Document:

Seventh Amendment and Restated Registration Rights Agreement

 Exhibit 4.2 
 NIMBLEGEN SYSTEMS, INC. 
 SEVENTH AMENDED AND RESTATED 
 REGISTRATION RIGHTS AGREEMENT 
 January 25, 2007 

 Table of Contents 
  

							
	 	 	 	 	 	  	Page
	 1.
	 	 DEFINED TERMS.
	  	2
			
	 2.
	 	 REGISTRATION RIGHTS.
	  	3
		 	 2.1
	 	 Demand Registration.
	  	3
		 	 2.2
	 	 Piggyback Registrations.
	  	6
		 	 2.3
	 	 Form S-3 Registration.
	  	7
		 	 2.4
	 	 Expenses of Registration.
	  	8
		 	 2.5
	 	 Obligations of the Company.
	  	9
		 	 2.6
	 	 Termination of Registration Rights.
	  	10
		 	 2.7
	 	 Delay of Registration; Furnishing Information.
	  	10
		 	 2.8
	 	 Indemnification.
	  	11
		 	 2.9
	 	 Assignment of Registration Rights.
	  	13
		 	 2.10
	 	 Rule 144 Reporting.
	  	13
			
	 3.
	 	 MISCELLANEOUS.
	  	14
		 	 3.1
	 	 Governing Law.
	  	14
		 	 3.2
	 	 Survival.
	  	14
		 	 3.3
	 	 Successors and Assigns.
	  	14
		 	 3.4
	 	 Entire Agreement.
	  	14
		 	 3.5
	 	 Severability.
	  	14
		 	 3.6
	 	 Amendment and Waiver.
	  	14
		 	 3.7
	 	 Delays or Omissions.
	  	15
		 	 3.8
	 	 Notices.
	  	15
		 	 3.9
	 	 Attorneys’ Fees.
	  	16
		 	 3.10
	 	 Titles and Subtitles.
	  	16
		 	 3.11
	 	 Counterparts, Facsimile Signatures.
	  	16
		 	 3.12
	 	 English as Official Language.
	  	16
		 	 3.13
	 	 Dispute Resolution.
	  	16
		 	 3.14
	 	 References to Dollars.
	  	16
		 	 3.15
	 	 Effective Date.
	  	16

 NIMBLEGEN SYSTEMS, INC. 
 SEVENTH AMENDED AND RESTATED 
 REGISTRATION RIGHTS AGREEMENT 
 This SEVENTH AMENDED AND RESTATED REGISTRATION RIGHTS AGREEMENT (this “Agreement”) is dated as of January 25, 2007 by and among NIMBLEGEN
SYSTEMS, INC., a Delaware corporation (the “Company”), and the individuals and entities listed on the signature pages hereof, and any other individuals or entities that may execute a counterpart signature page to this Agreement subsequent
to the date hereof (collectively, the parties hereto and such other persons or entities are referred to herein as the “Preferred Stockholders”), and amends and restates the Sixth Amended and Restated Registration Rights Agreement dated as
of December 22, 2006 (the “Amended Agreement”), by and among the Company and the individuals and entities listed on the signature pages thereof and any other individuals or entities that may have executed a counterpart signature page
thereto. 
 RECITALS 
 WHEREAS,
on or about September 28, 2004 or December 8, 2006, the Company issued shares of its Series E Preferred Stock to certain of the Preferred Stockholders who own Series E Preferred Stock in the Company and who are listed on
Exhibit A attached hereto as Series E Preferred Stockholders (collectively, the “Series E Preferred Stockholders”) pursuant to a Series E Preferred Stock Exchange Agreement dated September 28, 2004 (the
“Series E Preferred Stock Exchange Agreement”) or pursuant to the Company’s Sixth Amended and Restated Certificate of Incorporation (the “Recapitalization Charter Amendment”), as the case may be; 
 WHEREAS, on or about December 8, 2006, the Company issued shares of its Series F Preferred Stock to certain of the Preferred Stockholders who
own Series F Preferred Stock in the Company and who are listed on Exhibit A attached hereto as Series F Preferred Stockholders (collectively, the “Series F Preferred Stockholders”) pursuant to the Recapitalization
Charter Amendment and in respect of shares originally issued on or about September 28, 2004, June 24, 2005, November 23, 2005 pursuant to a Series F Preferred Stock Purchase Agreement dated September 28, 2004 (the “2004
Series F Preferred Stock Purchase Agreement”), respective Subscription Agreements, each dated June 24, 2005 (each a “Subscription Agreement”), a Series F Preferred Stock Purchase Agreement dated November 23, 2005
(the “2005 Series F Preferred Stock Purchase Agreement”), as the case may be, and on or about December 22, 2006, the Company issued shares of its Series F Preferred Stock to certain of the Preferred Stockholders pursuant to
a Series F Preferred Stock Purchase Agreement dated as of December 22, 2006 (the “2006 Series F Preferred Stock Purchase Agreement”); 
 WHEREAS, the Company is and will be issuing shares of its Series F Preferred Stock to Preferred Stockholders listed on Exhibit A attached hereto as Series F Preferred Stockholders (also, collectively, the
“Series F Preferred Stockholders”) in accordance with the terms and conditions of that certain Series F Preferred Stock Purchase Agreement dated as of January 25, 2007 (the “2007 Series F Preferred Stock
Purchase Agreement”); 

 WHEREAS, in connection with these transactions, the Company has granted and agreed to grant registration
rights to the Preferred Stockholders as set forth below in accordance with the terms and conditions set forth below; and 
 WHEREAS, the
Preferred Stockholders desire to set forth their agreements regarding such registration herein and in connection therewith the Company and the Preferred Stockholders desire to amend and restate the Amended Agreement as provided herein. 

NOW, THEREFORE, in consideration of the mutual promises, representations, warranties, covenants and conditions set forth in this Agreement, the
Series E Preferred Stock Exchange Agreement, the Recapitalization Charter Amendment, the 2004 Series F Preferred Stock Purchase Agreement, each Subscription Agreement, the 2005 Series F Preferred Stock Purchase Agreement, the 2006
Series F Preferred Stock Purchase Agreement, and the 2007 Series F Preferred Stock Purchase Agreement and for other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the parties hereto mutually
agree as follows: 
 AGREEMENT 
  

	1.	DEFINED TERMS. 

 As used in this Agreement, the following
terms shall have the following respective meanings: 
 “Exchange Act” means the Securities Exchange Act of 1934, as amended.

 “Form S-3” means such form under the Securities Act in effect on the date hereof or any successor registration form under the
Securities Act subsequently adopted by the SEC which permits inclusion or incorporation of substantial information by reference to other documents filed by the Company with the SEC. 
 “Holder” means any Series E Holder or Series F Holder. 
 “Initial Offering” means the Company’s first firm commitment underwritten public offering of its Common Stock registered under the Securities Act. 
 “Registration Expenses” shall mean all expenses incurred by the Company in complying with Sections 2.1, 2.2, and 2.3 hereof, including,
without limitation, all registration and filing fees, printing expenses, fees and disbursements of counsel for the Company, reasonable fees and disbursements of a single special counsel for the Holders, blue sky fees and expenses and the expense of
any special audits incident to or required by any such registration (but excluding the compensation of regular employees of the Company which shall be paid in any event by the Company, stock transfer taxes, underwriting discounts and commissions).

  

 2 

 “Registrable Securities” means Series E Registrable Securities or Series F
Registrable Securities. Notwithstanding the foregoing, Registrable Securities shall not include any securities sold by a person to the public pursuant to a registration statement or Rule 144 or sold in a private transaction in which the
transferor’s rights under Section 2 are not assigned. 
 “Register,” “registered” and “registration”
refer to a registration effected by preparing and filing a registration statement in compliance with the Securities Act, and the declaration or ordering of effectiveness of such registration statement or document. 
 “SEC” means the Securities and Exchange Commission. 
 “Securities Act” means the Securities Act of 1933, as amended. 
 “Series E Holder”
shall mean any holder of record of Series E Registrable Securities that have not been sold to the public or any assignee of record of any such Series E Registrable Securities in accordance with Section 2.9 hereof. 
 “Series F Holder” shall mean any holder of record of Series F Registrable Securities that have not been sold to the public or any
assignee of record of any such Series F Registrable Securities in accordance with Section 2.9 hereof. 
 “Series E Preferred
Stock” means the $0.001 par value, Series E Preferred Stock of the Company. 
 “Series F Preferred Stock” means the
$0.001 par value, Series F Preferred Stock of the Company. 
 “Series E Registrable Securities” means (1) Common
Stock of the Company issued or issuable upon conversion of the Series E Preferred Stock, and (2) any Common Stock of the Company issued as (or issuable upon the conversion or exercise of any warrant, right or other security which is issued as)
a dividend or other distribution with respect to, or in exchange for or replacement of, such above-described securities. 
 “Series F Registrable Securities” means (1) Common Stock of the Company issued or issuable upon conversion of the Series F Preferred Stock, and (2) any Common Stock of the Company issued as (or issuable upon the
conversion or exercise of any warrant, right or other security which is issued as) a dividend or other distribution with respect to, or in exchange for or replacement of, such above-described securities. 
  

	2.	REGISTRATION RIGHTS. 

 2.1 Demand Registration.

 (a) Subject to the conditions of this Section 2.1, if the Company shall receive a written request from Series F
Holders (the “Initiating Series F Holders”) who in the aggregate hold more than fifty percent (50%) of the Series F Registrable Securities that the Company file a registration statement under the Securities Act covering the
registration with an anticipated aggregate 

  

 3 

 
offering price, net of underwriting discounts and commissions, exceeding $5,000,000, then the Company shall, within thirty (30) days of the receipt
thereof, give written notice of such request to all Holders, and subject to the limitations of this Section 2.1, use its best efforts to effect, as soon as practicable, the registration under the Securities Act of all Series E Registrable
Securities that the Series E Holders request to be registered and all Series F Registrable Securities that the Series F Holders request to be registered. 
 (b) Subject to the conditions of this Section 2.1, if the Company shall receive a written request from Series E Holders (the
“Initiating Series E Holders”) who in the aggregate hold more than fifty percent (50%) of the Series E Registrable Securities that the Company file a registration statement under the Securities Act covering the registration
with an anticipated aggregate offering price, net of underwriting discounts and commissions, exceeding $5,000,000, then the Company shall, within thirty (30) days of the receipt thereof, give written notice of such request to all Holders, and
subject to the limitations of this Section 2.1, use its best efforts to effect, as soon as practicable, the registration under the Securities Act of all Series E Registrable Securities that the Series E Holders request to be
registered and all Series F Registrable Securities that the Series F Holders request to be registered. 
 (c) For
purposes of determining whether a sufficient number of Initiating Series E Holders and Initiating Series F Holders have exercised their rights to demand registration under Sections 2.1(a) or 2.1(b), above, respectively, the number of
Series E Registrable Securities and Series F Registrable Securities may, at the request of the Initiating Series E Holders or the Initiating Series F Holders be aggregated to determine whether Initiating Series E Holders or
Initiating Series F Holders holding in the aggregate at least fifty percent (50%) of all Series E Registrable Securities and Series F Registrable Securities have exercised rights under Sections 2.1(a) or 2.1(b). For purposes
hereof, Initiating Series E Holders and Initiating Series F Holders shall be referred to collectively herein as the “Initiating Holders”. 
 (d) If the Initiating Holders intend to distribute the Registrable Securities covered by their request by means of an underwriting, they
shall so advise the Company as a part of their request made pursuant to this Section 2.1 or any request pursuant to Section 2.3 and the Company shall include such information in the written notice referred to in Sections 2.1(a) or
2.1(b), or Section 2.3(a), as applicable. In such event, the right of any Holder to include its Registrable Securities in such registration shall be conditioned upon such Holder’s participation in such underwriting and the inclusion of
such Holder’s Registrable Securities in the underwriting to the extent provided herein. All Holders proposing to distribute their securities through such underwriting shall enter into an underwriting agreement in customary form with the
underwriter or underwriters selected for such underwriting by a majority in interest of the Initiating Holders (which underwriter or underwriters shall be reasonably acceptable to the Company). Notwithstanding any other provision of this
Section 2.1 or Section 2.3, if the underwriter advises the Company that marketing factors require a limitation of the number of securities to be underwritten (including Registrable Securities), then the Company shall so advise all Holders
of Registrable Securities which would 
  

 4 

 
otherwise be underwritten pursuant hereto, and the number of shares that may be included in the underwriting shall be allocated: (i) first to the
Holders of all Series F Registrable Securities on a pro rata basis based on the number of all Series F Registrable Securities held by all such Holders (including the Initiating Series F Holders); and (ii) second, to the Holders
of all Series E Registrable Securities on a pro rata basis based on the number of Series E Registrable Securities held by all such Holders (including the Initiating Series E Holders); provided, however, that the number of shares of
Registrable Securities to be included in such underwriting and registration shall not be reduced unless all other securities of the Company are first entirely excluded from the underwriting and registration. Any Registrable Securities excluded or
withdrawn from such underwriting shall be withdrawn from the registration. 
 (e) The Company shall not be required to effect
a registration pursuant to this Section 2.1: 
 (1) prior to the earlier of (i) one hundred eighty (180) days
following the effective date of the registration statement pertaining to the Initial Offering; or (ii) September 28, 2007; 
 (2) with respect to requests under Section 2.1(a), after the Company has effected two (2) registrations pursuant to Section 2.1(a) and such registrations have been declared or ordered effective, and with respect to requests
under Section 2.1(b), after the Company has effected two (2) registrations pursuant to Section 2.1(b) and such registrations have been declared or ordered effective; 
 (3) during the period starting with the date sixty (60) days prior to the Company’s estimated date of filing, and ending on the
date six (6) months following the effective date of the registration statement pertaining to a public offering (other than a registration of securities in a Rule 145 transaction or with respect to an employee benefit plan); provided that
the Company makes reasonable good faith efforts to cause such registration statement to become effective; 
 (4) if within
thirty (30) days of receipt of a written request from the Initiating Series F Holders pursuant to Section 2.1(a) and/or the Initiating Series E Holders pursuant to Section 2.1(b), the Company gives notice to the Holders of the
Company’s intention to make a public offering within thirty (30) days; provided, that such right to delay a request shall be exercised by the Company not more than twice in any twelve (12) month period; 
 (5) if the Company shall furnish to Holders requesting a registration statement pursuant to this Section 2.1 a certificate signed by
the Chairman of the Board stating that, in the good faith judgment of the Board of Directors of the Company, it would be seriously detrimental to the Company and its stockholders for such registration statement to be effected at such time, in which
event the Company shall have the right to defer such filing for a period of not more than 

  

 5 

 
ninety (90) days after receipt of the request of the Initiating Holders; provided that such right to delay a request shall be exercised by the Company
not more than once in any twelve (12) month period; or 
 (6) if the Initiating Series E Holders or the Initiating
Series F Holders propose to dispose of shares of Registrable Securities that may be immediately registered on Form S-3 pursuant to a request made pursuant to Section 2.3 below. 
 2.2 Piggyback Registrations. The Company shall notify all Holders in writing at least fifteen (15) days prior to the filing of any
registration statement under the Securities Act for purposes of a public offering of securities of the Company (including, but not limited to, registration statements relating to secondary offerings of securities of the Company, but excluding
registration statements relating to employee benefit plans or with respect to corporate reorganizations or other transactions under Rule 145 of the Securities Act) and will afford each such Holder an opportunity to include in such registration
statement all or part of such Registrable Securities held by such Holder. Each Holder desiring to include in any such registration statement all or any part of the Registrable Securities held by such Holder shall, within fifteen (15) days after
the above-described notice from the Company, so notify the Company in writing. Such notice shall state the intended method of disposition of the Registrable Securities by such Holder. If a Holder decides not to include all of its Registrable
Securities in any registration statement thereafter filed by the Company, such Holder shall nevertheless continue to have the right to include any Registrable Securities in any subsequent registration statement or registration statements as may be
filed by the Company with respect to offerings of its securities, all upon the terms and conditions set forth herein. 
 (a)
If the registration statement under which the Company gives notice under this Section 2.2 is for an underwritten offering, the Company shall so advise the Holders. In such event, the right of any such Holder to be included in a registration
pursuant to this Section 2.2 shall be conditioned upon such Holder’s participation in such underwriting and the inclusion of such Holder’s Registrable Securities in the underwriting to the extent provided herein. All Holders proposing
to distribute their Registrable Securities through such underwriting shall enter into an underwriting agreement in customary form with the underwriter or underwriters selected for such underwriting by the Company. Notwithstanding any other provision
of this Agreement, if the underwriter determines in good faith that marketing factors require a limitation of the number of shares to be underwritten below the aggregate number of shares that the Company, the Holders, and other stockholders of the
Company wish to offer for sale in such offering, the difference shall be applied: (1) first, to reduce the number of shares offered for sale by other stockholders; (2) second, to reduce the number of shares offered for sale by the Holders
to fifteen percent (15%) of the total number of shares registered in the offering; and (3) third, to reduce the number of shares offered by the Company and the number of shares offered by the Holders, pro rata. In no event will shares of
any other selling stockholder be included in such registration which would reduce the number of shares which may be included by Holders without the written consent of Holders of not less than sixty-six and two-thirds percent (66 2/3%) of the
Registrable Securities proposed to be sold in the offering. 
  

 6 

 
If any Holder disapproves of the terms of any such underwriting, such Holder may elect to withdraw therefrom by written notice to the Company and the
underwriter, delivered at least ten (10) business days prior to the effective date of the registration statement. Any Registrable Securities excluded or withdrawn from such underwriting shall be excluded and withdrawn from the registration. For
any Holder which is a partnership or corporation, the partners, retired partners and shareholders of such Holder, or the estates and family members of any such partners and retired partners and any trusts for the benefit of any of the foregoing
person shall be deemed to be a single Holder, and any pro rata reduction with respect to such Holder shall be based upon the aggregate amount of shares carrying registration rights owned by all entities and individuals included in such Holder, as
defined in this sentence. 
 (b) The Company shall have the right to terminate or withdraw any registration initiated by it
under this Section 2.2 prior to the effectiveness of such registration whether or not any Holder has elected to include securities in such registration. The Registration Expenses of such withdrawn registration shall be borne by the Company in
accordance with Section 2.4 hereof. 
  

