglas Mello
		Title:	Secretary
	of Schroder Venture Managers Inc. as General Partner
	Delaware
	Print jurisdiction of organization of entity
Address:	Address:
	c/o 22 Church Street
	Hamilton HM 11
	Bermuda

      IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
(Signature)	Schroder Ventures International
	Life Sciences Fund II L.P.2
	Print name of entity
(Printed Name)	By:	/s/ Gary Carr
		Name:	Gary Carr
		Title:	Director and Vice President
	By:	/s/ Douglas Mello
		Name:	Douglas Mello
		Title:	Secretary
	of Schroder Venture Managers Inc. as General Partner
	Delaware
	Print jurisdiction of organization of entity
Address:	Address:
	c/o 22 Church Street
	Hamilton HM 11
	Bermuda

      IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
(Signature)	Schroder Ventures International
	Life Sciences Fund II L.P.3
	Print name of entity
(Printed Name)	By:	/s/ Gary Carr
		Name:	Gary Carr
		Title:	Director and Vice President
	By:	/s/ Douglas Mello
		Name:	Douglas Mello
		Title:	Secretary
	of Schroder Venture Managers Inc. as General Partner
	Delaware
	Print jurisdiction of organization of entity
Address:	Address:
	c/o 22 Church Street
	Hamilton HM 11
	Bermuda

      IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
(Signature)	Schroder Ventures International
	Life Sciences Fund II Strategic
	Partners L.P.
	Print name of entity
(Printed Name)	By:	/s/ Gary Carr
		Name:	Gary Carr
		Title:	Director and Vice President
	By:	/s/ Douglas Mello
		Name:	Douglas Mello
		Title:	Secretary
	of Schroder Venture Managers Inc. as General Partner
	Delaware
	Print jurisdiction of organization of entity
Address:	Address:
	c/o 22 Church Street
	Hamilton HM 11
	Bermuda

      IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
(Signature)	Schroder Ventures International
	Life Sciences Fund II Group
	Co-Investment Scheme
	Print name of entity
(Printed Name)	By:	/s/ Gary Carr
		Name:	Gary Carr
		Title:	Director and Vice President
	By:	/s/ Douglas Mello
		Name:	Douglas Mello
		Title:	Secretary
	of SITCO Nominees Ltd. — VC01903 as Nominee
	Bermuda
	Print jurisdiction of organization of entity
Address:	Address:
	c/o 22 Church Street
	Hamilton HM 11
	Bermuda

      IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
(Signature)	SV (Nominees) Limited as Nominee
	for Schroder Ventures Investments Limited
	Print name of entity
(Printed Name)	By:	/s/ Lawrence S. McNairn
		Name:	Lawrence S. McNairn
		Title:	Director
	Guernsey, Channel Islands
	Print jurisdiction of organization of entity
Address:	Address:
	P.O. Box 255 Trafalgar Court
	Les Banques, St. Peter Port
	Guernsey, Channel Islands 941 3QJ

      IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
(Signature)	Abingworth Bioventures II A L.P.
	By:	Abingworth Management Ltd.
		its Manager
	Print name of entity
(Printed Name)	By:	/s/ James Abell
		Name: James Abell
		Title: Director
	England
	Print jurisdiction of organization of entity
Address:	Address:
	38 Jermyn Street
	London
	SW1Y 6DN

      IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
(Signature)	Abingworth Bioventures III A L.P.
	By:	Abingworth Management Ltd.
		its Manager
	Print name of entity
(Printed Name)	By:	/s/ James Abell
		Name: James Abell
		Title: Director
	England
	Print jurisdiction of organization of entity
Address:	Address:
	38 Jermyn Street
	London
	SW1Y 6DN

      IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
(Signature)	Abingworth Bioventures III B L.P.
	By:	Abingworth Management Ltd.
		its Manager
	Print name of entity
(Printed Name)	By:	/s/ James Abell
		Name: James Abell
		Title: Director
	England
	Print jurisdiction of organization of entity
Address:	Address:
	38 Jermyn Street
	London
	SW1Y 6DN

      IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
(Signature)	Abingworth Bioventures III C L.P.
	By:	Abingworth Management Ltd.
		its Manager
	Print name of entity
(Printed Name)	By:	/s/ James Abell
		Name: James Abell
		Title: Director
	England
	Print jurisdiction of organization of entity
Address:	Address:
	38 Jermyn Street
	London
	SW1Y 6DN

      IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
(Signature)	Abingworth Bioventures III Executives L.P.
	By:	Abingworth Management Ltd.
		its Manager
	Print name of entity
(Printed Name)	By:	/s/ James Abell
		Name: James Abell
		Title: Director
	England
	Print jurisdiction of organization of entity
Address:	Address:
	38 Jermyn Street
	London
	SW1Y 6DN

      IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
(Signature)	Amadeus II “A”
	By:	Amadeus Capital Partners Limited
		its Manager
	Print name of entity
(Printed Name)	By:	/s/ H. Hauser
		Name:	Hermann Hauser
		Title:
	Print jurisdiction of organization of entity
Address:	Address:
	Mt. Pleasant House, 2 Mount Pleasant
	Huntingdon Road
	Cambridge CB3 0RN
	United Kingdom

      IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
(Signature)	Amadeus II “B”
	By:	Amadeus Capital Partners Limited
		its Manager
	Print name of entity
(Printed Name)	By:	/s/ H. Hauser
		Name:	Hermann Hauser
		Title:
	Print jurisdiction of organization of entity
Address:	Address:
	Mt. Pleasant House, 2 Mount Pleasant
	Huntingdon Road
	Cambridge CB3 0RN
	United Kingdom

      IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
(Signature)	Amadeus II “C”
	By:	Amadeus Capital Partners Limited
		its Manager
	Print name of entity
(Printed Name)	By:	/s/ H. Hauser
		Name:	Hermann Hauser
		Title:
	Print jurisdiction of organization of entity
Address:	Address:
	Mt. Pleasant House, 2 Mount Pleasant
	Huntingdon Road
	Cambridge CB3 0RN
	United Kingdom

      IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
(Signature)	Amadeus II “D” GMBH & CO KG
	By:	Amadeus Capital Partners Limited
		its Manager
	Print name of entity
(Printed Name)	By:	/s/ H. Hauser
		Name:	Hermann Hauser
		Title:
	Print jurisdiction of organization of entity
Address:	Address:
	VCM Venture Capital Management and
	Beteiligungsgesellschaft mbH
	Max-Joseph Strasse 7, Munich, Germany

      IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
(Signature)	Amadeus II Affiliates Fund L.P.
	By:	Amadeus Capital Partners Limited
		its Manager
	Print name of entity
(Printed Name)	By:	/s/ H. Hauser
		Name:	Hermann Hauser
		Title:
	Delaware
	Print jurisdiction of organization of entity
Address:	Address:
	The Corporation Trust Company
	1209 Orange Street, Wilmington,
	New Castle County, Delaware, USA 19801

      IN WITNESS WHEREOF, the undersigned has executed this Purchase Agreement or caused its duly authorized officers to execute this Purchase Agreement as of the date first above written.

IF AN INDIVIDUAL:	IF A CORPORATION, PARTNERSHIP,
	TRUST, ESTATE OR OTHER ENTITY:
(Signature)	International Biotechnology Trust plc
	Print name of entity
(Printed Name)	By:	/s/ Nick Coleman
		Name:	Nick Coleman
		Title:	Signatory
	United Kingdom
	Print jurisdiction of organization of entity
Address:	Address:
	c/o Charmaine Obeyschera
	31 Gresham Street
	London EC2V 7QA
	United Kingdom

Exhibit A

FORM OF WARRANT

[The Form of Warrant is filed separately as Exhibit 10.59 of the Company’s Current Report on Form 8-K, filed on April 22, 2005.]

Exhibit A-1

Form of SF Capital Warrant

[The Form of SF Capital Warrant is filed separately as Exhibit 10.60 of the Company’s Current Report on Form 8-K, filed on April 22, 2005.]

Exhibit B

INSTRUCTION SHEET FOR PURCHASER
(to be read in conjunction with the entire
Securities Purchase Agreement)

A.   Complete the following items in the Securities Purchase Agreement:

1.	Provide the information regarding the Purchaser requested on the signature page. The Agreement must be executed by an individual authorized to bind the Purchaser.
2.	Exhibit B-1 – Stock Certificate Questionnaire:
	Provide the information requested by the Stock Certificate Questionnaire.
3.	Exhibit B-2 – Registration Statement Questionnaire:
	Provide the information requested by the Registration Statement Questionnaire.
4.	Exhibit B-3 – Purchaser Certificate:
	Provide the information requested by the Certificate for Individual Purchasers or the Certificate for Corporate, Partnership, Trust, Foundation and Joint Purchasers, as applicable.
5.	Return the signed Securities Purchase Agreement to:

John L. Brottem, Esq.
Cooley Godward llp
Five Palo Alto Square
3000 El Camino Real
Palo Alto, California 94306-2155
Fax: 650-745-3924

B.   Instructions regarding the transfer of funds for the purchase of Securities will be telecopied to the Purchaser at a later date.

C.   Upon the resale of the Registrable Shares by the Purchaser after the Registration Statement covering the Registrable Shares is effective, as described in the Securities Purchase Agreement, the Purchaser:

(i)   must deliver a current prospectus to the buyer (prospectuses may be obtained from the Company at the Purchaser’s request); and

(ii)   must send a letter in the form of Exhibit E to the Securities Purchase Agreement to the Company so that the Registrable Shares may be properly transferred.

Exhibit B-1

SOLEXA, INC.
STOCK CERTIFICATE QUESTIONNAIRE

Pursuant to Section 4.3 of the Agreement, please provide us with the following information:

1.	The exact name that the Securities are to be registered in (this is the name that will appear on the stock certificate(s)). You may use a nominee name if appropriate:
2.	The relationship between the Purchaser of the Securities and the Registered Holder listed in response to item 1 above:
3.	The mailing address of the Registered Holder listed in response to item 1 above:
4.	The Tax Identification Number of the Registered Holder listed in response to item 1 above:

B-1

Exhibit B-2

SOLEXA, INC.

REGISTRATION STATEMENT QUESTIONNAIRE

     In connection with the preparation of the Registration Statement, please provide us with the following information regarding the Purchaser.

A.   General Information

     1. Please state your organization’s name exactly as it should appear in the Registration Statement:                                                                       

     2. Have you or your organization had any position, office or other material relationship within the past three years with the Company or its affiliates other than as disclosed in the Prospectus included in the Registration Statement?

¨ Yes       ¨ No

     If yes, please indicate the nature of any such relationships below:

B.   Securities Holdings

     Please fill in all blanks in the following questions related to your beneficial ownershipof the Company’s capital stock. Generally, the term “beneficial ownership” refers to any direct or indirect interest in the securities which entitles you to any of the rights or benefits of ownership, even though you may not be the holder of record of the securities. For example, securities held in “street name” over which you exercise voting or investment power would be considered beneficially owned by you. Other examples of indirect ownership include ownership by a partnership in which you are a partner or by an estate or trust of which you or any member of your immediate family is a beneficiary. Ownership of securities held in the names of your spouse, minor children or other relatives who live in the same household may be attributed to you.

     Please note: If you have any reason to believe that any interest in securities of the Company which you may have, however remote, is a beneficial interest, please describe such interest. For purposes of responding to this questionnaire, it is preferable to err on the side of inclusion rather than exclusion. Where the SEC’s interpretation of beneficial ownership would require disclosure of your interest or possible interest in certain securities of the Company, and you believe that you do not actually possess the attributes of beneficial ownership, an appropriate response is to disclose the interest and at the same time disclaim beneficial ownership of the securities.

B-2.1

     1. As of [___], 2005, I owned outright (including shares registered in my name individually or jointly with others, shares held in the name of a bank, broker, nominee, depository or in “street name” for my account), the following number of shares of the Company’s capital stock: ___.

     2. In addition to the number of shares I own outright as indicated by my answer to question B(1), as of [___], 2005, I had or shared voting power or investment power, directly or indirectly, through a contract, arrangement, understanding, relationship or otherwise, over the following number of shares of the Company’s capital stock: ____________.

     If the answer to this question B(2) was not “zero,” please complete the following: with whom shared; and the nature of the relationship and any underlying voting trust agreement, investment arrangement or the like:

Shared Voting Power:

Number of Shares With Whom Shared Nature of Relationship

Shared Investment Power:

Number of Shares With Whom Shared Nature of Relationship

     3. As of [___], 2005, I will have the right to acquire ___shares of the Company’s capital stock pursuant to outstanding stock options issued under the Company’s stock option plans and ___shares pursuant to the exercise of outstanding warrants (none, indicated by “0” above).

Options and Warrants
Class	Number of Shares

B-2.2

     (4) Please identify the natural person or persons who have voting and/or investment control over the Company’s securities that you own, and state whether such person(s) disclaims beneficial ownership of the securities. For example, if you are a general partnership, please identify the general partners in the partnership.

B-2.3

C. NASD Questions

     1. Are you (i) a “member”¹ of the National Association of Securities Dealers, Inc. (the “NASD”), (ii) an “affiliate”² of a member of the NASD, (iii) a “person associated with a member” or an “associated person of a member”³ of the NASD or (iv) an immediate family member⁴ of any of the foregoing persons? If yes, please identify the member and describe such relationship (whether direct or indirect), and please respond to Question Number 2 below; if no, please proceed directly to Question Number 3.

Yes _____                     No _____

Description:

¹ NASD defines a “member” as any broker or dealer admitted to membership in the NASD, or any officer or partner or branch manager of such a member, or any person occupying a similar status or performing a similar function for such a member.

²The term “affiliate” means a person that directly, or indirectly through one or more intermediaries, controls, or is controlled by, or is in common control with, the person specified. Persons who have acted or are acting on behalf of or for the benefit of a person include, but are not necessarily limited to, directors, officers, employees, agents, consultants and sales representatives. The following should apply for purposes of the foregoing:

     (i) a person should be presumed to control a Member if the person beneficially owns 10 percent or more the outstanding voting securities of a Member which is a corporation, or beneficially owns a partnership interest in 10 percent or more of the distributable profits or losses of a Member which is a partnership;

     (ii) a Member should be presumed to control a person if the Member and Persons Associated With a Member beneficially own 10 percent or more of the outstanding voting securities of a person which is a corporation, or beneficially own a partnership interest in 10 percent or more of the distributable profits or losses of a person which is a partnership;

     (iii) a person should be presumed to be under common control with a Member if:

     (1) the same person controls both the Member and another person by beneficially owning 10 percent or more of the outstanding voting securities of a Member or person which is a corporation, or by beneficially owning a partnership interest in 10 percent or more of the distributable profits or losses of a Member or person which is a partnership; or

     (2) a person having the power to direct or cause the direction of the management or policies of the Member or such person also has the power to direct or cause the direction of the management or policies of the other entity in question.

³ The NASD defines a “person associated with a member” or an “associated person of a member” as being every sole proprietor, partner, equity owner, officer, director or branch manager of any member, or any natural person occupying a similar status or performing similar functions, or any natural person engaged in the investment banking or securities business who directly or indirectly controls or is controlled by such member (for example, any employee), whether or not any such person is registered or exempt from registration with the NASD.

⁴ Immediate family includes parents, mother-in-law, father-in-law, husband or wife, brother or sister, brother-in-law or sister-in-law, son-in-law or daughter-in-law, and children, or any other person who is supported, directly or indirectly, to a material extent, by a person associated with a member of the NASD or any other broker/dealer.

