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<H5 align="left" style="page-break-before:always"><A HREF="#toc">Table of Contents</A></H5><P>

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    <TD align="left" valign="top"><FONT style="white-space: nowrap">As filed with the Securities and Exchange Commission on October&nbsp;5, 2006</FONT>
</TD>
    <TD>&nbsp;</TD>
    <TD align="right" valign="top"><FONT style="white-space: nowrap">Registration No.&nbsp;333-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</FONT></TD>
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<DIV style="width: 100%; border-bottom: 2pt solid black; font-size: 1pt">&nbsp;</DIV>
<DIV style="width: 100%; border-bottom: 1pt solid black; font-size: 1pt">&nbsp;</DIV>




<DIV align="center" style="font-size: 14pt; margin-top: 12pt"><B>UNITED STATES SECURITIES AND EXCHANGE COMMISSION</B>
</DIV>

<DIV align="center" style="font-size: 12pt"><B>Washington, D.C. 20549<BR>
<DIV align="center"><DIV style="font-size: 3pt; margin-top: 6pt; width: 26%; border-bottom: 1px solid #000000">&nbsp;</DIV></DIV></B>
</DIV>

<DIV align="center" style="font-size: 18pt; margin-top: 6pt"><B>FORM S-8</B>
</DIV>

<DIV align="center" style="font-size: 12pt; margin-top: 6pt">REGISTRATION STATEMENT<br>
UNDER<br>
THE SECURITIES ACT OF 1933</DIV>


<DIV align="center" style="font-size: 10pt"><DIV align="center"><DIV style="font-size: 3pt; margin-top: 6pt; width: 26%; border-top: 1px solid #000000">&nbsp;</DIV></DIV></DIV>


<DIV align="center" style="font-size: 24pt; margin-top: 6pt"><B>SOLEXA, INC.</B>
</DIV>

<DIV align="center" style="font-size: 10pt"><DIV style="margin-top: 1px"><FONT style="border-top: 1px solid #000000">(Exact name of registrant as specified in its charter)</FONT></DIV></DIV>


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    <TD align="center" valign="top"><B>Delaware</B>
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top"><B>94-3161073</B></TD>
</TR>
<TR valign="bottom">
    <TD align="center" valign="top">(State of Incorporation)
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">(I.R.S. Employer Identification No.)</TD>
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<DIV align="Center" style="font-size: 10pt; margin-top: 6pt"><DIV align="center"><DIV style="font-size: 3pt; margin-bottom: 6pt; width: 26%; border-top: 1px solid #000000">&nbsp;</DIV></DIV>

</DIV>

<DIV align="Center" style="font-size: 10pt; margin-top: 6pt"><B>25861 Industrial Blvd.</B>

</DIV>

<DIV align="Center" style="font-size: 10pt; margin-top: 6pt"><B>Hayward, California 94545</B>

</DIV>

<DIV align="Center" style="font-size: 10pt; margin-top: 6pt">(Address of principal executive offices)

</DIV>

<DIV align="Center" style="font-size: 10pt; margin-top: 6pt"><DIV align="center"><DIV style="font-size: 3pt; margin-bottom: 6pt; width: 26%; border-top: 1px solid #000000">&nbsp;</DIV></DIV>

</DIV>

<DIV align="Center" style="font-size: 10pt; margin-top: 6pt"><B>2005 Equity Incentive Plan</B><BR>
(Full title of the plan)

</DIV>

<DIV align="Center" style="font-size: 10pt; margin-top: 6pt"><B>John West<BR>
Chief Executive Officer<BR>
Solexa, Inc.<BR>
25861 Industrial Blvd.<BR>
Hayward, California 94545<BR>
(510)&nbsp;670-9300</B><BR>
(Name, address, including zip code, and telephone number, including area code, of agent for service)

</DIV>

<DIV align="Center" style="font-size: 10pt; margin-top: 6pt"><DIV align="center"><DIV style="font-size: 3pt; margin-bottom: 6pt; width: 26%; border-top: 1px solid #000000">&nbsp;</DIV></DIV>

</DIV>

<DIV align="Center" style="font-size: 10pt; margin-top: 6pt"><B>COPIES TO:<BR>
James C. Kitch, Esq.<BR>
Cooley Godward LLP</B><BR>
Five Palo Alto Square<BR>
3000 El Camino Real<BR>
Palo Alto, CA 94306-2155<BR>
(650)&nbsp;843-5000<BR>
<DIV align="center"><DIV style="font-size: 3pt; margin-top: 6pt; width: 26%; border-bottom: 1px solid #000000">&nbsp;</DIV></DIV>

</DIV>

<DIV align="center" style="font-size: 10pt; margin-top: 6pt"><B>CALCULATION OF REGISTRATION FEE</B>
</DIV>

<DIV align="center">
<TABLE style="font-size: 10pt" cellspacing="0" border="0" cellpadding="0" width="100%">
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    <TD width="1%">&nbsp;</TD>
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    <TD nowrap align="left" colspan="22" style="border-bottom: 3px double #000000">&nbsp;</TD>
</TR>
<TR style="font-size: 8pt" valign="bottom">    <TD width="1%">&nbsp;</TD>

    <TD>&nbsp;</TD>
    <TD style="border-right: 2px solid #000000">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD style="border-right: 2px solid #000000">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center" colspan="3">Proposed Maximum</TD>
    <TD style="border-right: 2px solid #000000">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center" colspan="3">Proposed Maximum</TD>
    <TD style="border-right: 2px solid #000000">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center" colspan="3">&nbsp;</TD>
    <TD width="1%">&nbsp;</TD>
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<TR style="font-size: 8pt" valign="bottom">    <TD width="1%">&nbsp;</TD>

    <TD nowrap align="center">Title of Securities</TD>
    <TD style="border-right: 2px solid #000000">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center" colspan="3">Amount to be</TD>
    <TD style="border-right: 2px solid #000000">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center" colspan="3">Offering</TD>
    <TD style="border-right: 2px solid #000000">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center" colspan="3">Aggregate</TD>
    <TD style="border-right: 2px solid #000000">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center" colspan="3">Amount of</TD>
    <TD width="1%">&nbsp;</TD>
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<TR style="font-size: 8pt" valign="bottom">    <TD width="1%">&nbsp;</TD>

    <TD nowrap align="center">to be Registered</TD>
    <TD style="border-right: 2px solid #000000">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center" colspan="3">Registered</TD>
    <TD style="border-right: 2px solid #000000">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center" colspan="3">Price per Share</TD>
    <TD style="border-right: 2px solid #000000">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center" colspan="3">Offering Price</TD>
    <TD style="border-right: 2px solid #000000">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center" colspan="3">Registration Fee</TD>
    <TD width="1%">&nbsp;</TD>
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                    <TD style="border-top: 2px solid #000000"><DIV style="margin-left:15px; text-indent:-15px">Common Stock, par value $0.01 per share (1)</DIV></TD>
    <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
    <TD style="border-top: 2px solid #000000">&nbsp;</TD>

<TD colspan="3" align="right" style="border-top: 2px solid #000000" nowrap>3,000,000 shares</TD>
    <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
    <TD style="border-top: 2px solid #000000">&nbsp;</TD>
    <TD nowrap align="right" style="border-top: 2px solid #000000">&nbsp;</TD>

