Document:

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Exhibit 4.2

EXECUTION VERSION

BIOTROVE, INC.

Second Amended and Restated

Registration Rights Agreement

     This Second Amended and Restated Registration Rights Agreement (the “Agreement”) is
made as of this 10th day of December, 2007, by and among (I) BioTrove, Inc., a Delaware
corporation (the “Company”), (II) certain holders of the Company’s Common Stock (as defined
below) who are listed from time to time on Exhibit A hereto and who are identified on the
signature pages hereto or who shall become a party hereto by execution and delivery to the Company
of a Counterpart Signature Page for Common Stockholders in the form attached hereto as
Attachment I (the “Common Stockholders”), and (III) the holders of the Company’s
Series B/C Preferred Stock (as defined below) listed from time to time on Exhibit B hereto
and who are identified on the signature pages hereto or who shall become a party hereto by
execution and delivery to the Company of a Counterpart Signature Page for Investors in the form
attached hereto as Attachment II (the “Investors”). For the sake of clarity, any
person or entity holding both Common Stock and Series B/C Preferred Stock shall be considered a
“Common Stockholder” with respect to the shares of Common Stock (other than shares of Common Stock
issued upon conversion of Series B/C Preferred Stock) held by it and an “Investor” with respect to
the shares of Series B/C Preferred Stock (including shares of Common Stock issued upon conversion
of Series B/C Preferred Stock) held by it.

     WHEREAS, the Company and certain of the parties hereto are parties to that certain Amended and
Restated Registration Rights Agreement dated as of December 30, 2003, as amended, by and among the
Company and the parties listed on the signature pages thereto (the “Prior Registration Rights
Agreement”);

     WHEREAS, the parties executing signature pages hereto comprise the requisite parties necessary
to amend and restate in its entirety the Prior Registration Rights Agreement in accordance with its
terms;

     WHEREAS, contemporaneously with the execution and delivery of this Agreement, the Company and
certain of the Investors have entered into a Note Subscription Agreement, dated as of the date
hereof (as in effect from time to time, the “Note Subscription Agreement”) in connection
with the issuance and sale by the Company to certain Investors of promissory notes
(“Notes”) convertible into shares of the Series C Preferred Stock (as defined below);

     WHEREAS, in connection with the sale of the Notes, the parties hereto desire to amend and
restate the Prior Registration Rights Agreement as provided herein; and

     NOW, THEREFORE, in consideration of the foregoing recitals and the mutual covenants and
agreements herein contained, the parties hereto agree as follows:

 

 

1. Registration Rights.

     1.1. Definitions.

     (a) The term “1933 Act” means the Securities Act of 1933, as amended, or any successor
statute thereto, and the rules and regulations of the Securities and Exchange Commission
(the “SEC”) promulgated from time to time thereunder, all as the same shall be in
effect at the time.

     (b) The terms “Form S-1”, “Form S-3”, “Form S-4” and “Form S-8” mean such respective
forms under the 1933 Act as in effect on the date hereof or any successor registration forms
to Form S-1, Form S-3, Form S-4 and Form S-8, respectively, under the 1933 Act subsequently
adopted by the SEC.

     (c) The term “Common Stock” means the common stock, $0.01 par value per share,
of the Company.

     (d) The term “Holder” means any person owning Registrable Securities (as
defined below) or any assignee thereof in accordance with Section 1.13 hereof.

     (e) The term “Immediate Family” means, with respect to any natural person,
each of such person’s spouse, father, mother, brothers, sisters, aunts, uncles, nieces,
nephews and lineal descendants and ancestors and, with respect to any other entity, the
current stockholders, partners or members of such entity.

     (f) The term “Investor Holder” means any Holder who is an Investor or any
assignee thereof in accordance with Section 1.13 hereof.

     (g) The terms “register”, “registered”, and “registration”
refer to a registration effected by preparing and filing a registration statement or similar
document in compliance with the 1933 Act, and the automatic effectiveness or the declaration
or ordering of effectiveness of such registration statement or document.

     (h) The term “Registrable Securities” means (i) shares of Common Stock issued
upon conversion of any Series B/C Preferred Stock, (ii) any Common Stock issued as a
dividend or other distribution with respect to, in exchange for, or in replacement of, any
            shares of Common Stock which are deemed to be Registrable Securities pursuant to (i) above,
(iii) any other shares of Common Stock acquired on or after the date hereof by any Investor
which do not otherwise qualify as Registrable Securities under clauses (i) or (ii) above,
and (iv) any shares of Common Stock held by the Common Stockholders (the “Common
Stockholders’ Common Shares”) or any Common Stock issued as a dividend or other
distribution with respect to, in exchange for, or in replacement of the Common Stockholders’
Common Shares; provided, however, any and all shares described in clauses
(i)-(iv) above shall cease to be Registrable Securities upon any sale pursuant to a
registration statement under the 1933 Act or upon such time as such shares may be sold
within a 90 day period pursuant to Rule 144(k) under the 1933 Act.

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     (i) The term “Series B Preferred Stock” means the Company’s Series B
Convertible Participating Preferred Stock, $0.01 par value per share.