	2.3	Form S-3 Registration. In case the Company shall receive from any Holder or Holders of Registrable Securities a written request or requests that the Company effect a
registration on Form S-3 (or any successor to Form S-3) or any similar short-form registration statement and any related qualification or compliance with respect to all or a part of the Registrable Securities owned by such Holder or Holders, the
Company will: 

 (a) promptly give written notice of the proposed registration, and any related qualification or
compliance, to all other Holders of Registrable Securities; and 
 (b) as soon as practicable, effect such registration and
all such qualifications and compliances as may be so requested and as would permit or facilitate the sale and distribution of all or such portion of such Holder’s or Holders’ Registrable Securities as are specified in such request,
together with all or such portion of the Registrable Securities of any other Holder or Holders joining in such request as are specified in a written request given within fifteen (15) days after receipt of such written notice from the Company;
provided however, that the Company shall not be obligated to effect any such registration, qualification or compliance pursuant to this Section 2.3: 
 (1) if Form S-3 (or any successor or similar form) is not available for such offering by the Holders; 
 (2) if the Holders, together with the holders of any other securities of the Company entitled to inclusion in such registration, propose to sell Registrable Securities and such other securities (if any) at an
aggregate price to the public of less than $5,000,000; 
 (3) if within thirty (30) days of receipt of the written
request described in the preamble to this Section 2.3, the Company gives notice to the Holder or Holders of the Company’s intention to make a public offering within thirty 
  

 7 

 (30) days; provided, that such right to delay a request shall be exercised by the
Company not more than twice in any twelve (12) month period; 
 (4) during the period starting with the filing of, and
ending on the date six (6) months following the effective date of the registration statement pertaining to a public offering (other than a registration of securities in a Rule 145 transaction or with respect to an employee benefit plan);

 (5) if the Company shall furnish to the Holders a certificate signed by the Chairman of the Board of Directors of the
Company stating that in the good faith judgment of the Board of Directors of the Company, it would be seriously detrimental to the Company and its stockholders for such Form S-3 registration to be effected at such time, in which event the Company
shall have the right to defer the filing of the Form S-3 registration statement for a period of not more than ninety (90) days after receipt of the request of the Holder or Holders under this Section 2.3; provided, that such right to delay
a request shall be exercised by the Company not more than once in any twelve (12) month period; or 
 (6) in any
particular jurisdiction in which the Company would be required to qualify to do business or to execute a general consent to service of process in effecting such registration, qualification or compliance. 
 (c) Subject to the foregoing, the Company shall file a Form S-3 registration statement covering the Registrable Securities and other
securities so requested to be registered as soon as practicable after receipt of the request or requests of the Holders. Registrations effected pursuant to this Section 2.3 shall not be counted as demands for registration or registrations
effected pursuant to Sections 2.1 or 2.2, respectively. 
  

	2.4	Expenses of Registration. Except as specifically provided herein, all Registration Expenses incurred in connection with any registration, qualification or compliance pursuant
to Section 2.1 or any registration under Section 2.2 or Section 2.3 herein shall be borne by the Company. All underwriting discounts and selling commissions incurred in connection with any registrations hereunder shall be borne by the
holders of the securities so registered pro rata on the basis of the number of shares so registered. The Company shall not, however, be required to pay for expenses of any registration proceeding begun pursuant to Section 2.1, the request of
which has been subsequently withdrawn by the Initiating Holders unless (a) the withdrawal is based upon material adverse information concerning the Company of which the Initiating Holders were not aware at the time of such request or
(b) the Holders of a majority of Registrable Securities having the right to request a registration pursuant to Section 2.1 agree to forfeit their right to one (1) requested registration pursuant to Section 2.1, in which event
such right shall be forfeited by all Holders. If the Holders are required to pay the Registration Expenses, such expenses shall be borne by the holders of securities (including Registrable Securities) requesting such registration in proportion to
the number of shares for which registration was requested. If the Company is required to pay the Registration Expenses of a withdrawn offering pursuant to clause (a), above, then the Holders shall not forfeit their rights pursuant to
Section 2.1 to a demand registration. 

  

 8 

 2.5 Obligations of the Company. Whenever required to effect the registration of any Registrable
Securities, the Company shall, as expeditiously as reasonably possible: 
 (a) Prepare and file with the SEC a registration
statement with respect to such Registrable Securities and use all reasonable efforts to cause such registration statement to become effective, and, upon the request of the Holders of a majority of the Registrable Securities registered thereunder,
keep such registration statement effective for up to one hundred twenty (120) days or, if earlier, until the Holder or Holders have completed the distribution related thereto, provided that the Company shall not be required to file, cause to
become effective or maintain the effectiveness of any registration statement that contemplates a distribution of securities on a delayed or continuous basis pursuant to Rule 415 under the Securities Act; 
 (b) Prepare and file with the SEC such amendments and supplements to such registration statement and the prospectus used in connection
with such registration statement as may be necessary to comply with the provisions of the Securities Act with respect to the disposition of all securities covered by such registration statement for the period set forth in paragraph (a), above;

 (c) Furnish to the Holders such number of copies of a prospectus, including a preliminary prospectus, in conformity with
the requirements of the Securities Act, and such other documents as they may reasonably request in order to facilitate the disposition of Registrable Securities owned by them; 
 (d) Use its reasonable best efforts to register and qualify the securities covered by such registration statement under such other
securities or Blue Sky laws of such jurisdictions as shall be reasonably requested by the Holders; provided that the Company shall not be required in connection therewith or as a condition thereto to qualify to do business or to file a general
consent to service of process in any such states or jurisdictions; 
 (e) In the event of any underwritten public offering,
enter into and perform its obligations under an underwriting agreement, in usual and customary form, with the managing underwriter(s) of such offering; provided that each Holder participating in such underwriting shall also enter into and perform
its obligations under such an agreement; 
 (f) Notify each Holder of Registrable Securities covered by such registration
statement at any time when a prospectus relating thereto is required to be delivered under the Securities Act of the happening of any event as a result of which the prospectus included in such registration statement, as then in effect, includes an
untrue statement of a material fact or omits to state a material fact required to be stated therein or necessary to make the statements therein not misleading in the light of the circumstances then existing; 
  

 9 

 (g) Cause all such Registrable Securities registered pursuant hereunder to be listed on
each securities exchange on which similar securities issued by the Company are then listed; 
 (h) Provide a transfer agent
and registrar for all Registrable Securities registered pursuant hereunder and a CUSIP number for all such Registrable Securities, in each case not later than the effective date of such registration; and 
 (i) Use its best efforts to furnish, on the date that such Registrable Securities are delivered to the underwriters for sale, if such
securities are being sold through underwriters, (1) an opinion, dated as of such date, of the counsel representing the Company for the purposes of such registration, in form and substance as is customarily given to underwriters in an
underwritten public offering, addressed to the underwriters, if any, and (2) a letter dated as of such date, from the independent certified public accountants of the Company, in form and substance as is customarily given by independent
certified public accountants to underwriters in an underwritten public offering addressed to the underwriters. The opinion referred to in (1) above and, to the extent consistent with then applicable law and generally accepted accounting
principles and practices, the letter referred to in (2) above also shall be addressed to the Holders requesting registration of Registrable Securities. 
  

	2.6	Termination of Registration Rights. All registration rights granted under this Section 2 shall terminate and be of no further force and effect if (a) the Company
has completed its Initial Offering and is subject to the provisions of the Exchange Act, and (b) all Registrable Securities held by and issuable to such Holder (and its affiliates, partners, former partners, members and former members) may be
sold under Rule 144 during any ninety (90) day period. 

  

	2.7	Delay of Registration; Furnishing Information. 

 (a) No Holder shall have any right to obtain or seek an injunction restraining or otherwise delaying any such registration as the result of any controversy that might arise with respect to the interpretation or
implementation of this Section 2. 
 (b) It shall be a condition precedent to the obligations of the Company to take any
action pursuant to Section 2.1, 2.2 or 2.3 that the selling Holders shall furnish to the Company such information regarding themselves, the Registrable Securities held by them and the intended method of disposition of such securities as shall
be required to effect the registration of their Registrable Securities. 
 (c) The Company shall have no obligation with
respect to any registration requested pursuant to Section 2.1 or Section 2.3 if, due to the operation of Section 2.1(d), the number of shares or the anticipated aggregate offering price of the Registrable Securities to be included in
the registration does not equal or exceed the number of shares or the anticipated aggregate offering price required to originally trigger the Company’s obligation to initiate such registration as specified in Section 2.1 or
Section 2.3, whichever is applicable. 
  

 10 

 2.8 Indemnification. In the event any Registrable Securities are included in a registration
statement under Sections 2.1, 2.2 or 2.3: 
 (a) To the extent permitted by law, the Company will indemnify and hold
harmless each Holder, the partners, officers and directors of each Holder, any underwriter (as defined in the Securities Act) for such Holder and each person, if any, who controls such Holder or underwriter within the meaning of the Securities Act
or the Exchange Act, against any losses, claims, damages, or liabilities (joint or several) to which they may become subject under the Securities Act, the Exchange Act or other federal or state law, insofar as such losses, claims, damages or
liabilities (or actions in respect thereof) arise out of or are based upon any of the following statements, omissions or violations (collectively a “Violation”) by the Company: (1) any untrue statement or alleged untrue statement of a
material fact contained in such registration statement, including any preliminary prospectus or final prospectus contained therein or any amendments or supplements thereto, (2) the omission or alleged omission to state therein a material fact
required to be stated therein or necessary to make the statements therein not misleading, or (3) any violation or alleged violation by the Company of the Securities Act, the Exchange Act, any state securities law or any rule or regulation
promulgated under the Securities Act, the Exchange Act or any state securities law in connection with the offering covered by such registration statement; and the Company will pay as incurred to each such Holder, partner, officer, director,
underwriter or controlling person for any legal or other expenses reasonably incurred by them in connection with investigating or defending any such loss, claim, damage, liability or action; provided however, that the indemnity agreement contained
in this Section 2.8(a) shall not apply to amounts paid in settlement of any such loss, claim, damage, liability or action if such settlement is effected without the consent of the Company, which consent shall not be unreasonably withheld, nor
shall the Company be liable in any such case for any such loss, claim, damage, liability or action to the extent that it arises out of or is based upon a Violation which occurs in reliance upon and in conformity with written information furnished
expressly for use in connection with such registration by such Holder, partner, officer, director, underwriter or controlling person of such Holder. 
 (b) To the extent permitted by law, each Holder will, if Registrable Securities held by such Holder are included in the securities as to which such registration qualifications or compliance is being effected,
indemnify and hold harmless the Company, each of its directors, its officers and each person, if any, who controls the Company within the meaning of the Securities Act, any underwriter and any other Holder selling securities under such registration
statement or any of such other Holder’s partners, directors or officers or any person who controls such Holder, against any losses, claims, damages or liabilities (joint or several) to which the Company or any such director, officer,
controlling person, underwriter or other such Holder, or partner, director, officer or controlling person of such other Holder may become subject under the Securities Act, the Exchange Act or other federal or state law, insofar as such losses,
claims, damages or liabilities (or actions in respect thereto) arise out of or are based upon any Violation, in each case to the extent (and only to the extent) that such Violation occurs in reliance upon and in conformity with written information
furnished by such Holder under an instrument duly executed by such Holder 

  

 11 

 
and stated to be specifically for use in connection with such registration; and each such Holder will pay as incurred any legal or other expenses reasonably
incurred by the Company or any such director, officer, controlling person, underwriter or other Holder, or partner, officer, director or controlling person of such other Holder in connection with investigating or defending any such loss, claim,
damage, liability or action if it is judicially determined that there was such a Violation; provided, however, that the indemnity agreement contained in this Section 2.8(b) shall not apply to amounts paid in settlement of any such loss, claim,
damage, liability or action if such settlement is effected without the consent of the Holder, which consent shall not be unreasonably withheld; provided further, that in no event shall any indemnity under this Section 2.8 exceed the net
proceeds from the offering received by such Holder. 
 (c) Promptly after receipt by an indemnified party under this
Section 2.8 of notice of the commencement of any action (including any governmental action), such indemnified party will, if a claim in respect thereof is to be made against any indemnifying party under this Section 2.8, deliver to the
indemnifying party a written notice of the commencement thereof and the indemnifying party shall have the right to participate in, and, to the extent the indemnifying party so desires, jointly with any other indemnifying party similarly noticed, to
assume the defense thereof with counsel mutually satisfactory to the parties; provided, however, that an indemnified party shall have the right to retain its own counsel, with the fees and expenses to be paid by the indemnifying party, if
representation of such indemnified party by the counsel retained by the indemnifying party would be inappropriate due to actual or potential differing interests between such indemnified party and any other party represented by such counsel in such
proceeding. Without regard to the foregoing, the indemnified party will have an absolute right to participate in such proceeding using separate counsel at its own expense. The failure to deliver written notice to the indemnifying party within a
reasonable time of the commencement of any such action, if materially prejudicial to its ability to defend such action, shall relieve such indemnifying party of any liability to the indemnified party under this Section 2.8, but the omission so
to deliver written notice to the indemnifying party will not relieve it of any liability that it may have to any indemnified party otherwise than under this Section 2.8. 
 (d) If the indemnification provided for in this Section 2.8 is held by a court of competent jurisdiction to be unavailable to an
indemnified party with respect to any losses, claims, damages or liabilities referred to herein, the indemnifying party, in lieu of indemnifying such indemnified party thereunder, shall to the extent permitted by applicable law contribute to the
amount paid or payable by such indemnified party as a result of such loss, claim, damage or liability in such proportion as is appropriate to reflect the relative fault of the indemnifying party on the one hand and of the indemnified party on the
other in connection with the Violation(s) that resulted in such loss, claim, damage or liability, as well as any other relevant equitable considerations. The relative fault of the indemnifying party and of the indemnified party shall be determined
by a court of law by reference to, among other things, whether the untrue or alleged untrue statement of a material fact or the omission to state a material fact relates to information supplied by the indemnifying party or by the indemnified party
and the parties’ relative intent, knowledge, 

  

 12 

 
access to information and opportunity to correct or prevent such statement or omission; provided, that in no event shall any contribution by a Holder
hereunder exceed the net proceeds from the offering received by such Holder. 
 (e) Notwithstanding the foregoing, to the
extent that the provisions on indemnification and contribution contained in the underwriting agreement entered into in connection with the underwritten public offering are in conflict with the foregoing provisions, the provisions in the underwriting
agreement shall control. 
 (f) The obligations of the Company and Holders under this Section 2.8 shall survive
completion of any offering of Registrable Securities in a registration statement and the termination of this agreement. No indemnifying party, in the defense of any such claim or litigation, shall, except with the consent of each indemnified party,
consent to entry of any judgment or enter into any settlement which does not include as an unconditional term thereof the giving by the claimant or plaintiff to such indemnified party of a release from all liability in respect to such claim or
litigation. 
 2.9 Assignment of Registration Rights. The rights to cause the Company to register Registrable Securities pursuant to
this Section 2 may be assigned: (i) by any Holder of Series F Registrable Securities, to any third party, and (ii) by any Holder of Series E Registrable Securities, to any third party, which, in each case, (a) is a
subsidiary, parent, stockholder, general partner, limited partner, retired partner, member or retired member of such Holder, (b) is such Holder’s family member or a trust for the benefit of such Holder or such family member, or (c) an
Affiliate of such Holder; provided, however, that in the case of any transfer under clauses (i) or (ii) above, (a) the transferor shall, within twenty (20) days after such transfer, furnish to the Company written notice of the
name and address of such transferee or assignee and the securities with respect to which such registration rights are being assigned; (b) such transferee shall agree to be subject to all provisions set forth in this Agreement; and (c) such
transferee must not be a person deemed by the Board of Directors of the Company, in its reasonable judgment, to be a competitor or potential competitor of the Company. Otherwise, such rights may not be assigned. For purposes hereof,
“Affiliate” shall mean an entity controlling, controlled by or under common control with a Holder. 
 2.10 Rule 144
Reporting. With a view to making available to the Holders the benefits of certain rules and regulations of the SEC which may permit the sale of the Registrable Securities to the public without registration, the Company agrees to use its best
efforts to: 
 (a) Make and keep public information available, as those terms are understood and defined in SEC Rule 144
or any similar or analogous rule promulgated under the Securities Act, at all times after the effective date of the first registration filed by the Company for an offering of its securities to the general public; 
 (b) File with the SEC, in a timely manner, all reports and other documents required of the Company under the Exchange Act; and 

 

 13 

 (c) So long as a Holder owns any Registrable Securities, furnish to such Holder forthwith
upon request: a written statement by the Company as to its compliance with the reporting requirements of said Rule 144 of the Securities Act and of the Exchange Act (at any time after it has become subject to such reporting requirements); a
copy of the most recent annual or quarterly report of the Company; and such other reports and documents as a Holder may reasonably request in availing itself of any rule or regulation of the SEC allowing it to sell any such securities without
registration. 
  

	3.	MISCELLANEOUS. 

 3.1 Governing Law. This Agreement
shall be governed by and construed under the laws of the State of Wisconsin as applied to agreements among Wisconsin residents entered into and to be performed entirely within Wisconsin. 
 3.2 Survival. The representations, warranties, covenants, and agreements made herein shall survive any investigation made by any Holder and the
closing of the transactions contemplated hereby. All statements as to factual matters contained in any certificate or other instrument delivered by or on behalf of the Company pursuant hereto in connection with the transactions contemplated hereby
shall be deemed to be representations and warranties by the Company hereunder solely as of the date of such certificate or instrument. 
 3.3
Successors and Assigns. Except as otherwise expressly provided herein, the provisions hereof shall inure to the benefit of, and be binding upon, the successors, assigns, heirs, executors, and administrators of the parties hereto and shall
inure to the benefit of and be enforceable by each person who shall be a holder of Registrable Securities from time to time; provided however, that prior to the receipt by the Company of adequate written notice of the transfer of any Registrable
Securities specifying the full name and address of the transferee, the Company may deem and treat the person listed as the holder of such shares in its records as the absolute owner and holder of such shares for all purposes. 
 3.4 Entire Agreement. This Agreement constitutes the full and entire understanding and agreement among the parties with regard to the subjects
hereof and no party shall be liable or bound to any other in any manner by any representations, warranties, covenants and agreements with regard to the subjects hereof except as specifically set forth herein. 
 3.5 Severability. In the event one or more of the provisions of this Agreement should, for any reason, be held to be invalid, illegal or
unenforceable in any respect, such invalidity, illegality, or unenforceability shall not affect any other provisions of this Agreement, and this Agreement shall be construed as if such invalid, illegal or unenforceable provision had never been
contained herein. 
 3.6 Amendment and Waiver. 
 (a) Except as otherwise expressly provided, this Agreement may be amended or modified only upon the written consent of the Company (as
approved by a majority of the members of the Board of Directors then in office), the Holders of more than fifty percent (50%) of the Series E Registrable Securities then outstanding and the Holders of more than fifty percent (50%) of the
Series F Registrable Securities then outstanding. 
  

