Document:

Agreement between the Registrant and GATX Ventures, 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)Warrant issued by the Registrant to General Electric Capital Corporation

 Exhibit 4.4 
 NEITHER THIS WARRANT NOR THE SECURITIES ISSUABLE UPON EXERCISE OF THIS WARRANT HAVE BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED. NO SALE OR DISPOSITION MAY BE EFFECTED EXCEPT IN COMPLIANCE WITH
RULE 144 UNDER SAID ACT OR WITHOUT AN EFFECTIVE REGISTRATION STATEMENT RELATED THERETO OR AN OPINION OF COUNSEL FOR THE HOLDER, SATISFACTORY TO THE COMPANY, THAT SUCH REGISTRATION IS NOT REQUIRED UNDER THE ACT OR RECEIPT OF A NO-ACTION LETTER
FROM THE SECURITIES AND EXCHANGE COMMISSION. 
 WARRANT TO PURCHASE 4,000 SHARES OF SERIES E PREFERRED 
 STOCK AND 66,000 SHARES OF SERIES F PREFERRED STOCK 
 December 8, 2006 
 THIS CERTIFIES THAT, for value received, General Electric Capital
Corporation (“Holder”) is entitled to subscribe for and purchase (i) Four Thousand (4,000) shares of fully paid and nonassessable Series E Preferred Stock and (ii) Sixty Six Thousand (66,000) shares of fully paid
and nonassessable Series F Preferred Stock (collectively, the “Warrant Shares”) of NimbleGen Systems, Inc., a Delaware corporation (the “Company”), at the Warrant Price (as hereinafter defined), subject to the provisions
and upon the terms and conditions hereinafter set forth. As used herein, the term “Preferred Stock” shall mean the Company’s presently authorized Series E Preferred Stock and the Company’s presently authorized Series F
Preferred Stock, in each case pursuant to its Sixth Amended and Restated Certificate of Incorporation, and any stock into which such Preferred Stock may hereafter be converted or exchanged and the term “Warrant Shares” shall mean the
shares of Preferred Stock which Holder may acquire pursuant to this Warrant and any other shares of stock into which such shares of Preferred Stock may hereafter be converted or exchanged. 
 This Warrant is issued pursuant to an adjustment in accordance with Section 7 of, and amends, restates and supersedes in its entirety, that certain
warrant to purchase 40,000 shares of Series F Preferred Stock dated June 30, 2006 and issued by the Company to Holder (the “Amended and Superseded Warrant”). This Warrant is issued in exchange for, and upon surrender to the Company
for cancellation of, the Amended and Superseded Warrant. This Warrant is also being issued pursuant to the Amendment No. 2 and Consent to Loan and Security Agreement (“Amendment No. 2”) entered into as of even date herewith
between Company and Holder. 
 1. Warrant Price. The “Warrant Price” shall initially be $2.571428571 per share, subject to
adjustment as provided in Section 7 below. 
 2. Conditions to Exercise. The purchase right represented by this Warrant may be
exercised at any time for all, but not less than all, of the Warrant Shares during the term commencing on the date hereof and ending at 5:00 P.M. Pacific time on the tenth anniversary of the date of this Warrant. 

 3. Method of Exercise or Conversion; Payment; Issuance of Shares; Issuance of New Warrant.

 (a) Cash Exercise. Subject to Section 2 hereof, the purchase right represented by this Warrant may be exercised by the Holder
hereof by the surrender of this Warrant (with a duly executed Notice of Exercise in the form attached hereto) at the principal office of the Company (as set forth in Section 18 below) and by payment to the Company, by check, of an amount equal
to the then applicable Warrant Price per share multiplied by the number of shares then being purchased. In the event of any exercise of the rights represented by this Warrant, certificates for the shares of stock so purchased shall be in the name
of, and delivered to, the Holder hereof, or as such Holder may direct (subject to the terms of transfer contained herein and upon payment by such Holder hereof of any applicable transfer taxes). Such delivery shall be made within 30 days after
exercise of this Warrant and at the Company’s expense. 
 (b) Conversion. In lieu of exercising this Warrant as specified in
Section 3(a), Holder may from time to time convert this Warrant, in whole or in part, into Warrant Shares by surrender of this Warrant (with a duly executed Notice of Exercise in the form attached hereto) at the principal office of the Company,
in which event the Company shall issue to Holder the number of Warrant Shares computed using the following formula: 
 X = Y (A-B)

 A 
 Where X = the number of
Warrant Shares to be issued to Holder. 
  