     (j) The term “Series B-1 Preferred Stock” means the Company’s Series B-1
Convertible Participating Preferred Stock, $0.01 par value per share.

     (k) The term “Series B/C Preferred Stock” means, collectively, the Company’s
Series C Preferred Stock, Series B Preferred Stock and Series B-1 Preferred Stock.

     (l) The term “Series C Preferred Stock” means the Company’s Series C
Convertible Participating Preferred Stock, $0.01 par value per share.

     1.2. Request for Registration.

     (a) At any time after the earlier of (i) August 22, 2005 or (ii) the date that is 180
days after the closing date of the first registered public offering of equity securities of
the Company, if the Company shall receive a written request from any Investor Holder(s) of
at least twenty-five percent (25%) of the Registrable Securities then outstanding and
entitled to registration rights under this Section 1 (the “Initiating Holders”) that
the Company effect the registration under the 1933 Act of Registrable Securities, then the
Company shall, within fifteen days of the receipt thereof, give written notice of such
request to all Holders and shall, subject to the limitations of this Section 1.2, use its
best efforts to effect such a registration as soon as practicable and in any event to file
within 90 days of the receipt of such request a registration statement under the 1933 Act
covering all the Registrable Securities which the Holders shall in writing request (within
20 days of receipt of the notice given by the Company pursuant to this Section 1.2(a)) to be
included in such registration and to use its best efforts to have such registration
statement become effective; provided, however, that the Company will not be
required to effect the registration of Registrable Securities under this Section 1.2(a)
unless the Registrable Securities are offered at a proposed aggregate offering price of not
less than $15,000,000.

     (b) 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 part of
their request made pursuant to this Section 1.2 and the Company shall include such
information in the written notice referred to in Section 1.2(a). 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 (unless otherwise mutually agreed by
two-thirds in interest of the Initiating Holders and such Holder) to the extent provided
herein. All Holders proposing to distribute their securities through such underwriting
shall (together with the Company as provided in Section 1.4(d)) enter into an underwriting
agreement in customary form with the underwriter or underwriters selected for such
underwriting by the Company and reasonably acceptable to two-thirds in interest of the
Initiating Holders; provided, however, that if the underwriter is not reasonably acceptable
to two-thirds in interest of the Initiating Holders, such Initiating Holders may select an
underwriter or underwriters which shall be reasonably acceptable to the Company.

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Notwithstanding any other provision of this Section 1.2, if, in the case of a
registration requested pursuant to Section 1.2(a), the underwriter advises the Initiating
Holders in writing that marketing factors require a limitation of the number of shares to be
underwritten, then the Initiating Holders shall so advise the Company and all Holders of
Registrable Securities which would otherwise be underwritten pursuant hereto, and all the
securities other than Registrable Securities sought to be included in the underwriting shall
first be excluded. Next, to the extent that further limitation is required, Registrable
Securities held by the Common Stockholders sought to be included in the underwriting shall
be excluded pro rata among all such Common Stockholders (according to the number of
Registrable Securities then held by each such Common Stockholder). To the extent that
further limitation is required, the number of Registrable Securities that may be included in
the underwriting shall be allocated pro rata among all Investor Holders thereof desiring to
participate in such underwriting (according to the number of Registrable Securities then
held by each such Investor Holder). For the sake of clarity, no Registrable Securities
requested by any Initiating Holder to be included in a registration pursuant to Section
1.2(a) shall be excluded from the underwriting unless (i) all securities other than
Registrable Securities have first been excluded and (ii) all Registrable Securities held by
the Common Stockholders have first been excluded.

     (c) The Company is obligated to effect only three registrations pursuant to Section
1.2(a); provided, however, that no registration pursuant to Section 1.2(a)
shall be deemed to be a registration for any purpose of this sentence if (i) the number of
Registrable Securities included in the underwriting does not equal or exceed 75% of the
number of Registrable Securities proposed by the Holders to be distributed through such
underwriting and (ii) the Holders pay all expenses of such registration, including those
otherwise payable by the Company in accordance with Section 1.6; and provided,
further, that no registration of Registrable Securities which shall not have become
and remained effective in accordance with Section 1.4 shall be deemed to be a registration
for any purpose of this sentence unless such registration was withdrawn at the request of
the Holders except under the circumstances described in the second proviso in the
penultimate sentence of Section 1.6 hereof.