 14 

 (b) Except as otherwise expressly provided, the obligations of the Company and the rights
of the Holders of Series E Registrable Securities under this Agreement may be waived only with the written consent of the holders of more than fifty percent (50%) of the Series E Registrable Securities then outstanding unless such
waiver is effectuated by virtue of an amendment to this Agreement affecting all Holders equally in proportion to their holdings of Registrable Securities. 
 (c) Except as otherwise expressly provided, the obligations of the Company and the rights of the Holders of Series F Registrable Securities under this Agreement may be waived only with the written consent of the
holders of more than fifty percent (50%) of the Series F Registrable Securities then outstanding unless such waiver is effectuated by virtue of an amendment to this Agreement affecting all Holders equally in proportion to their holdings of
Registrable Securities. 
 (d) Notwithstanding the foregoing, the provisions of this Agreement may not be waived, amended or
otherwise modified in a manner that adversely affects one group of Holders differently from another group of Holders without the written consent of a majority of the shares of Registrable Securities held by the group of Holders so affected.

 (e) Notwithstanding the foregoing, this Agreement may be amended to add as a party any Series E Holder or
Series F Holder to the extent not otherwise a party hereto; provided, however, that such Holder shall have executed a counterpart to this Agreement agreeing to be bound by the terms of this Agreement as a Holder. 
 3.7 Delays or Omissions. It is agreed that no delay or omission to exercise any right, power, or remedy accruing to any Holder, upon any breach,
default or noncompliance of the Company under this Agreement shall impair any such right, power, or remedy, nor shall it be construed to be a waiver of any such breach, default or noncompliance, or any acquiescence therein, or of any similar breach,
default or noncompliance thereafter occurring. It is further agreed that any waiver, permit, consent, or approval of any kind or character on any Holder’s part of any breach, default or noncompliance under the Agreement or any waiver on such
Holder’s part of any provisions or conditions of this Agreement must be in writing and shall be effective only to the extent specifically set forth in such writing. All remedies, either under this Agreement, by law, or otherwise afforded to
Holders, shall be cumulative and not alternative. 
 3.8 Notices. All notices required or permitted hereunder shall be in writing and
shall be deemed effectively given: (a) upon personal delivery to the party to be notified, (b) when sent by confirmed facsimile if sent during normal business hours of the recipient; if not, then on the next business day, (c) five
(5) days after having been sent by registered or certified mail, return receipt requested, postage prepaid, or (d) one (1) day after deposit with a nationally recognized overnight courier, specifying next day delivery, with written
verification of receipt. All communications shall be sent to the party to be notified at the address as set forth on the signature pages hereof or Exhibit A hereto or at such other address as such party may designate by ten (10) days’
advance written notice to the other parties hereto. 
  

 15 

 3.9 Attorneys’ Fees. In the event that any suit or action is instituted to enforce any
provision in this Agreement, the prevailing party in such dispute shall be entitled to recover from the losing party all fees, costs and expenses of enforcing any right of such prevailing party under or with respect to this Agreement, including
without limitation, such reasonable fees and expenses of attorneys and accountants, which shall include, without limitation, all fees, costs and expenses of appeals. 
 3.10 Titles and Subtitles. The titles of the sections and subsections of this Agreement are for convenience of reference only and are not to be considered in construing this Agreement. 
 3.11 Counterparts, Facsimile Signatures. This Agreement may be executed in any number of counterparts, each of which shall be an original, but all
of which together shall constitute one instrument. This Agreement may be executed by facsimile and each facsimile signature will have the same effect as an original signature. 
 3.12 English as Official Language. The parties acknowledge and agree that English shall be the official language for the interpretation of this
Agreement. 
 3.13 Dispute Resolution. Any party to this Agreement who is not a U.S. resident or citizen or is a foreign entity shall
attempt to resolve through negotiation any disputes, controversies or other claims arising out of or in connection with this Agreement with any other party to this Agreement. To the extent that any such disputes, controversies or claims cannot be
resolved as a result of such discussions, such unresolved disputes, controversies and claims shall be settled by arbitration in accordance with the UNCITRAL Arbitration Rules in effect on the date of this Agreement. The appointing authority shall be
the International Chamber of Commerce. The number of arbitrators shall be three (3). The place of arbitration shall be Toronto, Canada. The language to be used in the arbitration shall be English. In connection with the arbitration, the Federal
Rules of Evidence in effect in the United States of America will govern evidentiary questions and the procedural and substantive rules of the State of Wisconsin, United States of America will apply. The parties acknowledge and agree that this
Agreement and all agreements, documents, instruments and certificates delivered in connection herewith (including the Related Agreements) and any award rendered pursuant hereto or thereto shall be governed by the 1958 United Nations Convention on
the Recognition and Enforcement of Foreign Arbitral Awards. In the event of any conflict between the UNCITRAL Arbitration Rules and this clause, this clause shall govern. Judgment upon the award rendered may be entered in any court having
jurisdiction. Application shall be made to such court for judicial acceptance of the award and an order of enforcement as the case may be. 
 3.14 References to Dollars. All references herein to “$” or “Dollars” shall be to United States Dollars. 
 3.15 Effective Date. If the “Closing Date” as defined in the 2007 Series F Preferred Stock Purchase Agreement is not January 25, 2007 but instead a later date not later than February 9, 2007 as provided in
Section 2.1 of the 2007 Series F Preferred 

  

 16 

 
Stock Purchase Agreement, then, notwithstanding the date of January 25, 2007 first written above in this Agreement, this Agreement shall be effective as
of such Closing Date and not as of January 25, 2007. 
  

 17 

 IN WITNESS WHEREOF, the parties hereto have executed this SEVENTH AMENDED AND RESTATED REGISTRATION
RIGHTS AGREEMENT as of the date set forth in the first paragraph hereof. 
  

			
	COMPANY:
	
	NIMBLEGEN SYSTEMS, INC.
		
	By:	 	 /s/ Stanley D. Rose

	Print Name:	 	Stanley D. Rose
	Title:	 	CEO
	
	STOCKHOLDERS:
	
	780 PARTNERS
		
	By:	 	 /s/ Richard J. Bliss

	Print Name:	 	Richard J. Bliss
	Title:	 	Managing Partner
	
	 BAIRD VENTURE PARTNERS I
 LIMITED
PARTNERSHIP

		
	By:	 	Baird Venture Partners Management Company I, LLC, its General Partner
		
	By:	 	 /s/ Peter K. Shagory

	Title:	 	Director
		
		 	  

		 	Frederick R. Blattner

 Signature Page – Seventh Amended And Restated Registration Rights Agreement 

			
	BVP I AFFILIATES FUND LIMITED
PARTNERSHIP
		
	By:	 	Baird Venture Partners Management Company I, LLC, its General Partner
		
	By:	 	 /s/ Peter K. Shagory

	Title	 	Director
	
	FHF PARTNERS
		
	By:	 	 /s/ Mitchell S. Fromstein

	Print Name:	 	Mitchell S. Fromstein
	Title:	 	General Partner
		
		 	 /s/ Roland Green

		 	Roland Green
	
	ICE NINE INVESTMENTS, LLC
		
	By:	 	 /s/ Nicholas Seay

	Print Name:	 	Nicholas Seay
	Title:	 	Managing Member
	
	ITX INTERNATIONAL EQUITY CORPORATION
		
	By:	 	 /s/ Takehito Jimro

	Print Name:	 	Takehito Jimro
	Title:	 	CEO
		
		 	 /s/ Emile Nuwaysir

		 	Emile Nuwaysir
		
		 	 /s/ Frank V. Sica

		 	Frank V. Sica

 Signature Page – Seventh Amended And Restated Registration Rights Agreement 

			
	 SKYLINE VENTURE PARTNERS
 QUALIFIED
PURCHASER FUND II, L.P.

		
	By:	 	Skyline Venture Management II LLC, its General Partner
		
	By:	 	 /s/ John G. Freund

		 	John G. Freund, Managing Director
	
	SKYLINE VENTURE PARTNERS II, L. P.
		
	By:	 	Skyline Venture Management II LLC, its General Partner
		
	By:	 	 /s/ John G. Freund

		 	John G. Freund, Managing Director
	
	SKYLINE EXPANSION FUND, L.P.
		
	By:	 	Skyline Expansion Fund Management, LLC
	Its:	 	General Partner
		
	By:	 	Skyline Venture Management III, LLC
	Its:	 	Managing Member
		
	By:	 	 /s/ John G. Freund

		 	John G. Freund, Managing Director
		
		 	 /s/ David C. Sneider

		 	David C. Sneider
	
	SCHOTT AG
		
	By:	 	 /s/ Gordon Weber

	Print Name:	 	Gordon Weber
	Title:	 	General Counsel

 Signature Page – Seventh Amended And Restated Registration Rights Agreement 

			
	 STATE OF WISCONSIN INVESTMENT
 BOARD

		
	By:	 	 /s/ Christopher D. Prestinacomo

	Print Name:	 	Christopher D. Prestinacomo
	Title:	 	Portfolio Manager
	
	TACTICS II LLC
		
	By:	 	 /s/ Robert J. Palay

	Print Name:	 	Robert J. Palay
	Title:	 	Member
		
		 	 /s/ Michael J. Treble

		 	Michael J. Treble
	
	VENTURE INVESTORS EARLY STAGE FUND III LIMITED PARTNERSHIP
		
	By:	 	Venture Investors LLC, its General Partner
		
	By:	 	 /s/ John Neis

		 	John Neis, Member
	
	WISCONSIN ALUMNI RESEARCH FOUNDATION
		
	By:	 	 /s/ Carrie Thome

	Print Name:	 	Carrie Thome
	Title:	 	Assoc. Dir. of Inv.
		
	By:	 	 /s/ Kenneth Lutz

	Print Name:	 	Kenneth Lutz
	Title:	 	Controller

 Signature Page – Seventh Amended And Restated Registration Rights Agreement 

			
	TEXAS INSTRUMENTS, INCORPORATED
		
	By:	 	  

	Print Name:	 	  

	Title:	 	  

		
		 	 /s/ Harold Garner

		 	Harold Garner
	
	STARTech SEED FUND II, L.P.
		
	By:	 	  

	Print Name:	 	  

	Title:	 	  

		
		 	 /s/ Stanley D. Rose

		 	Stanley D. Rose
		
		 	  

		 	Rodney Wallace
		
		 	 /s/ Steven W. Smith

		 	Steven W. Smith
		
		 	 /s/ Daniel Clutter

		 	Daniel Clutter
	
	CARGILL, INCORPORATED
		
	By:	 	 /s/ James Sayre

	Print Name:	 	James Sayre
	Title:	 	President, Cargill Ventures

 Signature Page – Seventh Amended And Restated Registration Rights Agreement 

			
	 TOPSPIN PARTNERS, L.P.

		
	By:	 	 /s/ Steven J. Winick

	Print Name:	 	Steven J. Winick
	Title:	 	Principal
	
	TOPSPIN ASSOCIATES, L.P.
		
	By:	 	 /s/ Steven J. Winick

	Print Name:	 	Steven J. Winick
	Title:	 	Principal
	
	BROOKSIDE CAPITAL PARTNERS FUND, L.P.
		
	By:	 	 /s/ Ted Pappendick

	Print Name:	 	Ted Pappendick
	Title:	 	Managing Director
	
	ADAGE CAPITAL PARTNERS, L.P.
		
	By:	 	 /s/ D. Labow

	Print Name:	 	D. Labow
	Title:	 	Chief Operating Officer
	
	STARK MASTER FUND LTD.
		
	By:	 	 /s/ Brian H. Davidson

	Print Name:	 	Brian H. Davidson
	Title:	 	 Authorized Signatory of Stark
 Offshore Management
LLC,
 Investment Manager of Stark Master Fund Ltd.

 Signature Page – Seventh Amended and Restated Registration Right Agreement 

			
	 BBT FUND, L.P.

		
	By:	 	BBT Genpar, L.P.
	Its:	 	General Partner
		 	By: FFT-FW, Inc.
		 	Its: General Partner
		
	By:	 	 /s/ William O. Reimann

	Print Name:	 	William O. Reimann
	Title:	 	Vice President
	
	CAP FUND, L.P.
		
	By:	 	Cap Genpar, L.P.
	Its:	 	General Partner
		 	By: Cap-FW, Inc.
		 	Its: General Partner
		
	By:	 	 /s/ William O. Reimann

	Print Name:	 	William O. Reimann
	Title:	 	Vice President
	
	SRI FUND, L.P.
		
	By:	 	SRI Genpar, L.P.
	Its:	 	General Partner
		 	By: BBT-FW, Inc.
		 	Its: General Partner
		
	By:	 	 /s/ William O. Reimann

	Print Name:	 	William O. Reimann
	Title:	 	Vice President
	
	QVT FUND LP
		
	By:	 	QVT Associates GP LLC
	Its:	 	General Partner
		
	By:	 	 /s/ Dan Gold

	Print Name:	 	Dan Gold
	Title:	 	Managing Member
		
	By:	 	 /s/ Nicholas Brumm

	Print Name:	 	Nicholas Brumm
	Title:	 	Managing Member

 Signature Page – Seventh Amended and Restated Registration Right Agreement 

			
	THE BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR UNIVERSITY (SBST-LS)
		
	By:	 	 /s/ Martina Poquet

		 	Martina Poquet, Director-Separate Investments
		
		 	 /s/ J. Warren Huff

		 	J. Warren Huff

 Signature Page – Seventh Amended and Restated Registration Right Agreement 

 EXHIBIT A 
 PREFERRED STOCKHOLDERS 
 Series E and F Preferred Shares: 
  

					
	 Stockholder
	  	Series E	  	Series F
	 780 Partners
 Attn: Richard Bliss
 780 North Water Street
 Milwaukee, WI 53202
 rbliss@gklaw.com
	  	250,298	  	276,014
			
	 Baird Venture Partners, L.P.
 Attn: Peter K.
Shagory
 227 West Monroe, Suite 2200
 Chicago, IL
60606
 pshagory@rwbaird.com
	  	171,565	  	303,105
			
	 Frederick Blattner
 Genetics Building, B10
 445 Henry Mall
 Madison, WI 53706
 fredblattner@scarabgenomics.com
	  	112,672	  	141,870
			
	 BVP I Affiliates Fund L.P.
 Attn: Peter K.
Shagory
 227 West Monroe, Suite 2200
 Chicago, IL
60606
 pshagory@rwbaird.com
	  	120,145	  	212,258
			
	 FHF Partners
 Attn: Mitchell Fromstein
 5301 North Ironwood Road
 Milwaukee, WI 53217
	  	248,331	  	263,182

  

					
	 Stockholder
	  	Series E	  	Series F
	 Roland Green
 506 Ozark Trail
 Madison, WI 53705
	  	407	  	6,720
			
	 Ice Nine Investments, LLC
 c/o Quarles & Brady,
LLP
 Attn: Nicholas Seay
 1 South Pinckney Street, Suite
600
 Madison, WI 53703
 njs@quarles.com
	  	12,543	  	10,529
			
	 ITX International Equity Corporation
 Attn: Takehita
Jimbo, President and CEO
 700 East El Camino Real, Suite 200
 Mountain View, CA 94040
	  	714,286	  	0
			
	 Emile Nuwaysir
 2022 Madison Street
 Madison, WI 53711
 enuwaysir@nimblegen.com
	  	3,673	  	1,680
			
	 Frank V. Sica
 Menemsha Capital Partners, Ltd.

c/o Tailwind Capital
 390 Park Avenue, 17th Floor
 New York, NY
10022
 frank.sica@menemshacpl.com
	  	249,521	  	335,268
			
	 Skyline Venture Partners Qualified Purchaser
 Fund II,
L.P.
 Attn: John G. Freund
 5255 University Avenue,
#520
 Palo Alto, CA 94301
 John@SkylineVentures.com
	  	1,010,155	  	905,643

					
	 Stockholder
	  	Series E	  	Series F
	 Skyline Venture Partners II, L.P.
 Attn: John G.
Freund
 525 University Avenue, #520
 Palo Alto, CA
94301
 John@SkylineVentures.com
	  	86,716	  	77,742
			
	 Skyline Expansion Fund, L.P.
 ATTN: John G.
Freund
 525 University Avenue, #520
 Palo Alto, CA
94301
 John@SkylineVentures.com
	  	22,222	  	666,667
			
	 David C. Sneider
 301 South Yellowstone Drive

Madison, WI 53705
 dsneider@gmail.com
	  	76,833	  	18,455
			
	 Schott AG
 Attn: Frank Mohler
 Hattenbergstrasse 10
 Mainz, Germany D-55122
 frank.mohler@schott.com
  
 Schott North America, Inc.
 Attn: Gerhard Kiewel
 555 Taxter Road
 Elmsford, NY, 10523
 gerhard.kiewel@us.schott.com
	  	2,690,477	  	0
			
	 State of Wisconsin Investment Board
 Attn: Chris
Prestigiacomo
 Wisconsin Private Equity Portfolio
 121 East
Wilson Street
 Madison, WI 53703-3455
 chris.prestigiacomo@swib.state.wi.us
	  	278,862	  	403,374

  

					
	 Stockholder
	  	Series E	  	Series F
	 Tactics II LLC
 Attn: Robert Palay
 5 Revere Drive, Suite 200
 Northbrook, IL 60062
 bpalay@tacticsii.com
	  	250,299	  	276,015
			
	 Michael J. Treble
 2820 Rancho Costero
 Carlsbad, CA 92009
 mtreble@sbcglobal.net
	  	24,942	  	18,671
			
	 Venture Investors Early Stage Fund III, L.P.
 Attn: John
Neis
 505 South Rosa Road
 Madison, WI 53719
 john@ventureinvestors.com
	  	438,936	  	791,720
			
	 Wisconsin Alumni Research Foundation
 Attn: Thomas H.
Weaver
 614 Walnut Street, 13th Floor
 Madison, WI 53707
 weaver@warf.org
	  	252,540	  	312,987
			
	 Texas Instruments, Incorporated
 Attn: Barbara C.
Papas
 7839 Churchill Way, MS 3995
 Dallas, TX
75251
	  	17,777	  	0
			
	 Harold Garner
 4100 Post Oak Road
 Flower Mound, TX 75028
	  	1,000	  	24,538
			
	 STARTech Seed Fund II, L.P.
 Attn: Matt
Blanton
 1302 East Collins Boulevard
 Richardson, TX
75081
	  	35,556	  	0

					
	 Stockholder
	  	Series E	  	Series F
	 Stanley D. Rose
 One Science Court
 Madison, WI 53711
 srose@nimblegen.com
	  	462,241	  	201,980
			