<TD align="right" style="border-top: 2px solid #000000">$8.79</TD>
    <TD nowrap style="border-top: 2px solid #000000">(2)</TD>
    <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
    <TD style="border-top: 2px solid #000000">&nbsp;</TD>
    <TD nowrap align="right" style="border-top: 2px solid #000000">&nbsp;</TD>

<TD align="right" style="border-top: 2px solid #000000">$26,370,000</TD>
    <TD nowrap style="border-top: 2px solid #000000">(2)</TD>
    <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
    <TD style="border-top: 2px solid #000000">&nbsp;</TD>
    <TD style="border-top: 2px solid #000000">&nbsp;</TD>

<TD align="right" style="border-top: 2px solid #000000">$2,821.59</TD>
    <TD style="border-top: 2px solid #000000">&nbsp;</TD>
    <TD width="1%" style="border-top: 2px solid #000000">&nbsp;</TD>
</TR>
<TR style="font-size: 1px" valign="bottom">
    <TD nowrap align="left" colspan="22" style="border-top: 3px double #000000">&nbsp;</TD>
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<TR valign="top" style="font-size: 10pt; color: #000000; background: transparent">
    <TD width="3%" nowrap align="left">(1)</TD>
    <TD width="1%">&nbsp;</TD>
    <TD>This Registration Statement shall cover any additional shares of Common Stock which become
issuable under the plan set forth herein by reason of any stock dividend, stock split,
recaptialization or any other similar transaction without receipt of consideration which results in
an increase in the number of shares of the Registrant&#146;s outstanding Common Stock.</TD>
</TR>

<TR>
    <TD style="font-size: 6pt">&nbsp;</TD>
</TR><TR valign="top" style="font-size: 10pt; color: #000000; background: transparent">
    <TD width="3%" nowrap align="left">(2)</TD>
    <TD width="1%">&nbsp;</TD>
    <TD>Estimated solely for the purpose of calculating the amount of the registration fee pursuant to
Rule 457(h) of the Securities Act. The price per share and aggregate offering price are based upon
the average of the high and low prices of Registrant&#146;s Common
Stock on September 29, 2006 as reported
on the Nasdaq Global Market, in accordance with Rule 457(c) of the Securities Act of 1933, as
amended (the &#147;Securities Act&#148;).</TD>
</TR>

</TABLE>
</DIV>

<DIV style="width: 100%; border-bottom: 1pt solid black; margin-top: 10pt; font-size: 1pt">&nbsp;</DIV>
<DIV style="width: 100%; border-bottom: 2pt solid black; font-size: 1pt">&nbsp;</DIV>





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<!-- TOC -->
<A name="toc"><DIV align="CENTER" style="page-break-before:always"><U><B>TABLE OF CONTENTS</B></U></DIV></A>

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<TR><TD colspan="9"><A HREF="#000">PART II. INFORMATION REQUIRED IN THE REGISTRATION STATEMENT</A></TD></TR>
<TR><TD></TD><TD colspan="8"><A HREF="#001">Item&nbsp;3. INCORPORATION OF CERTAIN DOCUMENTS BY REFERENCE</A></TD></TR>
<TR><TD></TD><TD colspan="8"><A HREF="#002">Item&nbsp;6. INDEMNIFICATION OF DIRECTORS AND OFFICERS</A></TD></TR>
<TR><TD></TD><TD colspan="8"><A HREF="#003">Item&nbsp;8. EXHIBITS</A></TD></TR>
<TR><TD></TD><TD colspan="8"><A HREF="#004">Item&nbsp;9. UNDERTAKINGS</A></TD></TR>
<TR><TD colspan="9"><A HREF="#005">SIGNATURES</A></TD></TR>
<TR><TD colspan="9"><A HREF="#006">EXHIBIT INDEX</A></TD></TR>
<TR><TD colspan="9"><A HREF="f23889exv3w1w3.htm">EXHIBIT 3.1.3</A></TD></TR>
<TR><TD colspan="9"><A HREF="f23889exv5w1.htm">EXHIBIT 5.1</A></TD></TR>
<TR><TD colspan="9"><A HREF="f23889exv23w1.htm">EXHIBIT 23.1</A></TD></TR>
<TR><TD colspan="9"><A HREF="f23889exv23w2.htm">EXHIBIT 23.2</A></TD></TR>
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<DIV align="center" style="font-size: 10pt; margin-top: 18pt"><B>EXPLANATORY NOTE</B>
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This Registration Statement on Form S-8 is being filed for the purpose of registering an
additional 3,000,000 shares of the Registrant&#146;s Common Stock to be issued pursuant ot the
Registrant&#146;s 2005 Equity Incentive Plan, as amended.
</DIV>

<!-- link1 "PART II. INFORMATION REQUIRED IN THE REGISTRATION STATEMENT" -->
<DIV align="left"><A NAME="000"></A></DIV>

<DIV align="center" style="font-size: 10pt; margin-top: 18pt"><B>PART II. INFORMATION REQUIRED IN THE REGISTRATION STATEMENT</B>
</DIV>

<!-- link2 "Item&nbsp;3. INCORPORATION OF CERTAIN DOCUMENTS BY REFERENCE" -->
<DIV align="left"><A NAME="001"></A></DIV>

<DIV align="left" style="font-size: 10pt; margin-top: 12pt"><B>Item&nbsp;3. INCORPORATION OF CERTAIN DOCUMENTS BY REFERENCE</B>
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The following documents filed by Solexa, Inc. (the &#147;Registrant&#148;) with the Securities and
Exchange Commission (the &#147;SEC&#148;) are incorporated by reference into this Registration Statement on
Form S-8:
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(a)&nbsp;Registrant&#146;s Annual Report on Form 10-K for the fiscal year ended December&nbsp;31, 2005 (File
No.&nbsp;000-22570), filed with the SEC on March&nbsp;31, 2006;
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(b)&nbsp;Registrant&#146;s Quarterly Report on Form 10-Q for the quarterly period ended June&nbsp;30, 2006
(File No.&nbsp;000-22570), filed with the SEC on August&nbsp;14, 2006;
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(c)&nbsp;Registrant&#146;s Current Reports on Form 8-K (File No.&nbsp;000-22570), filed with the SEC on
January&nbsp;23, 2006; March&nbsp;28, 2006; March&nbsp;30, 2006; May&nbsp;9, 2006; May&nbsp;15, 2006; May&nbsp;22, 2006; June&nbsp;13,
2006; July&nbsp;6, 2006; July&nbsp;19, 2006; August&nbsp;3, 2006; August&nbsp;14, 2006; August&nbsp;31, 2006; September&nbsp;20,
2006 and October 5, 2006.
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(d)&nbsp;Registrant&#146;s Registration Statement on Form S-8 (File No.&nbsp;333-127458) filed with the SEC
on August&nbsp;11, 2005; and
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(e)&nbsp;The description of the Registrant&#146;s Common Stock contained in the Registrant&#146;s
Registration Statement on Form&nbsp;10 (File No.&nbsp;000-22570), filed with the SEC on October&nbsp;5, 1993,
including any amendment or report filed for the purpose of updating such description.
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;All reports and other documents subsequently filed by the Registrant pursuant to Sections
13(a), 13(c), 14 and 15(d) of the Securities Exchange Act of 1934, as amended, prior to the filing
of a post-effective amendment which indicates that all securities offered have been sold or which
deregisters all securities then remaining unsold, shall be deemed to be incorporated by reference
herein and to be a part of this registration statement from the date of the filing of such reports
and documents.
</DIV>

