-----BEGIN PRIVACY-ENHANCED MESSAGE-----
Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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 TWSM7vrzLADbmYQaionwg5sDW3P6oaM5D3tdezXMm7z1T+B+twIDAQAB
MIC-Info: RSA-MD5,RSA,
 WDR26bGTsnqzNE7xMLid4SwE2rRM7KWPDHC+my94TRxP0JcDqdaPWmBQ5e9t+Tqe
 DbjnoclAZt0p9OwFJXKfkQ==

<SEC-DOCUMENT>0001129787-05-000092.txt : 20050714
<SEC-HEADER>0001129787-05-000092.hdr.sgml : 20050714
<ACCEPTANCE-DATETIME>20050714170259
ACCESSION NUMBER:		0001129787-05-000092
CONFORMED SUBMISSION TYPE:	3
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20050712
FILED AS OF DATE:		20050714
DATE AS OF CHANGE:		20050714

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			Solexa, Inc.
		CENTRAL INDEX KEY:			0000913275
		STANDARD INDUSTRIAL CLASSIFICATION:	MEDICINAL CHEMICALS & BOTANICAL PRODUCTS [2833]
		IRS NUMBER:				943161073
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	BUSINESS ADDRESS:	
		STREET 1:		25861 INDUSTRIAL BLVD
		CITY:			HAYWARD
		STATE:			CA
		ZIP:			94545
		BUSINESS PHONE:		5106709300

	MAIL ADDRESS:	
		STREET 1:		25861 INDUSTRIAL BLVD
		CITY:			HAYWARD
		STATE:			CA
		ZIP:			94545

	FORMER COMPANY:	
		FORMER CONFORMED NAME:	LYNX THERAPEUTICS INC
		DATE OF NAME CHANGE:	19931008

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			KAMIN PETER H
		CENTRAL INDEX KEY:			0000937541
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	FILING VALUES:
		FORM TYPE:		3
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-22570
		FILM NUMBER:		05955060

	BUSINESS ADDRESS:	
		STREET 1:		40 BRIARCLIFF RD
		CITY:			LONGMEADOW
		STATE:			MA
		ZIP:			01106
		BUSINESS PHONE:		6179605570

	MAIL ADDRESS:	
		STREET 1:		TWO INTERNATIONAL PLACE, 25TH FLOOR
		CITY:			BOSTON
		STATE:			MA
		ZIP:			02110

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			UBBEN JEFFREY W
		CENTRAL INDEX KEY:			0001159187
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	FILING VALUES:
		FORM TYPE:		3
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-22570
		FILM NUMBER:		05955061

	BUSINESS ADDRESS:	
		STREET 1:		ONE MARITIME PLAZA, SUITE 1400
		CITY:			SAN FRANCISCO
		STATE:			CA
		ZIP:			94111
		BUSINESS PHONE:		4153623700

	MAIL ADDRESS:	
		STREET 1:		435 PACIFIC AVENUE, FOURTH FLOOR
		CITY:			SAN FRANCISCO
		STATE:			CA
		ZIP:			94133

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			VA PARTNERS LLC
		CENTRAL INDEX KEY:			0001129787
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	FILING VALUES:
		FORM TYPE:		3
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-22570
		FILM NUMBER:		05955062

	BUSINESS ADDRESS:	
		STREET 1:		435 PACIFIC AVENUE
		STREET 2:		FOURTH FLOOR
		CITY:			SAN FRANCISCO
		STATE:			CA
		ZIP:			94133
		BUSINESS PHONE:		4153623700