	 Rodney Wallace
 20431 Peachtree Road
 Dickerson, MD 20842
	  	407	  	6,712
			
	 Steven W. Smith
 2854 Richardson Street
 Fitchburg, WI 53711
 ssmith@nimblegen.com
	  	136	  	2,237
			
	 Daniel Clutter
 NimbleGen Systems Inc.
 One Science Court
 Madison, WI 53711
 dclutter@nimblegen.com
	  	382	  	6,310
			
	 Cargill, Incorporated
 Attn: James Sayre
 1200 Park Place, Suite 300
 San Mateo, CA 94403
	  	156,017	  	2,674,277
			
	 Topspin Partners, L.P.
 Attn: Steve Winick
 3 Expressway Plaza
 Roslyn Heights, NY 11577
 swinick@topspinpartners.com
	  	41,916	  	691,619
			
	 Topspin Associates, L.P.
 Attn: Steve Winick

3 Expressway Plaza
 Roslyn Heights, NY 11577
 swinick@topspinpartners.com
	  	1,985	  	32,754

  

					
	 Stockholder
	  	Series E	  	Series F
	 Brookside Capital Partners Fund, L.P.
 c/o Brookside
Capital
 Attn: Jay Venkatesan
 111 Huntington Avenue

Boston, MA 02199
	  	0	  	1,644,806
			
	 Adage Capital Partners, L.P.
 c/o Adage Capital
Management, L.P.
 Attn: Dan Lehan
 200 Clarendon Street,
52nd Floor
 Boston, MA
02116
	  	0	  	600,000
			
	 Stark Master Fund Ltd.
 c/o Stark Offshore Management
LLC
 3600 South Lake Drive
 St. Francis, WI 53235
	  	0	  	500,000
			
	 BBT Fund, L.P.
 c/o BBT Genpar, L.P.
 201 Main Street, Suite 3200
 Fort Worth, TX 76102
	  	0	  	147,500
			
	 CAP Fund, L.P.
 c/o BBT Genpar, L.P.
 201 Main Street, Suite 3200
 Fort Worth, TX 76102
	  	0	  	67,500
			
	 SRI Fund, L.P.
 c/o BBT Genpar, L.P.
 201 Main Street, Suite 3200
 Fort Worth, TX 76102
	  	0	  	35,000

  

					
	 Stockholder
	  	Series E	  	Series F
	 QVT Fund LP
 c/o QVT Associates GP LLC
 1177 Avenue of the Americas, 9th
Floor
 New York, NY 10036
 legalnotices@qvt.com
	  	0	  	200,000
			
	 The Board of Trustees of Leland Stanford Junior University
  
 The Board of Trustees of Leland Stanford Junior University
 c/o Stanford
Management Company
 Attn: Martina Poquet
 2770 Sand Hill
Road
 Menlo Park, CA 94025
 martinapoquet@stanford.edu
  
 The Board of Trustees of Leland Stanford
Junior University
 c/o Stanford Management Company
 Attn: Jin
Gu
 2770 Sand Hill Road
 Menlo Park, CA 94025
 jingu@stanford.edu
	  	0	  	20,000
			
	 J. Warren Huff
 1002 Ashlawn Drive
 Southlake, TX 76092
	  	0	  	3,337
			
	 Total:
	  	7,732,840	  	11,880,470Agreement between the Registrant and GATX Venturs, Inc.

 Exhibit 4.3 
 This Agreement is made as of July 8, 2003 between GATX Ventures, Inc. (“Lender”) and Nimblegen Systems Inc. (“Borrower”). Reference is made to the Equipment Loan
and Security Agreement dated as of June 6, 2002 (the “Loan Agreement”) between Lender and Borrower. 
 Borrower issued two warrants to Lender
in connection with the Loan Agreement (the “2002 Warrants”). Lender shall return to Borrower the 2002 Warrants for Borrower in exchange for Borrower’s issuance to Lender of a new warrant, in the form of Exhibit A hereto
(which is equivalent to a return by Lender to Borrower of one third of the 2002 Warrants) (the “New Warrant”). Borrower represents and warrants that the lowest price per share of its Series D Preferred Stock (on a common
stock equivalent basis) was $4.20. The New Warrant shall be a “Warrant” under the Loan Agreement. Borrower agrees that it has no claims or damages against Lender in connection with Lender’s decision pursuant to Section 2.1(d) of
the Loan Agreement not to fund any additional Loans to Borrower after the first Loan was made as evidenced by Loan Agreement Supplement No. 1 (Borrower consented to Lender’s decision); to the extent any such claims or damages existed they
are hereby waived by Borrower. 
 This Agreement and the New Warrant constitute the entire agreement between the parties regarding the subject matter hereto.
This Agreement is governed by California law. This Agreement may be executed in counterparts, including by facsimile or electronic transmission, each of which, when executed and delivered, shall be deemed to be an original, and all of which, when
taken together, shall constitute but one and the same Agreement. 
  

											
	GATX VENTURES, INC.	 		 	NIMBLEGEN SYSTEMS INC.	 	
						
	By:	 	 /s/ Carl F.S.
	 		 	By:	 	 /s/ David S. Snyder
	 	
	Title:	 	VP	 		 	Title:	 	Chief Financial Officer and Vice President	 	

 Exhibit A 
 New Warrant 

 THIS WARRANT HAS NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED OR ANY STATE SECURITIES LAWS. NO SALE
OR DISPOSITION MAY BE EFFECTED WITHOUT (i) EFFECTIVE REGISTRATION STATEMENTS RELATED THERETO, (ii) AN OPINION OF COUNSEL OR OTHER EVIDENCE, REASONABLY SATISFACTORY TO THE COMPANY, THAT SUCH REGISTRATIONS ARE NOT REQUIRED,
(iii) RECEIPT OF NO-ACTION LETTERS FROM THE APPROPRIATE GOVERNMENT AUTHORITIES, OR (iv) OTHERWISE COMPLYING WITH THE PROVISIONS OF SECTION 7 OF THIS WARRANT. 
 NIMBLEGEN SYSTEMS, INC. 
 WARRANT TO PURCHASE 13,095 SHARES 
 OF SERIES D PREFERRED STOCK 
 THIS CERTIFIES
THAT, for value received, GATX VENTURES, INC. and its assignees are entitled to subscribe for and purchase 13,095 shared of the fully paid and nonassessable Series D Preferred Stock (as defined below and as adjusted pursuant to Section 4
hereof, the “Share”) of NIMBLEGEN SYSTEMS INC., a Delaware corporation (the “Company”), at $4.20 per share (such price and such other price as shall result, form time to time, from the adjustments specified in
Section 4 hereof is herein referred to as the “Warrant Price”), subject to the provisions and upon the terms and conditions hereinafter set forth. As used herein, (a) the term “Series Preferred”
shall mean the Company’s presently authorized Series D Preferred Stock, and after the automatic conversion of the Series D Preferred Stock issuable hereunder to common stock, the Company’s Common Stock; (b) the term “Date of
Grant” shall mean July 8, 2003; and (c) the term “Other Warrants” shall mean any other warrants issued by the Company in connection with the transaction with respect to which this Warrant was issued, and any
warrant issued upon transfer or partial exercise of or in lieu of this Warrant. The term “Warrant” as used herein shall be deemed to include Other Warrants unless the context clearly requires otherwise. 
 1. Term. The purchase right represented by this Warrant is exercisable, in whole or in part, at any time and from time to time from the Date of
Grant through the later of (i) ten (10) years after the Date of Grant or (ii) five (5) years after the closing of the company’s initial public offering of its Common Stock (“IPO”) effect pursuant to a
Registration Statement on Form S-1 (or its successor) filed under the Securities Act of 1933, as amended (the “Act”). 
 2.
Method of Exercise; Payment; Issuance of New Warrant. Subject to Section 1 hereof, the purchase right represented by this Warrant may be exercised by the holder hereof, in whole or in part and from time to time, at the election of
the holder hereof, by (a) the surrender of this Warrant (with the notice of exercise substantially in the form attached hereto as Exhibit A-1 duly completed and executed) at the principal office of the Company and by the payment to the
Company, by certified or bank check, or by wire transfer to an account designated by the Company (a “Wire Transfer”) of an amount equal to the then applicable Warrant Price multiplied by the number of Shares then being purchased;
(b) if in connection with a registered public offering of the Company’s securities, the surrender of this Warrant (with the notice of exercise form attached hereto as Exhibit A-2 duly completed and executed) at the principal office
of the Company together with notice of arrangements reasonably satisfactory to the Company for 

 
payment to the Company either by certified or bank check or by Wire Transfer from the proceeds of the sale of shares to be sold by the holder in such public
offering of an amount equal to the then applicable Warrant Price per share multiplied by the number of Shares then being purchased; or (c) exercise of the “net issuance” right provided for in Section 10.2 hereof. The
person or persons in whose name(s) any certificate(s) representing shares of Series Preferred shall be issuable upon exercise of this Warrant shall be deemed to have become the holder(s) of record of, and shall be treated for all purposes as the
record holder(s) of, the shares represented thereby (and such shares shall be deemed to have been issued) immediately prior to the close of business on the date or dates upon which this Warrant is exercised. In the event of any exercise of the
rights represented by this Warrant, certificates for the shares of stock so purchased shall be delivered to the holder hereof as soon as possible and in any event within thirty (30) days after such exercise and, unless this Warrant has been
fully exercised or expired, a new Warrant representing the portion of the Shares, if any, with respect to which this Warrant shall not then have been exercised shall also be issued to the holder hereof as soon as possible and in any event within
such thirty-day period; provided that at such time as the Company is subject to the reporting requirements of the Securities Exchange Act of 1934, as amended, if requested by the holder of this Warrant, the Company shall cause its transfer
agent to deliver the certificate representing Shares issued upon exercise of this Warrant to a broker or other person (as directed by the holder exercising this Warrant) within the time period required to settle any trade made by the holder after
exercise of this Warrant. 
 3. Stock Fully Paid; Reservation of Shares. All Shares that may be issued upon the exercise of the rights
represented by this Warrant will, upon issuance pursuant to the terms and conditions herein, be fully paid and nonassessable (except as provided in Section 180.0622(2)(h) of the Wisconsin Statutes and the cases decided thereunder) and free from
all preemptive rights and taxes, liens and charges with respect to the issue thereof. During the period within which the rights represented by this Warrant may be exercised, the Company will at all times have authorized, and reserved for the purpose
of the issue upon exercise of the purchase rights evidenced by this Warrant, a sufficient number of shares of its Series Preferred to provide for the exercise of the rights represented by this Warrant and a sufficient number of shares of its Common
Stock to provide for the conversion of the Series Preferred into Common Stock. 
 4. Adjustment of Warrant Price and Number of Shares.
Without duplication of any adjustment applicable to the securities issuable upon exercise of this Warrant resulting by operation of the terms of the Company’s Third Amended and Restated Certificate of Incorporation, a true and complete copy of
which is attached hereto as Exhibit B, as amended from time to time (the “Charter”), the number and kind of securities purchasable upon the exercise of this Warrant and the Warrant Price shall be subject to adjustment from
time to time upon the occurrence of certain events, as follows: 
 (a) Reclassification or Merger. In case of any reclassification or
change of securities of the class issuable upon exercise of this Warrant (other than a change in par value, or from par value to no par value, or from no par value to par value, or as a result of a subdivision or combination), or in case of any
merger of the company with or into another corporation (other than a merger with another corporation in which the Company is the acquiring and the surviving corporation and which does not result in any reclassification or change of outstanding
securities issuable upon exercise of this Warrant), or in case of any sale of all or substantially all of the assets of the Company, the Company, or such successor or purchasing corporation, as the case may be, shall duly execute 

 
and deliver to the holder of this Warrant a new Warrant (in form and substance satisfactory to the holder of this Warrant), or the Company shall make
appropriate provision without the issuance of a new Warrant, so that the holder of this Warrant shall have the right to receive upon exercise of this Warrant, at a total purchase price not to exceed that payable upon the exercise of the unexercised
portion of this Warrant, and in lieu of the shares of Series Preferred theretofore issuable upon exercise of this Warrant, (i) the kind and amount of shares of stock, other securities, money and property receivable upon such reclassification,
change, merger or sale by a holder of the number of shares of Series Preferred then purchasable under this Warrant, or (ii) in the case of such a merger or sale in which the consideration paid consists of all or in part of assets other than
securities of the successor or purchasing corporation, at the option of the holder of this Warrant, the securities of the success or purchasing corporation having a value at the time of the transaction equivalent to the value of the Series Preferred
purchasable upon exercise of this Warrant at the time of the transaction. Any new Warrant shall provide for adjustments that shall be as nearly equivalent as may be practicable to the adjustments provided for in this Section 4. The
provisions of this Section 4(a) shall similarly apply to successive reclassifications, changes, mergers and sales. 
 (b)
Subdivision or Combination of Shares. If the Company at any time while this Warrant remains outstanding and unexpired shall subdivide or combine its outstanding shares of Series Preferred, the Warrant Price shall be proportionately decreased
and the number of Shares issuable hereunder shall be proportionately increased in the case of a subdivision and the Warrant Price shall be proportionately increased and the number of Shares issuable hereunder shall be proportionately decreased in
the case of a combination. 
 (c) Stock Dividends and Other Distributions. If the Company at any time while this Warrant is outstanding
and unexpired shall (i) pay a dividend with respect to Series Preferred payable in Series Preferred, then the Warrant Price shall be adjusted, from and after the date of determination of shareholders entitled to receive such dividend or
distribution, to that price determined by multiplying the Warrant Price in effect immediately prior to such date of determination by a fraction (A) the numerator of which shall be the total number of shares of Series Preferred outstanding
immediately prior to such dividend or distribution, and (B) the denominator of which shall be the total number of shares of Series Preferred outstanding immediately after such dividend or distribution; or (ii) make any other distribution
with respect to Series Preferred (except any distribution specifically provided for in Sections 4(a) and 4(b)), then, in each such case, provision shall be made by the Company such that the holder of this Warrant shall receive upon exercise
of this Warrant a proportionate share of any such dividend or distribution as though it were the holder of the Series Preferred (or Common Stock issuable upon conversion thereof) as of the record date fixed for the determination of the shareholders
of the Company entitled to receive such dividend or distribution. 
 (d) Adjustment of Number of Shares. Upon each adjustment in the
Warrant Price, the number of Shares of Series Preferred purchasable hereunder shall be adjusted, to the nearest whole share, to the product obtained by multiplying the number of shares purchasable immediately prior to such adjustment in the Warrant
Price by a fraction, the numerator of which shall be the Warrant Price immediately prior to such adjustment and the denominator of which shall be the Warrant Price immediately thereafter. 

 (e) Antidilution Rights. The other antidilution rights applicable to the Shares of Series
Preferred purchasable hereunder are set forth in the Charter as amended through the Date of Grant. Such antidilution rights shall not be restated, amended, modified or waived in any manner that affects the holder hereof more adversely than the other
holders of shares of Series Preferred without such holder’s prior written consent. The Company shall promptly provide the holder hereof with any restatement, amendment, modification or waiver of the Charter promptly after the same has been
made. 
 5. Notice of Adjustments. Whenever the Warrant Price or the number of Shares purchasable hereunder shall be adjusted pursuant
to Section 4 hereof, the Company shall make a certificate signed by its chief financial officer setting forth, in reasonable detail, the event requiring the adjustment, the amount of the adjustment, the method by which such adjustment
was calculated, and the Warrant Price and the number of Shares purchasable hereunder after giving effect to such adjustment, and shall cause copies of such certificate to be mailed (without regard to Section 13 hereof, by first class
mail, postage prepaid) to the holder of this Warrant. In addition, whenever the conversion price or conversion ratio of the Series Preferred shall be adjusted, the Company shall make a certificate signed by its chief financial officer setting forth,
in reasonable detail, the event requiring the adjustment, the amount of the adjustment, the method by which such adjustment was calculated, and the conversion price or ratio of the Series Preferred after giving effect to such adjustment, and shall
cause copies of such certificate to be mailed (without regard to Section 13 hereof, by first class mail, postage prepaid) to the holder of this Warrant. Whenever the Warrant Price or the number of Shares purchasable hereunderafter shall
be adjusted pursuant to the occurrence of a Qualified Financing, the Company shall make a certificate signed by its chief financial officer setting forth, in reasonable detail, the event requiring the adjustment, the amount of the adjustment, the
method by which such adjustment was calculated, and the Warrant Price and the number of Shares purchasable hereunder giving the effect to such adjustment, and shall cause copies of such certificate to be mailed (without regard to
Section 13 hereof, by first class mail, postage prepaid) to the holder of this Warrant; provided that any certificate delivered by the Company to the holder of this Warrant in accordance with the Charter containing substantially
the same information shall be deemed compliance with the foregoing notice required by this sentence. 
 6. Fractional Shares. No
fractional Shares will be issued in connection with any exercise hereunder, but in lieu of such fractional shares the Company shall make a cash payment therefore based on the fair market value of the Shares on the date of exercise as reasonably
determined in good faith by the Company’s Board of Directors. 
 7. Compliance with Act; Disposition of Warrant or Shares of Series
Preferred. 
 (a) Compliance with Act. The holder of this Warrant, by acceptance hereof, agrees that this Warrant, and the share
of Series Preferred to be issued upon exercise hereof and any Common Stock issued upon conversion thereof are being acquired for investment and that such holder will not offer, sell or otherwise dispose of this Warrant, or any shares of Series
Preferred to be issued upon exercise hereof or any Common Stock issued upon conversion thereof except under circumstances which will not result in a violation of the Act or any applicable state securities laws. Upon exercise of this Warrant, unless
the Shares being acquired are registered under the Act and any applicable state securities laws or an exemption from such registration is available, the holder 

 
hereof shall confirm in writing that the shares of Series Preferred so purchased (and any shares of Common Stock issued upon conversion thereof) are being
acquired for investment and not with a view toward distribution or resale in violation of the Act and shall confirm such other matters related thereto as may be reasonably requested by the Company. This Warrant and all shares of Series Preferred
issued upon exercise of this Warrant and all shares of Common Stock issued upon conversion thereof (unless registered under the Act and any applicable state securities laws) shall be stamped or imprinted with a legend in substantially the following
form: 
 “THE SECURITIES EVIDENCED HEREBY HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED, OR ANY STATE SECURITIES LAWS. NO SALE
OR DISPOSITION MAY BE EFFECTED WITHOUT (i) EFFECTIVE REGISTRATION STATEMENTS RELATED THERETO, (ii) AN OPINION OF COUNSEL OR OTHER EVIDENCE, REASONABLY SATISFACTORY TO THE COMPANY, THAT SUCH REGISTRATIONS ARE NOT REQUIRED,
(iii) RECEIPT OF NO-ACTION LETTERS FROM THE APPROPRIATE GOVERNMENTAL AUTHORITIES, OR (iv) OTHERWISE COMPLYING WITH THE PROVISIONS OF SECTION 7 OF THE WARRANT UNDER WHICH THESE SECURITIES WERE ISSUED, DIRECTLY OR INDIRECTLY.”