B-2.4

     2. If you answered “yes” to Question Number 1, please furnish any information as to whether any such member intends to participate in any capacity in the private placement, including the details of such participation:

Description:

     3. Are you or have you been an “underwriter or related person”⁵ or a person associated with an underwriter or related person, including, without limitation, with respect to the proposed public offering? If yes, please identify the underwriter or related person and describe such relationship (whether direct or indirect).

Yes _____                     No _____

Description:

     4. If known, please describe in detail any underwriting compensations, arrangements or dealings entered into during the previous twelve months, or proposed to be consummated in the next twelve months, between (i) any underwriter or related person, member of the NASD, affiliate of a member of the NASD, person associated with a member or associated person of a member of the NASD or any immediate family member thereof, on the one hand, and (ii) the Company, or any director, officer or stockholder thereof, on the other hand, which provides for the receipt of any item of value and/or the transfer of any warrants, options or other securities from the Company to any such person (other than the information relating to the arrangements with any investment firm or underwriting organization which may participate in the proposed public offering).

Description:

     5. Have you purchased the securities in the ordinary course of business ?

Yes _____                     No _____

⁵ The term “underwriter or related person” includes underwriters, underwriters’ counsel, financial consultants and advisors, finders, members of the selling or distribution group, and any and all other persons associated with or related to any of such persons, including members of the immediate family of such persons.

B-2.5

     The answers to the foregoing questions are correctly stated to the best of my information and belief. I shall advise John L. Brottem at (650) 843-5358, the Company’s outside counsel, promptly of any changes in the foregoing information prior to the effectiveness of the registration statement.

(Print name of Selling Security Holder)

(Signature)

By:

(Name and title of signatory, if stockholder is an entity)

(Date)

B-2.6

Exhibit B-3

SOLEXA, INC.
CERTIFICATE FOR INDIVIDUAL PURCHASERS

     If the investor is an individual Purchaser (or married couple) the Purchaser must complete, date and sign this Certificate.

Certificate

     I certify that the representations and responses below are true and accurate:

     In order for the Company to offer and sell the Securities in conformance with state and federal securities laws, the following information must be obtained regarding your investor status. Please initial each category applicable to you as an investor in the Company.

     ___(1) A natural person whose net worth¹, either individually or jointly with such person’s spouse exceeds $1,000,000;

     ___(2) A natural person who had an income² in excess of $200,000, or joint income with the person’s spouse in excess of $300,000, in 2003 and 2004, and reasonably expects to have individual income reaching the same level in 2005;

     ___(3) An executive officer or director of the Company.

Date:
	Name(s) of Purchaser
	Signature
	Signature

¹ For purposes of this Certificate, “net worth” means the excess of total assets at fair market value over total liabilities, except that the principal residence owned by a natural person shall be valued either (a) at cost, including the cost of improvements, net of current encumbrances upon the property, or (b) at the appraised value of the residence as determined upon a written appraisal used by an institutional lender making a loan to the individual secured by the property, including the cost of subsequent improvements, net of current encumbrances upon the property. As used in the preceding sentence, “institutional lender” means a bank, savings and loan company, industrial loan company, credit union or personal property broker or a company whose principal business is as a lender of loans secured by real property and which has such loans receivable in the amount of $2,000,000 or more.

² For purposes of this Certificate, “income” means adjusted gross income, as reported for federal income tax purposes, increased by the following amounts: (a) the amount of any tax exempt interest income received, (b) the amount of losses claimed as a limited partner in a limited partnership, (c) any deduction claimed for depletion, (d) amounts contributed to an IRA or Keogh retirement plan, (e) alimony paid, and (f) any amounts by which income from long-term capital gains has been reduced in arriving at adjusted gross income pursuant to the provisions of Section 1202 of the Internal Revenue Code.

B-3

Exhibit B-4

SOLEXA, INC.
CERTIFICATE FOR CORPORATE, PARTNERSHIP,
TRUST, FOUNDATION, AND JOINT PURCHASERS

     If the investor is a corporation, partnership, trust, pension plan, foundation, joint purchaser (other than a married couple) or other entity, an authorized officer, partner, or trustee must complete, date and sign this Certificate.

Certificate

     The undersigned certifies that the representations and responses below are true and accurate:

     (a) The investor has been duly formed and is validly existing and has full power and authority to invest in the Company. The person signing on behalf of the undersigned has the authority to execute and deliver the Securities Purchase Agreement on behalf of the Purchaser and to take other actions with respect thereto.

     (b) Indicate the form of entity of the undersigned:

¨	Limited Partnership
¨	General Partnership
¨	Corporation
¨	Revocable Trust (identify each grantor and indicate under what circumstances the trust is revocable by the grantor:
	(Continue on a separate piece of paper, if necessary.)
¨	Other Type of Trust (indicate type of trust and, for trusts other than pension trusts, name the grantors and beneficiaries:
	(Continue on a separate piece of paper, if necessary.)
¨	Other form of organization (indicate form of organization (                                        ).

B-4.2

     (c) Indicate the approximate date the undersigned entity was formed:                                         .

     (d) In order for the Company to offer and sell the Securities in conformance with state and federal securities laws, the following information must be obtained regarding your investor status. Please initial each category applicable to you as an investor in the Company.

     ___ (1) A bank as defined in Section 3(a)(2) of the Securities Act, or any savings and loan association or other institution as defined in Section 3(a)(5)(A) of the Securities Act whether acting in its individual or fiduciary capacity;

     ___ (2) A broker or dealer registered pursuant to Section 15 of the Securities Exchange Act of 1934;

     ___ (3) An insurance company as defined in Section 2(13) of the Securities Act;

     ___ (4) An investment company registered under the Investment Company Act of 1940 or a business development company as defined in Section 2(a)(48) of that Act;

     ___ (5) A Small Business Investment Company licensed by the U.S. Small Business Administration under Section 301(c) or (d) of the Small Business Investment Act of 1958;

     ___ (6) A plan established and maintained by a state, its political subdivisions, or any agency or instrumentality of a state or its political subdivisions, for the benefit of its employees, if such plan has total assets in excess of $5,000,000;

     ___ (7) An employee benefit plan within the meaning of the Employee Retirement Income Security Act of 1974, if the investment decision is made by a plan fiduciary, as defined in Section 3(21) of such act, which is either a bank, savings and loan association, insurance company, or registered investment adviser, or if the employee benefit plan has total assets in excess of $5,000,000 or, if a self-directed plan, with investment decisions made solely by persons that are accredited investors;

     ___ (8) A private business development company as defined in Section 202(a)(22) of the Investment Advisers Act of 1940;

     ___ (9) An organization described in Section 501(c)(3) of the Internal Revenue Code, a corporation, Massachusetts or similar business trust, or partnership, not formed for the specific purpose of acquiring the Securities, with total assets in excess of $5,000,000;

     ___ (10) A trust, with total assets in excess of $5,000,000, not formed for the specific purpose of acquiring the Securities, whose purchase is directed by a sophisticated person who has such knowledge and experience in financial and business matters that such person is capable of evaluating the merits and risks of investing in the Company;

B-4.2

     ___   (11) An entity in which all of the equity owners qualify under any of the above subparagraphs. If the undersigned belongs to this investor category only, list the equity owners of the undersigned, and the investor category which each such equity owner satisfies:

(Continue on a separate piece of paper, if necessary.)

Dated:

Name of investor

Signature and title of authorized
officer, partner or trustee

B-4.2

Exhibit C

OPINION OF COMPANY COUNSEL

April [__], 2005

To the Purchasers listed on Exhibit A hereto

Re: Solexa, Inc. Private Placement
Dear Ladies and Gentlemen:

     We have acted as counsel for Solexa, Inc., a Delaware corporation (the “Company”), in connection with the issuance and sale of [                    ] shares of the Company’s common stock, par value $0.01 per share (“Common Stock”) (the “Shares”) and warrants (the “Warrants”) to purchase an aggregate of up to [___] shares of Common Stock (the “Warrant Shares” and collectively with the Shares and Warrants, the “Securities”), to the Purchasers at the First Closing under that certain Securities Purchase Agreement dated as of April [___], 2005 (the “Purchase Agreement”). We are rendering this opinion pursuant to Section [5.4] of the Purchase Agreement. Except as otherwise defined herein, capitalized terms used but not defined herein have the respective meanings given to them in the Purchase Agreement.

     In connection with this opinion, we have examined and relied upon the representations and warranties as to factual matters contained in and made pursuant to the Purchase Agreement by the various parties and originals or copies certified to our satisfaction, of such records, documents, certificates, opinions, memoranda and other instruments as in our judgment are necessary or appropriate to enable us to render the opinion expressed below.

     As to certain factual matters, we have relied upon certificates of officers of the Company and have not sought to independently verify such matters. Where we render an opinion “to our knowledge” or concerning an item “known to us” or our opinion otherwise refers to our knowledge, it is based solely upon (i) an inquiry of attorneys within this firm who have represented the Company in this transaction, (ii) receipt of a certificate executed by an officer of the Company covering such matters, and (iii) such other investigation, if any, that we specifically set forth herein.

     In rendering this opinion, we have assumed: the authenticity of all documents submitted to us as originals; the conformity to originals of all documents submitted to us as copies; the accuracy, completeness and authenticity of certificates of public officials; the due authorization, execution and delivery of all documents (except the due authorization, execution and delivery by the Company of the Purchase Agreement and the Warrants (together, the “Financing Agreements”)), where authorization, execution and delivery are prerequisites to the effectiveness of such documents; and the genuineness and authenticity of all signatures on original documents (except the signatures on behalf of the Company on the Financing Agreements). We have also assumed: that all individuals executing and delivering documents had the legal capacity to so execute and deliver; that the Financing Agreements are obligations binding upon the parties thereto other than the Company; that the parties to the Financing Agreements other than the Company have filed any required California franchise or income tax returns and have paid any required California franchise or income taxes; and that there are no extrinsic agreements or

C-1

understandings among the parties to the Financing Agreements that would modify or interpret the terms of the Financing Agreements or the respective rights or obligations of the parties thereunder.

     Our opinion is expressed only with respect to the federal laws of the United States of America and the laws of the State of California and the General Corporation Law of the State of Delaware. We express no opinion as to whether the laws of any particular jurisdiction apply, and no opinion to the extent that the laws of any jurisdiction other than those identified above are applicable to the subject matter hereof.

     We are not rendering any opinion as to any statute, rule, regulation, ordinance, decree or decisional law relating to antitrust, banking, land use, environmental, pension, employee benefit, tax, fraudulent conveyance, usury, laws governing the legality of investments for regulated entities, regulations T, U or X of the Board of Governors of the Federal Reserve System or local law. Furthermore, we express no opinion with respect to compliance with antifraud laws, rules or regulations relating to securities or the offer and sale thereof; compliance with fiduciary duties by the Company’s Board of Directors or stockholders; compliance with safe harbors for disinterested Board of Director or stockholder approvals; compliance with state securities or blue sky laws except as specifically set forth below; compliance with the Investment Company Act of 1940; compliance with laws that place limitations on corporate distributions; the enforceability of provisions in the Financing Agreements concerning the voting of the Company’s capital stock (other than solely administrative obligations of the Company).

     With regard to our opinion in paragraphs 1 and 3 below with respect to the good standing of the Company, we have relied solely upon certificates of the Secretaries of State of the indicated jurisdictions as of a recent date.

     With regard to our opinion in paragraph 3 below with respect to the Company’s qualifications to do business as a foreign corporation, we have based our opinion solely upon a certificate of an officer of the Company as to the states in which the Company maintains an office, has employees or owns or leases property, and an examination of the status of the Company in such states.

     With regard to our opinion in paragraph 6 below, we have examined and relied upon a certificate executed by an officer of the Company, to the effect that the consideration for all outstanding shares of capital stock of the Company was received by the Company in accordance with the provisions of the applicable Board of Directors resolutions and any plan or agreement relating to the issuance of such shares, and we have undertaken no independent verification with respect thereto.

     With regard to our opinion in paragraph 6 below with respect to securities of the Company to be issued after the date hereof, we express no opinion to the extent that, notwithstanding its current reservation of shares of Common Stock, future issuance of securities of the Company or anti-dilution adjustments to outstanding securities of the Company cause the Warrants to be convertible for more shares of Common Stock than the number that then remain authorized but unissued.

C-1.4

     With regard to our opinion in paragraph 8 below with respect to pending or overtly threatened litigation, we have made an inquiry of the attorneys within this firm who have represented the Company in this transaction, examined and relied upon a certificate executed by an officer of the Company covering such matters, and checked the records of this firm to ascertain that we are not acting as counsel of record for the Company in any such matter. We have made no further investigation.

     With regard to our opinion in paragraph 10 with respect to exemption from registration, no opinion is expressed with respect to the integration of the offer and sale of the Shares with any offers or sales of securities occurring prior to or subsequent to the date hereof.

     On the basis of the foregoing, in reliance thereon and with the foregoing qualifications, we are of the opinion that:

1.	The Company has been duly incorporated and is a validly existing corporation in good standing under the laws of the State of Delaware.
2.	The Company has the requisite corporate power to own its property and assets and to conduct its business as it is currently being conducted.
3.	The Company is duly qualified to do business as a foreign corporation and is in good standing under the laws of California.
4.	The Company has the corporate power to execute, deliver and perform its obligations under the Financing Agreements.
5.	Each of the Financing Agreements has been duly and validly authorized, executed and delivered by the Company and each such agreement constitutes a valid and binding agreement of the Company enforceable against the Company in accordance with its respective terms, except as rights to indemnity and contribution under section [7.3] of the Purchase Agreement may be limited by applicable laws and except as enforcement may be limited by applicable bankruptcy, insolvency, reorganization, arrangement, moratorium or other similar laws affecting creditors’ rights, and subject to general equity principles and to limitations on availability of equitable relief, including specific performance.
6.	The Company’s authorized capital stock consists of sixty million (60,000,000) shares of Common Stock, of which (excluding the Shares to be issued at First Closing) seventeen million six hundred six thousand four hundred seventy-one (17,606,471) shares are issued and outstanding, and (b) two million (2,000,000) shares of Preferred Stock, par value $0.01 per share, of which none are issued and outstanding. The outstanding shares of Common Stock have been duly authorized and validly issued and are fully paid and nonassessable. The Shares and Warrant Shares have been duly authorized and the Warrant Shares have been reserved for issuance upon exercise of the Warrants. The Shares and Warrants, when issued, sold and delivered against payment therefor in accordance with the terms of the Purchase Agreement and the Warrant Shares, if issued on the date hereof upon exercise of the Warrants and payment therefor in accordance with the terms of the Warrants, will be validly issued, outstanding, fully paid and

C-1.4

nonassessable. To our knowledge, except as provided in the SEC Documents, the Financing Agreements or the Disclosure Schedule, there are no options, warrants, conversion privileges, preemptive rights or other rights presently outstanding to purchase any of the authorized but unissued capital stock of the Company.