     (d) Notwithstanding the foregoing provisions of this Section 1.2, in the event that
the Company is requested to file any registration statement pursuant to this Section 1.2,
(i) the Company shall not be obligated to effect the filing of such registration statement:

     (A) during the 180 days following the effective date of any other registration
statement pertaining to an underwritten public offering of securities for the
account of the Company or any Holder;

     (B) if, in the case of the initial public offering of the Company’s
securities, the Company and the Initiating Holders are unable to obtain the
commitment of the underwriter selected pursuant to Section 1.2(b) to underwrite the
offering on a firm commitment basis; or

     (C) for a period of up to 90 days after the date of a request for registration
pursuant to this Section 1.2 if at the time of such request (1) the Company is

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engaged, or has fixed plans to engage, within 90 days of the time of such
request, in a firm commitment underwritten public offering of Common Stock in which
the holders of Registrable Securities include Registrable Securities pursuant to
Section 1.3 or (2) the Company is currently engaged in a self-tender or exchange
offer and the filing of a registration statement would cause a violation of the
Securities Exchange Act of 1934, as amended (the “1934 Act”);

or (ii) if the Company shall furnish to the Holders requesting such registration statement a
certificate signed by the Chief Executive Officer of the Company stating that, in the good faith
judgment of the Board of Directors, it would not be in the best interests of the Company and its
stockholders generally for such registration statement to be filed, the Company shall have the
right to defer such filing for a period of not more than 90 days after receipt of the request of
the relevant Initiating Holders; provided, however, that the Company may not
utilize the right set forth in this Section 1.2(d)(ii) more than once in any twelve-month period.

     (e) Each registration requested pursuant to Section 1.2(a) shall be effected by the
filing of a registration statement on Form S-1 (or if such form is not available, any other
form which includes substantially the same information (other than information which is
incorporated by reference) as would be required to be included in a registration statement
on such form as currently constituted). Notwithstanding the foregoing, with the prior
consent of the Initiating Holders, such consent not to be unreasonably withheld, the Company
may, if permitted by law, effect any registration request under this Section 1 by the filing
of a registration statement on Form S-3, provided that at the request of the Initiating
Holders the Company will include on such Form S-3 information which the Initiating Holders
determine in their reasonable discretion to be of material importance to the success of such
proposed registration.

     1.3. Company Registration. If (but without any obligation to do so) the Company
proposes to register (including for this purpose a registration effected by the Company for
stockholders other than the Holders) any of its capital stock or other equity securities (or other
securities convertible into equity securities) under the 1933 Act in connection with the public
offering of such securities solely for cash (other than a registration on Form S-8 relating solely
to the sale of securities to participants in a Company stock plan (or other stock arrangement) or a
registration on Form S-4), the Company shall, at such time, promptly give each Holder written
notice of such registration. Upon the written request of any Holder given within 20 days after
mailing of such notice by the Company, the Company shall, subject to the provisions of Section 1.8,
use its best efforts to cause a registration statement covering all of the Registrable Securities
that each such Holder has requested to be registered to become effective under the 1933 Act to the
extent that such registration is permissible under the 1933 Act. If in the case of an underwritten
registration requested pursuant to Section 1.3, the underwriter advises the Company in writing that
marketing factors require a limitation of the number of shares to be underwritten, then the Company
shall so advise all Holders of Registrable Securities which would otherwise be underwritten
pursuant hereto, and all the Registrable Securities held by the Common Stockholders sought to be
included in the underwriting shall be excluded pro rata among all such Common Stockholders
(according to the number of Registrable Securities then held by each such Common Stockholder) until
the number of shares by which the underwriters intend to reduce the registration has been reached.
To the extent that further limitation is

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required, all the Registrable Securities held by the Investor Holders sought to be included in the underwriting shall be
excluded pro rata among all such Investor Holders (according to the number of Registrable
Securities then held by each such Investor Holder) until the number of shares by which the
underwriters intend to reduce the registration has been reached. For the sake of clarity, no
Registrable Securities requested by any Investor Holder to be included in a registration pursuant
to Section 1.3 shall be excluded from the underwriting unless all Registrable Securities held by
the Common Stockholders have first been excluded. The Company shall be under no obligation to
complete any offering of its securities it proposes to make and shall incur no liability to any
Holder for its failure to do so.

     1.4. Obligations of the Company. Whenever required under this Section 1 to use its
best efforts to effect the registration of any Registrable Securities, the Company shall, as
expeditiously as reasonably possible, prepare and file with the SEC a registration statement with
respect to such Registrable Securities and use its best efforts to cause such registration
statement to become effective, and, upon the request of the Holders of two-thirds of the
Registrable Securities registered thereunder, keep such registration statement effective for up to
180 days or until such earlier time at which such Holders have informed the Company in writing that
the distribution of their securities has been completed (such 180-day or shorter period, the
“Effectiveness Period”). In addition, the Company shall:

     (a) Prepare and file with the SEC such amendments and supplements to such registration
statement and the prospectus used in connection with such registration statement, and use
its best efforts to cause each such amendment and supplement to become effective, as may be
necessary to comply with the provisions of the 1933 Act with respect to the disposition of
all securities covered by such registration statement during the Effectiveness Period.

     (b) Furnish to the Holders such number of copies of a prospectus, including a
preliminary prospectus, in conformity with the requirements of the 1933 Act, and such other
documents as they may reasonably request in order to facilitate the public sale or other
disposition of Registrable Securities owned by them.

     (c) Use its best efforts to register or qualify the securities covered by such
registration statement under such other securities or Blue Sky laws of such states and
jurisdictions as shall be reasonably requested by the Holders, except that the Company shall
not be required in connection therewith or as a condition thereto to qualify to do business,
subject itself to taxation or file a general consent to service of process in any such state
or jurisdiction.