 Said legend shall be removed by the Company, upon the request of a holder, at such time as the restrictions on the transfer of the
applicable security shall have terminated. In addition, in connection with the issuance of this Warrant, the holder specifically represents to the Company by acceptance of this Warrant as follows: 
 (1) The holder is aware of the Company’s business affairs and financial condition, and has acquired information about the Company sufficient to
reach an informed and knowledgeable decision to acquire this Warrant. The holder is acquiring this Warrant for its own account for investment purposes only and not with a view to, or for the resale in connection with, any “distribution”
thereof in violation of the Act. 
 (2) The holder understands that this Warrant has not been registered under the Act in reliance upon a
specific exemption therefrom, which exemption depends upon, among other things, the bona fide nature of the holder’s investment intent as expressed herein. 
 (3) The holder further understands that this Warrant must be held indefinitely unless subsequently registered under the Act and qualified under any applicable state securities laws, or unless exemptions from
registration and qualification are otherwise available. The holder is aware of the provisions of Rule 144, promulgated under the Act. 
 (4)
The holder is an “accredited investor” as such term is defined in Rule 501 of Regulation D promulgated under the Act. 
 (b)
Disposition of Warrant or Shares. With respect to any offer, sale or other disposition of this Warrant or any shares of Series Preferred acquired pursuant to the exercise of this Warrant prior to registration of such Warrant or shares, the
holder hereof agrees to give written notice to the Company prior thereto, describing briefly the manner thereof, together with a written opinion of such holder’s counsel, or other evidence, if reasonably satisfactory to the Company, to the
effect that such offer, sale or other 

 
disposition may be effected without registration or qualification (under the Act as then in effect or any federal or state securities law then in effect) of
this Warrant or such shares of Series Preferred or Common Stock and indicating whether or not under the Act certificates for this Warrant or such shares of Series Preferred to be sold or otherwise disposed of require any restrictive legend as to
applicable restrictions on transferability in order to ensure compliance with such law. Upon receiving such written notice and reasonably satisfactory opinion or other evidence, the Company, as promptly as practicable but no later than fifteen
(15) days after receipt of the written notice, shall notify such holder that such holder may sell or otherwise dispose of this Warrant or such shares of Series Preferred or Common Stock, all in accordance with the terms of the notice delivered
to the Company; provided that neither this Warrant nor the Shares may be transfer to a person deemed by the Board of Directors of the Company, in its reasonable judgment, to be a competitor or potential competitor of the Company. If a
determination has been made pursuant to this Section 7(b) that the opinion of counsel for the holder or other evidence is not reasonably satisfactory to the Company, the Company shall so notify the holder promptly with details thereof
after such determination has been made. Notwithstanding the foregoing, this Warrant or such shares of Series Preferred or Common Stock may, as to such federal laws, be offered, sold or otherwise disposed of in accordance with Rule 144 or 144A under
the Act, provided that the Company shall have been furnished with such information as the Company may reasonably request to provide a reasonable assurance that the provisions of Rule 144 or 144A have been satisfied. Each certificate representing
this Warrant or the shares of Series Preferred thus transferred (except a transfer pursuant to Rule 144 or 144A) shall bear a legend as to the applicable restrictions on transferability in order to ensure compliance with such laws, unless in the
aforesaid opinion of counsel for the holder, such legend is not required in order to ensure compliance with such laws. The Company may issue stop transfer instructions to its transfer agent in connection with such restrictions. 
 (c) Applicability of Restrictions. Neither any restrictions of any legend described in this Warrant nor the requirements of
Section 7(b) above shall apply to any transfer of, or grant of a security interest in, this Warrant (or the Series Preferred or Common Stock obtainable upon exercise thereof) or any part hereof (i) to a partner of the holder if the
holder is a partnership or to a member of the holder if the holder is a limited liability company, (ii) to a partnership of which the holder is a partner or to a limited liability company of which the holder is a member, or (iii) to any
affiliate of the holder if the holder is a corporation; provided that in any such transfer, if applicable, the transferee shall on the Company’s request agree in writing to be bound by the terms of this Warrant as if an original holder
hereof. 
 (d) “Market Standoff” Agreement. From and after June 6, 2002, the terms of Section 6 (“Market
Standoff” Agreement) of that certain Second Amended and Restated Stockholders Agreement dated as of January 23, 2002 by and among the Company and the stockholders party thereto (as amended from time to time, the “Stockholders
Agreement”), shall be equally applicable to the holder of this Warrant as if such holder where a “Stockholder” within the meaning of such Stockholders Agreement. 
 (e) Holder to Become Party to Stockholders Agreement. At any time following exercise of this Warrant, upon the Company’s written request, the
holder of Shares issued upon such exercise shall become a party to the Stockholders Agreement and subject to the terms thereof and such terms shall supercede and replace all corresponding terms of this Warrant relating to the transfer of the Shares.

 8. Rights as Shareholders; Information. No holder of this Warrant, as such, shall be entitled to
vote or receive dividends or be deemed the holder of Series Preferred or any other securities of the Company which may at any time be issuable upon the exercise hereof for any purpose, nor shall anything contained herein be construed to confer upon
the holder of this Warrant, as such, any of the rights of a shareholder of the Company or any right to vote for the election of directors or upon any matter submitted to shareholders at any meeting thereof, or to receive notice of meetings, or to
receive dividends or subscription rights or otherwise until this Warrant shall have been exercised and the Shares purchasable upon the exercise hereof shall have become deliverable, as provided herein. Notwithstanding the foregoing, the Company will
transmit to the holder of this Warrant such information, documents and reports as are generally distributed to the holders of any class or series of the securities of the Company concurrently with the distribution thereof to the shareholders.

 9. Registration Rights. The company grants registration rights to the holder of this Warrant for any Common Stock of the Company
obtained upon conversion of the Series Preferred, comparable to the registration rights granted to the investors in that certain Second Amended and Restated Registration Rights Agreement dated as of January 23, 2002 (the “Rights
Agreement”), with the following exceptions and clarifications: 
 (1) The holder will not have the right to demand registration, but
can otherwise participate in any registration demanded by others. 
 (2) The holder will be subject to the same provisions regarding
indemnification as contained in the Rights Agreement. 
 (3) The registration rights are freely assignable by the holder of this Warrant in
connection with a permitted transfer of this Warrant or the Shares; provided that the registration rights applicable to the Shares may not be transferred to a person deemed by the Board of Directors of the Company, in its reasonable judgment,
to be a competitor or potential competitor of the Company. 
 (4) In connection with the exercise of the registration rights herein
described, upon the Company’s written request, the holder of Shares to be included in the subject registration shall become a party to the Rights Agreement and subject to the terms thereof and such terms shall supercede and replace all
corresponding terms of this Warrant relating to the registration of the Shares. 
 10. Additional Rights. 
 10.1 Acquisition Transactions. The Company shall provide the holder of this Warrant with at least twenty (20) days’ written notice prior
to closing thereof of the terms and conditions of any of the following transactions (to the extent the Company has notice thereof): (i) the sale, lease, exchange, conveyance or other disposition of all or substantially all of the Company’s
property or business, or (ii) its merger into or consolidation with any other corporation (other than a wholly-owned subsidiary of the Company), or any transaction (including a merger or other reorganization) or series of related transactions,
in which more than fifty percent (50%) of the voting power of the Company is disposed of. 

 10.2 Right to Convert Warrant into Stock: Net Issuance. 
 (a) Right to Convert. In addition to and without limiting the rights of the holder under the terms of this Warrant, the holder shall have the
right to convert this Warrant or any portion thereof (the “Conversion Right”) into shares of Series Preferred as provided in this Section 10.2 at any time or from time to time during the term of this Warrant. Upon
exercise of the Conversion Right with respect to a particular number of shares subject to this Warrant (the “Converted Warrant Shares”), the Company shall deliver to the holder (without payment by the holder of any exercise price or
any cash or other consideration) that number of shares of fully paid and nonassessable Series Preferred as is determined according to the following formula: 
  

					
		 	X = B – A
		 	          Y
		 	Where:  X =	 	the number of shares of Series Preferred that shall be issued to holder
			
		 	Y =	 	the fair market value of one share of Series Preferred
			
		 	A =	 	the aggregate Warrant Price of the specified number of Converted Warrant Shares immediately prior to the exercise of the Conversion Right (i.e., the number of Converted Warrant Shares
multiplied by the Warrant Price)
			
		 	B =	 	the aggregate fair market value of the specified number of Converted Warrant Shares (i.e., the number of Converted Warrant Shares multiplied by the fair market value of one
Converted Warrant Share)

 No fractional shares shall be issuable upon exercise of the Conversion Right, and, if the number
of shares to be issued determined in accordance with the foregoing formula is other than a whole number, the Company shall pay to the holder an amount in cash equal to the fair market value of the resulting fractional share on the Conversion Date
(as hereinafter defined). For purposes of Section 10 of this Warrant, shares issued pursuant to the Conversion Right shall be treated as if they were issued upon the exercise of this Warrant. 
 (b) Method of Exercise. The Conversion Right may be exercised by the holder by the surrender of this Warrant at the principal office of the
Company together with a written statement (which may be in the form of Exhibit A-1 or Exhibit A-2 hereto) specifying that the holder thereby intends to exercise the Conversion Right and indicating the number of shares subject to this
Warrant which are being surrendered (referred to in Section 10.2(a) hereof as the Converted Warrant Shares) in exercise of the Conversion Right. Such conversion shall be effective upon receipt by the Company of this Warrant together with
the aforesaid written statement, or on such later date as is specified therein (the “Conversion Date”), and, at the election of the holder hereof, may be made contingent upon the closing of the sale of the Company’s Common
Stock to the public in a public offering pursuant to a Registration Statement under the Act (a “Public Offering”). Certificates for the shares issuable upon exercise of the Conversion Right and, if applicable, a new warrant
evidencing the balance of the shares remaining subject to this Warrant, shall be issued as of the Conversion Date and shall be delivered to the holder within thirty (30) days following the Conversion Date. 

 (c) Determination of Fair Market Value. For purposes of this Section 10.2, “fair
market value” of a share of Series Preferred (or Common Stock if the Series Preferred has been automatically converted into Common Stock) as of a particular date (the “Determination Date”) shall mean: 
 (i) If the Conversion Right is exercised in connection with and contingent upon a Public Offering, and if the Company’s Registration Statement
relating to such Public Offering (“Registration Statement”) has been declared effective by the Securities and Exchange Commission, then the initial “Price to Public” specified in the final prospectus with respect to such
offering. 
 (ii) If the Conversion Right is not exercised in connection with and contingent upon a Public Offering as contemplated pursuant
to the foregoing clause (i), then in all other cases as follows: 
 (A) If traded on a securities exchange, the fair market value of the
Common Stock shall be deemed to be the average of the closing prices of the Common Stock on such exchange over the five trading days immediately prior to the Determination Date, and the fair market value of the Series Preferred shall be deemed to be
such fair market value of the Common Stock multiplied by the number of shares of Common Stock into which each share of Series Preferred is then convertible; 
 (B) If traded on the Nasdaq Stock Market or other over-the-counter system, the fair market value of the Common Stock shall be deemed to be the average of the closing bid prices of the Common Stock over the five
trading days immediately prior to the Determination Date, and the fair market value of the Series Preferred shall be deemed to be such fair market value of the Common Stock multiplied by the number of shares of Common Stock into which each share of
Series Preferred is then convertible; and 
 (C) If there is no public market for the Common Stock, then fair market value shall be determined
by mutual agreement of the holder of this Warrant and the Company. In the event that the Company and the holder of this Warrant cannot agree upon such fair market value, then such fair market value shall be determined in good faith by the
Company’s Board of Directors. 
 In making a determination under clauses (A) and (B) above, if on the Determination Date, five trading days
had not passed since the IPO, then the fair market value of the Common Stock shall be the average closing prices or closing bid prices, as applicable, for the shorter period beginning on and including the date of the IPO and ending on the trading
day prior to the Determination Date (or if such period includes only one trading day the closing price or closing bid price, as applicable, for such trading day). If closing prices or closing bid prices are no longer reported by a securities
exchange or other trading system, the closing price or closing bid price shall be that which is reported by such securities exchange or other trading system at 4:00 p.m. New York City time on the applicable trading day. 

 10.3 Exercise Prior to Expiration. To the extent this Warrant is not previously exercised as to
all of the Shares subject hereto, and if the fair market value of one share of the Series Preferred is greater than the Warrant Price then in effect, this Warrant shall be deemed automatically exercised pursuant to Section 10.2 above
(even if not surrendered) immediately before its expiration. For purposes of such automatic exercise, the fair market value of one share of the Series Preferred upon such expiration shall be determined pursuant to Section 10.2(c). To the
extent this Warrant or any portion thereof is deemed automatically exercised pursuant to this Section 10.3, the Company agrees to promptly notify the holder hereof of the number of Shares, if any, the holder hereof is to receive by
reason of such automatic exercise. 
 11. Representations and Warranties. The Company represents and warrants to the holder of this
Warrant as follows: 
 (a) This Warrant has been duly authorized and executed by the Company and is a valid and binding obligation of the
Company enforceable in accordance with its terms, subject to laws of general application relating to bankruptcy, insolvency, fraudulent conveyance and the relief of debtors and the rules of law or principles at equity governing specific performance,
injunctive relief and other equitable remedies. 
 (b) The Shares have been duly authorized and reserved for issuance by the Company and, when
issued in accordance with the terms hereof, will be validly issued, fully paid and nonassessable (except as provided in Section 180.0622(2)(h) of the Wisconsin Statutes and the cases decided thereunder) and free from preemptive rights.

 (c) The rights, preferences, privileges and restrictions granted to or imposed upon the Series Preferred and the holders thereof are as set
forth in the Charter, and on the Date of Grant, each share of the Series Preferred represented by this Warrant is convertible into one share of Common Stock. 
 (d) The shares of Common Stock issuable upon conversion of the Shares have been duly authorized and reserved for issuance by the Company and, when issued in accordance with the terms of the Charter will be validly
issued, fully paid and nonassessable (except as provided in Section 180.0622(2)(h) of the Wisconsin Statutes and the cases decided thereunder). 
 (e) The execution and delivery of this Warrant are not, and the issuance of the Shares upon exercise of this Warrant in accordance with the terms hereof will not be, inconsistent with the Company’s Charter or by-laws, do not and will
not contravene any law, governmental rule or regulation, judgment or order applicable to the Company, and do not and will not conflict with or contravene any provision of, or constitute a default under, any indenture, mortgage, contract or other
instrument of which the Company is a party or by which it is bound or require the consent or approval of, the giving of notice to, the registration or filing with or the taking of any action in respect of or by, any Federal, state or local
government authority or agency or other person, except for the obtaining of consents which have been obtained and for the filing of notices pursuant to the federal and state securities laws, which filings will be effected by the time required
thereby. 

 (f) There are no actions, suits, audits, investigations or proceedings pending or, to the knowledge of
the Company, threatened against the Company in any court or before any governmental commission, board or authority which, if adversely determined, could have a material adverse effect on the ability of the Company to perform its obligations under
this Warrant. 
 (g) The number of shares of Common Stock of the Company outstanding on the date hereof, on a fully diluted basis (assuming
the conversion of all outstanding convertible securities and the exercise of all outstanding options and warrants) as of June 6, 2002 did not exceed 6,306,000 shares. 
 12. Modification and Waiver. This Warrant and any provision hereof may be changed, waived, discharged or terminated only by an instrument in
writing signed by the party against which enforcement of the same is sought. 
 13. Notices. Any notice, request, communication or
other document required or permitted to be given or delivered to the holder hereof or the Company shall be delivered, or shall be sent certified or registered mail, postage prepaid, to each such holder at its address as shown on the books of the
Company or to the Company at the address indicated therefor on the signature page of this Warrant. 
 14. Binding Effect on
Successors. This Warrant shall be binding upon any corporation succeeding the Company by merger, consolidation or acquisition of all or substantially all of the Company’s assets, and all of the obligations of the Company relating to the
Series Preferred issuable upon the exercise or conversion of this Warrant shall survive the exercise, conversion and termination of this Warrant and all of the covenants and agreements of the Company shall inure to the benefit of the successors and
assigns of the holder hereof. 
 15. Lost Warrants or Stock Certificates. The Company covenants to the holder hereof that, upon
receipt of evidence reasonably satisfactory to the Company of the loss, theft, destruction or mutilation of this Warrant or any stock certificate and, in the case of any such loss, theft or destruction, upon receipt of an indemnity reasonably
satisfactory to the Company, or in the case of any such mutilation upon surrender and cancellation of such Warrant or stock certificate, the Company will make and deliver a new Warrant or stock certificate, of like tenor, in lieu of the lost,
stolen, destroyed or mutilated Warrant or stock certificate. 
 16. Descriptive Headings. The descriptive headings of the various
Sections of this Warrant are inserted for convenience only and do not constitute a part of this Warrant. The language in this Warrant shall be construed as to its fair meaning without regard to which party drafted this Warrant. 
 17. Governing Law. This Warrant shall be construed and enforced in accordance with, and the rights of the parties shall be governed by, the laws
of the State of Delaware. 
 18. Survival of Representations, Warranties and Agreements. All representations and warranties of the
Company and the holder hereof contained herein shall survive the Date of Grant, the exercise or conversion of this Warrant (or any part hereof) or the termination or expiration of rights hereunder. All agreements of the Company and the holder hereof
contained herein shall survive indefinitely until, by their respective terms, they are no longer operative. 

 19. Remedies. In case any one or more of the covenants and agreements contained in this Warrant
shall have been breached, the holder hereof (in the case of a breach by the Company), or the Company (in the case of a breach by a holder), may proceed to protect and enforce their or its rights either by suit in equity and/or by action at law,
including, but not limited to, an action for damages as a result of any such breach and/or an action for specific performance of any such covenant or agreement contained in this Warrant. 
 20. No Impairment of Rights. The Company will not, by amendment of its Charter or through any other means, avoid or seek to avoid the observance
or performance of any of the terms of this Warrant, but will at all times in good faith assist in the carrying out of all such terms and in the taking of all such action as may be necessary or appropriate in order to protect the rights of the holder
of this Warrant against impairment. 
 21. Severability. The invalidity or unenforceability of any provision of this Warrant in any
jurisdiction shall not affect the validity or enforceability of such provision in any other jurisdiction, or affect any other provision of this Warrant, which shall remain in full force and effect. 
 22. Recovery of Litigation Costs. If any legal action or other proceeding is brought for the enforcement of this Warrant, or because of an alleged
dispute, breach, default, or misrepresentation in connection with any of the provisions of this Warrant, the successful or prevailing party or parties shall be entitled to recover reasonable attorneys’ fees and other costs incurred in that
action or proceeding, in addition to any other relief to which it or they may be entitled. 
 23. Entire Agreement; Modification. This
Warrant constitutes the entire agreement between the parties pertaining to the subject matter contained in it and supersedes all prior and contemporaneous agreements, representations, and undertakings of the parties, whether oral or written, with
respect to such subject matter. 
 [Remainder of page intentionally left blank.] 