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<DIV align="left"><A NAME="002"></A></DIV>

<DIV align="left" style="font-size: 10pt; margin-top: 12pt"><B>Item&nbsp;6. INDEMNIFICATION OF DIRECTORS AND OFFICERS</B>
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Our Bylaws provide that we will indemnify our directors and executive officers and may
indemnify our other officers, employees and other agents to the fullest extent permitted by
Delaware law. We are also empowered under our Bylaws to enter into indemnification agreements with
our directors and officers and to purchase insurance on behalf of any person whom we are required
or permitted to indemnify. Pursuant to this provision, we have entered into indemnity agreements
with each of our directors and executive officers. We have also obtained directors and officers
insurance to insure such persons against certain liabilities.
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;In addition, our Amended and Restated Certificate of Incorporation, as amended, provides that,
to the fullest extent permitted by Delaware law, our directors will not be liable for monetary
damages for breach of the directors&#146; fiduciary duty of care to Solexa and our stockholders. This
provision in the Amended and Restated Certificate of Incorporation does not eliminate the duty of
care, and in appropriate circumstances, equitable remedies such as an injunction or other forms of
non-monetary relief would remain available under Delaware law. Each director will continue to be
subject to liability for breach of the director&#146;s duty of loyalty to Solexa, for acts or omissions
not in good faith or involving intentional misconduct or knowing violations of law, for acts or
omissions that the director believes to be contrary to the best interests of Solexa or our
stockholders, for any transaction from which the director derived an improper personal benefit, for acts or omissions involving a
reckless disregard for the director&#146;s duty to Solexa or our stockholders when the director was
aware or should have been aware of a risk of
</DIV>

<P align="center" style="font-size: 10pt"><!-- Folio -->1.<!-- /Folio -->
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<DIV style="font-family: 'Times New Roman',Times,serif">
<DIV align="left" style="font-size: 10pt; margin-top: 6pt">serious injury to Solexa or our stockholders, for acts
or omissions that constitute an unexcused pattern of inattention that amounts to an abdication of
the director&#146;s duty to Solexa or our stockholders, for improper transactions between the director
and Solexa and for improper distributions to stockholders and loans to directors and officers. This
provision also does not affect a director&#146;s responsibilities under any other laws such as the
federal securities laws or state or federal environmental laws.
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;No pending material litigation or proceeding involving a director, officer, employee or other
agent of the Registrant as to which indemnification is being sought exists, and we are not aware of
any pending or threatened material litigation that may result in claims for indemnification by any
director, officer, employee or other agent.
</DIV>
<!-- link2 "Item&nbsp;8. EXHIBITS" -->
<DIV align="left"><A NAME="003"></A></DIV>

<DIV align="left" style="font-size: 10pt; margin-top: 12pt"><B>Item&nbsp;8. EXHIBITS</B>
</DIV>

<DIV align="center">
<TABLE style="font-size: 10pt" cellspacing="0" border="0" cellpadding="0" width="100%">
<!-- Begin Table Head -->
<TR valign="bottom">
    <TD width="2%">&nbsp;</TD>
    <TD width="5%">&nbsp;</TD>
    <TD width="93%">&nbsp;</TD>
</TR>
<TR style="font-size: 8pt" valign="bottom">
    <TD nowrap align="left"><B>Exhibit</B></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center">&nbsp;</TD>
</TR>
<TR style="font-size: 8pt" valign="bottom">
    <TD nowrap align="left"><B>Number</B></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center"><B>Description</B></TD>
</TR>

<!-- End Table Head -->
<!-- Begin Table Body -->
<TR valign="bottom"><!-- Blank Space -->
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">3.1
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Amended and Restated Certificate of Incorporation of the Registrant, incorporated by
reference to the indicated exhibit of the Registrant&#146;s Quarterly Report on Form&nbsp;10-Q
for the period ended June&nbsp;30, 2000.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">3.1
</DIV></TD>
    <TD align="left" valign="top">.1</TD>
    <TD align="left" valign="top">Certificate of Amendment to Amended and Restated Certificate of Incorporation of the
Registrant, incorporated by reference to the indicated exhibit of the Registrant&#146;s
Annual Report on Form&nbsp;10-K for the period ended December&nbsp;31, 2002.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">3.1
</DIV></TD>
    <TD align="left" valign="top">.2</TD>
    <TD align="left" valign="top">Certificate of Amendment to Amended and Restated Certificate of Incorporation of the
Registrant, incorporated by reference to the indicated exhibit of the Registrant&#146;s
Current Report on Form&nbsp;8-K filed on March&nbsp;7, 2005.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">3.1
</DIV></TD>
    <TD align="left" valign="top">.3</TD>
    <TD align="left" valign="top">Certificate of Amendment to Amended
and Restated Certificate of Incorporation of the
Registrant dated October 4, 2006.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">3.2
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Bylaws of the Registrant, as amended, incorporated by reference to the indicated
exhibit of the Registrant&#146;s Quarterly Report on Form&nbsp;10-Q for the period ended June&nbsp;30,
2000.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">3.3
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Certificate of Ownership and Merger of Lynx Therapeutics, Inc., incorporated by
reference to the indicated exhibit of the Registrant&#146;s Current Report on Form&nbsp;8-K filed
on March&nbsp;7, 2005.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">4.1
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Form of Common Stock Certificate, incorporated by reference to the indicated exhibit of
the Registrant&#146;s Quarterly Report on Form&nbsp;10-Q for the period ending March&nbsp;31, 2005.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">

<TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">10.63
</DIV></TD>
    <TD align="left" valign="top">&nbsp;</TD>
    <TD align="left" valign="top">2005 Equity Incentive Plan, as amended, incorporated by reference to the indicated
exhibit of the Registrant&#146;s Current Report on
Form&nbsp;8-K filed on October 5, 2006.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">5.1
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Opinion of Cooley Godward LLP<FONT style="font-variant: SMALL-CAPS">.</FONT></TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">23.1
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Consent of Independent Registered Public Accounting Firm.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">23.2
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Consent of Independent Registered Public Accounting Firm.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">23.3
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Consent of Cooley Godward LLP (contained in Exhibit&nbsp;5.1 to this Registration Statement).</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">24.1
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Power of Attorney (contained on the signature page to this Registration Statement).</TD>
</TR>
<!-- End Table Body -->
</TABLE>
</DIV>


<P align="center" style="font-size: 10pt"><!-- Folio -->2.<!-- /Folio -->
</DIV>

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<P><HR noshade><P>
<H5 align="left" style="page-break-before:always"><A HREF="#toc">Table of Contents</A></H5><P>

<DIV style="font-family: 'Times New Roman',Times,serif">
<!-- link2 "Item&nbsp;9. UNDERTAKINGS" -->
<DIV align="left"><A NAME="004"></A></DIV>

<DIV align="left" style="font-size: 10pt; margin-top: 12pt"><B>Item&nbsp;9. UNDERTAKINGS</B>
</DIV>


