e424b3
 

Prospectus Supplement No. 2
Filed Pursuant to
Rule 424(b)(3) and (c)
File No. 333-127460
13,657,101 Shares of Common Stock
SOLEXA, INC.
     This prospectus supplement supplements the prospectus, dated September 1, 2005, of Solexa, Inc. relating to the offering and sale by selling stockholders of Solexa (or by donees, pledgees, transferees and other successors in interest that receive such shares as a gift, pledge, partnership distribution or other non-sale transfer) of up to 13,657,101 shares of our common stock. This prospectus supplement should be read in conjunction with the prospectus, and is qualified by reference to the prospectus, except to the extent that the information presented herein supersedes the information contained in the prospectus. The term “Selling Stockholders” as used in the prospectus shall be deemed to include the selling stockholders identified in the table below. This prospectus supplement is not complete without, and may not be delivered or utilized except in connection with, the prospectus, including any amendments or supplements thereto.
     Investing in our common stock involves a high degree of risk. See “Risk Factors” beginning on page 2 of the prospectus.
     NEITHER THE SECURITIES AND EXCHANGE COMMISSION NOR ANY STATE SECURITIES COMMISSION HAS APPROVED OR DISAPPROVED OF THESE SECURITIES OR PASSED UPON THE ADEQUACY OR ACCURACY OF THIS PROSPECTUS. ANY REPRESENTATION TO THE CONTRARY IS A CRIMINAL OFFENSE.
The date of this prospectus is January 27, 2006.

 

 

     This prospectus supplement is being filed in connection with the distribution of shares held by (i) Abingworth Bioventures II S.I.C.A.V, (ii) Abingworth Bioventures IIA L.P., (iii) Abingworth Bioventures IIIA L.P., (iv) Abingworth Bioventures IIIB L.P., (v) Abingworth Bioventures IIIC L.P., and (vi) Abingworth Bioventures III Executives L.P., together the Abingworth Funds, each identified in the prospectus as selling stockholders, to their respective partners. No additional shares of Solexa common stock are being offered for resale hereunder. Except with respect to directors and officers of Solexa, the entities that have filed reports pursuant to Section 13(f) of the Securities Exchange Act of 1934, as amended, or the Act, and statements of beneficial ownership filed pursuant to Sections 13(d) and 13(g) of the Act, the ownership indicated in the table below is based solely on shares owned by the indicated selling stockholders as a result of a distribution of shares by the Abingworth Funds on January 26, 2006. The table appearing on pages 10-13 of the prospectus under the caption “Selling Stockholders” is supplemented and amended to include the following stockholders in addition to those identified in the prospectus:
                                         
    Shares of Common             Shares of Common  
    Stock Beneficially     Number     Stock Beneficially  
    Owned Prior to the     of     Owned After  
    Offering     Shares     Offering  
                    Being              
Security Holders   Shares     Percent*     Offered     Shares     Percent*  
Abingworth Bioventures II, S.I.C.A.V
     1,409,723       3.90 %     1,409,723       0       * *
Abingworth Bioventures IIA L.P.(1)
     508,279       1.40 %     133,279       375,000       1.03 %
Abingworth Bioventures IIIA L.P.(2)
     910,420       2.51 %     473,953       436,467       1.20 %
Abingworth Bioventures IIIB L.P.(3)
     555,749       1.53 %     289,312       266,437       * *
Abingworth Bioventures IIIC L.P.(4)
     332,900       * *     173,301       159,599       * *
Abingworth Bioventures III Executives L.P.(5)
     14,514       * *     7,558       6,956       * *
Abingworth Bioventures III GP LP
     2,136       * *     2,136       0       * *
Adams Street
                                        
Partnership Fund-2002 Non-U.S. Fund, L.P.
     3,027       * *     3,027       0       * *
Adams Street Partnership Fund-2002 U.S. Fund, L.P.
     12,366       * *     12,366       0       * *
Adams Street Partnership Fund-2003 Non-U.S. Fund, L.P.
     4,427       * *     4,427       0       * *
Adams Street Partnership Fund-2003 U.S. Fund, L.P.
     12,059       * *     12,059       0       * *
Alan Rowe Williamson
     1,022       * *     1,022       0       * *
AMP Society UK
     3,187       * *     3,187       0       * *
AMP Society UK v LLF a/c
     7,140       * *     7,140       0       * *
Bax Portfolios Inc.
     8,500       * *     8,500       0       * *
Blackboard Ventures, Inc
     40,889       * *     40,889       0       * *
Boston Safe Deposit & Trust Co. solely in its capacity as Trustee for the SBC Master Pension Trust (as directed by Adams Street Partners, LLC) & not in its individual capacity
     24,533       * *     24,533       0       * *
Brinson Partnership Fund Program Entity A
     20,357       * *     20,357       0       * *

 

 