     (d) 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 of such offering. Each Holder participating in such underwriting shall also
enter into and perform its obligations under such an underwriting agreement, including
furnishing an opinion of counsel or entering into a lock-up agreement reasonably requested
by the managing underwriter in accordance with Section 1.12.

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     (e) Notify each Holder of Registrable Securities covered by such registration
statement, at any time when a prospectus relating thereto covered by such registration
statement is required to be delivered under the 1933 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 and promptly file such amendments and supplements which
may be required pursuant to Section 1.4(b) on account of such event and use its best efforts
to cause each such amendment and supplement to become effective.

     (f) Furnish, at the request of any Holder requesting registration of Registrable
Securities pursuant to this Section 1, on the date that such Registrable Securities are
delivered to the underwriters for sale in connection with a registration pursuant to this
Section 1, if such securities are being sold through underwriters, or, if such securities
are not being sold through underwriters, on the date that the registration statement with
respect to such securities becomes effective, (i) an opinion or opinions, dated such date,
of the counsel representing the Company for the purposes of such registration, in form and
substance as is customarily given by company counsel to the underwriters in an underwritten
public offering, addressed to the underwriters, if any, and to the Holders requesting
registration of Registrable Securities and (ii) a letter dated such date, from the
independent certified public accountant 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, if any, and to the Holders
requesting registration of Registrable Securities.

     (g) Apply for listing and use its best efforts to list the Registrable Securities
being registered on any national securities exchange on which a class of the Company’s
equity securities is listed or, if the Company does not have a class of equity securities
listed on a national securities exchange, apply for qualification and use its best efforts
to qualify the Registrable Securities being registered for inclusion on the automated
quotation system of the National Association of Securities Dealers, Inc.

     (h) Without in any way limiting the types of registrations to which this Section 1
shall apply, in the event that the Company shall effect a “shelf registration” under Rule
415 promulgated under the 1933 Act, the Company shall take all necessary action, including,
without limitation, the filing of post-effective amendments, to permit the Holders to
include their Registrable Securities in such registration in accordance with the terms of
this Section 1.

     1.5. Furnish Information. It shall be a condition precedent to the obligations of the
Company to take any action pursuant to this Section 1 in respect of the Registrable Securities of
any selling Holder that such selling Holder shall furnish to the Company information regarding
itself, the Registrable Securities held by it, the intended method of disposition of such
securities and any other information that shall be required to effect the registration of its
Registrable Securities.

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     1.6. Expenses of Demand Registration. All expenses other than underwriting discounts
and commissions relating to Registrable Securities incurred in connection with each registration,
filing or qualification pursuant to Section 1.2(a) and each registration, filing or qualification
pursuant to Section 1.11, including (without limitation) all registration, filing and qualification
fees, printing and accounting fees, fees and disbursements of counsel for the Company, and the
reasonable fees and disbursements of one counsel for the selling Holders, shall be borne by the
Company; provided, however, that the Company shall not be required to pay for any
expenses of any registration begun pursuant to Section 1.2(a) if the registration request is
subsequently withdrawn at any time at the request of the Holders of two-thirds of the Registrable
Securities to be registered (in which case all participating Holders shall bear such expenses),
unless the Holders of two-thirds of the Registrable Securities agree to forfeit their right to one
demand registration pursuant to Section 1.2(a); and provided, further, that if at
the time of any withdrawal described in the foregoing clause the Holders have learned of a material
adverse change in the condition, business, or prospects of the Company (other than a change in
market demand for its securities or in the market price thereof) from that known to the Holders of
two-thirds of the Registrable Securities then outstanding at the time of their request (or of which
the Company advised them in writing within 20 days thereafter) that makes the proposed offering
unreasonable in the good faith judgment of two-thirds in interest of the Holders of the Registrable
Securities, then the Holders shall not be required to pay any of such expenses and the right to one
demand registration pursuant to Section 1.2(a) shall not be forfeited. All underwriting discounts
and commissions relating to Registrable Securities included in any registration effected pursuant
to Section 1.2(a) or 1.11 will be borne and paid ratably by the Holders of such Registrable
Securities.

     1.7. Expenses of Company Registration. The Company shall bear and pay all expenses
incurred in connection with any registration, filing or qualification of Registrable Securities
with respect to any registration pursuant to Section 1.3 for each Holder, including, without
limitation, all registration, filing and qualification fees, printing and accounting fees, fees and
disbursements of counsel for the Company and the reasonable fees and disbursements of one counsel
for the selling Holders. Underwriting discounts and commissions relating to Registrable Securities
included in any registration effected pursuant to Section 1.3 will be borne and paid ratably by the
Holders of such Registrable Securities.