<DIV style="margin-top: 6pt">
<TABLE width="100%" border="0" cellpadding="0" cellspacing="0" style="font-size: 10pt">

<TR valign="top" style="font-size: 10pt; color: #000000; background: transparent">
    <TD width="1%" nowrap align="left"><B>1.</B></TD>
    <TD width="1%">&nbsp;</TD>
    <TD>The undersigned registrant hereby undertakes:</TD>
</TR>

</TABLE>
</DIV>

<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>(a) </B>To file, during any period in which offers or sales are being made, a post-effective
amendment to this registration statement:
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>(i)&nbsp;</B>To include any prospectus required by section 10(a)(3) of the Securities Act of 1933;
</DIV>

<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>(ii)&nbsp;</B>To reflect in the prospectus any facts or events arising after the effective date of the
registration statement (or the most recent post-effective amendment thereof) which, individually or
in the aggregate, represent a fundamental change in the information set forth in the registration
statement. Notwithstanding the foregoing, any increase or decrease in volume of securities offered
(if the total dollar value of securities offered would not exceed that which was registered) and
any deviation from the low or high end of the estimated maximum offering range may be reflected in
the form of prospectus filed with the Commission pursuant to Rule 424(b) if, in the aggregate, the
changes in volume and price represent no more than 20% change in the maximum aggregate offering
price set forth in the &#147;Calculation of Registration Fee&#148; table in the effective registration
statement.
</DIV>

<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>(iii)&nbsp;</B>To include any material information with respect to the plan of distribution not
previously disclosed in the registration statement or any material change to such information in
the registration statement;
</DIV>

<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<I>Provided, however, </I>that paragraphs (a)(i) and (a)(ii) do not apply if the information required
to be included in a post-effective amendment by those paragraphs is contained in reports filed with
or furnished to the Commission by the registrant pursuant to section 13 or section 15(d) of the
Securities Exchange Act of 1934 that are incorporated by reference herein.
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>(b) </B>That, for the purpose of determining any liability under the Securities Act of 1933, each
such post-effective amendment shall be deemed to be a new registration statement relating to the
securities offered herein, and the offering of such securities at that time shall be deemed to be
the initial <I>bona fide </I>offering thereof.
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>(c) </B>To remove from registration by means of a post-effective amendment any of the securities
being registered which remain unsold at the termination of the offering.
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>(d) </B>That, for the purpose of determining liability of the registrant under the Securities Act
of 1933 to any purchaser in the initial distribution of the securities, the undersigned registrant
undertakes that in a primary offering of securities of the undersigned registrant pursuant to this
registration statement, regardless of the underwriting method used to sell the securities to the
purchaser, if the securities are offered or sold to such purchaser by means of any of the following
communications, the undersigned registrant will be a seller to the purchaser and will be considered
to offer or sell such securities to such purchaser:
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>(i)&nbsp;</B>Any preliminary prospectus or prospectus of the undersigned registrant relating to the
offering required to be filed pursuant to Rule&nbsp;424;
</DIV>

<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>(ii)&nbsp;</B>Any free writing prospectus relating to the offering prepared by or on behalf of the
undersigned registrant or used or referred to by the undersigned registrant;
</DIV>

<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>(iii)&nbsp;</B>The portion of any other free writing prospectus relating to the offering containing
material information about the undersigned registrant or its securities provided by or on behalf of
the undersigned registrant; and
</DIV>

<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>(iv)&nbsp;</B>Any other communication that is an offer in the offering made by the undersigned
registrant to the purchaser.
</DIV>

<P align="center" style="font-size: 10pt"><!-- Folio -->3.<!-- /Folio -->
</DIV>

<!-- PAGEBREAK -->
<P><HR noshade><P>
<H5 align="left" style="page-break-before:always"><A HREF="#toc">Table of Contents</A></H5><P>

<DIV style="font-family: 'Times New Roman',Times,serif">

<DIV style="margin-top: 6pt">
<TABLE width="100%" border="0" cellpadding="0" cellspacing="0" style="font-size: 10pt">

<TR valign="top" style="font-size: 10pt; color: #000000; background: transparent">
    <TD width="1%" nowrap align="left"><B>2.</B></TD>
    <TD width="1%">&nbsp;</TD>
    <TD>The undersigned registrant hereby undertakes that, for purposes of determining any liability
under the Securities Act of 1933, each filing of the registrant&#146;s annual report pursuant to
section 13(a) or section 15(d) of the Securities Exchange Act of 1934 (and, where applicable,
each filing of an employee benefit plan&#146;s annual report pursuant to section 15(d) of the
Securities Exchange Act of 1934) that is incorporated by reference in the registration
statement shall be deemed to be a new registration statement relating to the securities
offered herein, and the offering of such securities at that time shall be deemed to be the
initial <I>bona fide </I>offering thereof.</TD>
</TR>

</TABLE>
</DIV>

<DIV style="margin-top: 6pt">
<TABLE width="100%" border="0" cellpadding="0" cellspacing="0" style="font-size: 10pt">

<TR valign="top" style="font-size: 10pt; color: #000000; background: transparent">
    <TD width="1%" nowrap align="left"><B>3.</B></TD>
    <TD width="1%">&nbsp;</TD>
    <TD>Insofar as indemnification for liabilities arising under the Securities Act of 1933 may be
permitted to directors, officers and controlling persons of the registrant pursuant to the
foregoing provisions, or otherwise, the registrant has been advised that in the opinion of the
Securities and Exchange Commission such indemnification is against public policy as expressed
in the Act and is, therefore, unenforceable. In the event that a claim for indemnification
against such liabilities (other than the payment by the registrant of expenses incurred or
paid by a director, officer or controlling person of the registrant in the successful defense
of any action, suit or proceeding) is asserted by such director, officer or controlling person
in connection with the securities being registered, the registrant will, unless in the opinion
of its counsel the matter has been settled by controlling precedent, submit to a court of
appropriate jurisdiction the question whether such indemnification by it is against public
policy as expressed in the Act and will be governed by the final adjudication of such issue.</TD>
</TR>

</TABLE>
</DIV>

<P align="center" style="font-size: 10pt"><!-- Folio -->4.<!-- /Folio -->
</DIV>

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<H5 align="left" style="page-break-before:always"><A HREF="#toc">Table of Contents</A></H5><P>


<DIV style="font-family: 'Times New Roman',Times,serif">
<!-- link1 "SIGNATURES" -->
<DIV align="left"><A NAME="005"></A></DIV>

<DIV align="center" style="font-size: 10pt; margin-top: 18pt"><B>SIGNATURES</B>
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Pursuant to the requirements of the Securities Act of 1933, as amended, the Registrant
certifies that it has reasonable grounds to believe that it meets all of the requirements for
filing on Form S-8 and has duly caused this Registration Statement to be signed on its behalf by
the undersigned, thereunto duly authorized, in the City of Hayward, State of California, on October
5, 2006.
</DIV>