7.	The execution and delivery of the Financing Agreements by the Company and the issuance of the Shares and Warrants pursuant thereto do not violate any provision of the Company’s Amended and Restated Certificate of Incorporation, as amended, or Bylaws, as amended, and do not violate (a) any governmental statute, rule or regulation which in our experience is typically applicable to transactions of the nature contemplated by the Financing Agreements or (b) any order, writ, judgment, injunction, decree, determination or award which has been entered against the Company and of which we are aware, in each case to the extent the violation of which would materially and adversely affect the Company and its subsidiaries, taken as a whole.
8.	To our knowledge, there is no action, proceeding or investigation pending or overtly threatened against the Company before any court or administrative agency that questions the validity of the Purchase Agreement or that could reasonably be expected to result, either individually or in the aggregate, in a material adverse effect on the Company and its subsidiaries, taken as a whole that has not been disclosed in writing to the Investors.
9.	All consents, approvals, authorizations, or orders of, and filings, registrations, and qualifications with any U.S. Federal or California regulatory authority or governmental body required for the issuance of the Shares and Warrants, have been made or obtained, except (a) for the filing of a Form D pursuant to Securities and Exchange Commission Regulation D and (b) for the filing of the notice to be filed under California Corporations Code Section 25102.1(d).
10.	The offer and sale of the Shares and Warrants are exempt from the registration requirements of the Securities Act of 1933, as amended, subject to the timely filing of a Form D pursuant to Securities and Exchange Commission Regulation D.

     This opinion is intended solely for your benefit and is not to be made available to or be relied upon by any other person, firm, or entity without our prior written consent.

Very truly yours,

Cooley Godward llp

By:
	James C. Kitch

C-1.4

Exhibit D

SOLEXA, INC.

IMPORTANT — DO NOT REMOVE THIS INSTRUCTION SHEET FROM THE ATTACHED SHARE CERTIFICATE UNLESS AND UNTIL THE SHARES ARE SOLD AS FOLLOWS:

(1) THE SHARES ARE RESOLD PURSUANT TO THE REGISTRATION STATEMENT ON FORM S-3 (NO. [                                        ]), AND, IN CONNECTION WITH SUCH RESALE, THE HOLDER HAS DELIVERED TO THE PURCHASER OF THE SHARES A CURRENT PROSPECTUS AND HAS PROVIDED TO THE COMPANY OR TO THE TRANSFER AGENT FOR THE COMPANY’S STOCK A PURCHASER’S CERTIFICATE OF SUBSEQUENT SALE; OR

(2) THE SHARES ARE RESOLD IN A TRANSACTION EXEMPT FROM THE REGISTRATION REQUIREMENTS OF THE SECURITIES ACT OF 1933, AS AMENDED, PROVIDED THAT, PRIOR TO SUCH RESALE, THE HOLDER HAS NOTIFIED THE COMPANY OF SUCH DISPOSITION AND PROVIDED THE COMPANY WITH WRITTEN ASSURANCES, IN FORM AND SUBSTANCE SATISFACTORY TO THE COMPANY OF COMPLIANCE WITH THE REQUIREMENTS OF SUCH EXEMPTION.

DO NOT REMOVE THIS INSTRUCTION SHEET FROM
THE ATTACHED SHARE CERTIFICATE
EXCEPT IN ACCORDANCE WITH
THE INSTRUCTIONS SET FORTH ABOVE.

D-1

Exhibit E

PURCHASER’S CERTIFICATE OF SUBSEQUENT SALE

To: Cooley Godward llp

Attention: John Ketchum, Esq.

The undersigned, the selling securityholder or an officer of, or other duly authorized person,hereby certifies that

                                                                                                     represents that it has sold

            [fill in name of selling securityholder]

shares of the Common Stock of Solexa, Inc. and that such shares were sold on

                                         either (i) in accordance with the registration statement on Form S-3 with

            [date]

file number [                                        ], in which case the selling securityholder certifies that the requirement of delivering a current prospectus has been complied with or will be complied with in connection with such sale, or (ii) in accordance with Rule 144 under the Securities Act of 1933 (“Rule 144”), in which case the selling securityholder certifies that it has complied with the requirements of Rule 144.

Print or type:

Number of shares sold (if sold on multiple dates, please provide a breakdown by date):

Name of selling securityholder:

Name of individual representing selling securityholder (if an institution):

Title of individual representing selling securityholder (if an institution):

Signature by:

Selling securityholder or individual representative:

E-1

Exhibit F

Form of Amended and Restated Company Support Agreement

[The Form of Amended and Restated Company Support Agreement is filed separately as Exhibit 99.1 of the Company’s Current Report on Form 8-K, filed on April 22, 2005.]

E-2

EX-10.59

EXHIBIT 10.59

THIS WARRANT AND THE UNDERLYING SECURITIES HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”). THEY MAY NOT BE SOLD, OFFERED FOR SALE, PLEDGED OR HYPOTHECATED IN THE ABSENCE OF AN EFFECTIVE REGISTRATION STATEMENT AS TO SUCH SECURITIES UNDER THE ACT OR AN OPINION OF COUNSEL SATISFACTORY TO THE COMPANY THAT SUCH REGISTRATION IS NOT REQUIRED.

SOLEXA, INC.

WARRANT TO PURCHASE COMMON STOCK

April 25, 2005

Void After April 25, 2010

     This Certifies That, for value received, [___], or assigns (the “Holder”), is entitled to subscribe for and purchase at the Exercise Price (defined below) from Solexa, Inc., a Delaware corporation, with its principal office at 25861 Industrial Boulevard, Hayward, CA 94545 (the “Company”) up to [___] shares of the common stock of the Company, par value $0.01 per share (the “Common Stock”).

     1. Definitions. As used herein, the following terms shall have the following respective meanings:

         (a) “Exercise Period” shall mean the period commencing with the date that is one hundred and eighty (180) days after the date hereof and ending five (5) years from the date hereof, unless sooner terminated as provided below.

         (b) “Exercise Price” shall mean five dollars ($5.00) per share, subject to adjustment pursuant to Section 5 below.

         (c) “Exercise Shares” shall mean the shares of the Common Stock issuable upon exercise of this Warrant.

     2. Exercise of Warrant. The rights represented by this Warrant may be exercised in whole or in part at any time during the Exercise Period, by delivery of the following to the Company at its address set forth above (or at such other address as it may designate by notice in writing to the Holder):

         (a) An executed Notice of Exercise in the form attached hereto;

         (b) Payment of the Exercise Price in cash or by check; and

         (c) This Warrant.

     Certificates for shares purchased hereunder shall be transmitted by the transfer agent of the Company to the Holder by crediting the account of the Holder’s prime broker with the Depository Trust Company through its Deposit Withdrawal Agent Commission (“DWAC”)

1.

system if the Company is a participant in such system (and so long as the legend may be removed in accordance with Section 4.10 of the Purchase Agreement), and otherwise by physical delivery to the address specified by the Holder in the Notice of Exercise within 5 Trading Days from the delivery to the Company of the Notice of Exercise Form, surrender of this Warrant and payment of the aggregate Exercise Price as set forth above (“Warrant Share Delivery Date”). This Warrant shall be deemed to have been exercised on the date the Exercise Price is received by the Company. The Warrant Shares shall be deemed to have been issued, and Holder or any other person so designated to be named therein shall be deemed to have become a holder of record of such shares for all purposes, as of the date the Warrant has been exercised by payment to the Company of the Exercise Price.

     The person in whose name any certificate or certificates for Exercise Shares are to be issued upon exercise of this Warrant shall be deemed to have become the holder of record of such shares on the date on which this Warrant was surrendered and payment of the Exercise Price was made, irrespective of the date of delivery of such certificate or certificates, except that, if the date of such surrender and payment is a date when the stock transfer books of the Company are closed, such person shall be deemed to have become the holder of such shares at the close of business on the next succeeding date on which the stock transfer books are open.

     2.1 Net Exercise. Notwithstanding any provisions herein to the contrary, after the Filing Date (as defined in Section 7.2 of the Securities Purchase Agreement dated April 21, 2005, by and among the Company and the individuals and entities identified on the signature pages hereto (the “Purchase Agreement”)), if (i) the Registration Statement (as defined in the Purchase Agreement) has not been declared effective until such time as the Registration Statement is declared effective or at any time a Registration Statement is no longer effective and (ii) the fair market value of one share of the Company’s Common Stock is greater than the Exercise Price (at the date of calculation as set forth below), in lieu of exercising this Warrant by payment of cash, the Holder may elect to receive shares equal to the value (as determined below) of this Warrant (or the portion thereof being canceled) by surrender of this Warrant at the principal office of the Company together with the properly endorsed Notice of Exercise in which event the Company shall issue to the Holder a number of shares of Common Stock computed using the following formula:

X = Y (A-B)

             A

Where X =	the number of shares of Common Stock to be issued to the Holder
Y =	the number of shares of Common Stock purchasable under the Warrant or, if only a portion of the Warrant is being exercised, the portion of the Warrant being canceled (at the date of such calculation)
A =	the fair market value of one share of the Company’s Common Stock (at the date of such calculation)
B =	Exercise Price (as adjusted to the date of such calculation)

2.

     For purposes of the above calculation, the “fair market value” of one share of Common Stock shall mean (i) the average of the closing sales prices for the shares of Common Stock on the Nasdaq SmallCap Market or other trading market where such security is listed or traded as reported by Bloomberg Financial Markets (or a comparable reporting service of national reputation selected by the Company and reasonably acceptable to the holders if Bloomberg Financial Markets is not then reporting sales prices of such security) (collectively, “Bloomberg”) for the ten (10) consecutive trading days immediately preceding such date, or (ii) if the Nasdaq SmallCap Market is not the principal trading market for the shares of Common Stock, the average of the reported sales prices reported by Bloomberg on the principal trading market for the Common Stock during the same period, or, if there is no sales price for such period, the last sales price reported by Bloomberg for such period, or (iii) if neither of the foregoing applies, the last sales price of such security in the over-the-counter market on the pink sheets or bulletin board for such security as reported by Bloomberg, or if no sales price is so reported for such security, the last bid price of such security as reported by Bloomberg or (iv) if fair market value cannot be calculated as of such date on any of the foregoing bases, the fair market value shall be as determined by the Board of Directors of the Company in the exercise of its good faith judgment.

     Notwithstanding anything herein to the contrary, if there is no Registration Statement effective on the last day of the Exercise Period, this Warrant shall be automatically exercised via net exercise pursuant to this Section 2.1.

     2.2 Issuance of New Warrants. Upon any partial exercise of this Warrant, the Company, at its expense, will forthwith and, in any event within five (5) business days, issue and deliver to the Holder a new warrant or warrants of like tenor, registered in the name of the Holder, exercisable, in the aggregate, for the balance of the Warrant Shares.

     2.3 Payment of Taxes and Expenses. The Company shall pay any recording, filing, stamp or similar tax which may be payable in respect of any transfer involved in the issuance of, and the preparation and delivery of certificates (if applicable) representing, (i) any Warrant Shares purchased upon exercise of this Warrant and/or (ii) new or replacement warrants in the Holder’s name or the name of any transferee of all or any portion of this Warrant.

     2.4 Rescission Rights. If the Company fails to cause its transfer agent to transmit to the Holder a certificate or certificates representing the Warrant Shares pursuant to this Section 2 by the Warrant Share Delivery Date, then the Holder will have the right to rescind such exercise.

     3. Covenants of the Company.

     3.1 Covenants as to Exercise Shares. The Company covenants and agrees that all Exercise Shares that may be issued upon the exercise of the rights represented by this Warrant will, upon issuance, be validly issued and outstanding, fully paid and nonassessable, and free from all taxes, liens and charges with respect to the issuance thereof. The Company further covenants and agrees that the Company will at all times during the Exercise Period, have authorized and reserved, free from preemptive rights, a sufficient number of shares of its Common Stock to provide for the exercise of the rights represented by this Warrant. If at any time during the Exercise Period the number of authorized but unissued shares of Common Stock

3.

shall not be sufficient to permit exercise of this Warrant, the Company will take such corporate action as may, in the opinion of its counsel, be necessary to increase its authorized but unissued shares of Common Stock to such number of shares as shall be sufficient for such purposes.

     3.3 Notices of Record Date. In the event of any taking by the Company of a record of the holders of any class of securities for the purpose of determining the holders thereof who are entitled to receive any dividend (other than a cash dividend which is the same as cash dividends paid in previous quarters) or other distribution, the Company shall mail to the Holder, at least ten (10) days prior to the date specified herein, a notice specifying the date on which any such record is to be taken for the purpose of such dividend or distribution.

     4. Disposition of Warrant and Exercise Shares.

         (a) The Holder further agrees not to make any disposition of all or any part of the Warrant or Exercise Shares in any event unless and until:

               (i) The Company shall have received a letter secured by the Holder from the Securities and Exchange Commission stating that no action will be recommended to the Commission with respect to the proposed disposition; or

               (ii) There is then in effect a registration statement under the Act covering such proposed disposition and such disposition is made in accordance with said registration statement; or

               (iii) The Holder shall have notified the Company of the proposed disposition and shall have furnished the Company with a detailed statement of the circumstances surrounding the proposed disposition, and if reasonably requested by the Company, the Holder shall have furnished the Company with an opinion of counsel, reasonably satisfactory to the Company, for the Holder to the effect that such disposition will not require registration of such Warrant or Exercise Shares under the Act or any applicable state securities laws; provided, however, that no such opinion of counsel shall be required for sales (i) under Rule 144, (ii) to one of its nominees, affiliates or a nominee thereof, (iii) to a pension or profit-sharing fund established and maintained for its employees or for the employees of any affiliate, (iv) from a nominee to any of the aforementioned persons as beneficial owner of this Warrant or such Warrant Shares, or (v) to a qualified institutional buyer, so long as such transfer is effected in compliance with Rule 144A under the Securities Act.

         (b) The Holder understands and agrees that subject to Section 4.10 of the Purchase Agreement, all certificates evidencing the shares to be issued to the Holder may bear the following legend:

“THESE SECURITIES HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”). THEY MAY NOT BE SOLD, OFFERED FOR SALE, PLEDGED OR HYPOTHECATED IN THE ABSENCE OF AN EFFECTIVE REGISTRATION STATEMENT AS TO THE SECURITIES UNDER THE ACT OR AN OPINION OF COUNSEL SATISFACTORY TO THE COMPANY THAT SUCH REGISTRATION IS NOT REQUIRED.”

4.

     5. Adjustment of Exercise Price and Shares.

         (a) In the event of changes in the outstanding Common Stock of the Company by reason of stock dividends, split-ups, recapitalizations, reclassifications, combinations or exchanges of shares, separations, reorganizations, liquidations, consolidation, acquisition of the Company (whether through merger or acquisition of substantially all the assets or stock of the Company), or the like, the number and class of shares available under the Warrant in the aggregate and the Exercise Price shall be correspondingly adjusted to give the Holder of the Warrant, on exercise for the same aggregate Exercise Price, the total number, class, and kind of shares or other property as the Holder would have owned had the Warrant been exercised prior to the event and had the Holder continued to hold such shares until the event requiring adjustment. The form of this Warrant need not be changed because of any adjustment in the number of Exercise Shares subject to this Warrant.

         (b) If at any time or from time to time the holders of Common Stock of the Company (or any shares of stock or other securities at the time receivable upon the exercise of this Warrant) shall have received or become entitled to receive, without payment therefor,

               (i) Common Stock or any shares of stock or other securities which are at any time directly or indirectly convertible into or exchangeable for Common Stock, or any rights or options to subscribe for, purchase or otherwise acquire any of the foregoing by way of dividend or other distribution (other than a dividend or distribution covered in Section 5(a) above),

               (ii) any cash paid or payable otherwise than as a cash dividend or

               (iii) Common Stock or additional stock or other securities or property (including cash) by way of spinoff, split-up, reclassification, combination of shares or similar corporate rearrangement (other than shares of Common Stock pursuant to Section 5(a) above),

then and in each such case, the Holder hereof will, upon the exercise of this Warrant, be entitled to receive, in addition to the number of shares of Common Stock receivable thereupon, and without payment of any additional consideration therefor, the amount of stock and other securities and property (including cash in the cases referred to in clauses (ii) and (iii) above) which such Holder would hold on the date of such exercise had he been the holder of record of such Common Stock as of the date on which holders of Common Stock received or became entitled to receive such shares or all other additional stock and other securities and property.