     1.8. Underwriting Requirements. In connection with any offering involving an
underwriting of securities being issued by the Company, the Company shall not be required under
Section 1.3 to include any of the Holders’ securities in such underwriting unless such Holders
accept the terms of the underwriting as agreed upon between the Company and the underwriters
selected by it, and then only in such quantity, if any, as in the opinion of the underwriters,
marketing factors allow. If the managing underwriter for the offering shall advise the Company in
writing that the total amount of securities, including Registrable Securities, requested by
shareholders to be included in such offering exceeds the amount of securities to be sold other than
by the Company that marketing factors allow, then the Company shall be required to include in the
offering only that number of such securities, including Registrable Securities, which the managing
underwriter believes marketing factors allow (the securities so included to be reduced as follows:
(a) all securities which stockholders other than the Company and the Holders seek to include in the
offering shall be excluded from the offering to the extent limitation on the number of shares
included in the underwriting is required, (b) then all securities

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which the Common Stockholders seek to include in the offering shall be excluded from the
offering, pro rata, to the extent further limitation on the number of shares included in the
underwriting is required, and (c) if further limitation on the number of shares to be included in
the underwriting is required, then the number of shares held by Investors that may be included in
the underwriting shall be reduced so that the number of shares included in the underwriting are pro
rata in accordance with the number of shares of Registrable Securities held by each such Investor),
but in no event shall the amount of securities of the selling Investors included in the offering be
reduced below thirty percent (30%) of the total amount of securities included in such offering,
unless such offering is the initial public offering of the Company’s securities in which case the
selling Investors may be excluded if the managing underwriter makes the determination described
above and no securities other than those of the Company are included. For purposes of the
preceding parenthetical concerning apportionment, for any selling shareholder which is a Holder of
Registrable Securities and which is a partnership, a limited liability company or a corporation,
the partners, retired partners, members, retired members and shareholders of such Holder, or the
estates and family members of such partners, retired partners, members and retired members and any
trusts for the benefit of any of the foregoing persons shall collectively be deemed to be a
“selling Holder,” and any pro rata reduction with respect to such “selling Holder” shall be based
upon the aggregate amount of shares carrying registration rights owned by all entities and
individuals included in such “selling Holder,” as defined in this sentence.

     1.9. Indemnification. In the event any Registrable Securities are included in a
registration statement under this Section 1:

     (a) The Company will indemnify and hold harmless each Holder, the officers, directors,
partners, members, agents and employees of each Holder, any underwriter (as defined in the
1933 Act) for such Holder and each person, if any, who controls such Holder or underwriter
within the meaning of the 1933 Act or the 1934 Act, against any losses, claims, damages or
liabilities (joint or several) to which they may become subject under the 1933 Act, the 1934
Act or any 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 (each a “Violation”): (i) 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, (ii) the omission or alleged omission to state therein a
material fact required to be stated therein or necessary to make the statements therein, in
light of the circumstances in which they were made, not misleading, or (iii) any violation
or alleged violation by the Company of the 1933 Act, the 1934 Act, any state securities law
or any rule or regulation promulgated under the 1933 Act, the 1934 Act or any state
securities law in connection with any matter relating to such registration statement. The
Company will reimburse each such Holder, officer, director, partner, member, agent,
employee, 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. The indemnity agreement contained in this Section 1.9(a) shall not
apply to amounts paid in settlement of any 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 to an Holder in any such case for
any such loss, claim, damage, liability or action

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(1) 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 or on behalf of such Holder, underwriter or controlling
person or (2) in the case of a sale directly by an Holder of Registrable Securities
(including a sale of such Registrable Securities through any underwriter retained by such
Holder engaging in a distribution solely on behalf of such Holder), such untrue statement or
alleged untrue statement or omission or alleged omission was contained in a preliminary
prospectus and corrected in a final or amended prospectus, and such Holder failed to deliver
a copy of the final or amended prospectus at or prior to the confirmation of the sale of the
Registrable Securities to the person asserting any such loss, claim, damage or liability in
any case in which such delivery is required by the 1933 Act.

     (b) Each Holder which includes any Registrable Securities in any registration
statement, as a condition to including any Registrable Securities in such registration
statement, will, severally and not jointly, indemnify and hold harmless the Company, each of
its directors, each of its officers who have signed the registration statement, each person,
if any, who controls the Company within the meaning of the 1933 Act, each employee, agent,
and any underwriter for the Company, and any other Holder or other stockholder selling
securities in such registration statement or any of its directors, officers, partners,
members, agents or employees or any person who controls such Holder or such other
stockholder or such underwriter, against any losses, claims, damages, or liabilities (joint
or several) to which the Company or any such director, officer, controlling person,
employee, agent, or underwriter or controlling person, or other such Holder, stockholder,
director, officer or controlling person may become subject, under the 1933 Act, the 1934 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 or on behalf of such Holder expressly for
use in connection with such registration, and each such Holder will reimburse any legal or
other expenses reasonably incurred by the Company or any such director, officer, controlling
person, agent or underwriter or controlling person, other Holder or other stockholder,
officer, director, partner, member, agent, employee, or controlling person in connection
with investigating or defending any such loss, claim, damage, liability, or action;
provided, however, that the liability of any Holder hereunder shall be
limited to the amount of net proceeds (after deduction of all underwriters’ discounts and
commissions paid by such Holder in connection with the registration in question) received by
such Holder, in the offering giving rise to the Violation; and provided,
further, that the indemnity agreement contained in this Section 1.9(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 or delayed nor, in the case of a sale directly by the Company of its
securities (including a sale of such securities through any underwriter retained by the
Company to engage in a distribution solely on behalf of the Company), shall the Holder be
liable to the Company in any case in which such untrue statement or alleged untrue statement
or omission or alleged omission was contained in a preliminary prospectus and corrected in a
final or amended prospectus, and the Company failed to deliver a copy of

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the final or amended prospectus at or prior to the confirmation of the sale of the
securities to the person asserting any such loss, claim, damage or liability in any case in
which such delivery is required by the 1933 Act. As noted above, the obligations of the
Holders under this Section 1.9(b) are several, not joint.