	MAIL ADDRESS:	
		STREET 1:		435 PACIFIC AVENUE
		STREET 2:		FOURTH FLOOR
		CITY:			SAN FRANCISCO
		STATE:			CA
		ZIP:			94133
</SEC-HEADER>
<DOCUMENT>
<TYPE>3
<SEQUENCE>1
<FILENAME>primary_doc.xml
<DESCRIPTION>PRIMARY DOCUMENT
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2005-07-12</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0000913275</issuerCik>
        <issuerName>Solexa, Inc.</issuerName>
        <issuerTradingSymbol>SLXA</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001129787</rptOwnerCik>
            <rptOwnerName>VA PARTNERS LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>435 PACIFIC AVENUE</rptOwnerStreet1>
            <rptOwnerStreet2>FOURTH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>SAN FRANCISCO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94133</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001159187</rptOwnerCik>
            <rptOwnerName>UBBEN JEFFREY W</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>435 PACIFIC AVENUE, FOURTH FLOOR</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>SAN FRANCISCO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94133</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0000937541</rptOwnerCik>
            <rptOwnerName>KAMIN PETER H</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>TWO INTERNATIONAL PLACE, 25TH FLOOR</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>BOSTON</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02110</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock, par value $.01 per share</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>1875000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Warrant to Purchase Common Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>5</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2005-10-22</value>
            </exerciseDate>
            <expirationDate>
                <value>2010-04-25</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock, par value $.01 per share</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>404684</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnote</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Warrant to Purchase Common Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>5</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2006-01-08</value>
            </exerciseDate>
            <expirationDate>
                <value>2010-07-12</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock, par value $.01 per share</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>532816</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnote</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">As General Partner of ValueAct Capital Master Fund, L.P. and ValueAct Capital Partners Co-Investors, L.P.</footnote>
        <footnote id="F2">These securities are also beneficially owned by Jeffrey W. Ubben, George F. Hamel, Jr., and Peter H. Kamin as Managing Members, Principal Owners and Controlling Persons of VA Partners, LLC. The reporting persons disclaim beneficial ownership except to the extent of their pecuniary interest therein.</footnote>
    </footnotes>

    <remarks>Joint Filer Information

Name: ValueAct Capital Master Fund, L.P.
Address: 435 Pacific Avenue, 4th Floor, San Francisco, CA  94133
Designated Filer: VA Partners, L.L.C.
Issuer and Ticker Symbol: Solexa, Inc. (SLXA)
Date of Event Requiring Statement: July 12, 2005

Name: ValueAct Capital Partners Co-Investors, L.P.
Address: 435 Pacific Avenue, 4th Floor, San Francisco, CA  94133
Designated Filer: VA Partners, L.L.C.
Issuer and Ticker Symbol: Solexa, Inc. (SLXA)
Date of Event Requiring Statement: July 12, 2005

Name: Jeffrey W. Ubben
Address: 435 Pacific Avenue, 4th Floor, San Francisco, CA  94133
Designated Filer: VA Partners, L.L.C.
Issuer and Ticker Symbol: Solexa, Inc. (SLXA)
Date of Event Requiring Statement: July 12, 2005

Name: George F. Hamel, Jr.
Address: 435 Pacific Avenue, 4th Floor, San Francisco, CA  94133
Designated Filer: VA Partners, L.L.C.
Issuer and Ticker Symbol: Solexa, Inc. (SLXA)
Date of Event Requiring Statement: July 12, 2005

Name: Peter H. Kamin
Address: Two International Place, Suite 2500, Boston, MA 02110
Designated Filer: VA Partners, L.L.C.
Issuer and Ticker Symbol: Solexa, Inc. (SLXA)
Date of Event Requiring Statement: July 12, 2005</remarks>

    <ownerSignature>
        <signatureName>VALUEACT CAPITAL MASTER FUND, L.P., BY VA PARTNERS, L.L.C., ITS GENERAL PARTNER By: /s/ George F. Hamel, Jr. Managing Member</signatureName>
        <signatureDate>2005-07-14</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>VALUEACT CAPITAL PARTNERS CO-INVESTORS, L.P., BY VA PARTNERS, L.L.C., ITS GENERAL PARTNER By: /s/ George F. Hamel, Jr. Managing Member</signatureName>
        <signatureDate>2005-07-14</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>VA PARTNERS, L.L.C. By: /s/ George F. Hamel, Jr. Managing Member</signatureName>
        <signatureDate>2005-07-14</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>By: /s/ Jeffrey W. Ubben</signatureName>
        <signatureDate>2005-07-14</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>By: /s/ George F. Hamel, Jr.</signatureName>
        <signatureDate>2005-07-14</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>By: /s/ Peter H. Kamin</signatureName>
        <signatureDate>2005-07-14</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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