 The Company has caused this Warrant to be duly executed and delivered as of the Date of Grant specified
above. 
  

			
	 NIMBLEGEN SYSTEMS INC.

		
	 By
	 	  

	 Title
	 	  

	 Address: One Science Court Madison, WI 53711

 EXHIBIT A-1 
 NOTICE OF EXERCISE 
 To: NIMBLEGEN SYSTEMS INC. (the “Company”) 
  

	 	1.	The undersigned hereby: 

  

	 	r	elects to purchase                      shares of [Series Preferred
Stock][Common Stock] of the Company pursuant to the terms of the attached Warrant, and tenders herewith payment of the purchase price of such shares in full, or 

  

	 	r	elects to exercise its net issuance rights pursuant to section 10.2 of the attached Warrant with respect to
                     Shares of [Series Preferred Stock][Common Stock]. 

 2. Please issue a certificate or certificates representing
                     shares in the name of the undersigned or in such other name or names as are specified below: 
  

					
		 	  
 (Name)
	 	
		 	  
	 	
		 	  
 (Address)
	 	

 3. The undersigned represents that the aforesaid shares are being acquired for the account of the
undersigned for investment and not with a view to, or for resale in connection with, the distribution thereof and that the undersigned has no present intention of distributing or reselling such shares, all except as in compliance with applicable
securities laws. 
  

							
		 		 	  
 (Signature)
	 	
				
	  
 (Date)
	 		 		 	

 EXHIBIT A-2 
 NOTICE OF EXERCISE 
 To: NIMBLEGEN SYSTEMS INC. (the “Company”) 
 1. Contingent upon and effective immediately prior to the closing (the “Closing”) of the Company’s public offering contemplated by the
Registration Statement on Form S    , filed                    ,
,             the undersigned hereby: 
  

	 	r	elects to purchase                      shares of [Series Preferred
Stock][Common Stock] of the Company (or such lesser number of shares as may be sold on behalf of the undersigned at the Closing) pursuant to the terms of the attached Warrant, or 

  

	 	r	elects to exercise its net issuance rights pursuant to section 10.2 of the attached Warrant with respect to
                     Shares of [Series Preferred Stock][Common Stock]. 

 2. Please deliver to the custodian for the selling shareholders a stock certificate representing such
                     shares. 
 3.
The undersigned has instructed the custodian for the selling shareholders to deliver to the Company $                     or, if less, the net
proceeds due the undersigned from the sale of shares in the aforesaid public offering. If such net proceeds are less than the purchase price for such shares, the undersigned agrees to deliver the difference to the Company prior to the Closing.

  

					
		 		 	  

	 	 	 	 	(Signature)
	  
	 	 	 	 
	 (Date)
	 		 	

 EXHIBIT B 
 CHARTER 
 THIRD AMENDED AND RESTATED 
 CERTIFICATE OF INCORPORATION 
 OF 
 NIMBLEGEN SYSTEMS INC. 
 The
undersigned officers of NimbleGen Systems Inc., a corporation organized and existing under and by virtue of the General Corporation Law of the State of Delaware, originally incorporated on August 25, 2000, do hereby certify as follows:

 1. Pursuant to the unanimous written consent of the Board of Directors and the holders of all of the issued and outstanding voting stock
of the corporation, the following resolutions were duly adopted approving the amendment and restatement of Article I through VIII of the Certificate of Incorporation of NimbleGen Systems Inc.: 
 ARTICLE I 
 The name of the corporation is
NimbleGen Systems Inc. 
 ARTICLE II 
 The address of the registered office of the corporation is 1209 Orange Street, Wilmington, New Castle County, Delaware. The name of its registered agent at such address is The Corporation Trust Company. 
 ARTICLE III 
 The purpose of the corporation
is to engage in any lawful act or activity for which corporations may be organized under the General Corporation Law of Delaware. 
 ARTICLE
IV 
 A. The corporation is authorized to issue two classes of stock to be designated, respectively, “Common Stock” and
“Preferred Stock.” The total number of shares of all classes of stock that the corporation is authorized to issue is 17,225,465 shares. The total number of shares of Common Stock that the corporation is authorized to issue is 9,895,821
with a par value 

  

 18 

 
of $0.001 per share. The total number of shares of Preferred Stock that the corporation is authorized to issue is 7,329,644 with a par value of $0.001 per
share, of which 1,230,001 shares shall be designated as “Series A Preferred Stock”, of which 2,080,000 shares shall be designated as “Series B Preferred Stock”, of which 1,035,715 shares shall be designated as
“Series C Preferred Stock”, and of which 2,983,928 shares shall be designated as “Series D Preferred Stock.” Series A Preferred Stock, Series B Preferred Stock, Series C Preferred Stock, and Series D
Preferred Stock are referred to herein collectively as “Preferred Stock.” 
 B. A statement of rights, preferences, privileges and
restrictions granted to or imposed upon the Common Stock and the Preferred Stock and the holders thereof is as follows: 
 1.
Dividends. 
 (a) Series A Preferred Stock. The holders of the Series A Preferred Stock shall be
entitled to receive, when, as and if declared by the board of directors, out of any funds legally available therefor, noncumulative dividends at the rate per share of Series A Preferred Stock of $0.24 per annum (as adjusted for any stock
dividends, combinations, splits, recapitalizations and the like with respect to such shares) (the “Series A Preferred Annual Dividend”). So long as the Series A Preferred Stock shall be outstanding, no dividend shall be paid on
the Common Stock, the Series B Preferred Stock, the Series C Preferred Stock, or the Series D Preferred Stock in any year, other than dividends payable solely in capital stock, until the Series A Preferred Annual Dividend has
been paid in full, except that dividends may be declared and paid on the Series B Preferred Stock, the Series C Preferred Stock, and the Series D Preferred Stock pro rata with any dividends simultaneously declared and paid on
Series A Preferred Stock. 
 (b) Series B Preferred Stock. The holders of the Series B Preferred Stock
shall be entitled to receive, when, as and if declared by the board of directors, out of any funds legally available therefor, noncumulative dividends at the rate per share of Series B Preferred Stock of $0.40 per annum (as adjusted for any
stock dividends, combinations, splits, recapitalizations and the like with respect to such shares) (the “Series B Preferred Annual Dividend”). So long as the Series B Preferred Stock shall be outstanding, no dividend shall be
paid on the Common Stock, the Series A Preferred Stock, the Series C Preferred Stock, or the Series D Preferred Stock in any year, other than dividends payable solely in capital stock, until the Series B Preferred Annual Dividend
has been paid in full, except that dividends may be declared and paid on the Series A Preferred Stock , the Series C Preferred Stock, and the Series D Preferred Stock pro rata with any dividends simultaneously declared and paid on
Series B Preferred Stock. 
 (c) Series C Preferred Stock. The holders of the Series C Preferred Stock
shall be entitled to receive, when, as and if declared by the board of directors, out of any funds legally available therefor, noncumulative dividends at the rate per share of Series C Preferred Stock of $0.448 per annum (as adjusted for any
stock dividends, combinations, splits, recapitalizations and the like with respect to such shares) (the “Series C Preferred Annual Dividend”). So long as 

  

 19 

 
the Series C Preferred Stock shall be outstanding, no dividend shall be paid on the Common Stock, the Series A Preferred Stock, the Series B
Preferred Stock or the Series D Preferred Stock in any year, other than dividends payable solely in capital stock, until the Series C Preferred Annual Dividend has been paid in full, except that dividends may be declared and paid on the
Series A Preferred Stock, Series B Preferred Stock and the Series D Preferred Stock pro rata with any dividends simultaneously declared and paid on Series C Preferred Stock. 
 (d) Series D Preferred Stock. The holders of the Series D Preferred Stock shall be entitled to receive, when, as and if
declared by the board of directors, out of any funds legally available therefor, noncumulative dividends at the rate per share of Series D Preferred Stock of $0.336 per annum (as adjusted for any stock dividends, combinations, splits,
recapitalizations and the like with respect to such shares) (the “Series D Preferred Annual Dividend”). So long as the Series D Preferred Stock shall be outstanding, no dividend shall be paid on the Common Stock, the
Series A Preferred Stock, the Series B Preferred Stock or the Series C Preferred Stock in any year, other than dividends payable solely in capital stock, until the Series D Preferred Annual Dividend has been paid in full, except
that dividends may be declared and paid on the Series A Preferred Stock, the Series B Preferred Stock and the Series C Preferred Stock pro rata with any dividends simultaneously declared and paid on Series D Preferred Stock.

 2. Liquidation Preference. 
 (a) Preferred Stock. In the event of any liquidation, dissolution or winding up of the corporation, prior and in preference to any
distribution of any of the assets or funds of the corporation to the holders of the Common Stock by reason of their ownership of such stock, the holders of Preferred Stock shall be entitled to receive the following: 
 (1) the holders of Series D Preferred Stock shall be entitled to receive, prior to the payment of any amounts to the holders of
Series A Preferred Stock, Series B Preferred Stock or Series C Preferred Stock for each outstanding share of Series D Preferred Stock then held an amount equal to $4.20 per share (as adjusted for any stock dividends,
combinations, splits, recapitalizations and the like with respect to such shares), plus any declared but unpaid dividends on such share, and 
 (2) after payment of any amount due to the holders of Series D Preferred Stock under subparagraph (1), above, the holders of Series A Preferred Stock shall be entitled to receive for each outstanding
share of Series A Preferred Stock then held, $3.00 per share (as adjusted for any stock dividends, combinations, splits, recapitalizations and the like with respect to such shares), plus declared but unpaid dividends on such share, the holders
of Series B Preferred Stock shall be entitled to receive for each outstanding share of Series B Preferred Stock then held, $5.00 per share (as adjusted for any stock dividends, combinations, splits, recapitalizations 

  

 20 

 
and the like with respect to such shares), plus declared but unpaid dividends on such share, and the holders of Series C Preferred Stock shall be
entitled to receive for each outstanding share of Series C Preferred Stock then held, $5.60 per share (as adjusted for any stock dividends, combinations, splits, recapitalizations and the like with respect to such shares), plus declared but
unpaid dividends on such share. If, upon the occurrence of a liquidation, dissolution or winding up, the assets and funds of the corporation legally available for distribution to stockholders by reason of their ownership of stock of the corporation
shall be insufficient to permit the payment to such holders of Series A Preferred Stock, Series B Preferred Stock, and Series C Preferred Stock of the full aforementioned preferential amount under this subparagraph (2), then the
entire assets and funds of the corporation legally available for distribution to stockholders by reason of their ownership of stock of the corporation shall be distributed ratably among the holders of Series A Preferred Stock, Series B
Preferred Stock, and Series C Preferred Stock, based upon the total preferential amount each holder would be entitled to receive if sufficient funds were legally available to pay the full preferential amounts. 
 (b) Common Stock. Upon a liquidation, dissolution or winding up of the corporation, and after payment to the holders of Preferred
Stock of the amounts to which they are entitled pursuant to Section B2(a) of this Article IV, all assets and funds of the corporation that remain legally available for distribution to stockholders by reason of their ownership of stock of the
corporation shall be distributed ratably among the holders of the Common Stock in proportion to the number of shares of Common Stock held by them. 
 (c) Other Events Considered a Liquidation. For purposes of this Section B2, the following events shall be considered a liquidation of the corporation: 
 (1) any consolidation or merger of the corporation with or into any other corporation or other entity in which the corporation is not the
surviving entity, or in which the stockholders of the corporation immediately prior to such consolidation or merger own less than fifty percent (50%) of the corporation’s voting power immediately after such consolidation or merger,
excluding any consolidation or merger effected exclusively to change the domicile of the corporation (a “Merger”); or 
 (2) a sale, lease or other disposition of all or substantially all of the assets of the corporation (an “Asset Transfer”). 
 If the consideration issued in a Merger or received by the corporation in an Asset Transfer is other than cash, its value will be deemed its fair market value as determined in good faith by the board of directors. Any securities shall be
valued as follows: 
  

 21 

 (A) For securities not subject to investment letter or other similar restrictions on free
marketability covered by subsection (B), below: 
 (i) if traded on a securities exchange or through the Nasdaq National
Market, the value shall be deemed to be the average of the closing prices of the securities on such quotation system over the thirty-day period ending three (3) days prior to the closing; 
 (ii) if actively traded over-the-counter, the value shall be deemed to be the average of the closing bid or sale prices (whichever is
applicable) over the thirty-day period ending three (3) days prior to the closing; and 
 (iii) if there is no active
public market the value shall be the fair market value thereof as determined in good faith by the board of directors. 
 (B)
The method of valuation of securities subject to investment letter or other restrictions on free marketability (other than restrictions arising solely by virtue of a shareholder’s status as an affiliate or former affiliate) shall be to make an
appropriate discount from the market value determined as provided in subsection (A), above to reflect the approximate fair market value thereof, as determined by at least sixty-six and two-thirds percent (66-2/3%) of the members of the board of
directors. 
 3. Voting. 
 (a) General. Except as otherwise required by law and except as provided under Section B3(b), below, each holder of Common Stock shall have one vote for each share of Common Stock so held, and each holder
of Preferred Stock shall be entitled to the number of votes equal to the whole number of shares of Common Stock into which the shares of Preferred Stock so held could be converted at the record date for determination of the stockholders entitled to
vote, or, if no such record date is established, at the date such vote is taken or any written consent of the stockholders is solicited. With respect to such vote, except as provided under Section B3(b), below, each holder of Preferred Stock
shall have full voting rights and powers equal to the voting rights and powers of the holders of Common Stock and shall be entitled, notwithstanding any provision hereof, to notice of any stockholders’ meeting in accordance with the bylaws of
the Corporation. Except as otherwise set forth herein and except as may be required by Section 242(b)(2) of the Delaware General Corporation Law, all shares of Common Stock and Preferred Stock shall vote together as a single class on all
matters. 
  

 22 

 (b) Protective Provisions 
 (1) Protective Provisions Applicable to Series A Preferred Stock. So long as any Series A Preferred Stock shall be
outstanding, the affirmative vote or written consent of the holders of more than sixty percent (60%) of the outstanding Series A Preferred Stock voting together as a single class shall be required: 
 (i) to increase the number of authorized shares of Series A Preferred Stock or to authorize or issue any class or series of stock
(other than Series B Preferred Stock, Series C Preferred Stock or Series D Preferred Stock) having any preference or priority as to dividends, liquidation preferences, conversion rights, or voting rights, superior to or on a parity
with any preference or priority over the Series A Preferred Stock; 
 (ii) to authorize or issue any bonds, debentures,
notes or other obligations convertible into or exchangeable for, or having option rights to purchase, any shares of stock of the corporation (other than Series B Preferred Stock, Series C Preferred Stock or Series D Preferred Stock)
having any preference or priority as to dividends, liquidation preferences, conversion rights, or voting rights, superior to or on a parity with any preference or priority over the Series A Preferred Stock; 
 (iii) to reclassify any shares of capital stock of the corporation into shares having any preference or priority as to dividends,
liquidation preferences, conversion rights, or voting rights, superior to or on a parity with any preference or priority over the Series A Preferred Stock; or 
 (iv) to amend or repeal any provision of, or add any provision to, the corporation’s Certificate of Incorporation or Bylaws if such
action would alter or change the preferences, rights, privileges or powers of, or the restrictions provided for the benefit of, the Series A Preferred Stock. 
 (2) Protective Provisions Applicable to Series B Preferred Stock. So long as any Series B Preferred Stock shall be
outstanding, the affirmative vote or written consent of the holders of more than fifty percent (50%) of the outstanding Series B Preferred Stock voting together as a single class shall be required: 
 (i) to increase the number of authorized shares of Series B Preferred Stock or to authorize or issue any class or series of stock
(other than Series B Preferred Stock, Series C Preferred Stock or Series D Preferred Stock) having any preference or 

  

 23 

 
priority as to dividends, liquidation preferences, conversion rights, or voting rights, superior to or on a parity with any preference or priority over the
Series B Preferred Stock; 
 (ii) to authorize or issue any bonds, debentures, notes or other obligations convertible
into or exchangeable for, or having option rights to purchase, any shares of stock of the corporation (other than Series B Preferred Stock, Series C Preferred Stock or Series D Preferred Stock) having any preference or priority as to
dividends, liquidation preferences, conversion rights, or voting rights, superior to or on a parity with any preference or priority over the Series B Preferred Stock; 
 (iii) to reclassify any shares of capital stock of the corporation into shares having any preference or priority as to dividends,
liquidation preferences, conversion rights, or voting rights, superior to or on a parity with any preference or priority of the Series B Preferred Stock; or 
 (iv) to amend or repeal any provision of, or add any provision to, the corporation’s Certificate of Incorporation or By-Laws if such
action would alter or change the preferences, rights, privileges or powers of, or the restrictions provided for the benefit of, the Series B Preferred Stock. 
 (3) Protective Provisions Applicable to Series C Preferred Stock. So long as any Series C Preferred Stock shall be
outstanding, the affirmative vote or written consent of the holders of more than fifty percent (50%) of the outstanding Series C Preferred Stock voting together as a single class shall be required to amend this Certificate of Incorporation
if such amendment would (i) require class voting under Section 242(b)(2) of the Delaware General Corporation Law, as amended or modified from time to time or (ii) increase the number of authorized shares of Series C Preferred
Stock. For purposes hereof, any Merger in which all holders of Preferred Stock receive the same consideration per share or the creation of any new series or classes of capital stock will not require class voting by the holders of Series C Preferred
Stock. 
 (4) Protective Provisions Applicable to Series D Preferred Stock. So long as any Series D
Preferred Stock shall be outstanding, the affirmative vote or written consent of the holders of more than fifty-five percent (55%) of the outstanding Series D Preferred Stock voting together as a single class shall be required to amend
this Certificate of Incorporation if such amendment would (i) require class voting under Section 242(b)(2) of the Delaware General Corporation Law, as amended or modified from time to time or (ii) increase the number of authorized
shares of Series D Preferred Stock. For purposes hereof, any Merger in 

  

 24 

 
which all holders of Preferred Stock receive the same consideration per share or the creation of any new series or classes of capital stock will not require
class voting by the holders of Series D Preferred Stock. 
 (5) Protective Provisions Applicable to Series A
Preferred Stock and Series B Preferred Stock. So long as any Series A Preferred Stock or Series B Preferred Stock shall be outstanding, the affirmative vote or written consent of the holders of more than fifty percent
(50%) of the then outstanding Series A Preferred Stock and Series B Preferred Stock voting together as a single class shall be required: 
 (i) to increase the number of authorized shares of capital stock of the corporation; 
 (ii)
to effect a Merger, an Asset Transfer, or any transaction or series of related transactions to which the corporation is a party which results in the holders of the corporation’s capital stock prior to the transaction or transactions owning less
than fifty percent (50%) of the voting power of the corporation’s capital stock after the transaction or transactions; 
 (iii) to declare or pay any dividend on or make any other distribution with respect to the corporation’s capital stock; or 
 (iv) to apply assets of the corporation to the redemption, retirement, purchase or acquisition, directly or indirectly, through subsidiaries (as defined in Section 425 of the Internal Revenue Code of 1986) or
otherwise, of any shares of any class or series of Common Stock, other than pursuant to plans or agreements with employees, officers, directors, consultants, or other persons performing services for the corporation or its subsidiaries on terms
approved by the board of directors, if the number of shares of stock so redeemed retired, purchased or acquired exceeds five percent (5%) of the total number of the then issued and outstanding shares of Common Stock and Preferred Stock.