<TABLE width="100%" border="0" cellspacing="0" cellpadding="0" style="font-size: 10pt">
<TR>
    <TD width="48%">&nbsp;</TD>
    <TD width="1%">&nbsp;</TD>
    <TD width="1%">&nbsp;</TD>
    <TD width="35%">&nbsp;</TD>
    <TD width="15%">&nbsp;</TD>
</TR>
<TR>
    <TD valign="top" align="left">&nbsp;</TD>
    <TD colspan="3" align="left"><FONT style="font-variant: SMALL-CAPS"><B>Solexa, Inc.</B></FONT><BR>
&nbsp;</TD>
    <TD>&nbsp;</TD>
</TR><TR>
    <TD align="left">&nbsp;</TD>
    <TD valign="top">By:&nbsp;&nbsp;</TD>

<TD colspan="2" style="border-bottom: 1px solid #000000" align="left">/s/
Linda M. Rubinstein</TD>
    <TD>&nbsp;</TD>
</TR><TR>
    <TD align="left">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD colspan="2" align="left"><FONT style="font-variant: SMALL-CAPS">Linda M. Rubinstein</FONT>&nbsp;</TD>
    <TD>&nbsp;</TD>
</TR><TR>
    <TD align="left">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD colspan="2" align="left">Vice President and Chief Financial Officer&nbsp;</TD>
    <TD>&nbsp;</TD>
</TR>
<TR>
    <TD colspan="5">&nbsp;</TD>
</TR>
</TABLE>


<P align="center" style="font-size: 10pt"><!-- Folio -->5.<!-- /Folio -->
</DIV>

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<P><HR noshade><P>
<H5 align="left" style="page-break-before:always"><A HREF="#toc">Table of Contents</A></H5><P>


<DIV style="font-family: 'Times New Roman',Times,serif">

<DIV align="center" style="font-size: 10pt; margin-top: 18pt"><B>POWER OF ATTORNEY</B>
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<FONT style="font-variant: SMALL-CAPS"><B>Know All Persons By These Presents</B>,</FONT> that each person whose signature appears below
constitutes and appoints John West and Linda M. Rubinstein, and each or any one of them, his true
and lawful attorney-in-fact and agent, with full power of substitution and resubstitution, for him
and in his name, place and stead, in any and all capacities, to sign any and all amendments
(including post-effective amendments) to this Registration Statement, and to file the same, with
all exhibits thereto, and other documents in connection therewith, with the Securities and Exchange
Commission, granting unto said attorneys-in-fact and agents, and each of them, full power and
authority to do and perform each and every act and thing requisite and necessary to be done in
connection therewith, as fully to all intents and purposes as he might or could do in person,
hereby ratifying and confirming all that said attorneys-in-fact and agents, or any of them, or
their or his substitutes or substitute, may lawfully do or cause to be done by virtue hereof.
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Pursuant to the requirements of the Securities Act of 1933, this Registration Statement has
been signed by the following persons in the capacities and on the dates indicated.
</DIV>

<DIV align="center">
<TABLE style="font-size: 10pt" cellspacing="0" border="0" cellpadding="0" width="100%">
<!-- Begin Table Head -->
<TR valign="bottom">
    <TD width="35%">&nbsp;</TD>
    <TD width="10%">&nbsp;</TD>
    <TD width="30%">&nbsp;</TD>
    <TD width="10%">&nbsp;</TD>
    <TD width="15%">&nbsp;</TD>
</TR>
<TR style="font-size: 8pt" valign="bottom">
    <TD nowrap align="center"><B>Signature</B></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center"><B>Title</B></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center"><B>Date</B></TD>
</TR>

<!-- End Table Head -->
<!-- Begin Table Body -->
<TR valign="bottom"><!-- Blank Space -->
    <TD align="center" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">

<TD align="center" valign="top"><DIV style="margin-left:0px; text-indent:-0px">/s/ John West
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top" rowspan="2">Chief Executive Officer
and Director (<I>Principal
Executive Officer</I>)
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">October 5, 2006</TD>
</TR>
<TR valign="bottom">
    <TD align="center" valign="top"><DIV style="margin-left:0px; text-indent:-0px"><DIV style="font-size: 1pt; border-top: 1px solid #000000">&nbsp;</DIV>
<FONT style="font-variant: SMALL-CAPS">John West</FONT>
</DIV></TD>
    <TD>&nbsp;</TD>

    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="center" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">

<TD align="center" valign="top"><DIV style="margin-left:0px; text-indent:-0px">/s/
Linda M. Rubinstein
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" rowspan="2" valign="top">Chief Financial Officer
(<I>Principal Financial and
Accounting Officer</I>)
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">October 5, 2006</TD>
</TR>
<TR valign="bottom">
    <TD align="center" valign="top"><DIV style="margin-left:0px; text-indent:-0px"><DIV style="font-size: 1pt; border-top: 1px solid #000000">&nbsp;</DIV>
<FONT style="font-variant: SMALL-CAPS">Linda M. Rubinstein</FONT>
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="center" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">

<TD align="center" valign="top"><DIV style="margin-left:0px; text-indent:-0px">/s/
Stephen D. Allen
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Director
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">October 5, 2006</TD>
</TR>
<TR valign="bottom">
    <TD align="center" valign="top"><DIV style="margin-left:0px; text-indent:-0px"><DIV style="font-size: 1pt; border-top: 1px solid #000000">&nbsp;</DIV>
<FONT style="font-variant: SMALL-CAPS">Stephen D. Allen</FONT>
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="center" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">

<TD align="center" valign="top"><DIV style="margin-left:0px; text-indent:-0px">/s/
A. Blaine Bowman
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Director
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">October 5, 2006</TD>
</TR>
<TR valign="bottom">
    <TD align="center" valign="top"><DIV style="margin-left:0px; text-indent:-0px"><DIV style="font-size: 1pt; border-top: 1px solid #000000">&nbsp;</DIV>
<FONT style="font-variant: SMALL-CAPS">A. Blaine Bowman</FONT>
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="center" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">

<TD align="center" valign="top"><DIV style="margin-left:0px; text-indent:-0px">/s/
Hermann Hauser
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Director
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">October 5, 2006</TD>
</TR>
<TR valign="bottom">
    <TD align="center" valign="top"><DIV style="margin-left:0px; text-indent:-0px"><DIV style="font-size: 1pt; border-top: 1px solid #000000">&nbsp;</DIV>
<FONT style="font-variant: SMALL-CAPS">Hermann Hauser</FONT>
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="center" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">

<TD align="center" valign="top"><DIV style="margin-left:0px; text-indent:-0px">/s/
G. Mason Morfit
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Director
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">October 5, 2006</TD>
</TR>
<TR valign="bottom">
    <TD align="center" valign="top"><DIV style="margin-left:0px; text-indent:-0px"><DIV style="font-size: 1pt; border-top: 1px solid #000000">&nbsp;</DIV>
<FONT style="font-variant: SMALL-CAPS">G. Mason Morfit</FONT>
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="center" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">

<TD align="center" valign="top"><DIV style="margin-left:0px; text-indent:-0px">/s/
Joseph E. Whitters
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Director
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">October 5, 2006</TD>
</TR>
<TR valign="bottom">
    <TD align="center" valign="top"><DIV style="margin-left:0px; text-indent:-0px"><DIV style="font-size: 1pt; border-top: 1px solid #000000">&nbsp;</DIV>
<FONT style="font-variant: SMALL-CAPS">Joseph E. Whitters</FONT>
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="center" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">