     6. Subsequent Financings.

               (i) If, at any time prior to the second and one half (2 1/2) year anniversary of the date hereof, the Company issues additional shares of Common Stock or rights, warrants, options or other securities or debt convertible, exercisable or exchangeable for shares of Common Stock or otherwise entitling any individual or entity to acquire shares of Common Stock (collectively, “Common Stock Equivalents”) at an effective net price to the Company per share of Common Stock (the “Effective Price”) less than four dollars ($4.00) (as adjusted for any stock dividends, combinations, splits, recapitalizations and the like after the date hereof), then the Exercise Price shall be reduced to equal the product of (A) the Exercise Price in effect

5.

immediately prior to such issuance of Common Stock or Common Stock Equivalents times (B) a fraction, the numerator of which is the sum of (1) the number of shares of Common Stock outstanding immediately prior to such issuance, plus (2) the number of shares of Common Stock which the aggregate Effective Price of the Common Stock issued (or deemed to be issued) would purchase at the Exercise Price, and the denominator of which is the aggregate number of shares of Common Stock outstanding or deemed to be outstanding immediately after such issuance. For purposes of this paragraph, in connection with any issuance of any Common Stock Equivalents, (A) the maximum number of shares of Common Stock potentially issuable at any time upon conversion, exercise or exchange of such Common Stock Equivalents (the “Deemed Number”) shall be deemed to be outstanding upon issuance of such Common Stock Equivalents, (B) the Effective Price applicable to such Common Stock shall equal the minimum dollar value of consideration payable to the Company to purchase such Common Stock Equivalents and to convert, exercise or exchange them into Common Stock (net of any discounts, fees, commissions and other expenses), divided by the Deemed Number, and (C) no further adjustment shall be made to the Exercise Price upon the actual issuance of Common Stock upon conversion, exercise or exchange of such Common Stock Equivalents.

               (ii) If, at any time while this Warrant is outstanding, the Company issues Common Stock Equivalents with an Effective Price or a number of underlying shares that floats or resets or otherwise varies or is subject to adjustment based (directly or indirectly) on market prices of the Common Stock (a “Floating Price Security”) in a transaction the primary purpose of which is to raise capital, then for purposes of applying the preceding paragraph in connection with any subsequent exercise, the Effective Price will be determined separately on each Exercise Date and will be deemed to equal the lowest Effective Price at which any holder of such Floating Price Security is entitled to acquire Common Stock on such Exercise Date (regardless of whether any such holder actually acquires any shares on such date).

               (iii) Notwithstanding the foregoing, no adjustment will be made under this Section 6 in respect to any issuance of Common Stock (A) upon exercise or conversion of any options or other securities described in the SEC Documents (as defined in the Purchase Agreement) or Disclosure Schedule to the Purchase Agreement or otherwise pursuant to any employee benefit plan of the Company or its subsidiaries or hereafter adopted by the Company, or (B) in connection with any grant of options to employees, officers, directors or consultants of the Company pursuant to a stock option plan duly adopted by the Company’s board of directors or in respect of the issuance of Common Stock upon exercise of any such options.

     7. Fractional Shares. No fractional shares shall be issued upon the exercise of this Warrant as a consequence of any adjustment pursuant hereto. All Exercise Shares (including fractions) issuable upon exercise of this Warrant may be aggregated for purposes of determining whether the exercise would result in the issuance of any fractional share. If, after aggregation, the exercise would result in the issuance of a fractional share, the Company shall, in lieu of issuance of any fractional share, pay the Holder otherwise entitled to such fraction a sum in cash equal to the product resulting from multiplying the then current fair market value of an Exercise Share by such fraction.

     8. Fundamental Transactions. If, at any time while this Warrant is outstanding, (i) the Company effects any merger of the Company with or into another entity, (ii)

6.

the Company effects any sale of all or substantially all of its assets in one or a series of related transactions, (iii) any tender offer or exchange offer (whether by the Company or another individual or entity) is completed pursuant to which holders of Common Stock are permitted to tender or exchange their shares for other securities, cash or property, or (iv) the Company effects any reclassification of the Common Stock or any compulsory share exchange pursuant to which the Common Stock is effectively converted into or exchanged for other securities, cash or property (other than as a result of a subdivision or combination of shares of Common Stock covered by Section 5 above) (in any such case, a “Fundamental Transaction”), then, upon any subsequent exercise of this Warrant, the Holder shall have the right to receive, for each Warrant Share that would have been issuable upon such exercise immediately prior to the occurrence of such Fundamental Transaction, at the option of the Holder, (a) upon exercise of this Warrant, the number of shares of Common Stock of the successor or acquiring corporation or of the Company, if it is the surviving corporation, and any additional consideration (the “Alternate Consideration”) receivable upon or as a result of such reorganization, reclassification, merger, consolidation or disposition of assets by a Holder of the number of shares of Common Stock for which this Warrant is exercisable immediately prior to such event. For purposes of any such exercise, the determination of the Exercise Price shall be appropriately adjusted to apply to such Alternate Consideration based on the amount of Alternate Consideration issuable in respect of one share of Common Stock in such Fundamental Transaction, and the Company shall apportion the Exercise Price among the Alternate Consideration in a reasonable manner reflecting the relative value of any different components of the Alternate Consideration. If holders of Common Stock are given any choice as to the securities, cash or property to be received in a Fundamental Transaction, then the Holder shall be given the same choice as to the Alternate Consideration it receives upon any exercise of this Warrant following such Fundamental Transaction. To the extent necessary to effectuate the foregoing provisions, any successor to the Company or surviving entity in such Fundamental Transaction shall issue to the Holder a new warrant consistent with the foregoing provisions and evidencing the Holder’s right to exercise such warrant into Alternate Consideration. The terms of any agreement pursuant to which a Fundamental Transaction is effected shall include terms requiring any such successor or surviving entity to comply with the provisions of this Section 8 and insuring that this Warrant (or any such replacement security) will be similarly adjusted upon any subsequent transaction analogous to a Fundamental Transaction.

     9. No Stockholder Rights. This Warrant in and of itself shall not entitle the Holder to any voting rights or other rights as a shareholder of the Company.

     10. Registration Rights. The Holder of the Warrant Shares shall be entitled to the registration rights to such Warrant Shares provided by the Purchase Agreement.

     11. Transfer of Warrant. Subject to applicable laws and the restriction on transfer set forth on the first page of this Warrant, this Warrant and all rights hereunder are transferable, by the Holder in person or by duly authorized attorney, upon delivery of this Warrant and the form of assignment attached hereto to any transferee designated by Holder. The transferee shall sign an investment letter in form and substance reasonably satisfactory to the Company and its counsel.

7.

     12. Lost, Stolen, Mutilated or Destroyed Warrant. If this Warrant is lost, stolen, mutilated or destroyed, the Company may, on such terms as to indemnity or otherwise as it may reasonably impose (which shall, in the case of a mutilated Warrant, include the surrender thereof), issue a new Warrant of like denomination and tenor as the Warrant so lost, stolen, mutilated or destroyed. Any such new Warrant shall constitute an original contractual obligation of the Company, whether or not the allegedly lost, stolen, mutilated or destroyed Warrant shall be at any time enforceable by anyone.

     13. Notices, etc. All notices required or permitted hereunder shall be in writing and shall be deemed effectively given: (a) upon personal delivery to the party to be notified, (b) when sent by confirmed telex or facsimile if sent during normal business hours of the recipient, if not, then on the next business day, (c) five (5) days after having been sent by registered or certified mail, return receipt requested, postage prepaid, or (d) one (1) day after deposit with a nationally recognized overnight courier, specifying next day delivery, with written verification of receipt. All communications shall be sent to the Company at the address listed on the signature page and to Holder at:

[_____]

or at such other address as the Company or Holder may designate by ten (10) days advance written notice to the other parties hereto.

     14. Acceptance. Receipt of this Warrant by the Holder shall constitute acceptance of and agreement to all of the terms and conditions contained herein.

     15. Governing Law. This Warrant and all rights, obligations and liabilities hereunder shall be governed by the laws of the State of California.

     16. Remedies. The Holder, in addition to being entitled to exercise all rights granted by law, including recovery of damages, will be entitled to specific performance of its rights under this Warrant. The Company agrees that monetary damages would not be adequate compensation for any loss incurred by reason of a breach by it of the provisions of this Warrant and hereby agrees to waive the defense in any action for specific performance that a remedy at law would be adequate. In any action or proceeding brought to enforce any provision of this Warrant or where any provision hereof is validly asserted as a defense, the successful party to such action or proceeding shall be entitled to recover reasonable attorneys’ fees in addition to any other available remedy.

8.

     In Witness Whereof, the Company has caused this Warrant to be executed by its duly authorized officer as of April 25, 2005.

SOLEXA, INC.

By:

Name:

Title:

Address: 25861 Industrial Boulevard

                Hayward, CA 94545

NOTICE OF EXERCISE

TO: Solexa, Inc.

     (1) ¨ The undersigned hereby elects to purchase ______shares of the Common Stock of Solexa, Inc. (the “Company”) pursuant to the terms of the attached Warrant, and tenders herewith payment of the exercise price in full, together with all applicable transfer taxes, if any.

          ¨ The undersigned hereby elects to purchase ______shares of Common Stock of the Company pursuant to the terms of the net exercise provisions set forth in Section 2.1 of the attached Warrant, and shall tender payment of all applicable transfer taxes, if any.

     (2) Please issue a certificate or certificates representing said shares of Common Stock of the Company in the name of the undersigned or in such other name as is specified below:

(Name)

(Address)

     (3) The undersigned represents that (i) the aforesaid shares of Common Stock are being acquired for the account of the undersigned for investment and not with a view to, or for resale in connection with, the distribution thereof and that the undersigned has no present intention of distributing or reselling such shares, other than as contemplated by Article 7 of the Securities Purchase Agreement dated as of April 21, 2005 by and among the Company and the purchasers named therein (the “Purchase Agreement”); (ii) the undersigned is aware of the Company’s business affairs and financial condition and has acquired sufficient information about the Company to reach an informed and knowledgeable decision regarding its investment in the Company; (iii) the undersigned is experienced in making investments of this type and has such knowledge and background in financial and business matters that the undersigned is capable of evaluating the merits and risks of this investment and protecting the undersigned’s own interests; (iv) the undersigned understands that the shares of Common Stock issuable upon exercise of this Warrant have not been registered (except to the extent a registration statement pursuant to and as contemplated by Article 7 of the Purchase Agreement is effective) under the Securities Act of 1933, as amended (the “Securities Act”), by reason of a specific exemption from the registration provisions of the Securities Act, which exemption depends upon, among other things, the bona fide nature of the investment intent as expressed herein, and, because such securities have not been registered under the Securities Act, they must be held indefinitely unless subsequently registered under the Securities Act or an exemption from such registration is available; (v) the undersigned is aware that the aforesaid shares of Common Stock may not be sold pursuant to Rule 144 adopted under the Securities Act unless certain conditions are met and until the undersigned has held the shares for the number of years prescribed by Rule 144, that among the conditions for use of the Rule is the availability of current information to the public about the

Company; and (vi) the undersigned agrees not to make any disposition of all or any part of the aforesaid shares of Common Stock unless and until there is then in effect a registration statement under the Securities Act covering such proposed disposition and such disposition is made in accordance with said registration statement, or the undersigned has provided upon the Company’s reasonable request, an opinion of counsel satisfactory to the Company, stating that such registration is not required.

(Date)	(Signature)
	(Print name)

ASSIGNMENT FORM

(To assign the foregoing Warrant, execute this form and supply required information.
Do not use this form to purchase shares.)

     For Value Received, the foregoing Warrant and all rights evidenced thereby are hereby assigned to

Name:

(Please Print)

Address:

(Please Print)

Dated: __________, 20__

Holder’s

Signature:                                                            

Holder’s

Address:                                                             

NOTE: The signature to this Assignment Form must correspond with the name as it appears on the face of the Warrant, without alteration or enlargement or any change whatever. Officers of corporations and those acting in a fiduciary or other representative capacity should file proper evidence of authority to assign the foregoing Warrant.

EX-10.60

EXHIBIT 10.60

THIS WARRANT AND THE UNDERLYING SECURITIES HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”). THEY MAY NOT BE SOLD, OFFERED FOR SALE, PLEDGED OR HYPOTHECATED IN THE ABSENCE OF AN EFFECTIVE REGISTRATION STATEMENT AS TO SUCH SECURITIES UNDER THE ACT OR AN OPINION OF COUNSEL SATISFACTORY TO THE COMPANY THAT SUCH REGISTRATION IS NOT REQUIRED.

SOLEXA, INC.

WARRANT TO PURCHASE COMMON STOCK¹

April 25, 2005

Void After April 25, 2010

     This Certifies That, for value received, [___], or assigns (the “Holder”), is entitled to subscribe for and purchase at the Exercise Price (defined below) from Solexa, Inc., a Delaware corporation, with its principal office at 25861 Industrial Boulevard, Hayward, CA 94545 (the “Company”) up to [___] shares of the common stock of the Company, par value $0.01 per share (the “Common Stock”).

     1. Definitions. As used herein, the following terms shall have the following respective meanings:

          (a) “Exercise Period” shall mean the period commencing with the date that is one hundred and eighty (180) days after the date hereof and ending five (5) years from the date hereof, unless sooner terminated as provided below.

          (b) “Exercise Price” shall mean five dollars ($5.00) per share, subject to adjustment pursuant to Section 5 below.

          (c) “Exercise Shares” shall mean the shares of the Common Stock issuable upon exercise of this Warrant.

     2. Exercise of Warrant. The rights represented by this Warrant may be exercised in whole or in part at any time during the Exercise Period, by delivery of the following to the Company at its address set forth above (or at such other address as it may designate by notice in writing to the Holder):

          (a) An executed Notice of Exercise in the form attached hereto;

          (b) Payment of the Exercise Price in cash or by check; and

          (c) This Warrant.

¹ Form of Warrant to be issued to SF Capital Partners, Ltd.

1.

     Certificates for shares purchased hereunder shall be transmitted by the transfer agent of the Company to the Holder by crediting the account of the Holder’s prime broker with the Depository Trust Company through its Deposit Withdrawal Agent Commission (“DWAC”) system if the Company is a participant in such system (and so long as the legend may be removed in accordance with Section 4.10 of the Purchase Agreement), and otherwise by physical delivery to the address specified by the Holder in the Notice of Exercise within 5 Trading Days from the delivery to the Company of the Notice of Exercise Form, surrender of this Warrant and payment of the aggregate Exercise Price as set forth above (“Warrant Share Delivery Date”). This Warrant shall be deemed to have been exercised on the date the Exercise Price is received by the Company. The Warrant Shares shall be deemed to have been issued, and Holder or any other person so designated to be named therein shall be deemed to have become a holder of record of such shares for all purposes, as of the date the Warrant has been exercised by payment to the Company of the Exercise Price.

     The person in whose name any certificate or certificates for Exercise Shares are to be issued upon exercise of this Warrant shall be deemed to have become the holder of record of such shares on the date on which this Warrant was surrendered and payment of the Exercise Price was made, irrespective of the date of delivery of such certificate or certificates, except that, if the date of such surrender and payment is a date when the stock transfer books of the Company are closed, such person shall be deemed to have become the holder of such shares at the close of business on the next succeeding date on which the stock transfer books are open.