 (6) Protective Provisions Applicable to Common Stock and Preferred Stock. The affirmative vote or written consent
of the holders of more than fifty percent (50%) of the then outstanding Common Stock and Preferred Stock voting together as a single class shall be required: 
 (i) to increase the number of shares of authorized capital stock of the corporation; 
 (ii) to effect a Merger, an Asset Transfer, or any transaction or series of related transactions to which the corporation is a party
which results in the holders of the corporation’s capital stock prior to the transaction or transactions 

  

 25 

 
owning less than fifty percent (50%) of the voting power of the corporation’s capital stock after the transaction or transactions; 
 (iii) to declare or pay any dividend on or make any other distribution with respect to the corporation’s capital stock; or

 (iv) to apply assets of the corporation to the redemption, retirement, purchase or acquisition, directly or indirectly,
through subsidiaries (as defined in Section 425 of the Internal Revenue Code of 1986) or otherwise, of any shares of any class or series of Common Stock, other than pursuant to plans or agreements with employees, officers, directors,
consultants, or other persons performing services for the corporation or its subsidiaries on terms approved by the board of directors, if the number of shares of stock so redeemed retired, purchased or acquired exceeds five percent (5%) of the
total number of then issued and outstanding shares of Common Stock and Preferred Stock. 
 4. Conversion Rights. The
holders of the Preferred Stock shall have conversion rights as follows: 
 (a) Optional Conversion for Series A
Preferred Stock. Subject to and in compliance with the provisions of this Section B4, any shares of Series A Preferred Stock may, at the option of the holder, be converted at any time into fully paid and nonassessable shares of Common
Stock. The number of shares of Common Stock to which a holder of Series A Preferred Stock shall be entitled upon conversion shall be the product obtained by multiplying the Series A Conversion Rate then in effect by the number of shares of
Series A Preferred Stock being converted. The “Series A Conversion Rate” shall be the quotient obtained by dividing $3.00 by the Series A Conversion Price. The “Series A Conversion Price” shall initially be
$3.00, which shall be adjusted from time to time as provided below. As of the date of this Third Amended and Restated Certificate of Incorporation, the Series A Conversion Price is $3.00. 
 (b) Optional Conversion for Series B Preferred Stock. Subject to and in compliance with the provisions of this
Section B4, any shares of Series B Preferred Stock may, at the option of the holder, be converted at any time into fully paid and nonassessable shares of Common Stock. The number of shares of Common Stock to which a holder of Series B
Preferred Stock shall be entitled upon conversion shall be the product obtained by multiplying the Series B Conversion Rate then in effect by the number of shares of Series B Preferred Stock being converted. The “Series B
Conversion Rate” shall be the quotient obtained by dividing $5.00 by the Series B Conversion Price. The “Series B Conversion Price” shall initially be $5.00, which shall be adjusted from time to time as provided below. As of
the date of this Third Amended and Restated Certificate of Incorporation, the Series B Conversion Price is $4.7391. 
  

 26 

 (c) Optional Conversion for Series C Preferred Stock. Subject to and in
compliance with the provisions of this Section B4, any shares of Series C Preferred Stock may, at the option of the holder, be converted at any time into fully paid and nonassessable shares of Common Stock. The number of shares of Common
Stock to which a holder of Series C Preferred Stock shall be entitled upon conversion shall be the product obtained by multiplying the Series C Conversion Rate then in effect by the number of shares of Series C Preferred Stock being
converted. The “Series C Conversion Rate” shall be the quotient obtained by dividing $5.60 by the Series C Conversion Price. The “Series C Conversion Price” shall initially be $5.60, which shall be adjusted from
time to time as provided below. As of the date of this Third Amended and Restated Certificate of Incorporation, the Series C Conversion Price is $5.1435. 
 (d) Optional Conversion for Series D Preferred Stock. Subject to and in compliance with the provisions of this
Section B4, any shares of Series D Preferred Stock may, at the option of the holder, be converted at any time into fully paid and nonassessable shares of Common Stock. The number of shares of Common Stock to which a holder of Series D
Preferred Stock shall be entitled upon conversion shall be the product obtained by multiplying the Series D Conversion Rate then in effect by the number of shares of Series D Preferred Stock being converted. The “Series D
Conversion Rate” shall be the quotient obtained by dividing $4.20 by the Series D Conversion Price. The “Series D Conversion Price” shall initially be $4.20, which shall be adjusted from time to time as provided below. As of
the date of this Third Amended and Restated Certificate of Incorporation, the Series D Conversion Price is $4.20. 
 (e)
Mechanics of Conversion. Each holder of Preferred Stock who desires to convert the same into shares of Common Stock pursuant to this Section B4 shall surrender the certificate or certificates therefor, duly endorsed, at the office of the
corporation or any transfer agent for the Preferred Stock, and shall give written notice to the corporation at such office that holder elects to convert the same. Such notice shall state the number of shares of Preferred Stock being converted.
Thereupon, the corporation shall promptly issue and deliver at such office to such holder a certificate or certificates for the number of shares of Common Stock to which such holder is entitled and shall promptly pay (1) in cash or, to the
extent sufficient funds are not then legally available therefor, in Common Stock (at the Common Stock’s fair market value determined by the board of directors as of the date of such conversion), any declared and unpaid dividends on the shares
of Preferred Stock being converted and (2) in cash (at the Common Stock’s fair market value determined by the board of directors as of the date of conversion) the value of any fractional share of Common Stock otherwise issuable to such
holder. Such conversion shall be deemed to have been made at the close of business on the date of such surrender of the certificates, duly endorsed representing the shares of Preferred Stock to be converted together with such written notice, and the
person entitled to receive the shares of Common Stock issuable upon such conversion shall be treated for all purposes as the record holder of such shares of Common Stock at such time. If the conversion is in 

  

 27 

 
connection with an underwritten offering of securities registered pursuant to the Securities Act of 1933, as amended, the conversion may, at the option of
any holder tendering Preferred Stock for conversion, be conditioned upon the closing with the underwriters of the sale of securities pursuant to each offering, in which event the persons entitled to receive the Common Stock upon conversion of the
Preferred Stock shall not be deemed to have converted such Preferred Stock until immediately prior to the closing of such sale of securities. 
 (f) Adjustment for Stock Splits and Combinations. If the corporation shall at any time or from time to time after the date that the first share of Series D Preferred Stock is issued (the “Original
Issue Date”) effect a subdivision of the outstanding Common Stock without a corresponding subdivision of the Series A Preferred Stock, the Series B Preferred Stock, the Series C Preferred Stock, and the Series D Preferred
Stock, the Series A Conversion Price, the Series B Conversion Price, the Series C Conversion Price, and the Series D Conversion Price, in effect immediately before that subdivision shall each be proportionately decreased.
Conversely, if the corporation shall at any time or from time to time after the Original Issue Date combine the outstanding shares of Common Stock into a smaller number of shares without a corresponding combination of the Series A Preferred
Stock, the Series B Preferred Stock, the Series C Preferred Stock, and the Series D Preferred Stock, the Series A Conversion Price, the Series B Conversion Price, the Series C Conversion Price and the Series D
Conversion Price in effect immediately before the combination shall each be proportionately increased. Any adjustment under this Section B(4)(f) shall become effective at the time the subdivision or combination becomes effective. 
 (g) Adjustment for Common Stock Dividends and Distributions. If the corporation at any time or from time to time after the Original
Issue Date makes, or fixes a record date for the determination of holders of Common Stock entitled to receive, a dividend or other distribution payable in additional shares of Common Stock, in each such event each of the Series A Conversion
Price, the Series B Conversion Price, the Series C Conversion Price and the Series D Conversion Price that is then in effect shall be decreased as of the time of such issuance or, in the event such record date is fixed, as of the
close of business on such record date, by multiplying each of the Series A Conversion Price, the Series B Conversion Price, the Series C Conversion Price and the Series D Conversion Price then in effect by a fraction (1) the
numerator of which is the total number of shares of Common Stock issued and outstanding immediately prior to the time of such issuance or the close of business on such record date, and (2) the denominator of which is the total number of shares
of Common Stock issued and outstanding immediately prior to the time of such issuance or the close of business on such record date plus the number of shares of Common Stock issuable in payment of such dividend or distribution; provided, however,
that if such record date is fixed and such dividend is not fully paid or if such distribution is not fully made on the date fixed therefor, each of the Series A Conversion Price, the Series B Conversion Price, the Series C Conversion
Price and the Series D Conversion Price shall be recomputed accordingly as of the close of 

  

 28 

 
business on such record date and thereafter the Series A Conversion Price, the Series B Conversion Price, the Series C Conversion Price and
the Series D Conversion Price shall be adjusted pursuant to this Section B4(g) to reflect the actual payment of such dividend or distribution. 
 (h) Adjustment for Reclassification, Exchange and Substitution. If at any time or from time to time after the Original Issue Date, the Common Stock is changed into the same or a different number of shares of
any class or classes of stock, whether by recapitalization, reclassification or otherwise (other than a Merger or Asset Transfer or a subdivision or combination of shares or stock dividend or a reorganization, merger, consolidation or sale of assets
provided for elsewhere in this Section B4), in any such event each holder of Preferred Stock shall have the right thereafter to convert such stock into the kind and amount of stock and other securities and property receivable upon such
recapitalization, reclassification or other change by holders of the maximum number of shares of Common Stock into which such shares of Preferred Stock could have been converted immediately prior to such recapitalization, reclassification or change,
all subject to further adjustment as provided herein or with respect to such other securities or property by the terms thereof. 
 (i) Reorganizations, Mergers, Consolidations or Sales of Assets. If at any time or from time to time after the Original Issue Date, there is a capital reorganization of the Common Stock (other than a Merger or Asset Transfer or a
recapitalization, subdivision, combination, reclassification, exchange or substitution of shares provided for elsewhere in this Section B4), as a part of such capital reorganization, provision shall be made so that the holders of the Preferred
Stock shall thereafter be entitled to receive upon conversion of the Preferred Stock the number of shares of stock or other securities or property of the corporation to which a holder of the number of shares of Common Stock deliverable upon
conversion would have been entitled on such capital reorganization, subject to adjustment in respect of such stock or securities by the terms thereof. In any such case, appropriate adjustment shall be made in the application of the provisions of
this Section B4(i) with respect to the rights of the holders of Preferred Stock after the capital reorganization to the end that the provisions of this Section B4(i) (including adjustment of the Series A Conversion Price, the Series B
Conversion Price, the Series C Conversion Price and the Series D Conversion Price then in effect and the number of shares issuable upon conversion of the Preferred Stock) shall be applicable after that event and be as nearly equivalent as
practicable. 
 (j) Sale of Shares Below Series A Conversion Price, Series B Conversion Price, Series C
Conversion Price or Series D Conversion Price. 
 (1) If at any time or from time to time after the Original Issue
Date, the corporation issues or sells or is deemed by the express provisions of this subsection (1) to have issued or sold, Additional Shares of Common Stock (as defined below), other than as a dividend or other 

  

 29 

 
distribution on any class of stock and other than a subdivision or combination of shares of Common Stock, for an Effective Price (as defined below) less than
the then effective Series A Conversion Price, then and in each such case the then existing Series A Conversion Price shall be reduced, as of the opening of business on the date of such issue or sale, to a price determined by multiplying
the Series A Conversion Price by a fraction (i) the numerator of which shall be (A) the number of shares of Common Stock deemed outstanding immediately prior to such issue or sale, plus (B) the number of shares of Common Stock
which the aggregate Consideration Received (as defined below) by the corporation for the total number of Additional Shares of Common Stock so issued would purchase at such Series A Conversion Price, and (ii) the denominator of which shall
be the number of shares of Common Stock deemed outstanding immediately prior to such issue or sale plus the total number of Additional Shares of Common Stock so issued. For the purposes of the preceding sentence, the number of shares of Common Stock
deemed to be outstanding as of a given date shall be the sum of (i) the number of shares of Common Stock actually outstanding, (ii) the number of shares of Common Stock into which the then outstanding shares of Series A Preferred
Stock could be converted if fully converted on the day immediately preceding the given date, and (iii) the number of shares of Common Stock which could be obtained through the exercise or conversion of all other rights, options and convertible
securities or debt instruments of the corporation outstanding on the day immediately preceding the given date, including the shares of common stock which could be obtained upon conversion of all other series of Preferred Stock. 
 (2) If at any time or from time to time after the Original Issue Date, the corporation issues or sells or is deemed by the express
provisions of this subsection (2) to have issued or sold, Additional Shares of Common Stock, other than as a dividend or other distribution on any class of stock and other than a subdivision or combination of shares of Common Stock, for an
Effective Price less than the then effective Series B Conversion Price, then and in each such case the then existing Series B Conversion Price shall be reduced, as of the opening of business on the date of such issue or sale, to a price
determined by multiplying the Series B Conversion Price by a fraction (i) the numerator of which shall be (A) the number of shares of Common Stock deemed outstanding immediately prior to such issue or sale, plus (B) the number of
shares of Common Stock which the aggregate Consideration Received by the corporation for the total number of Additional Shares of Common Stock so issued would purchase at such Series B Conversion Price, and (ii) the denominator of which
shall be the number of shares of Common Stock deemed outstanding immediately prior to such issue or sale plus the total number of Additional Shares of Common Stock so issued. For the purposes of the preceding sentence, the number of shares of Common
Stock deemed to be outstanding as of a given date shall be the sum of (i)

  

 30 

 
the number of shares of Common Stock actually outstanding, (ii) the number of shares of Common Stock into which the then outstanding shares of
Series B Preferred Stock could be converted if fully converted on the day immediately preceding the given date, and (iii) the number of shares of Common Stock which could be obtained through the exercise or conversion of all other rights,
options and convertible securities or debt instruments of the corporation outstanding on the day immediately preceding the given date, including the shares of common stock which could be obtained upon conversion of all other series of Preferred
Stock. 
 (3) If at any time or from time to time after the Original Issue Date, the corporation issues or sells or is deemed
by the express provisions of this subsection (3) to have issued or sold, Additional Shares of Common Stock, other than as a dividend or other distribution on any class of stock and other than a subdivision or combination of shares of Common
Stock, for an Effective Price less than the then effective Series C Conversion Price, then and in each such case the then existing Series C Conversion Price shall be reduced, as of the opening of business on the date of such issue or sale,
to a price determined by multiplying the Series C Conversion Price by a fraction (i) the numerator of which shall be (A) the number of shares of Common Stock deemed outstanding immediately prior to such issue or sale, plus
(B) the number of shares of Common Stock which the aggregate Consideration Received by the corporation for the total number of Additional Shares of Common Stock so issued would purchase at such Series C Conversion Price, and (ii) the
denominator of which shall be the number of shares of Common Stock deemed outstanding immediately prior to such issue or sale plus the total number of Additional Shares of Common Stock so issued. For the purposes of the preceding sentence, the
number of shares of Common Stock deemed to be outstanding as of a given date shall be the sum of (i) the number of shares of Common Stock actually outstanding, (ii) the number of shares of Common Stock into which the then outstanding
shares of Series C Preferred Stock could be converted if fully converted on the day immediately preceding the given date, and (iii) the number of shares of Common Stock which could be obtained through the exercise or conversion of all
other rights, options and convertible securities or debt instruments of the corporation outstanding on the day immediately preceding the given date, including the shares of common stock which could be obtained upon conversion of all other series of
Preferred Stock. 
 (4) If at any time or from time to time after the Original Issue Date, the corporation issues or sells or
is deemed by the express provisions of this subsection (4) to have issued or sold, Additional Shares of Common Stock, other than as a dividend or other distribution on any class of stock and other than a subdivision or combination of shares of
Common Stock, for an Effective Price less than the then effective Series D Conversion Price, then and in each such case the then existing Series D 

  

 31 

 
Conversion Price shall be reduced, as of the opening of business on the date of such issue or sale, to a price determined by multiplying the Series D
Conversion Price by a fraction (i) the numerator of which shall be (A) the number of shares of Common Stock deemed outstanding immediately prior to such issue or sale, plus (B) the number of shares of Common Stock which the aggregate
Consideration Received by the corporation for the total number of Additional Shares of Common Stock so issued would purchase at such Series D Conversion Price, and (ii) the denominator of which shall be the number of shares of Common Stock
deemed outstanding immediately prior to such issue or sale plus the total number of Additional Shares of Common Stock so issued. For the purposes of the preceding sentence, the number of shares of Common Stock deemed to be outstanding as of a given
date shall be the sum of (i) the number of shares of Common Stock actually outstanding, (ii) the number of shares of Common Stock into which the then outstanding shares of Series D Preferred Stock could be converted if fully converted
on the day immediately preceding the given date, and (iii) the number of shares of Common Stock which could be obtained through the exercise or conversion of all other rights, options and convertible securities or debt instruments of the
corporation outstanding on the day immediately preceding the given date, including the shares of common stock which could be obtained upon conversion of all other series of Preferred Stock. 
 (5) For the purpose of making any adjustment required under this Section B4(j), the consideration received by the corporation for
any issue or sale of securities (the “Consideration Received”) shall (i) to the extent it consists of cash, be computed at the net amount of cash received by the corporation after deduction of any underwriting or similar commissions,
compensation or concessions paid or allowed by the corporation in connection with such issue or sale but without deduction of any expenses payable by the corporation, (ii) to the extent it consists of property other than cash, be computed at
the fair value of that property as determined in good faith by the board of directors, and (iii) if Additional Shares of Common Stock, Convertible Securities (as defined below) or rights or options to purchase either Additional Shares of Common
Stock or Convertible Securities are issued or sold together with other stock or securities or other assets of the corporation for a consideration which covers both, be computed as the portion of the consideration so received that may be reasonably
determined in good faith by the board of directors to be allocable to such Additional Shares of Common Stock, Convertible Securities or rights or options. 
 (6) For the purpose of the adjustment required under this Section B4(j), if the corporation issues or sells (i) stock or other securities convertible into Additional Shares of Common Stock (such convertible
stock or securities being herein referred to as “Convertible Securities”) or (ii) rights or options for the purchase of Additional Shares of Common 