<TD align="center" valign="top"><DIV style="margin-left:0px; text-indent:-0px">/s/
Roy A. Whitfield
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Director
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">October 5, 2006</TD>
</TR>
<TR valign="bottom">
    <TD align="center" valign="top"><DIV style="margin-left:0px; text-indent:-0px"><DIV style="font-size: 1pt; border-top: 1px solid #000000">&nbsp;</DIV>
<FONT style="font-variant: SMALL-CAPS">Roy A. Whitfield</FONT>
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
<!-- End Table Body -->
</TABLE>
</DIV>


<P align="center" style="font-size: 10pt"><!-- Folio -->6.<!-- /Folio -->
</DIV>

<!-- PAGEBREAK -->
<P><HR noshade><P>
<H5 align="left" style="page-break-before:always"><A HREF="#toc">Table of Contents</A></H5><P>

<DIV style="font-family: 'Times New Roman',Times,serif">
<!-- link1 "EXHIBIT INDEX" -->
<DIV align="left"><A NAME="006"></A></DIV>

<DIV align="center" style="font-size: 10pt; margin-top: 18pt"><B>EXHIBIT INDEX</B>
</DIV>

<DIV align="center">
<TABLE style="font-size: 10pt" cellspacing="0" border="0" cellpadding="0" width="100%">
<!-- Begin Table Head -->
<TR valign="bottom">
    <TD width="2%">&nbsp;</TD>
    <TD width="5%">&nbsp;</TD>
    <TD width="93%">&nbsp;</TD>
</TR>
<TR style="font-size: 8pt" valign="bottom">
    <TD nowrap align="left"><B>Exhibit</B></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center">&nbsp;</TD>
</TR>
<TR style="font-size: 8pt" valign="bottom">
    <TD nowrap align="left"><B>Number</B></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center"><B>Description</B></TD>
</TR>

<!-- End Table Head -->
<!-- Begin Table Body -->
<TR valign="bottom"><!-- Blank Space -->
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">3.1
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Amended and Restated Certificate of Incorporation of the Registrant, incorporated by
reference to the indicated exhibit of the Registrant&#146;s Quarterly Report on Form&nbsp;10-Q
for the period ended June&nbsp;30, 2000.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">3.1
</DIV></TD>
    <TD align="left" valign="top">.1</TD>
    <TD align="left" valign="top">Certificate of Amendment to Amended and Restated Certificate of Incorporation of the
Registrant, incorporated by reference to the indicated exhibit of the Registrant&#146;s
Annual Report on Form&nbsp;10-K for the period ended December&nbsp;31, 2002.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">3.1
</DIV></TD>
    <TD align="left" valign="top">.2</TD>
    <TD align="left" valign="top">Certificate of Amendment to Amended and Restated Certificate of Incorporation of the
Registrant, incorporated by reference to the indicated exhibit of the Registrant&#146;s
Current Report on Form&nbsp;8-K filed on March&nbsp;7, 2005.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">3.1
</DIV></TD>
    <TD align="left" valign="top">.3</TD>
    <TD align="left" valign="top">Certificate of Amendment to Amended
and Restated Certificate of Incorporation of the
Registrant dated October 4, 2006.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">3.2
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Bylaws of the Registrant, as amended, incorporated by reference to the indicated
exhibit of the Registrant&#146;s Quarterly Report on Form&nbsp;10-Q for the period ended June&nbsp;30,
2000.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">3.3
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Certificate of Ownership and Merger of Lynx Therapeutics, Inc., incorporated by
reference to the indicated exhibit of the Registrant&#146;s Current Report on Form&nbsp;8-K filed
on March&nbsp;7, 2005.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">4.1
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Form of Common Stock Certificate, incorporated by reference to the indicated exhibit of
the Registrant&#146;s Quarterly Report on Form&nbsp;10-Q for the period ending March&nbsp;31, 2005.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">5.1
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Opinion of Cooley Godward LLP.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">

<TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">10.63</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">2005 Equity Incentive Plan, as amended, incorporated by reference to the indicated
exhibit of the Registrant&#146;s Current Report on
Form&nbsp;8-K filed on October 5, 2006.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">23.1
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Consent of Independent Registered Public Accounting Firm.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">23.2
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Consent of Independent Registered Public Accounting Firm.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">23.3
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Consent of Cooley Godward LLP (contained in Exhibit&nbsp;5.1 to this Registration Statement).</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD align="right" valign="top"><DIV style="margin-left:0px; text-indent:-0px">24.1
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Power of Attorney (contained on the signature page to this Registration Statement).</TD>
</TR>
<!-- End Table Body -->
</TABLE>
</DIV>