     2.1 Net Exercise. Notwithstanding any provisions herein to the contrary, after the Filing Date (as defined in Section 7.2 of the Securities Purchase Agreement dated April [21], 2005, by and among the Company and the individuals and entities identified on the signature pages hereto (the “Purchase Agreement”)), if (i) the Registration Statement (as defined in the Purchase Agreement) has not been declared effective until such time as the Registration Statement is declared effective or at any time a Registration Statement is no longer effective and (ii) the fair market value of one share of the Company’s Common Stock is greater than the Exercise Price (at the date of calculation as set forth below), in lieu of exercising this Warrant by payment of cash, the Holder may elect to receive shares equal to the value (as determined below) of this Warrant (or the portion thereof being canceled) by surrender of this Warrant at the principal office of the Company together with the properly endorsed Notice of Exercise in which event the Company shall issue to the Holder a number of shares of Common Stock computed using the following formula:

	X = Y (A-B)
	A
Where X =	the number of shares of Common Stock to be issued to the Holder
Y =	the number of shares of Common Stock purchasable under the Warrant or, if only a portion of the Warrant is being exercised, the portion of the Warrant being canceled (at the date of such calculation)

2.

A =	the fair market value of one share of the Company’s Common Stock (at the date of such calculation)
B =	Exercise Price (as adjusted to the date of such calculation)

     For purposes of the above calculation, the “fair market value” of one share of Common Stock shall mean (i) the average of the closing sales prices for the shares of Common Stock on the Nasdaq SmallCap Market or other trading market where such security is listed or traded as reported by Bloomberg Financial Markets (or a comparable reporting service of national reputation selected by the Company and reasonably acceptable to the holders if Bloomberg Financial Markets is not then reporting sales prices of such security) (collectively, “Bloomberg”) for the ten (10) consecutive trading days immediately preceding such date, or (ii) if the Nasdaq SmallCap Market is not the principal trading market for the shares of Common Stock, the average of the reported sales prices reported by Bloomberg on the principal trading market for the Common Stock during the same period, or, if there is no sales price for such period, the last sales price reported by Bloomberg for such period, or (iii) if neither of the foregoing applies, the last sales price of such security in the over-the-counter market on the pink sheets or bulletin board for such security as reported by Bloomberg, or if no sales price is so reported for such security, the last bid price of such security as reported by Bloomberg or (iv) if fair market value cannot be calculated as of such date on any of the foregoing bases, the fair market value shall be as determined by the Board of Directors of the Company in the exercise of its good faith judgment.

     Notwithstanding anything herein to the contrary, if there is no Registration Statement effective on the last day of the Exercise Period, this Warrant shall be automatically exercised via net exercise pursuant to this Section 2.1.

     2.2 Issuance of New Warrants. Upon any partial exercise of this Warrant, the Company, at its expense, will forthwith and, in any event within five (5) business days, issue and deliver to the Holder a new warrant or warrants of like tenor, registered in the name of the Holder, exercisable, in the aggregate, for the balance of the Warrant Shares.

     2.3 Payment of Taxes and Expenses. The Company shall pay any recording, filing, stamp or similar tax which may be payable in respect of any transfer involved in the issuance of, and the preparation and delivery of certificates (if applicable) representing, (i) any Warrant Shares purchased upon exercise of this Warrant and/or (ii) new or replacement warrants in the Holder’s name or the name of any transferee of all or any portion of this Warrant.

     2.4 Rescission Rights. If the Company fails to cause its transfer agent to transmit to the Holder a certificate or certificates representing the Warrant Shares pursuant to this Section 2 by the Warrant Share Delivery Date, then the Holder will have the right to rescind such exercise.

     3. Covenants of the Company.

     3.1 Covenants as to Exercise Shares. The Company covenants and agrees that all Exercise Shares that may be issued upon the exercise of the rights represented by this Warrant will, upon issuance, be validly issued and outstanding, fully paid and nonassessable, and free from all taxes, liens and charges with respect to the issuance thereof. The Company further

3.

covenants and agrees that the Company will at all times during the Exercise Period, have authorized and reserved, free from preemptive rights, a sufficient number of shares of its Common Stock to provide for the exercise of the rights represented by this Warrant. If at any time during the Exercise Period the number of authorized but unissued shares of Common Stock shall not be sufficient to permit exercise of this Warrant, the Company will take such corporate action as may, in the opinion of its counsel, be necessary to increase its authorized but unissued shares of Common Stock to such number of shares as shall be sufficient for such purposes.

     3.3 Notices of Record Date. In the event of any taking by the Company of a record of the holders of any class of securities for the purpose of determining the holders thereof who are entitled to receive any dividend (other than a cash dividend which is the same as cash dividends paid in previous quarters) or other distribution, the Company shall mail to the Holder, at least ten (10) days prior to the date specified herein, a notice specifying the date on which any such record is to be taken for the purpose of such dividend or distribution.

     4. Disposition of Warrant and Exercise Shares.

          (a) The Holder further agrees not to make any disposition of all or any part of the Warrant or Exercise Shares in any event unless and until:

               (i) The Company shall have received a letter secured by the Holder from the Securities and Exchange Commission stating that no action will be recommended to the Commission with respect to the proposed disposition; or

               (ii) There is then in effect a registration statement under the Act covering such proposed disposition and such disposition is made in accordance with said registration statement; or

               (iii) The Holder shall have notified the Company of the proposed disposition and shall have furnished the Company with a detailed statement of the circumstances surrounding the proposed disposition, and if reasonably requested by the Company, the Holder shall have furnished the Company with an opinion of counsel, reasonably satisfactory to the Company, for the Holder to the effect that such disposition will not require registration of such Warrant or Exercise Shares under the Act or any applicable state securities laws; provided, however, that no such opinion of counsel shall be required for sales (i) under Rule 144, (ii) to one of its nominees, affiliates or a nominee thereof, (iii) to a pension or profit-sharing fund established and maintained for its employees or for the employees of any affiliate, (iv) from a nominee to any of the aforementioned persons as beneficial owner of this Warrant or such Warrant Shares, or (v) to a qualified institutional buyer, so long as such transfer is effected in compliance with Rule 144A under the Securities Act.

          (b) The Holder understands and agrees that subject to Section 4.10 of the Purchase Agreement, all certificates evidencing the shares to be issued to the Holder may bear the following legend:

“THESE SECURITIES HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”). THEY MAY NOT BE SOLD, OFFERED FOR SALE, PLEDGED OR HYPOTHECATED IN

4.

THE ABSENCE OF AN EFFECTIVE REGISTRATION STATEMENT AS TO THE SECURITIES UNDER THE ACT OR AN OPINION OF COUNSEL SATISFACTORY TO THE COMPANY THAT SUCH REGISTRATION IS NOT REQUIRED.”

     5. Adjustment of Exercise Price and Shares.

          (a) In the event of changes in the outstanding Common Stock of the Company by reason of stock dividends, split-ups, recapitalizations, reclassifications, combinations or exchanges of shares, separations, reorganizations, liquidations, consolidation, acquisition of the Company (whether through merger or acquisition of substantially all the assets or stock of the Company), or the like, the number and class of shares available under the Warrant in the aggregate and the Exercise Price shall be correspondingly adjusted to give the Holder of the Warrant, on exercise for the same aggregate Exercise Price, the total number, class, and kind of shares or other property as the Holder would have owned had the Warrant been exercised prior to the event and had the Holder continued to hold such shares until the event requiring adjustment. The form of this Warrant need not be changed because of any adjustment in the number of Exercise Shares subject to this Warrant.

          (b) If at any time or from time to time the holders of Common Stock of the Company (or any shares of stock or other securities at the time receivable upon the exercise of this Warrant) shall have received or become entitled to receive, without payment therefor,

               (i) Common Stock or any shares of stock or other securities which are at any time directly or indirectly convertible into or exchangeable for Common Stock, or any rights or options to subscribe for, purchase or otherwise acquire any of the foregoing by way of dividend or other distribution (other than a dividend or distribution covered in Section 5(a) above),

               (ii) any cash paid or payable otherwise than as a cash dividend or

               (iii) Common Stock or additional stock or other securities or property (including cash) by way of spinoff, split-up, reclassification, combination of shares or similar corporate rearrangement (other than shares of Common Stock pursuant to Section 5(a) above),

then and in each such case, the Holder hereof will, upon the exercise of this Warrant, be entitled to receive, in addition to the number of shares of Common Stock receivable thereupon, and without payment of any additional consideration therefor, the amount of stock and other securities and property (including cash in the cases referred to in clauses (ii) and (iii) above) which such Holder would hold on the date of such exercise had he been the holder of record of such Common Stock as of the date on which holders of Common Stock received or became entitled to receive such shares or all other additional stock and other securities and property.

     6. Subsequent Financings.

          (i) If, at any time prior to the second and one half (2 1/2) year anniversary of the date hereof, the Company issues additional shares of Common Stock or rights, warrants, options or other securities or debt convertible, exercisable or exchangeable for shares

5.

of Common Stock or otherwise entitling any individual or entity to acquire shares of Common Stock (collectively, “Common Stock Equivalents”) at an effective net price to the Company per share of Common Stock (the “Effective Price”) less than four dollars ($4.00) (as adjusted for any stock dividends, combinations, splits, recapitalizations and the like after the date hereof), then the Exercise Price shall be reduced to equal the product of (A) the Exercise Price in effect immediately prior to such issuance of Common Stock or Common Stock Equivalents times (B) a fraction, the numerator of which is the sum of (1) the number of shares of Common Stock outstanding immediately prior to such issuance, plus (2) the number of shares of Common Stock which the aggregate Effective Price of the Common Stock issued (or deemed to be issued) would purchase at the Exercise Price, and the denominator of which is the aggregate number of shares of Common Stock outstanding or deemed to be outstanding immediately after such issuance. For purposes of this paragraph, in connection with any issuance of any Common Stock Equivalents, (A) the maximum number of shares of Common Stock potentially issuable at any time upon conversion, exercise or exchange of such Common Stock Equivalents (the “Deemed Number”) shall be deemed to be outstanding upon issuance of such Common Stock Equivalents, (B) the Effective Price applicable to such Common Stock shall equal the minimum dollar value of consideration payable to the Company to purchase such Common Stock Equivalents and to convert, exercise or exchange them into Common Stock (net of any discounts, fees, commissions and other expenses), divided by the Deemed Number, and (C) no further adjustment shall be made to the Exercise Price upon the actual issuance of Common Stock upon conversion, exercise or exchange of such Common Stock Equivalents.

          (ii) If, at any time while this Warrant is outstanding, the Company issues Common Stock Equivalents with an Effective Price or a number of underlying shares that floats or resets or otherwise varies or is subject to adjustment based (directly or indirectly) on market prices of the Common Stock (a “Floating Price Security”) in a transaction the primary purpose of which is to raise capital, then for purposes of applying the preceding paragraph in connection with any subsequent exercise, the Effective Price will be determined separately on each Exercise Date and will be deemed to equal the lowest Effective Price at which any holder of such Floating Price Security is entitled to acquire Common Stock on such Exercise Date (regardless of whether any such holder actually acquires any shares on such date).

          (iii) Notwithstanding the foregoing, no adjustment will be made under this Section 6 in respect to any issuance of Common Stock (A) upon exercise or conversion of any options or other securities described in the SEC Documents (as defined in the Purchase Agreement) or Disclosure Schedule to the Purchase Agreement or otherwise pursuant to any employee benefit plan of the Company or its subsidiaries or hereafter adopted by the Company, or (B) in connection with any grant of options to employees, officers, directors or consultants of the Company pursuant to a stock option plan duly adopted by the Company’s board of directors or in respect of the issuance of Common Stock upon exercise of any such options.

     7. Fractional Shares. No fractional shares shall be issued upon the exercise of this Warrant as a consequence of any adjustment pursuant hereto. All Exercise Shares (including fractions) issuable upon exercise of this Warrant may be aggregated for purposes of determining whether the exercise would result in the issuance of any fractional share. If, after aggregation, the exercise would result in the issuance of a fractional share, the Company shall, in lieu of issuance of any fractional share, pay the Holder otherwise entitled to such fraction a sum in cash

6.

equal to the product resulting from multiplying the then current fair market value of an Exercise Share by such fraction.

     8. Fundamental Transactions. If, at any time while this Warrant is outstanding, (i) the Company effects any merger of the Company with or into another entity, (ii) the Company effects any sale of all or substantially all of its assets in one or a series of related transactions, (iii) any tender offer or exchange offer (whether by the Company or another individual or entity) is completed pursuant to which holders of Common Stock are permitted to tender or exchange their shares for other securities, cash or property, or (iv) the Company effects any reclassification of the Common Stock or any compulsory share exchange pursuant to which the Common Stock is effectively converted into or exchanged for other securities, cash or property (other than as a result of a subdivision or combination of shares of Common Stock covered by Section 5 above) (in any such case, a “Fundamental Transaction”), then, upon any subsequent exercise of this Warrant, the Holder shall have the right to receive, for each Warrant Share that would have been issuable upon such exercise immediately prior to the occurrence of such Fundamental Transaction, at the option of the Holder, (a) upon exercise of this Warrant, the number of shares of Common Stock of the successor or acquiring corporation or of the Company, if it is the surviving corporation, and any additional consideration (the “Alternate Consideration”) receivable upon or as a result of such reorganization, reclassification, merger, consolidation or disposition of assets by a Holder of the number of shares of Common Stock for which this Warrant is exercisable immediately prior to such event. For purposes of any such exercise, the determination of the Exercise Price shall be appropriately adjusted to apply to such Alternate Consideration based on the amount of Alternate Consideration issuable in respect of one share of Common Stock in such Fundamental Transaction, and the Company shall apportion the Exercise Price among the Alternate Consideration in a reasonable manner reflecting the relative value of any different components of the Alternate Consideration. If holders of Common Stock are given any choice as to the securities, cash or property to be received in a Fundamental Transaction, then the Holder shall be given the same choice as to the Alternate Consideration it receives upon any exercise of this Warrant following such Fundamental Transaction. To the extent necessary to effectuate the foregoing provisions, any successor to the Company or surviving entity in such Fundamental Transaction shall issue to the Holder a new warrant consistent with the foregoing provisions and evidencing the Holder’s right to exercise such warrant into Alternate Consideration. The terms of any agreement pursuant to which a Fundamental Transaction is effected shall include terms requiring any such successor or surviving entity to comply with the provisions of this Section 8 and insuring that this Warrant (or any such replacement security) will be similarly adjusted upon any subsequent transaction analogous to a Fundamental Transaction.

9. Limitations on Exercise.

          (i) Notwithstanding anything herein to the contrary, in no event shall the Holder be entitled to exercise any portion of this Warrant in excess of that portion of this Warrant upon exercise of which the sum of (1) the number of shares of Common Stock beneficially owned by the Holder and its Affiliates (other than shares of Common Stock which may be deemed beneficially owned through the ownership of the unexercised portion of the Warrant or the unexercised or unconverted portion of any other security of the Holder subject to a limitation on conversion analogous to the limitations contained herein) and (2) the number of

7.

shares of Common Stock issuable upon the exercise of the portion of this Warrant with respect to which the determination of this proviso is being made, would result in beneficial ownership by the Holder and its Affiliates of more than 4.99% of the then outstanding shares of Common Stock. As used herein, the term “Affiliate” means any person or entity that, directly or indirectly through one or more intermediaries, controls or is controlled by or is under common control with a person or entity, as such terms are used in and construed under Rule 144 under the Act. For purposes of the proviso to the immediately preceding sentence, beneficial ownership shall be determined in accordance with Section 13(d) of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), and Regulations 13D-G thereunder, except as otherwise provided in clause (1) of such proviso.