					
	 Y
	 	=	 	the number of Warrant Shares of the series of Preferred Stock as to which this Warrant is being so converted (the “Applicable Preferred Stock”) purchasable under this Warrant (at
the date of such calculation).
			
	 A
	 	=	 	the Fair Market Value of one share of the Applicable Preferred Stock (at the date of such calculation).
			
	 B
	 	=	 	Warrant Price (as adjusted to the date of such calculation).

 (c) Fair Market Value. For purposes of this Section 3, Fair Market Value of one share
of the Company’s Preferred Stock shall mean: 
 (i) In the event of an exercise in connection with an Initial Public
Offering, the per share Fair Market Value for the Applicable Preferred Stock shall be the Offering Price at which the underwriters initially sell Common Stock to the public multiplied by the number of shares of Common Stock into which each share of
the Applicable Preferred Stock is then convertible; or 
 (ii) The average of the closing bid and asked prices of Common Stock
quoted in the Over-The-Counter Market Summary, the last reported sale price quoted on the Nasdaq National Market (“NNM”) or on any exchange on which the Common Stock is listed, whichever is applicable, as published in the Western Edition
of the Wall Street Journal for the three (3) trading days prior to the date of determination of Fair Market Value, multiplied by the number of shares of Common Stock into which each share of the Applicable Preferred Stock is then
convertible; or 
 (iii) In the event of an exercise in connection with a merger, acquisition or other consolidation in which
the Company is not the surviving entity, the per share Fair Market Value for the Applicable Preferred Stock shall be the value to be 

  

 2 

 
received per share of the Applicable Preferred Stock by all holders of the Applicable Preferred Stock in such transaction as determined by the Board of
Directors; or 
 (iv) In any other instance, the per share Fair Market Value for the Applicable Preferred Stock shall be as
determined in the reasonable good faith judgment of the Company’s Board of Directors. 
 In the event of 3(c)(iii) or 3(c)(iv), above, the
Company’s Board of Directors shall prepare a certificate, to be signed by an authorized officer of the Company, setting forth in reasonable detail the basis for and method of determination of the per share Fair Market Value of the Applicable
Preferred Stock. The Board will also certify to the Holder that this per share Fair Market Value will be applicable to all holders of the Applicable Preferred Stock. Such certification must be made to Holder at least thirty (30)
business days prior to the proposed effective date of the merger, consolidation, sale, or other triggering event as defined in 3(c)(iii) or 3(c)(iv). 
 (d) Automatic Exercise. To the extent this Warrant is not previously exercised, it shall be automatically exercised in accordance with Sections 3(b) and 3(c) hereof (even if not surrendered)
immediately before its expiration, involuntary termination or cancellation unless Holder notifies the Company to the contrary prior to such automatic exercise. 
 (e) Treatment of Warrant Upon Acquisition of Company. 
 (i) Certain
Definitions. For the purpose of this Warrant, “Acquisition” means (x) any sale, license, or other disposition of all or substantially all of the assets of the Company, or (y) any reorganization, consolidation, or merger of
Company, or (z) any sale of Company securities, in any such case described in (x)-(z) to a third party that is not an Affiliate of the Company (or of any of the Company’s existing security-holders), where the holders of Company’s
securities before the transaction beneficially own less than 50% of the outstanding voting securities of the surviving entity after the transaction, and “Affiliate” with respect to any person or entity shall mean any other person or entity
that controls or is controlled by or is under common control with such person or entity, and each of such person’s or entity’s officers, directors, joint venturers or partners, as applicable. 
 (ii) Cash Acquisition. In the event of an Acquisition (other than a True Asset Sale as defined below) in which the sole
consideration is cash, Holder may either (a) exercise its conversion or purchase right under this Warrant and such exercise will be deemed effective immediately prior to the consummation of such Acquisition or (b) permit the Warrant to
expire upon the consummation of such Acquisition. Company shall provide Holder with written notice of any proposed Acquisition together with such reasonable information as the Holder may request in connection with such contemplated Acquisition
giving rise to such notice, which is to be delivered to Holder not less than ten (10) business days prior to the closing of the proposed Acquisition. 
  