     (c) Promptly after receipt by an indemnified party under this Section 1.9 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 1.9, 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 and control 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, as reasonably
determined by either party, between such indemnified party and any other party represented
by such counsel in such proceeding. The failure to deliver written notice to the
indemnifying party within a reasonable time of the commencement of any such action, if
prejudicial to its ability to defend such action, shall relieve such indemnifying party of
any liability to the indemnified party under this Section 1.9 to the extent of such
prejudice, 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 1.9.

     (d) The obligations of the Company and the Holders under this Section 1.9 shall
survive the conversion, if any, of the Registrable Securities and the completion of any
offering of Registrable Securities in a registration statement whether under this Section 1
or otherwise.

     1.10. Reports Under Securities Exchange Act of 1934.

     (a) Resales Under Rule 144; Form S-3 Registration. With a view to making
available to the Holders the benefits of Rule 144 promulgated under the 1933 Act (“Rule
144”) and any other rule or regulation of the SEC that may at any time permit a Holder to
sell securities of the Company to the public without registration, and with a view to making
it possible for Holders to have the resale of the Registrable Securities registered pursuant
to a registration statement on Form S-3, the Company agrees to:

     (i) use its best efforts to make and keep public information available, as
those terms are understood and defined in Rule 144, at all times after 90 days after
the effective date of the first registration statement filed by the Company for the
offering of its securities to the general public;

     (ii) as soon as practicable after the first registered public offering, take
such action, including the voluntary registration of its Common Stock under Section
12 of the 1934 Act or compliance with the reporting requirements of

-11-

 

Section 15(d) of the 1934 Act, as is necessary to enable the Holders to utilize
Form S-3 for the sale of their Registrable Securities.

     (iii) use its best efforts, after the first registered public offering, to
file with the SEC in a timely manner all reports and other documents required of the
Company under the 1933 Act and the 1934 Act; and

     (iv) furnish to any Holder, so long as the Holder owns any Registrable
Securities, forthwith upon request (1) a written statement by the Company as to its
compliance with the reporting requirements of Rule 144 (at any time after 90 days
after the effective date of the first registration statement filed by the Company
for the offering of the securities to the general public), the 1933 Act and the 1934
Act (at any time after it has become subject to such reporting requirements), or as
to its qualification as a registrant whose securities may be resold pursuant to Form
S-3 (at any time after it so qualifies), (2) a copy of the most recent annual or
quarterly report of the Company and such other reports and documents so filed by the
Company, and (3) such other documents as may be reasonably requested in availing any
Holder of any rule or regulation of the SEC which permits the selling of any such
securities without registration or pursuant to such form.

     1.11. Form S-3 Registration.

     (a) In case the Company shall receive a written request from any Investor Holder(s) of
at least twenty-five percent (25%) of the Registrable Securities then outstanding and
entitled to registration rights under Section 1 hereof that the Company effect a
registration on Form S-3 (or on any successor form to Form S-3 regardless of its
designation) 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:

     (i) promptly give written notice of the proposed registration, and any related
qualification or compliance, to all other Holders; and

     (ii) use its best efforts to effect, as soon as practicable, such registration
(and to keep such registration effective for up to six months), qualification or
compliance 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 20 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 1.11 if: (1) Form S-3 (or any successor form to Form S-3
regardless of its designation) is not available for such offering by the Holders;
(2) the aggregate net offering price (after deduction of underwriting discounts and
commissions) of the Registrable Securities specified in such request is not at least
$500,000; (3) the Company has already effected two registrations on Form S-3 or
pursuant to Section 1.2 hereof within the previous twelve-month period; or (4) the

-12-

 

Company shall furnish to the Holders a certificate signed by the president of
the Company stating that, in the good faith judgment of the Board of Directors, it
would not be in the best interests of 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 for a period of not more
than 45 days after receipt of the request of the Holder or Holders under this
Section 1.11; provided, however, that the Company shall not utilize
this right more than once in any twelve-month period.

     (b) In the event that the Company consummates the initial public offering of its
securities, then as soon as reasonably possible following a written request from two-thirds
in interest of the Registrable Securities, and in any event not before 366 days after the
effective date of the registration statement filed in connection with such initial public
offering, the Company shall file a shelf registration statement on Form S-3 (or on any
successor form to Form S-3 regardless of its designation) which would permit or facilitate
the sale and distribution of the Holders’ Registrable Securities, and the Company shall use
best efforts to keep such shelf registration effective in accordance with applicable
regulations.