          (ii) Notwithstanding anything to the contrary contained herein, the number of shares of Common Stock that may be acquired by the Holder upon any exercise of this Warrant (or otherwise in respect hereof) shall be limited to the extent necessary to insure that, following such exercise (or other issuance), the total number of shares of Common Stock then beneficially owned by such Holder and its Affiliates and any other individuals or entities whose beneficial ownership of Common Stock would be aggregated with the Holder’s for purposes of Section 13(d) of the Exchange Act, does not exceed 9.999% of the total number of issued and outstanding shares of Common Stock (including for such purpose the shares of Common Stock issuable upon such exercise). For such purposes, beneficial ownership shall be determined in accordance with Section 13(d) of the Exchange Act and the rules and regulations promulgated thereunder.

     10. No Stockholder Rights. This Warrant in and of itself shall not entitle the Holder to any voting rights or other rights as a shareholder of the Company.

     11. Registration Rights. The Holder of the Warrant Shares shall be entitled to the registration rights to such Warrant Shares provided by the Purchase Agreement.

     12. Transfer of Warrant. Subject to applicable laws and the restriction on transfer set forth on the first page of this Warrant, this Warrant and all rights hereunder are transferable, by the Holder in person or by duly authorized attorney, upon delivery of this Warrant and the form of assignment attached hereto to any transferee designated by Holder. The transferee shall sign an investment letter in form and substance reasonably satisfactory to the Company and its counsel.

     13. Lost, Stolen, Mutilated or Destroyed Warrant. If this Warrant is lost, stolen, mutilated or destroyed, the Company may, on such terms as to indemnity or otherwise as it may reasonably impose (which shall, in the case of a mutilated Warrant, include the surrender thereof), issue a new Warrant of like denomination and tenor as the Warrant so lost, stolen, mutilated or destroyed. Any such new Warrant shall constitute an original contractual obligation of the Company, whether or not the allegedly lost, stolen, mutilated or destroyed Warrant shall be at any time enforceable by anyone.

     13. Notices, etc. All notices required or permitted hereunder shall be in writing and shall be deemed effectively given: (a) upon personal delivery to the party to be notified, (b) when sent by confirmed telex or facsimile if sent during normal business hours of the recipient, if not,

8.

then on the next business day, (c) five (5) days after having been sent by registered or certified mail, return receipt requested, postage prepaid, or (d) one (1) day after deposit with a nationally recognized overnight courier, specifying next day delivery, with written verification of receipt. All communications shall be sent to the Company at the address listed on the signature page and to Holder at:

[_____]

or at such other address as the Company or Holder may designate by ten (10) days advance written notice to the other parties hereto.

     14. Acceptance. Receipt of this Warrant by the Holder shall constitute acceptance of and agreement to all of the terms and conditions contained herein.

     15. Governing Law. This Warrant and all rights, obligations and liabilities hereunder shall be governed by the laws of the State of California.

     16. Remedies. The Holder, in addition to being entitled to exercise all rights granted by law, including recovery of damages, will be entitled to specific performance of its rights under this Warrant. The Company agrees that monetary damages would not be adequate compensation for any loss incurred by reason of a breach by it of the provisions of this Warrant and hereby agrees to waive the defense in any action for specific performance that a remedy at law would be adequate. In any action or proceeding brought to enforce any provision of this Warrant or where any provision hereof is validly asserted as a defense, the successful party to such action or proceeding shall be entitled to recover reasonable attorneys’ fees in addition to any other available remedy.

9.

     In Witness Whereof, the Company has caused this Warrant to be executed by its duly authorized officer as of April 25, 2005.

SOLEXA, INC.

By:                                                                                

Name:

Title:

Address: 25861 Industrial Boulevard
               Hayward, CA 94545

NOTICE OF EXERCISE

TO: Solexa, Inc.

     (1) o The undersigned hereby elects to purchase ______shares of the Common Stock of Solexa, Inc. (the “Company”) pursuant to the terms of the attached Warrant, and tenders herewith payment of the exercise price in full, together with all applicable transfer taxes, if any.

          o The undersigned hereby elects to purchase ______shares of Common Stock of the Company pursuant to the terms of the net exercise provisions set forth in Section 2.1 of the attached Warrant, and shall tender payment of all applicable transfer taxes, if any.

     (2) Please issue a certificate or certificates representing said shares of Common Stock of the Company in the name of the undersigned or in such other name as is specified below:

(Name)

(Address)

     (3) The undersigned represents that (i) the aforesaid shares of Common Stock are being acquired for the account of the undersigned for investment and not with a view to, or for resale in connection with, the distribution thereof and that the undersigned has no present intention of distributing or reselling such shares, other than as contemplated by Article 7 of the Securities Purchase Agreement dated as of April 21, 2005 by and among the Company and the purchasers named therein (the “Purchase Agreement”); (ii) the undersigned is aware of the Company’s business affairs and financial condition and has acquired sufficient information about the Company to reach an informed and knowledgeable decision regarding its investment in the Company; (iii) the undersigned is experienced in making investments of this type and has such knowledge and background in financial and business matters that the undersigned is capable of evaluating the merits and risks of this investment and protecting the undersigned’s own interests; (iv) the undersigned understands that the shares of Common Stock issuable upon exercise of this Warrant have not been registered (except to the extent a registration statement pursuant to and as contemplated by Article 7 of the Purchase Agreement is effective) under the Securities Act of 1933, as amended (the “Securities Act”), by reason of a specific exemption from the registration provisions of the Securities Act, which exemption depends upon, among other things, the bona fide nature of the investment intent as expressed herein, and, because such securities have not been registered under the Securities Act, they must be held indefinitely unless subsequently registered under the Securities Act or an exemption from such registration is available; (v) the undersigned is aware that the aforesaid shares of Common Stock may not be sold pursuant to Rule 144 adopted under the Securities Act unless certain conditions are met and until the undersigned has held the shares for the number of years prescribed by Rule 144, that among the conditions for use of the Rule is the availability of current information to the public about the

Company; and (vi) the undersigned agrees not to make any disposition of all or any part of the aforesaid shares of Common Stock unless and until there is then in effect a registration statement under the Securities Act covering such proposed disposition and such disposition is made in accordance with said registration statement, or the undersigned has provided upon the Company’s reasonable request, an opinion of counsel satisfactory to the Company, stating that such registration is not required.

(Date)	(Signature)
	(Print name)

ASSIGNMENT FORM

(To assign the foregoing Warrant, execute this form and supply required information. Do not use this form to purchase shares.)

     For Value Received, the foregoing Warrant and all rights evidenced thereby are hereby assigned to

Name:

(Please Print)

Address:

(Please Print)

Dated: __________, 20__

Holder’s

Signature:                                                                                 

Holder’s

Address:                                                                                 

NOTE: The signature to this Assignment Form must correspond with the name as it appears on the face of the Warrant, without alteration or enlargement or any change whatever. Officers of corporations and those acting in a fiduciary or other representative capacity should file proper evidence of authority to assign the foregoing Warrant.

EX-10.61

EXHIBIT 10.61

[Solexa, Inc. Letterhead]

April 21, 2005

ValueAct Capital
435 Pacific Avenue, 4th Floor
San Francisco, CA 94133
Attn: G. Mason Morfit

Re: Board Of Directors Representative

Dear Mason:

     This purpose of this letter is to confirm the understanding between Solexa, Inc., a Delaware company (the “Company”)and ValueAct Capital Master Fund, L.P. (“ValueAct”) in connection with the Company’s private placement of common stock and warrants pursuant to that certain Securities Purchase Agreement, dated April 21, 2005, by and between the Company and the individuals and entities identified on the signature pages hereto (the “Purchase Agreement”).

     Effective and contingent upon of the First Closing (as defined in the Purchase Agreement) and until ValueAct no longer owns at least 734,500 shares of the Company’s common stock (as appropriately adjusted for any stock dividend, stock split, reverse split, reclassification or the like), ValueAct shall have the right to nominate one member of the Company’s Board of Directors, which nominee shall initially be G. Mason Morfit.

Very truly yours,

Solexa, Inc.

/s/ John West

John West

Chief Executive Officer

Accepted and Agreed:

ValueAct Capital Master Fund, L.P.

/s/ George F. Hamel 

By its General Partner, VA Partners, LLC

George F. Hamel, Jr.

Managing Member

EX-99.1

EXHIBIT 99.1

AMENDED AND RESTATED COMPANY SUPPORT AGREEMENT

     This Amended and Restated Company Support Agreement (the “Agreement”) is made and entered into as of April 21, 2005, between Solexa, Inc., a Delaware corporation (formerly Lynx Therapeutics, Inc.) (the “Company”), and the undersigned stockholder (“Holder”) of the Company.

RECITALS

     Whereas, the Holder and the Company are parties to that certain Company Support Agreement, dated September 28, 2004 (the “Prior Agreement”), entered into in connection with the business combination between the Company and Solexa Limited, a company registered in England and Wales (“Solexa Limited”);

     Whereas, Holder is the registered owner of such number of the Company’s common stock, par value $0.01 per share (“Common Stock”) issued pursuant to that certain Acquisition Agreement, dated as of September 28, 2004, by and between the Company and Solexa Limited (the “Acquisition Agreement”) (the “Shares”) and such number of options to purchase Common Stock as indicated beneath Holder’s signature on the last page of this Agreement;

     Whereas, the Holder is purchasing shares of Common Stock and warrants to purchase shares of Common Stock pursuant to that certain Securities Purchase Agreement (the “Purchase Agreement”) of even date herewith (the “Private Placement”);

     Whereas, the obligations in the Purchase Agreement are conditioned upon the execution and delivery of this Agreement;

     Whereas, the Company and the Holder desire to amend and restate the Prior Agreement and accept the rights and covenants hereof in lieu of their rights and covenants under the Prior Agreement; and

     Whereas, in connection with the consummation of the Private Placement, the Company and Holder have agreed to provide for the voting of the Holder’s Shares and the rights as set forth below.

     Now, Therefore, in consideration of these premises and for other good and valid consideration, the receipt and sufficiency of which are hereby acknowledged, the parties hereto agree as follows:

AGREEMENT

     1. Amendment and Restatement of Prior Agreement. The Prior Agreement is hereby amended in its entirety and restated herein. Such amendment and restatement is effective upon the execution of the Agreement by the Company and the Holder.

     2. Agreement to Retain Shares.

          (a) Transfer and Encumbrance. Except as contemplated by the Acquisition Agreement and except as provided in Sections 2(b), 3, and 4 below, during the period beginning on the date hereof and ending on August 31, 2005, Holder agrees not to, directly or indirectly, (x) transfer (except as may be specifically required by court order), sell, exchange, tender, pledge, assign, contribute to the capital of any entity, hypothecate or otherwise dispose of (including by merger, consolidation or otherwise by operation of law) or encumber the Shares or any New Shares (as defined below), enter into any short sale with respect to the Shares or any New Shares, enter into or acquire an offsetting derivative contract with respect to such Shares or any New Shares, enter into or acquire a futures or forward contract to deliver such Shares or any New Shares or enter into any other hedging or other derivative transaction that has the effect of materially changing the economic benefits and risks of ownership of the Shares or any New Shares, or to, directly or indirectly, make any offer or agreement relating thereto, (y) grant any proxies or powers of attorney, deposit any of such Shares or New Shares into a voting trust or enter into a voting agreement with respect to any of such Shares or New Shares, or enter into any agreement or arrangement providing for any of the actions described in this clause (y), or (z) take any action that could reasonably be expected to have the effect of preventing or disabling Holder from performing Holder’s obligations under this Agreement, and Holder warrants that it has not agreed to carry out any of the foregoing matters in relation to the Shares or any New Shares.

          (b) Permitted Transfers. Section 2(a) shall not prohibit a transfer of Shares or New Shares by Holder (i) if Holder is an individual (A) to any member of Holder’s immediate family, or to a trust for the benefit of Holder or any member of Holder’s immediate family, or (B) upon the death of Holder, or (ii) if Holder is a partnership or limited liability company, to one or more partners or members of Holder or to an affiliated Person under common control or common management with Holder; provided, however, that any such transfer pursuant to either clause (i) or (ii) of this Section 2(b) shall be permitted only if, as a precondition to such transfer, the transferee agrees in writing to be bound by all of the terms of this Agreement.

          (c) New Shares. Holder agrees that any shares of capital stock or interests in shares or other securities of the Company, that Holder purchases or with respect to which Holder otherwise acquires registered or beneficial ownership after the date hereof and prior to August 31, 2005 (“New Shares”) shall be subject to the terms and conditions of this Agreement to the same extent as if they constituted Shares.

     3. Agreement to Vote Shares. Until August 31, 2005, Holder shall, at any meeting (whether annual or extraordinary and whether or not an adjourned or postponed meeting) of stockholders of the Company or of any class of stockholders of the Company, however called, or in connection with any written resolution of the holders of shares or any class of shares in the capital of the Company, vote the Shares and any New Shares held by Holder in favor of the issuance of Common Stock and warrants pursuant to the Private Placement and any other transactions contemplated by the Purchase Agreement. The Holder hereby agrees that he or she will not vote the Shares and New Shares in favor of the approval of any action the consummation of which would frustrate the purposes, or prevent or delay the consummation of, the transactions contemplated by the Purchase Agreement. This Agreement is intended to bind Holder as a

2

holder of the Company only with respect to the specific matters set forth herein. Except as set forth this Section 3, Holder shall not be restricted from voting in favor of, against or abstaining with respect to any other matter presented to the stockholders of the Company.

     4. Irrevocable Proxy. Concurrently with the execution of this Agreement, Holder agrees to deliver to the Company a proxy in the form attached hereto as Exhibit A (the “Proxy”), which shall be irrevocable to the fullest extent permitted by law.

     5. Affiliate Agreement.

          (a) General. Holder has been advised that, as of the date of the Prior Agreement, Holder may have been deemed to be an “affiliate” of Solexa Limited, as the term “affiliate” is defined for purposes of paragraphs (c) and (d) of Rule 145 of the rules and regulations (the “Rules and Regulations”) of the SEC under the Securities Act. Notwithstanding anything to the contrary set forth in this Section 5, the execution of this Agreement should not be considered an admission on Holder’s part that Holder is or was an “affiliate” of Solexa Limited, nor as a waiver of any rights Holder may have to object to any claim that Holder is such an affiliate on or after the date of the Prior Agreement.

          (b) Holder Representations; Restrictions on Transfer; Legends. Holder represents, warrants and covenants to the Company:

               (i) Holder shall not make any sale, transfer or other disposition of the Shares in violation of the Securities Act.

               (ii) Holder has carefully read this Agreement and discussed the requirements of this Agreement and other applicable limitations upon Holder’s ability to sell, transfer or otherwise dispose of the Shares, to the extent Holder has felt necessary, with Holder’s counsel.

               (iii) Holder has been advised that the resale of the Shares may be subject to restrictions set forth in Rule 145 under the Securities Act. Holder has been advised that, because Holder may be deemed to be an “affiliate” of the Company, Holder may not sell, transfer or otherwise dispose of the Shares issued to Holder, unless (i) such sale, transfer or other disposition is made in conformity with the limitations of Rule 145 promulgated by the SEC under the Securities Act, (ii) such sale, transfer or other disposition has been registered under the Securities Act or (iii) in the opinion of counsel reasonably acceptable to the Company, such sale, transfer or other disposition is otherwise exempt from registration under the Securities Act.