 3 

 (iii) Asset Sale. In the event of an Acquisition that is an arms length sale of
all or substantially all of Company’s assets (and only its assets) to a third party that is not an Affiliate of Company (a “True Asset Sale”), Holder may either (a) exercise its conversion or purchase right under this Warrant and
such exercise will be deemed effective immediately prior to the consummation of such Acquisition or (b) permit the Warrant to continue until the Expiration Date if Company continues as a going concern following the closing of any such True
Asset Sale. Company shall provide the Holder with written notice of any proposed asset sale together with such reasonable information as the Holder may request in connection with such asset sale giving rise to such notice, which is to be delivered
to Holder not less than ten (10) business days prior to the closing of the proposed asset sale. 
 (iv) Assumption of
Warrant. Upon the closing of any Acquisition other than those particularly described in subsections (ii) and (iii) above, the successor entity shall assume the obligations of this Warrant, and this Warrant shall be exercisable for the
same securities, cash, and property as would be payable for the Warrant Shares issuable upon exercise of this Warrant as if such Warrant Shares were outstanding on the record date for the Acquisition and subsequent closing. The terms of this Warrant
shall be adjusted accordingly. 
 4. Representations and Warranties of Holder and the Company. 
 (a) Representations and Warranties by Holder. The Holder represents and warrants to the Company with respect to this purchase as follows:

 (i) The Holder has substantial experience in evaluating and investing in private placement transactions of securities of
companies similar to the Company so that the Holder is capable of evaluating the merits and risks of its investment in the Company and has the capacity to protect its interests. 
 (ii) Except for transfers to a Holder affiliate, the Holder is acquiring this Warrant and the Warrant Shares issuable upon exercise of
this Warrant (collectively the “Securities”) for investment for its own account and not with a view to, or for resale in connection with, any distribution thereof. The Holder understands that the Securities have not been registered under
the Securities Act of 1933, as amended (the “Act”) by reason of a specific exemption from the registration provisions of the Act which depends upon, among other things, the bona fide nature of the investment intent as expressed herein.

 (iii) The Holder acknowledges that the Securities must be held indefinitely unless subsequently registered under the Act or
an exemption from such registration is available. The Holder is aware of the provisions of Rule 144 promulgated under the Act. 
 (iv) The Holder is an “accredited investor” within the meaning of Regulation D promulgated under the Act. 
 (v) The Holder has had an opportunity to discuss the Company’s business, management and financial affairs with its management and an opportunity to review the Company’s facilities. The Holder understands that such discussions,

  

 4 

 
as well as the written information issued by the Company, were intended to describe the aspects of the Company’s business and prospects which the
Company believes to be material but were not necessarily a thorough or exhaustive description. 
 (b) Representations and Warranties by
Company. Company hereby represents and warrants to Holder that the statements in the following paragraphs of this Section 4(b) are true and correct (a) as of the date hereof and (b) except where any such representation and
warranty relates specifically to an earlier date, as of the date of any exercise of this Warrant. 
 (i) Corporate
Organization and Authority. Company (a) is a corporation duly organized, validly existing, and in good standing in its jurisdiction of incorporation, (b) has the corporate power and authority to own and operate its properties and to
carry on its business as now conducted and as proposed to be conducted; and (c) is qualified as a foreign corporation in all jurisdictions where such qualification is required except where the failure to be so qualified could not reasonably be
expected to have a material adverse effect. 
 (ii) Corporate Power. Company has all requisite legal and corporate
power and authority to execute, issue and deliver this Warrant, to issue the Warrant Shares issuable upon exercise or conversion of this Warrant, and to carry out and perform its obligations under this Warrant and any related agreements. 