     1.12. Lock-up Agreements. If reasonably requested by the Company and the managing
underwriter, each Holder agrees to enter into lock-up agreements (the “Lock-up Agreements”)
pursuant to which he, she or it will not, for a period of no more than 180 days following the
effective date of the first registration statement for a public offering of the Company’s
securities, offer, sell or otherwise dispose of the Registrable Securities or other equity
securities of the Company other than to its members or partners, as the case may be, except the
Registrable Securities sold pursuant to such registration statement, without the prior consent of
the Company and the underwriter, provided that the officers, directors and all holders of more than
five percent (5%) of the shares of Common Stock (calculated for the purpose as if all securities
convertible into or exercisable for Common Stock, directly or indirectly, are so converted or
exercised) of the Company enter into Lock-up Agreements for the same period and on the same terms.
The Lock-up Agreements shall provide that the provisions thereof may be waived with the consent of
the Company and the managing underwriter, provided that with the exception of the
release of a Holder from the provisions of the Lock-up Agreement for reasons of financial hardship,
which release shall prohibit the disposition of equity securities of the Company by such Holder in
excess of $50,000, any release from the provisions of the Lock-up Agreement shall be allocated pro
rata among all Holders.

     1.13. Assignment of Registration Rights. The rights to cause the Company to register
Registrable Securities pursuant to this Section 1 may be assigned by any Holder to a permitted
transferee, and by such transferee to a subsequent permitted transferee, but only if such rights
are transferred (a)(i) to an affiliate, subsidiary, partner, member or stockholder of such Holder
or transferee or an account managed or advised by the manager or adviser of such Holder or
transferee, (ii) by gift or bequest or through inheritance to, or for the benefit of, any member or
members of a Common Stockholder’s Immediate Family or to a trust for the benefit of such Common
Stockholder or any member or members of such Common Stockholder’s Immediate Family, or (iii) to a
limited partnership or limited liability company, all partners or members of which are members of
such Common Stockholder’s Immediate Family, and (b) in connection

-13-

 

with the sale or other transfer of not less than an aggregate of 100,000 Registrable
Securities (as adjusted for stock splits, combinations, stock dividends and recapitalizations) or
some lesser number, if such lesser number represents all the Registrable Securities then held by
such Holder. Any transferee to whom rights under this Agreement are transferred shall (i) as a
condition to such transfer, deliver to the Company a written instrument by which such transferee
agrees to be bound by the obligations imposed upon Holders under this Agreement to the same extent
as if such transferee were a Holder under this Agreement and (ii) be deemed to be a Holder
hereunder.

     1.14. Limitations on Subsequent Registration Rights. From and after the date of this
Agreement, the Company shall not, without the prior written consent of the Investor Holders of a
majority of the Registrable Securities then outstanding and held by the Investor Holders, enter
into any agreement with any holder or prospective holder of any securities of the Company relating
to registration rights unless such agreement includes (a) to the extent such agreement would allow
such holder or prospective holder to include such securities in any registration filed under
Section 1.2, 1.3 or 1.11 hereof, a provision that such holder or prospective holder may include
such securities in any such registration only to the extent that the inclusion of its securities
will not reduce the amount of the Registrable Securities of the Investor Holders which would
otherwise be included, and (b) no provision which would allow such holder or prospective holder to
make a demand registration which could result in such registration statement being declared
effective prior to the earlier of the dates set forth in Section 1.2(a), and (c) a provision which
permits the Holders to include in such registration and in any underwriting involved therewith,
Registrable Securities pro rata with the sellers of securities in such registration based on the
number of equivalent shares of Common Stock held by each person (where an equivalent share is
either a share of Common Stock held directly or the number of shares of Common Stock receivable
upon conversion or exercise of securities held directly).

2. Miscellaneous.

     2.1. Notices. All notices, requests, consents and demands shall be in writing and
shall be personally delivered (effective upon receipt), mailed, postage prepaid (effective three
business days after dispatch), telecopied or telegraphed (effective upon receipt of the telecopy in
complete, readable form), or sent via a reputable overnight courier service (effective the
following business day), to the Company at:

BioTrove, Inc.

12 Gill Street

Suite 4000

Woburn, Massachusetts 01801

Attn: Chief Executive Officer

Fax number: (781) 721-3601

with a copy sent at the same time and by the same means, which shall not constitute notice, to:

Jonathan M. Lourie, Esq.

Edwards, Angell Palmer & Dodge LLP

111 Huntington Avenue

-14-

 

Boston, Massachusetts 02199

Fax number: (617) 227-4420

or to each Investor at its address set out on Exhibit B hereto, as the case may be, with a
copy sent at the same time and by the same means, which shall not constitute notice, to:

Steven A. Wilcox, Esq.

Ropes & Gray LLP

One International Place

Boston, Massachusetts 02110

Fax number: (617) 951-7050

or to each Common Stockholder at its address set out on Exhibit A hereto, or such other
address of any party as may be furnished in writing to the other parties hereto.