<P align="center" style="font-size: 10pt"><!-- Folio -->7.<!-- /Folio -->
</DIV>

</BODY>
</HTML>
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sv8
Table of Contents
As filed with the Securities and Exchange Commission on October 5, 2006
Registration No. 333-
UNITED STATES SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549
FORM S-8
REGISTRATION STATEMENT
UNDER
THE SECURITIES ACT OF 1933
SOLEXA, INC.
(Exact name of registrant as specified in its charter)
Delaware
94-3161073
(State of Incorporation)
(I.R.S. Employer Identification No.)
25861 Industrial Blvd.
Hayward, California 94545
(Address of principal executive offices)
2005 Equity Incentive Plan
(Full title of the plan)
John West
Chief Executive Officer
Solexa, Inc.
25861 Industrial Blvd.
Hayward, California 94545
(510) 670-9300
(Name, address, including zip code, and telephone number, including area code, of agent for service)
COPIES TO:
James C. Kitch, Esq.
Cooley Godward LLP
Five Palo Alto Square
3000 El Camino Real
Palo Alto, CA 94306-2155
(650) 843-5000
CALCULATION OF REGISTRATION FEE
Proposed Maximum
Proposed Maximum
Title of Securities
Amount to be
Offering
Aggregate
Amount of
to be Registered
Registered
Price per Share
Offering Price
Registration Fee
Common Stock, par value $0.01 per share (1)
3,000,000 shares
$8.79
(2)
$26,370,000
(2)
$2,821.59
(1)
This Registration Statement shall cover any additional shares of Common Stock which become
issuable under the plan set forth herein by reason of any stock dividend, stock split,
recaptialization or any other similar transaction without receipt of consideration which results in
an increase in the number of shares of the Registrant's outstanding Common Stock.
(2)
Estimated solely for the purpose of calculating the amount of the registration fee pursuant to
Rule 457(h) of the Securities Act. The price per share and aggregate offering price are based upon
the average of the high and low prices of Registrant's Common
Stock on September 29, 2006 as reported
on the Nasdaq Global Market, in accordance with Rule 457(c) of the Securities Act of 1933, as
amended (the "Securities Act").
TABLE OF CONTENTS
PART II. INFORMATION REQUIRED IN THE REGISTRATION STATEMENT
Item 3. INCORPORATION OF CERTAIN DOCUMENTS BY REFERENCE
Item 6. INDEMNIFICATION OF DIRECTORS AND OFFICERS
Item 8. EXHIBITS
Item 9. UNDERTAKINGS
SIGNATURES
EXHIBIT INDEX
EXHIBIT 3.1.3
EXHIBIT 5.1
EXHIBIT 23.1
EXHIBIT 23.2
Table of Contents
EXPLANATORY NOTE
This Registration Statement on Form S-8 is being filed for the purpose of registering an
additional 3,000,000 shares of the Registrant's Common Stock to be issued pursuant ot the
Registrant's 2005 Equity Incentive Plan, as amended.
PART II. INFORMATION REQUIRED IN THE REGISTRATION STATEMENT
Item 3. INCORPORATION OF CERTAIN DOCUMENTS BY REFERENCE
The following documents filed by Solexa, Inc. (the "Registrant") with the Securities and
Exchange Commission (the "SEC") are incorporated by reference into this Registration Statement on
Form S-8:
(a) Registrant's Annual Report on Form 10-K for the fiscal year ended December 31, 2005 (File
No. 000-22570), filed with the SEC on March 31, 2006;
(b) Registrant's Quarterly Report on Form 10-Q for the quarterly period ended June 30, 2006
(File No. 000-22570), filed with the SEC on August 14, 2006;
(c) Registrant's Current Reports on Form 8-K (File No. 000-22570), filed with the SEC on
January 23, 2006; March 28, 2006; March 30, 2006; May 9, 2006; May 15, 2006; May 22, 2006; June 13,
2006; July 6, 2006; July 19, 2006; August 3, 2006; August 14, 2006; August 31, 2006; September 20,
2006 and October 5, 2006.
(d) Registrant's Registration Statement on Form S-8 (File No. 333-127458) filed with the SEC
on August 11, 2005; and
(e) The description of the Registrant's Common Stock contained in the Registrant's
Registration Statement on Form 10 (File No. 000-22570), filed with the SEC on October 5, 1993,
including any amendment or report filed for the purpose of updating such description.
All reports and other documents subsequently filed by the Registrant pursuant to Sections
13(a), 13(c), 14 and 15(d) of the Securities Exchange Act of 1934, as amended, prior to the filing
of a post-effective amendment which indicates that all securities offered have been sold or which
deregisters all securities then remaining unsold, shall be deemed to be incorporated by reference
herein and to be a part of this registration statement from the date of the filing of such reports
and documents.
Item 6. INDEMNIFICATION OF DIRECTORS AND OFFICERS
Our Bylaws provide that we will indemnify our directors and executive officers and may
indemnify our other officers, employees and other agents to the fullest extent permitted by
Delaware law. We are also empowered under our Bylaws to enter into indemnification agreements with
our directors and officers and to purchase insurance on behalf of any person whom we are required
or permitted to indemnify. Pursuant to this provision, we have entered into indemnity agreements
with each of our directors and executive officers. We have also obtained directors and officers
insurance to insure such persons against certain liabilities.
In addition, our Amended and Restated Certificate of Incorporation, as amended, provides that,
to the fullest extent permitted by Delaware law, our directors will not be liable for monetary
damages for breach of the directors' fiduciary duty of care to Solexa and our stockholders. This
provision in the Amended and Restated Certificate of Incorporation does not eliminate the duty of
care, and in appropriate circumstances, equitable remedies such as an injunction or other forms of
non-monetary relief would remain available under Delaware law. Each director will continue to be
subject to liability for breach of the director's duty of loyalty to Solexa, for acts or omissions
not in good faith or involving intentional misconduct or knowing violations of law, for acts or
omissions that the director believes to be contrary to the best interests of Solexa or our
stockholders, for any transaction from which the director derived an improper personal benefit, for acts or omissions involving a
reckless disregard for the director's duty to Solexa or our stockholders when the director was
aware or should have been aware of a risk of
1.
Table of Contents
serious injury to Solexa or our stockholders, for acts
or omissions that constitute an unexcused pattern of inattention that amounts to an abdication of
the director's duty to Solexa or our stockholders, for improper transactions between the director
and Solexa and for improper distributions to stockholders and loans to directors and officers. This
provision also does not affect a director's responsibilities under any other laws such as the
federal securities laws or state or federal environmental laws.
No pending material litigation or proceeding involving a director, officer, employee or other
agent of the Registrant as to which indemnification is being sought exists, and we are not aware of
any pending or threatened material litigation that may result in claims for indemnification by any
director, officer, employee or other agent.
Item 8. EXHIBITS
Exhibit
Number
Description
3.1
Amended and Restated Certificate of Incorporation of the Registrant, incorporated by
reference to the indicated exhibit of the Registrant's Quarterly Report on Form 10-Q
for the period ended June 30, 2000.
3.1
.1
Certificate of Amendment to Amended and Restated Certificate of Incorporation of the
Registrant, incorporated by reference to the indicated exhibit of the Registrant's
Annual Report on Form 10-K for the period ended December 31, 2002.
3.1
.2
Certificate of Amendment to Amended and Restated Certificate of Incorporation of the
Registrant, incorporated by reference to the indicated exhibit of the Registrant's
Current Report on Form 8-K filed on March 7, 2005.
3.1
.3
Certificate of Amendment to Amended
and Restated Certificate of Incorporation of the
Registrant dated October 4, 2006.
3.2
Bylaws of the Registrant, as amended, incorporated by reference to the indicated
exhibit of the Registrant's Quarterly Report on Form 10-Q for the period ended June 30,
2000.
3.3
Certificate of Ownership and Merger of Lynx Therapeutics, Inc., incorporated by
reference to the indicated exhibit of the Registrant's Current Report on Form 8-K filed
on March 7, 2005.
4.1
Form of Common Stock Certificate, incorporated by reference to the indicated exhibit of
the Registrant's Quarterly Report on Form 10-Q for the period ending March 31, 2005.
10.63
2005 Equity Incentive Plan, as amended, incorporated by reference to the indicated
exhibit of the Registrant's Current Report on
Form 8-K filed on October 5, 2006.
5.1
Opinion of Cooley Godward LLP
.
23.1
Consent of Independent Registered Public Accounting Firm.
23.2
Consent of Independent Registered Public Accounting Firm.
23.3
Consent of Cooley Godward LLP (contained in Exhibit 5.1 to this Registration Statement).
24.1
Power of Attorney (contained on the signature page to this Registration Statement).
2.
Table of Contents
Item 9. UNDERTAKINGS
1.
The undersigned registrant hereby undertakes:
(a)
To file, during any period in which offers or sales are being made, a post-effective
amendment to this registration statement:
(i)
To include any prospectus required by section 10(a)(3) of the Securities Act of 1933;