(iii) Authorization; Enforceability. All corporate action on the part of Company, its officers, directors and shareholders
necessary for the authorization, execution, delivery and performance of its obligations under this Warrant and for the authorization, issuance and delivery of this Warrant and the Warrant Shares issuable upon exercise of this Warrant has been taken
and this Warrant constitutes the legally binding and valid obligation of Company enforceable in accordance with its terms. 
 (iv) Valid Issuance of Warrant and Warrant Shares. This Warrant has been validly issued and is free of restrictions on transfer other than restrictions on transfer set forth herein and under applicable state and federal securities
laws. The Warrant Shares issuable upon conversion of this Warrant, when issued, sold and delivered in accordance with the terms of this Warrant for the consideration expressed herein, will be duly and validly issued, fully paid and nonassessable,
and will be free of restrictions on transfer other than restrictions on transfer under this Warrant and under applicable state and federal securities laws. Subject to applicable restrictions on transfer, the issuance and delivery of this Warrant and
the Warrant Shares issuable upon exercise or conversion of this Warrant are not subject to any preemptive or other similar rights or any liens or encumbrances except as specifically set forth in the Company’s Certificate of Incorporation or
this Warrant. The offer, sale and issuance of the Warrant Shares, as contemplated by this Warrant, are exempt from the prospectus and registration requirements of applicable United States federal and state security laws, and neither Company nor any
authorized agent acting on its behalf has or will take any action hereafter that would cause the loss of such exemption. 
  

 5 

 (v) No Conflict. The execution, delivery, and performance of this Warrant will not
result in (a) any violation of, be in conflict with, or constitute a default under, with or without the passage of time or the giving of notice (1) any provision of Company’s Certificate of Incorporation or by-laws; (2) any
provision of any judgment, decree, or order to which Company is a party, by which it is bound, or to which any of its material assets are subject; (3) any contract, obligation, or commitment to which Company is a party or by which it is bound;
or (4) any statute, rule, or governmental regulation applicable to Company, or (b) the creation of any material lien, charge or encumbrance upon any material assets of Company. 
 (vi) Capitalization. The capitalization table of Company delivered to Holder pursuant to Amendment No. 2 is complete and
accurate as of the date hereof and reflects both immediately before and on a pro forma basis immediately after the recapitalization of Company (the (“Recapitalization”) described in Amendment No. 2 (a) all outstanding capital
stock of Company as of such date and (b) all outstanding warrants, options, conversion privileges, or other rights or agreements to purchase or otherwise acquire or issue any equity securities or convertible securities of Company as of such
date. Company has reserved 70,000 shares of Common Stock for issuance upon conversion of the Preferred Stock. 
 (vii)
Warrant Price. As of June 30, 2006, the “Warrant Price” applicable under and as set forth in the Amended and Superseded Warrant was no greater than the lowest price at which Company then had issued its then authorized Series F
Preferred Stock to an unrelated third party in an arm’s length transaction. 
 5. Legends. 
 (a) Legend. Each certificate representing the Warrant Shares shall be endorsed with the following legend: 
 THESE SECURITIES HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933 AND MAY NOT BE TRANSFERRED UNLESS COVERED BY AN EFFECTIVE REGISTRATION
STATEMENT UNDER SAID ACT, A “NO ACTION” LETTER FROM THE SECURITIES AND EXCHANGE COMMISSION WITH RESPECT TO SUCH TRANSFER, A TRANSFER MEETING THE REQUIREMENTS OF RULE 144 OF THE SECURITIES AND EXCHANGE COMMISSION, OR (IF REASONABLY
REQUIRED BY THE COMPANY) AN OPINION OF COUNSEL SATISFACTORY TO THE ISSUER TO THE EFFECT THAT ANY SUCH TRANSFER IS EXEMPT FROM SUCH REGISTRATION. 
 The
Company need not enter into its stock records a transfer of Warrant Shares unless the conditions specified in the foregoing legend are satisfied. The Company may also instruct its transfer agent not to allow the transfer of any of the Warrant Shares
unless the conditions specified in the foregoing legend are satisfied. 
  