                                         
    Shares of Common             Shares of Common  
    Stock Beneficially     Number     Stock Beneficially  
    Owned Prior to the     of     Owned After  
    Offering     Shares     Offering  
                    Being              
Security Holders   Shares     Percent*     Offered     Shares     Percent*  
Brinson Partnership Fund 2001 Primary Fund, LP
     12,807       * *     12,807       0       * *
Brinson Partnership Fund-2003 Primary Fund, L.P.
     4,645       * *     4,645       0       * *
Chancellor Offshore Partnership Fund
     57,897       * *     57,897       0       * *
Chancellor Partnership Fund
     42,039       * *     42,039       0       * *
Charles Schwab & Co. for benefit of Michael Sherman, IRA
     204       * *     204       0       * *
Christopher Egan
     4,250       * *     4,250       0       * *
Credit Suisse Anlagestiftung
     6,133       * *     6,133       0       * *
Crescent International Holdings Ltd.
     26,611       * *     26,611       0       * *
De Soto Finance Co.
     4,250       * *     4,250       0       * *
EDS Retirement Plan Trust
     16,356       * *     16,356       0       * *
Equitable Life Assurance Society
     42,500       * *     42,500       0       * *
Europe Select Private Equity II Ltd.
     40,889       * *     40,889       0       * *
Ewing Marion Kauffman Foundation
     72,194       * *     72,194       0       * *
Fitzgerald Partners IV
     17,000       * *     17,000       0       * *
Fortis Banque (Crescent Int Holdings)
     17,000       * *     17,000       0       * *
Frank A. Bonsal, Jr.
     5,175       * *     5,175       0       * *
G.I.M.V. N.V.
     45,945       * *     45,945       0       * *
General Practitioner LLC
     1,840       * *     1,840       0       * *
Hajod A/S
     4,454       * *     4,454       0       * *
HarbourVest International Private Equity Partners IV-Partnership Fund L.P.
     102,223       * *     102,223       0       * *
HarbourVest Partners V-Partnership Fund L.P.
     150,890       * *     150,890       0       * *
HarbourVest Partners V-Parallel P/S Fund L.P.
     25,148       * *     25,148       0       * *
Henderson Private Capital (GP) Limited
     40,889       * *     40,889       0       * *
Herbert L. Heyneker
     204       * *     204       0       * *
HIPEP IV-European Venture Partnership Fund LP
     10,222       * *     10,222       0       * *
HSBC Global Custody 813247
     8,500       * *     8,500       0       * *
INVESCO Venture Partnership Fund III, L.P.
     20,445       * *     20,445       0       * *
James A. Wells
     204       * *     204       0       * *
Joel Franklin Martin
     204       * *     204       0       * *
John Egan
     4,250       * *     4,250       0       * *
Key Capital Corporation
     17,556       * *     17,556       0       * *
Knightsbridge Associated Investors X, LP
     31,050       * *     31,050       0       * *
Knightsbridge Associated Investors XI, LP
     20,445       * *     20,445       0       * *
Finnish Local Government Pension Institution
     40,889       * *     40,889       0       * *
Logan Family 1992 Trust dated 3/3/1992 Robert W. Logan
     204       * *     204       0       * *
Luna PCC Limited 2000 Cell
     409       * *     409       0       * *
Lysander LLC
     12,267       * *     12,267       0       * *
Montagu Newhall Global Partners II, L.P.
     3,476       * *     3,476       0       * *
Montagu Newhall Global Partners II-A, L.P.
     82       * *     82       0       * *
Montagu Newhall Global Partners II-B, L.P.
     532       * *     532       0       * *
Montagu Newhall Global Partners, LP
     8,178       * *     8,178       0       * *
Montauk Partners II, L.P.
     16,679       * *     16,679       0       * *
Novartis AG
     42,500       * *     42,500       0       * *

 

 