               (iv) Holder understands and agrees that stop transfer instructions will be given to the Company’s transfer agent with respect to the Shares issued to Holder and that there will be placed on the certificates for the Shares issued to Holder, or any substitutions therefor, a legend stating in substance: “THE SHARES REPRESENTED BY THIS CERTIFICATE WERE ISSUED IN A TRANSACTION TO WHICH RULE 145 PROMULGATED UNDER THE SECURITIES ACT OF 1933, AS AMENDED, APPLIES. THE SHARES REPRESENTED BY THIS CERTIFICATE MAY ONLY BE TRANSFERRED

3

IN ACCORDANCE WITH THE TERMS OF A COMPANY SUPPORT AGREEMENT DATED SEPTEMBER28, 2004 BETWEEN THE REGISTERED HOLDER HEREOF AND LYNX THERAPEUTICS, INC., A COPY OF WHICH AGREEMENT IS ON FILE AT THE PRINCIPAL OFFICES OF LYNX THERAPEUTICS, INC.” If a sale or transfer is made prior to such legend being removed pursuant to Section 5(c) below, certificates with the above legend will be substituted by delivery of certificates without such legend upon delivery of a declaration to the Company (the “Declaration”), which Declaration shall be reasonably satisfactory in form and substance to Parent, that the requirements of Rule 145(d)(1) have been complied with.

               (v) Holder understands and agrees that stop transfer instructions will be given to the Company’s transfer agent with respect to the Shares issued to Holder and there will be placed on the certificates for the Shares issued to Holder, or any substitutions therefore, a legend stating in substance: “THE SHARES REPRESENTED BY THIS CERTIFICATE MAY NOT BE TRANSFERRED UNTIL THE DATE THAT IS 180 DAYS FOLLOWING THE FIRST CLOSING DATE (AS DEFINED IN THE ACQUISITION AGREEMENT DATED SEPTEMBER 28, 2004 BETWEEN LYNX THERAPEUTICS, INC. AND SOLEXA LIMITED) IN ACCORDANCE WITH THE TERMS OF A COMPANY SUPPORT AGREEMENT DATED SEPTEMBER 28, 2004 BETWEEN THE REGISTERED HOLDER HEREOF AND LYNX THERAPEUTICS, INC., A COPY OF WHICH AGREEMENT IS ON FILE AT THE PRINCIPAL OFFICES OF LYNX THERAPEUTICS, INC.”

          (c) Company Representations.

               (i) The Company hereby agrees that, unless previously sold pursuant to the applicable requirements of Rule 145, it is understood and agreed that certificates with the legend set forth in Section 5(b)(iv) above will be substituted by delivery of certificates without such legend, and any stop transfer instructions then in effect will be terminated, if (i) one year shall have elapsed from the date Holder acquired the Shares received in the Offer (as defined in the Acquisition Agreement) and the provisions of Rule 145(d)(2) are then available to Holder, (ii) two years shall have elapsed from the date Holder acquired the Shares received in the Offer and the provisions of Rule 145(d)(3) are then available to Holder, or (iii) the Company has received either an opinion of counsel, which opinion and counsel shall be reasonably satisfactory to the Company, or a “no action” letter obtained by Holder from the staff of the SEC, to the effect that the restrictions imposed by Rule 145 under the Securities Act no longer apply to Holder. For as long as resales of any shares of Common Stock owned by Holder are subject to Rule 145, the Company will use its reasonable efforts to make all filings of the nature specified in paragraph (c)(1) of Rule 144 under the Securities Act. Upon receipt of a properly completed Declaration, the Company shall use its reasonable efforts to instruct its transfer agent to deliver shares of Common Stock without the legend set forth in Section 5(b)(iv) above in accordance with the terms of the transfer set forth in the Declaration as soon as practicable following receipt of such Declaration.

               (ii) The Company hereby agrees that it is understood and agreed that certificates with the legend set forth in Section 5(b)(v) above will, to the extent required to enable the shares represented by such certificate to be transferred by the holder thereof, be substituted by delivery of certificates without such legend upon the written request of the Holder

4

if 180 days shall have elapsed from March 4, 2005. Upon receipt of any such written request, the Company shall use its reasonable efforts to instruct its transfer agent to deliver shares of Common Stock without the legend set forth in Section 5(b)(v) above as soon as practicable following receipt of such written request.

     6. Resale Registration Rights.

          (a) Registrable Shares. For purposes of this Agreement, “Registrable Shares” shall mean the shares of Common Stock issued to stockholders who executed a Prior Agreement (the “Original Holder Group”), including Holder, pursuant to the Offer (as defined in the Acquisition Agreement).

          (b) Required Registration. The Company shall use its commercially reasonable efforts to (i) file a post-effective amendment to the Registration Statement on Form S-3 registering the resale of the Registrable Shares within 60 days following March 4, 2005 (the “Amendment”), so long as the holders of such Registrable Shares shall provide the information necessary for inclusion therein in a timely manner to enable the Company to file the Amendment within such period, (ii) to cause such Amendment to be declared effective by the SEC as soon thereafter as possible and in any event no later than August 31, 2005, (iii) to file such amendments or supplements as may be necessary so that the prospectus contained in the Amendment will not include an untrue statement of a material fact or omit to state a material fact required to be stated therein or necessary to make the statements therein not misleading in light of the circumstances then existing, and (iv) to effect all such registrations, qualifications and compliances (including, without limitation, obtaining appropriate qualifications under applicable state securities or “blue sky” laws and compliance with any other applicable governmental requirements or regulations) as Holder may reasonably request and that would permit or facilitate the sale of all Holder’s Registrable Shares (provided, however, that the Company shall not be required in connection therewith to qualify to do business or to file a general consent to service of process in any such state or jurisdiction), and in each case the Company will use its commercially reasonable efforts to cause such Amendment and all other such registrations, qualifications and compliances to be declared effective as promptly as practicable thereafter. As soon as reasonably practicable after the date hereof, the Company will provide to each holder of Registrable Securities a questionnaire setting forth the information that the Company will require from each such holder to include such holder’s Registrable Shares in the Registration Statement. If Holder shall fail to furnish such information to the Company within twenty (20) days following the date on which such questionnaire shall be delivered to the Holders, the Company may exclude Holder from the Registration Statement.

          (c) Effectiveness; Delivery of Prospectus; Suspension Right.

               (i) The Company will use its commercially reasonable efforts to maintain the effectiveness of the Amendment and other applicable registrations, qualifications and compliances until such time as fewer than 25% of the Registrable Securities remain held by the Original Holder Group, calculated on an aggregate basis (the “Registration Effective Period”). As soon as practicable following the effectiveness of the Amendment, the Company will furnish to each holder of Registrable Shares such number of copies of the prospectus

5

contained in the Amendment in conformity with the requirements of the Securities Act, and such other documents as such holder may reasonably request in order to facilitate the public sale or other disposition of such shares.

               (ii) For any offer or sale of any of the Registrable Shares by a stockholder in a transaction that is not exempt under the Securities Act, the stockholder, in addition to complying with any other federal securities laws, will deliver a copy of the final prospectus (or amendment of or supplement to such prospectus) of the Company covering the Registrable Shares in the form furnished to the stockholder by the Company to the purchaser of any of the Registrable Shares on or before the settlement date for the purchase of such Registrable Shares.

               (iii) Following the date on which the Amendment is first declared effective, the holder of Registrable Shares will be permitted (subject in all cases to Section 7 below) to offer and sell Registrable Shares pursuant to the Amendment during the Registration Effective Period in the manner described in the Amendment provided that the Amendment remains effective and has not been suspended.

               (iv) Notwithstanding any other provision of this Section 6 but subject to Section 7, the Company shall have the right at any time to require that all holders of Registrable Shares suspend further open market offers and sales of Registrable Shares pursuant to the Amendment whenever, and for so long as, in the reasonable judgment of the Company after consultation with counsel there is or may be in existence material undisclosed information or events with respect to the Company (the “Suspension Right”) ; provided, however, that the Company shall not be entitled to invoke the Suspension Right unless such right or an equivalent restriction has been imposed on, and is then applicable to, all of the Company’s executive officers, directors and other holders of Common Stock which are registered for resale under the Securities Act. In the event the Company exercises the Suspension Right, such suspension will continue for the period of time reasonably necessary for disclosure (including any necessary filings with the SEC) to occur at a time that is not detrimental to the Company and its stockholders or until such time as the information or event is no longer material, each as determined in good faith by the Company (it being understood that the Company will use all reasonably commercial efforts to minimize the duration of the suspension period). The termination of the Registration Effective Period will extend by one (1) day for each day during which the holders of Registrable Shares suspend further open market offers and sales of Registrable Shares pursuant to the Company’s exercise of the Suspension Right.

          (d) Expenses. The costs and expenses to be borne by the Company for purposes of this Section 6 shall include, without limitation, printing expenses (including a reasonable number of prospectuses for circulation by the selling holders of Registrable Shares, including the Holder (the “Selling Stockholders”)), legal fees and disbursements of counsel for the Company, “blue sky” expenses, accounting fees and filing fees, but shall not include underwriting commissions or similar charges, or any legal fees and disbursements of counsel to the Selling Stockholders.

          (e) Indemnification.

6

               (i) To the extent permitted by law, the Company will indemnify and hold harmless each holder of Registrable Shares, any underwriter (as defined in the Securities Act) for such stockholder, its officers, directors, stockholders or partners and each person, if any, who controls such stockholder or underwriter within the meaning of the Securities Act or the Exchange Act, against any losses, claims, damages, or liabilities (joint or several) to which they may become subject under the Securities Act, the Exchange Act or other federal or state law, insofar as such losses, claims, damages, or liabilities (or actions in respect thereof) arise out of or are based upon any of the following statements, omissions or violations (collectively a “Violation”): (A) any untrue statement or alleged untrue statement of a material fact contained in the Amendment, including any preliminary prospectus or final prospectus contained therein or any amendments or supplements thereto, (B) the omission or alleged omission to state therein a material fact required to be stated therein, or necessary to make the statements therein not misleading, or (C) any violation or alleged violation by the Company of the Securities Act, the Exchange Act, any state securities law or any rule or regulation promulgated under the Securities Act, the Exchange Act or any state securities law; and the Company will pay to each such stockholder (and its officers, directors, stockholders or partners), underwriter or controlling person, any legal or other expenses reasonably incurred by them in connection with investigating or defending any such loss, claim, damage, liability, or action; provided, however, that the indemnity agreement contained in this Section 6(e)(i) shall not apply to amounts paid in settlement of any such loss, claim, damage, liability, or action if such settlement is effected without the consent of the Company; nor shall the Company be liable in any such case for any such loss, claim, damage, liability, or action to the extent that it arises out of or is based upon (a) a Violation which occurs in reliance upon and in conformity with written information furnished expressly for use in the Amendment by any such stockholder, or (b) a Violation that would not have occurred if such stockholder had delivered to the purchaser the version of the Prospectus most recently provided by the Company to the stockholder as of the date of such sale.

               (ii) To the extent permitted by law, each Selling Stockholder will indemnify and hold harmless the Company, each of its directors, each of its officers who has signed the Amendment, each person, if any, who controls the Company within the meaning of the Securities Act, any underwriter, any other Selling Stockholder selling securities pursuant to the Amendment and any controlling person of any such underwriter or other stockholder, against any losses, claims, damages, or liabilities (joint or several) to which any of the foregoing persons may become subject, under the Securities Act, the Exchange Act or other federal or state law, insofar as such losses, claims, damages, or liabilities (or actions in respect thereto) arise out of or are based upon any Violation (which includes without limitation the failure of the stockholder to comply with the prospectus delivery requirements under the Securities Act, and the failure of the stockholder to deliver the most current prospectus provided by the Company prior to such sale), in each case to the extent (and only to the extent) that such Violation occurs in reliance upon and in conformity with written information furnished by such Selling Stockholder expressly for use in the Amendment or such Violation is caused by the stockholder’s failure to deliver to the purchaser of the Selling Stockholder’s Registrable Shares a prospectus (or amendment or supplement thereto) that had been made available to the stockholder by the Company; and each such Selling Stockholder will pay any legal or other expenses reasonably incurred by any person intended to be indemnified pursuant to this Section 6(e)(ii) in connection with investigating or

7

defending any such loss, claim, damage, liability, or action; provided, however, that the indemnity agreement contained in this Section 6.5(e)(ii) shall not apply to amounts paid in settlement of any such loss, claim, damage, liability or action if such settlement is effected without the consent of the Selling Stockholder, which consent shall not be unreasonably withheld. The aggregate indemnification liability of each Selling Stockholder under this Section 6(e)(ii) shall not exceed the net proceeds received by such Selling Stockholder in connection with sale of shares pursuant to the Amendment.

               (iii) Each person entitled to indemnification under this Section 6(e) (the “Indemnified Party”) shall give notice to the party required to provide indemnification (the “Indemnifying Party”) promptly after such Indemnified Party has actual knowledge of any claim as to which indemnity may be sought and shall permit the Indemnifying Party to assume the defense of any such claim and any litigation resulting therefrom, provided that counsel for the Indemnifying Party who conducts the defense of such claim or any litigation resulting therefrom shall be approved by the Indemnified Party (whose approval shall not unreasonably be withheld), and the Indemnified Party may participate in such defense at such party’s expense, and provided further that the failure of any Indemnified Party to give notice as provided herein shall not relieve the Indemnifying Party of its obligations under this Section 6.5 unless the Indemnifying Party is materially prejudiced thereby. No Indemnifying Party, in the defense of any such claim or litigation, shall (except with the consent of each Indemnified Party) consent to entry of any judgment or enter into any settlement that does not include as an unconditional term thereof the giving by the claimant or plaintiff to such Indemnified Party of a release from all liability in respect to such claim or litigation. Each Indemnified Party shall furnish such information regarding itself or the claim in question as an Indemnifying Party may reasonably request in writing and as shall be reasonably required in connection with the defense of such claim and litigation resulting therefrom.

               (iv) To the extent that the indemnification provided for in this Section 6(e) is held by a court of competent jurisdiction to be unavailable to an Indemnified Party with respect to any loss, liability, claim, damage or expense referred to herein, then the Indemnifying Party, in lieu of indemnifying such Indemnified Party hereunder, shall contribute to the amount paid or payable by such Indemnified Party as a result of such loss, liability, claim, damage or expense in such proportion as is appropriate to reflect the relative fault of the Indemnifying Party on the one hand and of the Indemnified Party on the other in connection with the statements or omissions which resulted in such loss, liability, claim, damage or expense, as well as any other relevant equitable considerations. The relative fault of the Indemnifying Party and of the Indemnified Party shall be determined by reference to, among other things, whether the untrue or alleged untrue statement of a material fact or the omission or alleged omission to state a material fact relates to information supplied by the Indemnifying Party or by the Indemnified Party and the parties’ relative intent, knowledge, access to information and opportunity to correct or prevent such statement or omission. The aggregate contribution liability of each Selling Stockholder under this Section 6.5(e)(iv) shall not exceed the net proceeds received by such Selling Stockholder in connection with sale of shares pursuant to the Amendment.