 6 

 (b) Removal of Legend and Transfer Restrictions. The legend relating to the Act endorsed on a
certificate pursuant to paragraph 5(a) of this Warrant shall be removed and the Company shall issue a certificate without such legend to the Holder of the Securities if (i) the Securities are registered under the Act and a prospectus meeting
the requirements of Section 10 of the Act is available or (ii) the Holder provides to the Company an opinion of counsel for the Holder reasonably satisfactory to the Company, a no-action letter or interpretive opinion of the staff of the
SEC reasonably satisfactory to the Company, or other evidence reasonably satisfactory to the Company, to the effect that public sale, transfer or assignment of the Securities may be made without registration and without compliance with any
restriction such as Rule 144. 
 6. Condition of Transfer or Exercise of Warrant. It shall be a condition to any transfer or
exercise of this Warrant that at the time of such transfer or exercise, Holder shall provide the Company with a representation in writing that Holder or transferee is acquiring this Warrant and the shares of Preferred Stock to be issued upon
exercise for investment purposes only and not with a view to any sale or distribution, or will provide the Company with a statement of pertinent facts covering any proposed distribution. As a further condition to any transfer of this Warrant or any
or all of the shares of Preferred Stock issuable upon exercise of this Warrant, other than a transfer registered under the Act, the Company may request a legal opinion, in form and substance satisfactory to the Company and its counsel, reciting the
pertinent circumstances surrounding the proposed transfer and stating that such transfer is exempt from the registration and prospectus delivery requirements of the Act. The Company shall not require Holder to provide an opinion of counsel if the
transfer is to an affiliate of Holder. Each certificate evidencing the shares issued upon exercise of this Warrant or upon any transfer of the Warrant Shares (other than a transfer registered under the Act or any subsequent transfer of shares so
registered) shall, at the Company’s option, if the Shares are not freely saleable under Rule 144(k) under the Act, contain a legend in form and substance satisfactory to the Company and its counsel, restricting the transfer of the shares to
sales or other dispositions exempt from the requirements of the Act. As further condition to each transfer, at the request of the Company, Holder shall surrender this Warrant to the Company and the transferee shall receive and accept a Warrant, of
like tenor and date, executed by the Company. 
 7. Adjustment for Certain Events. 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 (a) 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), (b) 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 (c) any transfer of all or substantially all of the assets of the Company which is
not an Acquisition, the Company, or such successor, purchaser or transferee, as the case may be, shall duly execute and deliver to Holder a new Warrant (in form and substance satisfactory to Holder of this Warrant), or the Company shall make
appropriate provision without the issuance of a new Warrant, so that the Holder shall have the right to receive, at a total purchase price not to exceed that payable upon the exercise of this Warrant, and in lieu of the Warrant Shares theretofore
issuable upon exercise or conversion of this Warrant, the kind and amount of shares of stock, other securities, money and property receivable 

  

 7 

 
upon such reclassification, change, merger or transfer by a holder of the number of shares of Preferred Stock then purchasable under this Warrant, or in the
case of such a merger or transfer in which the consideration paid consists all or in part of assets other than securities of the successor or transferee, at the option of the Holder, the securities of the successor or purchasing corporation having a
value at the time of the transaction equivalent to the value of the Warrant Shares 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 7. The provisions of this subparagraph (a) shall similarly apply to successive reclassifications, changes, mergers and transfers. 
 (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 Preferred Stock, the Warrant Price shall be proportionately decreased and the number of Warrant 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 Warrant Shares issuable hereunder shall be proportionately decreased in the case of a combination. 
 (c) Stock Dividends and Other Distributions. If Company at any time while this Warrant is outstanding and unexpired shall (i) pay a dividend with respect to Preferred Stock payable in Preferred Stock, 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 Preferred Stock outstanding immediately prior to such dividend or distribution, and (B) the denominator of which shall be the total number of shares of Preferred
Stock outstanding immediately after such dividend or distribution; or (ii) make any other distribution with respect to Preferred Stock (except any distribution specifically provided for in Sections 7(a) and 7(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 Warrant Shares 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 Warrant Shares purchasable hereunder shall be adjusted, to the nearest whole share, to the product obtained by multiplying the number of Warrant 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) Adjustment for Dilutive Issuance. The Warrant Price and the number of Warrant Shares issuable upon exercise of this Warrant or,
if the Warrant Shares are Preferred Stock, the number of shares of common stock issuable upon conversion of the Shares, shall be subject to adjustment, from time to time in the manner set forth in the Company’s Certificate of Incorporation as
if the Warrant Shares were issued and outstanding on and as of the date of any such required adjustment. The provisions set forth for the Warrant Shares in the Company’s Certificate of Incorporation relating to the above in effect as of the
date hereof may not be amended, modified or waived, without the prior written consent of Holder unless such amendment, modification or waiver affects the rights associated with the Warrant Shares in the same manner as such amendment, modification or
waiver affects the rights associated with all other shares of the same series and class as the Warrant Shares. 
  