(ii)
To reflect in the prospectus any facts or events arising after the effective date of the
registration statement (or the most recent post-effective amendment thereof) which, individually or
in the aggregate, represent a fundamental change in the information set forth in the registration
statement. Notwithstanding the foregoing, any increase or decrease in volume of securities offered
(if the total dollar value of securities offered would not exceed that which was registered) and
any deviation from the low or high end of the estimated maximum offering range may be reflected in
the form of prospectus filed with the Commission pursuant to Rule 424(b) if, in the aggregate, the
changes in volume and price represent no more than 20% change in the maximum aggregate offering
price set forth in the "Calculation of Registration Fee" table in the effective registration
statement.
(iii)
To include any material information with respect to the plan of distribution not
previously disclosed in the registration statement or any material change to such information in
the registration statement;
Provided, however,
that paragraphs (a)(i) and (a)(ii) do not apply if the information required
to be included in a post-effective amendment by those paragraphs is contained in reports filed with
or furnished to the Commission by the registrant pursuant to section 13 or section 15(d) of the
Securities Exchange Act of 1934 that are incorporated by reference herein.
(b)
That, for the purpose of determining any liability under the Securities Act of 1933, each
such post-effective amendment shall be deemed to be a new registration statement relating to the
securities offered herein, and the offering of such securities at that time shall be deemed to be
the initial
bona fide
offering thereof.
(c)
To remove from registration by means of a post-effective amendment any of the securities
being registered which remain unsold at the termination of the offering.
(d)
That, for the purpose of determining liability of the registrant under the Securities Act
of 1933 to any purchaser in the initial distribution of the securities, the undersigned registrant
undertakes that in a primary offering of securities of the undersigned registrant pursuant to this
registration statement, regardless of the underwriting method used to sell the securities to the
purchaser, if the securities are offered or sold to such purchaser by means of any of the following
communications, the undersigned registrant will be a seller to the purchaser and will be considered
to offer or sell such securities to such purchaser:
(i)
Any preliminary prospectus or prospectus of the undersigned registrant relating to the
offering required to be filed pursuant to Rule 424;
(ii)
Any free writing prospectus relating to the offering prepared by or on behalf of the
undersigned registrant or used or referred to by the undersigned registrant;
(iii)
The portion of any other free writing prospectus relating to the offering containing
material information about the undersigned registrant or its securities provided by or on behalf of
the undersigned registrant; and
(iv)
Any other communication that is an offer in the offering made by the undersigned
registrant to the purchaser.
3.
Table of Contents
2.
The undersigned registrant hereby undertakes that, for purposes of determining any liability
under the Securities Act of 1933, each filing of the registrant's annual report pursuant to
section 13(a) or section 15(d) of the Securities Exchange Act of 1934 (and, where applicable,
each filing of an employee benefit plan's annual report pursuant to section 15(d) of the
Securities Exchange Act of 1934) that is incorporated by reference in the registration
statement shall be deemed to be a new registration statement relating to the securities
offered herein, and the offering of such securities at that time shall be deemed to be the
initial
bona fide
offering thereof.
3.
Insofar as indemnification for liabilities arising under the Securities Act of 1933 may be
permitted to directors, officers and controlling persons of the registrant pursuant to the
foregoing provisions, or otherwise, the registrant has been advised that in the opinion of the
Securities and Exchange Commission such indemnification is against public policy as expressed
in the Act and is, therefore, unenforceable. In the event that a claim for indemnification
against such liabilities (other than the payment by the registrant of expenses incurred or
paid by a director, officer or controlling person of the registrant in the successful defense
of any action, suit or proceeding) is asserted by such director, officer or controlling person
in connection with the securities being registered, the registrant will, unless in the opinion
of its counsel the matter has been settled by controlling precedent, submit to a court of
appropriate jurisdiction the question whether such indemnification by it is against public
policy as expressed in the Act and will be governed by the final adjudication of such issue.
4.
Table of Contents
SIGNATURES
Pursuant to the requirements of the Securities Act of 1933, as amended, the Registrant
certifies that it has reasonable grounds to believe that it meets all of the requirements for
filing on Form S-8 and has duly caused this Registration Statement to be signed on its behalf by
the undersigned, thereunto duly authorized, in the City of Hayward, State of California, on October
5, 2006.
Solexa, Inc.
By:
/s/
Linda M. Rubinstein
Linda M. Rubinstein
Vice President and Chief Financial Officer
5.
Table of Contents
POWER OF ATTORNEY
Know All Persons By These Presents
,
that each person whose signature appears below
constitutes and appoints John West and Linda M. Rubinstein, and each or any one of them, his true
and lawful attorney-in-fact and agent, with full power of substitution and resubstitution, for him
and in his name, place and stead, in any and all capacities, to sign any and all amendments
(including post-effective amendments) to this Registration Statement, and to file the same, with
all exhibits thereto, and other documents in connection therewith, with the Securities and Exchange
Commission, granting unto said attorneys-in-fact and agents, and each of them, full power and
authority to do and perform each and every act and thing requisite and necessary to be done in
connection therewith, as fully to all intents and purposes as he might or could do in person,
hereby ratifying and confirming all that said attorneys-in-fact and agents, or any of them, or
their or his substitutes or substitute, may lawfully do or cause to be done by virtue hereof.
Pursuant to the requirements of the Securities Act of 1933, this Registration Statement has
been signed by the following persons in the capacities and on the dates indicated.
Signature
Title
Date
/s/ John West
Chief Executive Officer
and Director (
Principal
Executive Officer
)
October 5, 2006
John West
/s/
Linda M. Rubinstein
Chief Financial Officer
(
Principal Financial and
Accounting Officer
)
October 5, 2006
Linda M. Rubinstein
/s/
Stephen D. Allen
Director
October 5, 2006
Stephen D. Allen
/s/
A. Blaine Bowman
Director
October 5, 2006
A. Blaine Bowman
/s/
Hermann Hauser
Director
October 5, 2006
Hermann Hauser
/s/
G. Mason Morfit
Director
October 5, 2006
G. Mason Morfit
/s/
Joseph E. Whitters
Director
October 5, 2006
Joseph E. Whitters
/s/
Roy A. Whitfield
Director
October 5, 2006
Roy A. Whitfield
6.
Table of Contents
EXHIBIT INDEX
Exhibit
Number
Description
3.1
Amended and Restated Certificate of Incorporation of the Registrant, incorporated by
reference to the indicated exhibit of the Registrant's Quarterly Report on Form 10-Q
for the period ended June 30, 2000.
3.1
.1
Certificate of Amendment to Amended and Restated Certificate of Incorporation of the
Registrant, incorporated by reference to the indicated exhibit of the Registrant's
Annual Report on Form 10-K for the period ended December 31, 2002.
3.1
.2
Certificate of Amendment to Amended and Restated Certificate of Incorporation of the
Registrant, incorporated by reference to the indicated exhibit of the Registrant's
Current Report on Form 8-K filed on March 7, 2005.
3.1
.3
Certificate of Amendment to Amended
and Restated Certificate of Incorporation of the
Registrant dated October 4, 2006.
3.2
Bylaws of the Registrant, as amended, incorporated by reference to the indicated
exhibit of the Registrant's Quarterly Report on Form 10-Q for the period ended June 30,
2000.
3.3
Certificate of Ownership and Merger of Lynx Therapeutics, Inc., incorporated by
reference to the indicated exhibit of the Registrant's Current Report on Form 8-K filed
on March 7, 2005.
4.1
Form of Common Stock Certificate, incorporated by reference to the indicated exhibit of
the Registrant's Quarterly Report on Form 10-Q for the period ending March 31, 2005.
5.1
Opinion of Cooley Godward LLP.
10.63
2005 Equity Incentive Plan, as amended, incorporated by reference to the indicated
exhibit of the Registrant's Current Report on
Form 8-K filed on October 5, 2006.
23.1
Consent of Independent Registered Public Accounting Firm.
23.2
Consent of Independent Registered Public Accounting Firm.
23.3
Consent of Cooley Godward LLP (contained in Exhibit 5.1 to this Registration Statement).
24.1
Power of Attorney (contained on the signature page to this Registration Statement).
7.