     7. Procedures for Sale of Shares Under Registration Statement.

8

          (a) Notice and Approval. If any stockholder shall propose to sell any Registrable Shares pursuant to the Amendment, it shall notify the Company of its intent to do so (including the proposed manner and timing of all sales) at least three (3) full trading days prior to such sale, and the provision of such notice to the Company shall conclusively be deemed to reestablish and reconfirm an agreement by such Selling Stockholder to comply with the registration provisions set forth in this Agreement. Unless otherwise specified in such notice, such notice shall be deemed to constitute a representation that any information previously supplied by such Selling Stockholder expressly for inclusion in the Amendment (as the same may have been superseded by subsequent such information) is accurate as of the date of such notice. The Company may delay the resale by such Selling Stockholder of any Registrable Shares pursuant to the Amendment by delivering to such Selling Stockholder a written notification that the Company’s Suspension Right has been exercised and is then in effect (the "Suspension Notice"); provided, however, that the Suspension Notice must be delivered within the three (3) trading-day period following receipt of such Selling Stockholder’s notice of intent to sell Registrable Securities under the Amendment so long as such notice included a working facsimile number for purposes of delivery of the Company’s response. Upon receipt of the Suspension Notice, such Selling Stockholder shall refrain from selling any Registrable Shares pursuant to the Amendment in the open market until his, her or its receipt of a supplemented or amended prospectus pursuant to Section 7(b) below or written notice from the Company that the suspension period has ended and use of the prospectus previously furnished to such Selling Stockholder may be resumed.

          (b) Copies of Prospectus. Subject to the provisions of this Section 7, when a Selling Stockholder is entitled to sell and gives notice of its intent to sell Registrable Shares pursuant to the Amendment, the Company shall, within two (2) trading days following the request or, in the event that the Company’s Suspension Right has been exercised and is then in effect, as soon as practicable following the termination of the suspension period, furnish to such Selling Stockholder a reasonable number of copies of a supplement to or an amendment of such prospectus as may be necessary so that, as thereafter delivered to the purchasers of such Registrable Shares, such prospectus shall not as of the date of delivery to the Selling Stockholder include an untrue statement of a material fact or omit to state a material fact required to be stated therein or necessary to make the statements therein not misleading or incomplete in the light of the circumstances then existing.

8. Representations, Warranties and Covenants of Holder. Holder hereby represents, warrants and covenants to the Company that Holder (i) is the registered owner and, as set forth on the signature page, beneficial owner, of the Shares and options to purchase Common Stock, if any, indicated below Holder’s signature on the signature page to this Agreement, which at the date of this Agreement and at all times up until August 31, 2005, are, and will be, free and clear of any liens, claims, options, charges or other encumbrances, and (ii) is not the registered owner of any shares, options or other securities in, or convertible into, capital stock of the Company, other than the Shares and the options to purchase Common Stock, if any, indicated below Holder’s signature on the last page of this Agreement. Holder has the legal capacity, power and authority to enter into and perform all of Holder’s obligations under this Agreement (including under the Proxy). This Agreement (including the Proxy) has been duly and validly executed and

9

delivered by Holder and constitutes a valid and binding agreement of Holder, enforceable against Holder in accordance with its terms, subject to (a) laws of general application relating to bankruptcy, insolvency and the relief of debtors and (b) rules of law governing specific performance, injunctive relief and other equitable remedies.

     9 Further Assurances. Holder shall perform such further acts and execute such further documents and instruments as may reasonably be required to vest in the Company the power to carry out and give effect to the provisions of this Agreement.

     10. Fiduciary Duties. Notwithstanding anything in this Agreement to the contrary: (i) Holder makes no agreement or understanding herein in any capacity other than in Holder’s capacity as a registered owner of the Shares and, to the extent applicable, any New Shares, (ii) nothing in this Agreement shall be construed to limit or affect any action or inaction by Holder, or any officer, partner, member or employee, as applicable, of Holder, serving on the Company’s Board of Directors acting in such person’s capacity as a director or fiduciary of the Company, and (iii) Holder shall have no liability to Parent or any its affiliates under this Agreement as a result of any action or inaction by Holder, or any officer, partner, member or employee, as applicable, of Holder, serving on the Company’s Board of Directors acting in such person’s capacity as a director or fiduciary of the Company.

     11. Miscellaneous.

          (a) Amendments and Waivers. Any term of this Agreement may be amended or waived with the written consent of the parties or their respective successors and assigns. Any amendment or waiver effected in accordance with this Section 12(a) shall be binding upon the parties and their respective successors and assigns.

          (b) Governing Law. This Agreement and all acts and transactions pursuant hereto and the rights and obligations of the parties hereto shall be governed, construed and interpreted in accordance with the laws of the State of Delaware, without giving effect to principles of conflicts of law.

          (c) Counterparts. This Agreement may be executed in two or more counterparts, each of which shall be deemed an original and all of which together shall constitute one instrument.

          (d) Titles and Subtitles. The titles and subtitles used in this Agreement are used for convenience only and are not to be considered in construing or interpreting this Agreement.

          (e) Notices. Any notice or other communication required or permitted to be delivered to any party under this Agreement shall be in writing and shall be deemed properly delivered, given and received (i) when delivered by hand; (ii) on the day sent by facsimile, provided that the sender has received confirmation of transmission as of or prior to 5:00 p.m. local time of the recipient, on such day; (iii) the first Business Day after sent by facsimile (to the extent that (A) the sender has received confirmation of transmission after 5:00 p.m. local time of

10

the recipient on the day sent by facsimile, or (B) notice is sent on a day that is not a Business Day); or (iv) the third Business Day after sent by registered mail or by courier or express delivery service, in each case to the address or facsimile number set forth on the signature page to this Agreement beneath the name of such party, or to such other address or facsimile number as such party shall have specified in a written notice given to the other party hereto).

          (f) Severability. If one or more provisions of this Agreement are held to be invalid or unenforceable under the applicable law of any jurisdiction, the parties agree to renegotiate such provision in good faith, in order to maintain the economic position enjoyed by each party as close as possible to that under the provision rendered unenforceable. In the event that the parties cannot reach a mutually agreeable and enforceable replacement for such provision, then (i) such provision shall be excluded from this Agreement, (ii) the balance of the Agreement shall be interpreted as if such provision were so excluded and (iii) the balance of the Agreement shall be valid and enforceable in accordance with its terms. Each provision of this Agreement is separable from any other provisions of this Agreement, and each part of each provision of this Agreement is severable from every other part of such provision.

          (g) Specific Performance. Each of the parties hereto recognizes and acknowledges that a breach of any covenants or agreements contained in this Agreement will cause the Company to sustain damages for which it would not have an adequate remedy at law for money damages, and therefore each of the parties hereto agrees that in the event of any such breach the Company shall be entitled to the remedy of specific performance of such covenants and agreements and injunctive and other equitable relief in addition to any other remedy to which they may be entitled, at law or in equity.

          (h) Acknowledgement. Holder hereby agrees and acknowledges that the terms and provisions of Section 7.6 of the Subscription and Stockholders’ Agreement dated July 30, 2004 shall survive and remain in full force and effect following the consummation of the Offer.

[signature page follows]

11

     The parties have caused this Agreement to be duly executed on the date first above written.

COMPANY

By:                                                                                      

Name:                                                                                 

Title:                                                                                   

Address: Solexa, Inc.

25861 Industrial Boulevard

Hayward, California 94545

Attention: Chief Executive Officer

Facsimile No.: 650.670.9303

Signature Page to Amended and Restated Company Support Agreement

HOLDER

By:                                                                                              

                         [Name]

Holder’s Address for Notice:

Attention:
Facsimile No.:

Common Stock of the Company held of record:                                        

Options to Purchase Common Stock of the Company:                             

Additional Securities of the Company Beneficially Owned:                    

EXHIBIT A

IRREVOCABLE PROXY

TO VOTE SHARES OF

SOLEXA, INC.

     The undersigned stockholder (“Holder”) of Solexa, Inc, a Delaware corporation (the “Company”), hereby irrevocably (to the fullest extent permitted under the laws of Delaware) appoints the Chief Executive Officer and each of the other members of the Board of Directors of the Company, and each of them, as the sole and exclusive attorneys and proxies of the undersigned, with full power of substitution and resubstitution, to vote and exercise all voting and related rights (to the full extent that the undersigned is entitled to do so) with respect to all of the capital stock of the Company that now are or hereafter may be owned of record by and/or registered in the name of the undersigned, and any and all other shares or securities of the Company issued or issuable in respect thereof on or after the date hereof (collectively, the “Shares”) in accordance with the terms of this Proxy, the Shares and that certain Amended and Restated Company Support Agreement of even date herewith, by and between Company and the undersigned (the “Company Support Agreement”). The shares of, and/or options over, the common stock of the Company owned by the undersigned stockholder of the Company as of the date of this Proxy are listed beneath the undersigned’s signature on the final page of this Proxy. Upon the undersigned’s execution of this Proxy, any and all prior proxies given by the undersigned with respect to any Shares are hereby revoked and the undersigned agrees not to grant any subsequent proxies with respect to the Shares until August 31, 2005. Terms used herein and not defined herein shall have the meaning set forth in the Company Support Agreement.

     This Proxy is coupled with an interest, is irrevocable (to the fullest extent permitted by law), is granted pursuant to the Company Support Agreement and is granted in consideration of the Company entering into that certain Securities Purchase Agreement, of even date herewith, among the Company and the individuals and entities listed on the Schedule of Purchasers attached thereto as Exhibit A-1 and Exhibit A-2 (the “Purchase Agreement”).

     The attorneys and proxies named above, and each of them, are hereby further authorized and empowered by the undersigned, at any time prior to August 31, 2005, to act as the undersigned’s attorney and proxy to vote the Shares in favor of the issuance of Common Stock and warrants pursuant to the Purchase Agreement and any other transactions contemplated by the Purchase Agreement, and to exercise all voting and other rights of the undersigned with respect to the Shares (including, without limitation, the power to execute and deliver written resolutions), at every annual, extraordinary or adjourned meeting of the stockholders or any class of stockholders of the Company and in every written resolution in lieu of any such meeting

     This Proxy and all acts and transactions pursuant hereto and the rights and obligations of the parties hereto shall be governed, construed and interpreted in accordance with the laws of the State of Delaware, without giving effect to principles of conflicts of law.

     Any obligation of the undersigned hereunder shall be binding upon the successors and assigns of the undersigned.

     This Proxy is irrevocable to the fullest extent permitted by law.

[signature page follows]

2

Dated: April        , 2005

                                                            
[Name]

Common Stock of the Company held of record:                                        

Options to Purchase Common Stock of the Company:                             

Additional Securities of the Company Beneficially Owned:                    

Signature Page to Irrevocable Proxy

EX-99.2

EXHIBIT 99.2

CONTACTS:

Solexa, Inc.
John West, CEO
510/670-9300
John.West@solexa.com

Press Contact:	Investor Contacts:
Northbank Communications	Lippert/Heilshorn & Associates
Sue Charles, CEO	Jody Cain (jcain@lhai.com)
+44 (0)20 7886 8152	Bruce Voss (bvoss@lhai.com)
s.charles@northbankcommunications.com	310/691-7100

Solexa Announces Agreement for $32.5 Million Private Equity Financing

Appoints G. Mason Morfit to Board of Directors

HAYWARD, Calif. (April 22, 2005) – Solexa, Inc. (Nasdaq: SLXA) today announced that it has entered into a definitive agreement for a $32.5 million private sale of common stock and warrants for the purchase of common stock with a group of leading institutional investors in the health care sector. The transaction is led by ValueAct Capital. Solexa also announced that G. Mason Morfit, CFA, a partner of ValueAct Capital, has been appointed to its board of directors, bringing board membership to eight.

Under terms of the financing, Solexa will sell approximately 8.1 million shares of common stock at $4.00 per share and will issue warrants to purchase approximately 4.1 million shares of common stock at an exercise price of $5.00 per share. Approximately 2.1 million shares of common stock and approximately 1.1 million warrants will be issued in a closing expected on or about April 25, 2005, and the balance of approximately 6.0 million shares of common stock and warrants to purchase approximately 3.0 million shares of common stock will be issued on the same terms in a second closing subject to stockholder approval at the 2005 annual meeting. Solexa’s intended use of proceeds includes the development and launch of its first-generation Sequencing-by-Synthesis (SBS) molecular array platform for genetic analysis and repayment of its loan from Silicon Valley Bank. All of Solexa’s previous venture capital investors, including funds affiliated with Abingworth Management Limited, Amadeus Capital Partners Limited, Oxford Bioscience Partners and SV Life Sciences, will be investing a total of approximately $10.8 million in the financing at the second closing of the financing and have entered into agreements with Solexa to vote in favor of the financing at the 2005 annual meeting. SG Cowen & Co., LLC served as the exclusive placement agent for the transaction.

“We are delighted to bring in funding for the introduction of our first SBS system at the end of 2005, which we expect will dramatically lower the cost of DNA sequencing and gene expression analysis, and for our commercialization ramp in 2006,” said John West, Solexa’s chief executive officer. “I am pleased to welcome Mason, with his capital markets experience and leadership abilities, to Solexa’s board.”

“I envision a significant commercial opportunity for Solexa as the Company brings to market its next-generation technology for DNA sequencing,” said G. Mason Morfit. “I’m pleased my board appointment comes on the heels of Solexa’s announcement that it has completed its first full genome sequence, for the virus Phi-X174, which represents a major milestone for Solexa’s SBS technology. On behalf of ValueAct Capital, I look forward to working actively with Solexa’s management and board.”

These securities have not been registered under the Securities Act of 1933, as amended, or any state securities laws and may not be offered or sold in the United States absent registration with the Securities and Exchange Commission (SEC) or an applicable exemption from the registration requirements. Solexa has agreed to file a registration statement with respect to the shares within the earlier of ten days following the second closing of the financing or eighty days following the first closing. This news release is not an offer to sell or the solicitation of an offer to buy the securities discussed herein.

About the Market for SBS Technology

Solexa is designing its initial system with the goal of enabling users to ascertain a human genome sequence for about $100,000. This is approximately 100 times lower than the costs of conventional sequencing. Solexa’s initial strategy is to focus on the well established research market. This market includes DNA sequencing, gene expression and genotyping, all at full genome scale. These together already represent an approximately $1 billion market. According to IDC, the DNA sequencing segment has the potential to grow to $1.6 billion with the advent of the $100,000 genome.*

About Solexa

Solexa, Inc. is developing and preparing to commercialize a new platform for genetic analysis, based on Sequencing-by-Synthesis (SBS) and molecular arrays. This one platform is expected to support many types of genetic analysis, including DNA sequencing, gene expression, genotyping and micro-RNA analysis. This technology can potentially generate over a billion bases of DNA sequence from a single experiment with a single sample preparation. Solexa’s long-term goal is to reduce the cost of human re-sequencing to a few thousand dollars for use in a wide range of applications from basic research through clinical diagnostics. The company anticipates an initial product launch by the end of 2005. For further information, please visit www.solexa.com.

* Zachary Zimmerman, Ph.D., “The $1,000 Human Genome — Implications for Life Science, Healthcare and IT”, IDC, 2004.

This press release contains “forward-looking” statements, including statements related to the current views of Solexa management as to future products, product development, the expansion and success of Solexa’s commercial application of its genomics technologies, and the future financial performance of Solexa. Any statements contained in this press release that are not statements of historical fact may be deemed to be forward-looking statements. Words such as “believes,” “anticipates,” “plans,” “predicts,” “expects,” “envisions,” “hopes,” “estimates,” “intends,” “will,” “continue,” “may,” “potential,” “should,” “confident,” “could” and similar expressions are intended to identify forward-looking statements. There can be no assurance that such expectations of any of the forward-looking statements will prove to be correct, and actual results could differ materially from those projected or assumed in the forward-looking statements. There are a number of important factors that could cause the results of Solexa to differ materially from those indicated by these forward-looking statements including, among others, risks detailed from time to time in the Company’s SEC reports, including its Annual Report on Form 10-K for the year ended December 31, 2004. Solexa does not undertake any obligation to update forward-looking statements.

# # #