 8 

 8. Notice of Adjustments. Whenever any Warrant Price or the kind or number of securities issuable
under this Warrant shall be adjusted pursuant to Section 7 hereof, the Company shall prepare a certificate signed by an officer of the Company 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 number or kind of shares issuable upon exercise of this Warrant after giving effect to such adjustment, and shall cause copies of such certificate to be mailed
(by certified or registered mail, return receipt required, postage prepaid) within thirty (30) days of such adjustment to the Holder of this Warrant as set forth in Section 18 hereof. 
 9. Transferability of Warrant. This Warrant is transferable in whole, but not in part, on the books of the Company at its principal office by the
registered Holder hereof upon surrender of this Warrant properly endorsed, subject to compliance with Section 6 and applicable federal and state securities laws. The Company shall issue and deliver to the transferee a new Warrant representing
the Warrant so transferred. Holder shall not have any right to transfer any portion of this Warrant or any Warrant Shares issued upon exercise or conversion of this Warrant (or, prior to the Company’s initial public offering under the Act, any
shares of Common Stock of the Company into which the Warrant Shares have been converted), to any direct competitor of the Company (unless such competitor is the acquirer in an Acquisition). 
 10. Registration Rights. The Company hereby grants “piggyback” registration rights to the Holder on the terms and subject to the
conditions provided in Section 2.2 of that certain Fifth Amended and Restated Registration Rights Agreement dated November 23, 2005, among the Company and certain other parties (the “Registration Rights Agreement”), with respect
to any Common Stock of the Company obtained by the Holder upon exercise or conversion of this Warrant, and/or subsequent conversion of the Preferred Stock, as if the Holder was a “Holder” and such stock constituted “Registrable
Securities” under the Registration Rights Agreement. Notwithstanding the foregoing, in the application of such terms and conditions in circumstances where the underwriter(s) determines to limit the number of shares to be included in a
particular registration statement, (a) the Company shall use commercially reasonable efforts to include the Holder’s shares in such registration statement and (b) the Holder acknowledges that Holder’s shares shall be subject to
the senior registration rights of “Holders” under the Registration Rights Agreement and accordingly may not ultimately be included in such registration statement. Furthermore, the Holder agrees to enter into customary “lock-up”
or comparable agreements with the underwriter(s) in the Company’s initial public offering pursuant to a registration statement under the Securities Act of 1933, as amended, to the extent that other non-affiliate shareholders that hold
comparable amounts of the Company’s Common Stock are so required by such underwriter(s) as a condition of such offering. 
 11. No
Fractional Shares. No fractional share of Preferred Stock will be issued in connection with any exercise or conversion hereunder, but in lieu of such fractional share the Company shall make a cash payment therefor upon the basis of the Warrant
Price then in effect. 
 12. Charges, Taxes and Expenses. Issuance of certificates for shares of Preferred Stock upon the exercise or
conversion of this Warrant shall be made without charge to Holder for any United States or state of the United States documentary stamp tax or other incidental expense with respect to the issuance of such certificate, all of which taxes and expenses
shall be paid by Company, and such certificates shall be issued in the name of Holder. 
  

 9 

 13. No Shareholder Rights Until Exercise. Except as expressly provided herein, this Warrant does
not entitle Holder to any voting rights or other rights as a shareholder of Company prior to the exercise hereof. 
 14. Registry of
Warrant. Company shall maintain a registry showing the name and address of the registered Holder of this Warrant. This Warrant may be surrendered for exchange or exercise, in accordance with its terms, at such office or agency of Company, and
Company and Holder shall be entitled to rely in all respects, prior to written notice to the contrary, upon such registry. 
 15. Loss,
Theft, Destruction or Mutilation of Warrant. Upon receipt by Company of evidence reasonably satisfactory to it of the loss, theft, destruction or mutilation of this Warrant, and, in the case of loss, theft, or destruction, of indemnity
reasonably satisfactory to it, and, if mutilated, upon surrender and cancellation of this Warrant, Company will execute and deliver a new Warrant, having terms and conditions substantially identical to this Warrant, in lieu hereof. 
 16. Miscellaneous. 
 (a) Issue
Date. The provisions of this Warrant shall be construed and shall be given effect in all respect as if it had been issued and delivered by Company on the date hereof. 
 (b) Successors. This Warrant shall be binding upon any successors or assigns of Company. 
 (c)
Governing Law. This Warrant shall be governed by and construed in accordance with the laws of the State of Delaware. 
 (d)
Headings. The headings used in this Warrant are used for convenience only and are not to be considered in construing or interpreting this Warrant. 
 (e) Saturdays, Sundays, Holidays. If the last or appointed day for the taking of any action or the expiration of any right required or granted herein shall be a Saturday or a Sunday or shall be a legal holiday
in the State of Delaware, then such action may be taken or such right may be exercised on the next succeeding day not a legal holiday. 
 (f)
Waiver of Jury Trial. Each of the parties hereto hereby waives to the fullest extent permitted by applicable law, any right it may have to a trial by jury in respect of any litigation directly or indirectly arising out of, under or in
connection with this Warrant or the Preferred Shares. 
 (g) Attorney’s Fees. In the event of any dispute between the parties
concerning the terms and provisions of this Warrant, the party prevailing in such dispute shall be entitled to collect from the other party all costs incurred in such dispute, including reasonable attorney’s fees. 
  