  

 32 

 
Stock or Convertible Securities, and if the Effective Price of such Additional Shares of Common Stock is less than the Series A Conversion Price (with
respect to the provisions of Section B4(j)(1), above), the Series B Conversion Price (with respect to the provisions of Section B4(j)(2), above), the Series C Conversion Price (with respect to the provisions of Section B4(j)(3),
above) or the Series D Conversion Price (with respect to the provisions of Section B4(j)(4), above, in each case the corporation shall be deemed to have issued at the time of the issuance of such rights or options or Convertible Securities
the maximum number of Additional Shares of Common Stock issuable upon exercise or conversion thereof and to have received as consideration for the issuance of such shares an amount equal to the total amount of the consideration, if any, received by
the corporation for the issuance of such rights or options or Convertible Securities, plus, in the case of such rights or options, the minimum amounts of consideration, if any, payable to the corporation upon the exercise of such rights or options,
plus, in the case of Convertible Securities, the minimum amounts of consideration, if any, payable to the corporation upon the conversion thereof; provided that if in the case of Convertible Securities the minimum amounts of such consideration
cannot be ascertained, but are a function of antidilution or similar protective clauses, the corporation shall be deemed to have received the minimum amounts of consideration without reference to such clauses; provided further that if the minimum
amount of consideration payable to the corporation upon the exercise or conversion of rights, options or Convertible Securities is reduced over time or on the occurrence or nonoccurrence of specified events other than by reason of antidilution
adjustments, the Effective Price shall be recalculated at that time using the figure to which such minimum amount of consideration is reduced; provided further that if the minimum amount of consideration payable to the corporation upon the exercise
or conversion of such rights, options or Convertible Securities is subsequently increased, the Effective Price shall be again recalculated using the increased minimum amount of consideration payable to the corporation upon the exercise or conversion
of such rights, options or Convertible Securities. No further adjustment of the Series A Conversion Price, the Series B Conversion Price, the Series C Conversion Price, or the Series D Conversion Price as adjusted pursuant to the
foregoing, shall be made as a result of the actual issuance of Additional Shares of Common Stock on the exercise of any such rights or options or the conversion of any such Convertible Securities. If any such rights or options or the conversion
privilege represented by any such Convertible Securities shall expire without having been exercised, the Series A Conversion Price, the Series B Conversion Price, the Series C Conversion Price or the Series D Conversion Price as
adjusted pursuant to the foregoing shall be readjusted to the Series A Conversion Price, the Series B Conversion Price, the Series C Conversion Price and the Series D Conversion Price which would have been in effect had an
adjustment been 
  

 33 

 made on the basis that the only Additional Shares of Common Stock so issued were the Additional Shares
of Common Stock, if any, actually issued or sold on the exercise of such rights or options or rights of conversion of such Convertible Securities, and such Additional Shares of Common Stock, if any, were issued or sold for the consideration actually
received by the corporation upon such exercise, plus the consideration, if any, actually received by the corporation for the granting of all such rights or options, whether or not exercised, plus the consideration received for issuing or selling the
Convertible Securities actually converted, plus the consideration, if any, actually received by the corporation on the conversion of such Convertible Securities, provided that such readjustment shall not apply to prior conversions of Preferred
Stock. 
 (7) For purposes of this Section B4(j), “Additional Shares of Common Stock” shall mean all shares of
Common Stock issued by the corporation or deemed to be issued pursuant to this Section B4(j), other than (i) shares of Common Stock issued upon conversion of the Preferred Stock, (ii) shares of Common Stock and/or options, warrants or
other Common Stock purchase rights, and the Common Stock issued pursuant to such options, warrants or other rights (as adjusted for any stock dividends, combinations, splits, recapitalizations and the like) to employees, officers, directors,
consultants, advisors, or other persons performing services for the corporation or any subsidiary pursuant to stock purchase or stock option plans or other arrangements that are approved by the board of directors, (iii) shares of Common Stock
issued to financial institutions or other lenders or lessors in connection with leases, equipment financings, revolving lines of credit or borrowings to support working capital, or similar borrowings in the ordinary course of business as approved by
the board of directors, (iv) shares of Common Stock issued in connection with bona fide acquisitions, mergers or similar transactions as approved by the board of directors, (v) shares of Common Stock issued in connection with any future
licensing of technology from third parties as approved by the board of directors, (vi) shares of Common Stock issued pursuant to the exercise of options, warrants or convertible securities outstanding as of the Original Issue Date, and
(vii) shares of Common Stock issued in connection with the transactions contemplated under Sections B4(f), (g) and (h) of this Article IV. For purposes of this Section B4(j), the “Effective Price” of Additional Shares
of Common Stock shall mean the quotient determined by dividing the total number of Additional Shares of Common Stock issued or sold, or deemed to have been issued or sold by the corporation under this Section B4(j), into the aggregate Consideration
Received, or deemed to have been received by the corporation for such issue under this Section B4(j), for such Additional Shares of Common Stock. 
 (k) Certificate of Adjustment. In each case of an adjustment or readjustment of the Series A Conversion Price, the Series B Conversion Price or 

  

 34 

 
the Series C Conversion Price, if the Series A Preferred Stock, the Series B Preferred Stock, the Series C Preferred Stock or the
Series D Preferred Stock is then convertible pursuant to this Section B4(k), the corporation, at its expense, shall compute such adjustment or readjustment in accordance with the provisions hereof and prepare a certificate showing such
adjustment or readjustment, and shall mail such certificate, by first class mail, postage prepaid, to each registered holder of Preferred Stock at the holder’s address as shown in the corporation’s books. The certificate shall set forth
such adjustment or readjustment, showing in detail the facts upon which such adjustment or readjustment is based, including a statement of (i) the Consideration Received or deemed to be received by the corporation for any Additional Shares of
Common Stock issued or sold or deemed to have been issued or sold, (ii) the Series A Conversion Price, the Series B Conversion Price, the Series C Conversion Price and the Series D Conversion Price at the time in effect,
(iii) the number of Additional Shares of Common Stock and (iv) the type and amount, if any, of other property which at the time would be received upon conversion of the Preferred Stock. 
 (l) Notices of Record Date. Upon (i) any taking by the corporation of a record of the holders of any class of securities for
the purpose of determining the holders thereof who are entitled to receive any dividend or other distribution, or (ii) any Merger or other capital reorganization of the corporation, any reclassification or recapitalization of the capital stock
of the corporation, any merger or consolidation of the corporation with or into any other corporation, any Asset Transfer, or any voluntary or involuntary dissolution, liquidation or winding up of the corporation, the corporation shall mail to each
holder of Preferred Stock at least twenty (20) days prior to the record date specified therein (or such shorter period approved by a majority of the outstanding shares of the Series A Preferred Stock, a majority of the outstanding shares
of the Series B Preferred Stock, a majority of the outstanding shares of the Series C Preferred Stock and a majority of the outstanding shares of Series D Preferred Stock) a notice specifying (i) the date on which any such record
is to be taken for the purpose of such dividend or distribution and description of such dividend or distribution, (ii) the date on which any such Merger, reorganization, reclassification, transfer, consolidation, merger, Asset Transfer,
dissolution, liquidation or winding up is expected to become effective, and (iii) the date, if any, that is to be fixed as to when the holders of record of Common Stock (or other securities) shall be entitled to exchange their shares of Common
Stock (or other securities) for securities or other property deliverable upon such Merger, reorganization, reclassification, transfer, consolidation, merger, Asset Transfer, dissolution, liquidation or winding up. 
 (m) Automatic Conversion. 
 (1) Each share of Series A Preferred Stock shall automatically be converted into shares of Common Stock, based on the then effective Series A Conversion Rate (i) at any time upon the affirmative
election of the holders of at least sixty percent (60%) of the outstanding shares of the Series A Preferred Stock, or (ii) immediately upon the closing of a firm 

  

 35 

 
commitment underwritten public offering pursuant to an effective registration statement under the Securities Act of 1933, as amended, covering the offer and
sale of Common Stock in which (A) the per share price is at least $10.50 (as adjusted for stock splits, dividends, recapitalizations and the like), and (B) the gross proceeds to the corporation (before underwriting discounts, commissions
and fees) are at least $20,000,000 (for purposes hereof, a “Qualified IPO”). Upon such automatic conversion, any declared and unpaid dividends shall be paid in accordance with the provisions of Section B1 of this Article IV. 
 (2) Each share of Series B Preferred Stock shall automatically be converted into shares of Common Stock, based on the then effective
Series B Conversion Rate (i) at any time upon the affirmative election of the holders of more than fifty percent (50%) of the outstanding shares of the Series B Preferred Stock, or (ii) immediately upon the closing of a
Qualified IPO. Upon such automatic conversion, any declared and unpaid dividends shall be paid in accordance with the provisions of Section B1 of this Article IV. 
 (3) Each share of Series C Preferred Stock shall automatically be converted into shares of Common Stock, based on the then effective
Series C Conversion Rate (i) at any time upon the affirmative election of the holders of more than fifty percent (50%) of the outstanding shares of the Series C Preferred Stock, or (ii) immediately upon the closing of a
Qualified IPO. Upon such automatic conversion, any declared and unpaid dividends shall be paid in accordance with the provisions of Section B1 of this Article IV. 
 (4) Each share of Series D Preferred Stock shall automatically be converted into shares of Common Stock, based on the then effective
Series D Conversion Rate (i) at any time upon the affirmative election of the holders of more than fifty-five percent (55%) of the outstanding shares of the Series D Preferred Stock, or (ii) immediately upon the closing of a
Qualified IPO. Upon such automatic conversion, any declared and unpaid dividends shall be paid in accordance with the provisions of Section B1 of this Article IV. 
 (5) Upon the occurrence of either of the events specified in Section B4(m)(1), above, the outstanding shares of Series A
Preferred Stock shall be converted automatically without any further action by the holders of such shares and whether or not the certificates representing such shares are surrendered to the corporation or its transfer agent, upon the occurrence of
either of the events specified in Section B4(m)(2), above, the outstanding shares of Series B Preferred Stock shall be converted automatically without any further action by the holders of such shares and whether or not the certificates
representing such shares are 

  

 36 

 
surrendered to the corporation or its transfer agent, upon the occurrence of either of the events specified in Section B4(m)(3), above, the outstanding
shares of Series C Preferred Stock shall be converted automatically without any further action by the holders of such shares and whether or not the certificates representing such shares are surrendered to the corporation or its transfer agent,
and upon the occurrence of either events specified in Section B4(m)(4), above, the outstanding shares of Series D Preferred Stock shall be converted automatically without any further action by the holders of such shares and whether or not
the certificates representing such shares are surrendered by the corporation or its transfer agent; provided, however, in each case, that the corporation shall not be obligated to issue certificates evidencing the shares of Common Stock issuable
upon such conversion unless the certificates evidencing such shares of Preferred Stock are either delivered to the corporation or its transfer agent or the holder notifies the corporation or its transfer agent that such certificates have been lost,
stolen or destroyed and executes an agreement satisfactory to the corporation to indemnify the corporation from any loss incurred by it in connection with such certificates. Upon the occurrence of such automatic conversion of the Preferred Stock,
the holders thereof shall surrender the certificates representing such shares at the office of the corporation or any transfer agent for the Preferred Stock. Thereupon, there shall be issued and delivered to such holder promptly at such office and
in its name as shown on such surrendered certificate or certificates, a certificate or certificates for the number of shares of Common Stock into which the shares of Preferred Stock surrendered were convertible on the date on which such automatic
conversion occurred, and any declared and unpaid dividends shall be paid in accordance with the provisions of Section B(1) of this Article IV. 
 (n) Fractional Shares. No fractional shares of Common Stock shall be issued upon conversion of Preferred Stock. All shares of Common Stock (including fractions thereof) issuable upon conversion of more than one
share of Preferred Stock by a holder thereof shall be aggregated for purposes of determining whether the conversion would result in the issuance of any fractional share. If, after the aforementioned aggregation, the conversion would result in the
issuance of any fractional share, the corporation shall, in lieu of issuing any fractional share, pay cash equal to the product of such fraction multiplied by the Common Stock’s fair market value (as determined by the board of directors) on the
date of conversion. 
 (o) Reservation of Stock Issuable Upon Conversion. The corporation shall at all times reserve
and keep available out of its authorized but unissued shares of Common Stock, solely for the purpose of effecting the conversion of the shares of the Preferred Stock, such number of its shares of Common Stock as shall from time to time be sufficient
to effect the conversion of all outstanding shares of the Preferred Stock. If at any time the number of authorized but unissued shares of Common Stock shall not be sufficient to effect the conversion 

  

 37 

 
of all then outstanding shares of the Preferred Stock, the corporation will take such corporate action as may, in the opinion of its counsel, be necessary to
increase its authorized but unissued shares of Common Stock to such number of shares as shall be sufficient for such purpose. 
 (p) Notices. Any notice required by the provisions of this Section B4 shall be in writing and shall be deemed effectively given: (i) upon personal delivery to the party to be notified, (ii) when sent by confirmed telex or
facsimile if sent during normal business hours of the recipient; if not, then on the next business day, (iii) five (5) days after having been sent by registered or certified mail, return receipt requested, postage prepaid, or (iv) one
(1) day after deposit with a nationally recognized overnight courier, specifying next day delivery, with written verification of receipt. All notices shall be addressed to each holder of record at the address of such holder appearing on the
books of the corporation. 
 (q) Payment of Taxes. The corporation will pay all taxes (other than taxes based upon
income) and other governmental charges that may be imposed with respect to the issue or delivery of shares of Common Stock upon conversion of shares of Preferred Stock, excluding any tax or other charge imposed in connection with any transfer
involved in the issue and delivery of shares of Common Stock in a name other than that in which the shares of Preferred Stock so converted were registered. 
 (r) No Dilution or Impairment. Without the consent of the holders of then outstanding Preferred Stock as required under
Section B4 of this Article IV, the corporation shall not amend its Certificate of Incorporation or participate in any reorganization, transfer of assets, consolidation, merger, dissolution, issue or sale of securities or take any other
voluntary action, for the purpose of avoiding or seeking to avoid the observance or performance of any of the terms to be observed or performed hereunder by the corporation, but shall at all times in good faith assist in carrying out all such action
as may be reasonably necessary or appropriate in order to protect the conversion rights of the holders of the Preferred Stock against dilution or other impairment. 
 5. Waiver of Rights, Preferences or Privileges. 
 (a) Series A Preferred Stock. Any right, preference or privilege which is specific to the Series A Preferred Stock may
be waived if holders of at least sixty percent (60%) of the outstanding shares of Series A Preferred Stock approve such waiver in writing, in which event such waiver shall be binding on all holders of Series A Preferred Stock.

 (b) Series B Preferred Stock. Any right, preference or privilege which is specific to the Series B
Preferred Stock may be waived if holders of more than fifty percent (50%) of the outstanding shares of Series B Preferred Stock approve 

  

 38 

 
such waiver in writing, in which event such waiver shall be binding on all holders of Series B Preferred Stock. 
 (c) Series C Preferred Stock. Any right, preference or privilege which is specific to the Series C Preferred Stock may
be waived if holders of more than fifty percent (50%) of the outstanding shares of Series C Preferred Stock approve such waiver in writing, in which event such waiver shall be binding on all holders of Series C Preferred Stock.

 (d) Series D Preferred Stock. Any right, preference or privilege which is specific to the Series D
Preferred Stock may be waived if holders of more than fifty-five percent (55%) of the outstanding shares of Series D Preferred Stock approve such waiver in writing, in which event such waiver shall be binding on all holders of
Series D Preferred Stock. 
 6. United States Dollars. All references herein to “$” or Dollars means
United States dollars. 
 ARTICLE V 
 The name and address of the incorporator is Kenneth C. Hunt, 780 North Water Street, Milwaukee, Wisconsin 53202. 
 ARTICLE VI

 Election of directors need not be by written ballot unless the Bylaws of the corporation shall so provide. 
 ARTICLE VII 
 In furtherance and not in
limitation of the powers conferred by statute, the board of directors of the corporation is expressly authorized to make, alter, amend or repeal the Bylaws of the corporation. 
 ARTICLE VIII 
 A. To the fullest extent not prohibited by the General Corporation Law
of Delaware as the same exists or as it may hereafter be amended, a director of the corporation shall not be personally liable to the corporation or its stockholders for monetary damages for conduct as a director. 
 B. The corporation shall indemnify to the fullest extent not prohibited by law any person made or threatened to be made a party to an action or
proceeding, whether criminal, civil, administrative or investigative, by reason of the fact that such person is or was a director, officer, employee benefit plan fiduciary, or employee of the corporation or any predecessor of the corporation or
serves or served at the request of the corporation or any predecessor of the corporation as a director, officer, agent, employee benefit plan fiduciary or employee of another 

  

 39 

 
corporation, partnership, limited liability company, joint venture, trust or other entity or enterprise. 
 C. Neither any amendment or repeal of this Article VIII, nor the adoption of any provision of the corporation’s Certificate of Incorporation
inconsistent with this Article VIII, shall eliminate or reduce the effect of this Article VIII in respect of any matter occurring, or any action or proceeding accruing or arising or that, but for this Article VIII, would accrue or arise, prior to
such amendment, repeal or adoption of an inconsistent provision. 
 2. That this Amendment and Restatement was adopted in accordance with the
provisions of Sections 242 and 245 of the General Corporation Law of the State of Delaware. 
 Executed in duplicate this
             day of February, 2003. 
  
  

			
	NIMBLEGEN SYSTEMS INC.
		
	By:	 	  
		 	(Title)

  

			
		
	Attest:	 	  
		 	Kenneth C. Hunt, Secretary

 This document was drafted by: 
 Mark T. Ehrmann 
 Godfrey & Kahn, S.C. 
 780 North Water Street 
 Milwaukee, WI 53202 
  

 40

Source: [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00122-of-00352.parquet"}, [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00122-of-00352.parquet"}]]