                                         
    Shares of Common             Shares of Common  
    Stock Beneficially     Number     Stock Beneficially  
    Owned Prior to the     of     Owned After  
    Offering     Shares     Offering  
                    Being              
Security Holders   Shares     Percent*     Offered     Shares     Percent*  
Orange County Employees Retirement System
     4,089       * *     4,089       0       * *
Pantheon International Participations PLC
     42,500       * *     42,500       0       * *
Partners Group Private Equity Performance Holding Ltd.
     8,178       * *     8,178       0       * *
PAT Pensions
     13,727       * *     13,727       0       * *
Paul Associates II, L.P.
     188       * *     188       0       * *
Paul Capital Partners VII Holdings
     5,521       * *     5,521       0       * *
Paul Capital Partners VII, L.P.
     964       * *     964       0       * *
Paul Capital Partners VII-C, L.P.
     49       * *     49       0       * *
Pearl Assurance PLC
     103,445       * *     103,445       0       * *
Pearl Holding Limited
     26,578       * *     26,578       0       * *
Pensionskasse der UBS
     20,445       * *     20,445       0       * *
Pomona Capital V Fund, L.P.
     2,260       * *     2,260       0       * *
Pomona Capital V, L.P.
     4,461       * *     4,461       0       * *
Prime Edge Investments N.V.
     17,173       * *     17,173       0       * *
Princess Private Equity Subholding Ltd.
     10,222       * *     10,222       0       * *
Quilvest European Venture Ltd.
     16,356       * *     16,356       0       * *
SIF Investment Company Ltd.
     25,416       * *     25,416       0       * *
Sir Winfriend Franz Wihelm Bischoff
     2,044       * *     2,044       0       * *
State Universities Retirement System
     16,356       * *     16,356       0       * *
Stuart J. Collinson
     204       * *     204       0       * *
Tachbrook Investments Limited
     4,089       * *     4,089       0       * *
Technopreneur Investment Pte Ltd.
     12,267       * *     12,267       0       * *
The 1995 Michael Egan Revocable Trust
     4,250       * *     4,250       0       * *
The 2001 Primary Brinson Non US Partnership Fund Offshore Series Company Ltd.
     8,644       * *     8,644       0       * *
The 2001 Primary Brinson Partnership Fund Offshore Series Co. Ltd.
     9,775       * *     9,775       0       * *
The 2003 Primary Brinson Non-U.S. Partnership Fund Offshore Series Co. Ltd.
     3,564       * *     3,564       0       * *
The 2003 Primary Brinson Partnership Fund Offshore Series Co. Ltd.
     3,159       * *     3,159       0       * *
The Brinson Non US Partnership - 2001 Primary Fund, L.P.
     5,389       * *     5,389       0       * *
The Brinson U.S. Partnership Fund - 2003 Primary Fund, L.P.
     1,615       * *     1,615       0       * *
The General Trust Company S.A.
     8,687       * *     8,687       0       * *
The James Irvine Foundation
     62,622       * *     62,622       0       * *
The John Egan Revocable Trust dtd 10/29/91
     20,445       * *     20,445       0       * *
The Jon S. Saxe & Myrna G. Marshall 1997 Trust
     204       * *     204       0       * *
The Meadows Foundation
     30,667       * *     30,667       0       * *
The Wellcome Trust Limited, as Trustee of the Wellcome Trust
     221,828       * *     221,828       0       * *
Timothy Haines
     204       * *     204       0       * *
Timothy James Rink
     204       * *     204       0       * *
UBS Global Asset Management Trust Co. as Trustee of The Brinson Non-U.S. Partnership Fund Trust - 2003 Primary Fund, L.P.
     7,064       * *     7,064       0       * *

 

 

                                         
    Shares of Common             Shares of Common  
    Stock Beneficially     Number     Stock Beneficially  
    Owned Prior to the     of     Owned After  
    Offering     Shares     Offering  
                    Being              
Security Holders   Shares     Percent*     Offered     Shares     Percent*  
UBS Global Asset Management Trust Co. as Trustee of The Brinson Partnership Fund Trust-2003 Primary Fund
     9,737       * *     9,737       0       * *
UBS Global Asset Management Trust Company as Trustee of the Brinson Non US Partnership Fund Trust-2001 Primary Fund
     34,915       * *     34,915       0       * *
UBS Global Asset Management Trust Company as Trustee of The Brinson Partnership Fund Trust-2001 Primary Fund
     30,780       * *     30,780       0       * *
UBS Jersey Nominees Ltd.
     6,133       * *     6,133       0       * *
UBS Private Banking Nominees Ltd. As Nominee for Sachsen LB Corporate
                                        
Finance Holding GMBH
     4,089       * *     4,089       0       * *
Unicapital II (Guernsey) Limited
     6,141       * *     6,141       0       * *
Valinco Investment Limited
     10,757       * *     10,757       0       * *
Varma Mutual Pension Insurance Company
     40,889       * *     40,889       0       * *
Vega Invest (Guernsey) Limited
     8,178       * *     8,178       0       * *
Wilden Ltd.
     4,250       * *     4,250       0       * *
Total Shares Being Offered
     5,731,585       15.78 %     4,487,126       1,244,459       3.4 %
  *   Percentage calculations based on 36,300,335 shares of our common stock that were issued and outstanding as of January 26, 2006.
 
  **   Represents beneficial ownership of less than 1%.
(1)   Includes 125,000 shares of common stock issuable upon exercise of a warrant.
 
(2)   Includes 145,489 shares of common stock issuable upon exercise of a warrant.
 
(3)   Includes 88,812 shares of common stock issuable upon exercise of a warrant.
 
(4)   Includes 53,200 shares of common stock issuable upon exercise of a warrant.
 
(5)   Includes 2,319 shares of common stock issuable upon exercise of a warrant.