 10 

 17. No Impairment. Company will not, by amendment of its Certificate of Incorporation or any other
voluntary action, 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 hereof against impairment. Without limiting the breadth of the foregoing, Company will not cause the Series F Preferred Stock into which this Warrant is exercisable or convertible unless such
conversion is effected as part of the conversion of all Company’s outstanding series of preferred stock and other senior securities into Common Stock. 
 18. Addresses. Any notice required or permitted hereunder shall be in writing and shall be mailed by overnight courier, registered or certified mail, return receipt required, and postage prepaid, or otherwise
delivered by hand or by messenger, addressed as set forth below, or at such other address as the Company or the Holder hereof shall have furnished to the other party. 
  

			
	 If to Company:
	    	NimbleGen Systems, Inc.
		    	One Science Court
		    	Madison WI 53711
		    	Attn: Chief Executive Officer
		
	 If to Holder:
	    	General Electric Capital Corporation
		    	83 Wooster Heights Road
		    	Danbury, CT 06810
		    	Attn: Credit Manager-Life Science Finance
		
	 With a copy to:
	    	General Electric Capital Corporation
		    	Two Bethesda Metro Center
		    	Suite 600
		    	Bethesda, MD 20814
		    	Attn: General Counsel

  

 11 

 [SIGNATURES FOLLOW] 
  

 12 

 IN WITNESS WHEREOF, Company has caused this Warrant to be executed by its officers thereunto duly authorized. 

 

					
	 Dated as of December 8, 2006.
	 	NIMBLEGEN SYSTEMS, INC.
			
		 	By:	 	 /s/ David S. Snyder

		 	Name:	 	 David S. Snyder

		 	Title:	 	Vice President and Chief Financial Officer

  

 S-1 

 NOTICE OF EXERCISE 
 TO: 
  

	1.	The undersigned Warrantholder (“Holder”) elects to acquire shares of the Series E Preferred Stock and shares of the Series F Preferred Stock (collectively, the
“Preferred Stock”) of NimbleGen Systems, Inc., (the “Company”) pursuant to the terms of the Warrant to purchase 4,000 shares of Series E Preferred Stock and 66,000 shares of Series F Preferred Stock dated December
    , 2006 (the “Warrant”). 

  

	2.	The Holder exercises its rights under the Warrant as set forth below: 

  

					
	 (    )
	  	 Holder elects to purchase the shares of Preferred
  
 Stock as provided in Section 3(a) and tenders herewith a check in
  
 the amount of $180,000 as payment of the purchase price.
	 	
			
	 (    )
	  	 Holder elects to convert the purchase rights into shares of
  
 Preferred Stock as provided in Section 3(b) of the Warrant
  
 as to the following number and series of such Preferred Stock:
	 	
			
		  	                                      
                                        
                          .	 	

  

	3.	Holder surrenders the Warrant with this Notice of Exercise. 

 Holder
represents that it is acquiring the aforesaid shares of Preferred Stock for investment and not with a view to or for resale in connection with distribution and that the Holder has no present intention of distributing or reselling the shares.

 Please issue a certificate representing the shares of the Preferred Stock in the name of Holder or in such other name as is specified below: 

 

					
	 Name:
	 	  
	 	
	 Address:
	 	  
	 	
			
	 Taxpayer I.D.:
	 	  
	 	

  

			
	  

	 (Holder)
	 	
		
	 By:
	 	  

	 Title:
	 	  

	 Date:

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