     2.2. Entire Agreement. This Agreement and the Second Amended and Restated
Stockholders’ Agreement dated December 10, 2007, between the Company and the parties listed on
Exhibit A and Exhibit B thereto, as amended from time to time, constitute the
entire understanding of the parties with respect to the subject matter hereof and thereof and
supersede any and all prior understandings and agreements, whether written or oral, with respect to
such subject matter.

     2.3. Amendments, Waivers and Consents. Modifications or amendments to this Agreement
may be made, and compliance with any covenant or provision herein set forth may be omitted or
waived, if the Company shall agree thereto and (a) shall obtain consent thereto in writing from (i)
Investors holding a majority of the Registrable Securities then held by such Investors and (ii)
Common Stockholders holding a majority of the Common Stockholders’ Common Shares then held by such
Common Stockholders and (b) shall, in each such case, deliver copies of such consent in writing to
any Holders who did not execute the same; provided, however, that no Holder shall,
without its consent, be adversely affected by any such modification, amendment or waiver in any
manner in which the other Holders are not likewise adversely affected.

     2.4. Binding Effect; Assignment. This Agreement shall be binding upon and inure to
the benefit of the personal representatives, successors and permitted assigns of the respective
parties hereto. The Company shall not have the right to assign its obligations hereunder or any
interest herein without obtaining the prior written consent of the Investors holding or having the
right to acquire in the aggregate a majority of the aggregate Registrable Securities then
outstanding.

     2.5. General. The headings contained in this Agreement are for reference purposes
only and shall not in any way affect the meaning or interpretation of this Agreement. In this
Agreement the singular includes the plural, the plural includes the singular, and the masculine
gender includes the neuter, masculine and feminine genders. This Agreement shall be governed by
and construed in accordance with the laws of The Commonwealth of Massachusetts as such laws apply
to agreements between residents of Massachusetts.

-15-

 

     2.6. Severability. If any provision of this Agreement shall be found by any court of
competent jurisdiction to be invalid or unenforceable, the parties hereby waive such provision to
the extent that it is found to be invalid or unenforceable. Such provision shall, to the maximum
extent allowable by law, be modified by such court so that it becomes enforceable, and, as
modified, shall be enforced as any other provision hereof, all the other provisions hereof
continuing in full force and effect.

     2.7. Counterparts. This Agreement may be executed in one or more counterparts, each
of which shall be deemed an original, but all of which together shall constitute one and the same
agreement. Counterparts of this Agreement (or applicable signature pages hereof) that are manually
signed and delivered by facsimile transmission shall be deemed to constitute signed original
counterparts hereof and shall bind the parties signing and delivering in such manner.

     2.8. Specific Performance. The Company recognizes that the rights of the Holders
under this Agreement are unique, and, accordingly, the Holders shall, in addition to such other
remedies as may be available to them at law or in equity, have the right to enforce their rights
hereunder by actions for injunctive relief and specific performance to the extent permitted by law.
This Agreement is not intended to limit or abridge any rights of the Holders which may exist apart
from this Agreement.

     2.9. Termination of Registration Rights. The registration of obligations of the
Company under Section 1 will terminate on the earlier of (i) five years after the closing date of
the first registered public offering of the Common Stock of the Company or (ii) with respect to any
holder of Registrable Securities, at such time as all Registrable Securities of such holder may be
sold within a 90 day period pursuant to Rule 144(k).

     2.10. Aggregation of Stock. All shares of Registrable Securities acquired by
affiliated entities or persons of any Investor shall be aggregated together for the purposes of
determining the availability of any rights under this Agreement.

[REMAINDER OF PAGE INTENTIONALLY LEFT BLANK]

-16-

 

IN WITNESS WHEREOF, the Company, the Investors and Stockholders have executed this Second Amended
and Restated Registration Rights Agreement as of the day and year first above written.

	 	 	 	 	 
	 	COMPANY:

BIOTROVE, INC.

 	 
	 	By:  	/s/ Albert Luderer
 	 
	 	 	Name:  	Albert Luderer 	 
	 	 	Title:  	CEO 	 
	 

[Second Amended and Restated Registration Rights Agreement of BioTrove, Inc.]

 

 

	 	 	 	 	 
	 

	 	STOCKHOLDERS:	 	 
	 
	 	 	 	 
	 
	 	 	 	 
	 

	 	/s/ Colin Brenan	 	 
	 
	 	 
	 	 
	 
	 	Colin Brenan	 	 
	 
	 	 	 	 
	 
	 	 	 	 
	 

	 	 

Ian W. Hunter 2002 Grantor Retained
	 	 
	 

	 	Annuity Trust	 	 
	 
	 	 	 	 
	 
	 	 	 	 
	 

	 	/s/ Tanya Kanigan	 	 
	 

	 	Tanya Kanigan	 	 
	 
	 	 	 	 
	 
	 	 	 	 
	 

	 	Serge Lafontaine	 	 
	 
	 	 	 	 
	 
	 	 	 	 
	 

	 	/s/ Lynette Jones	 	 
	 

	 	Lynette Jones 
	 	 
	 
	 	 	 	 
	 
	 	 	 	 
	 

	 	Ian W. Hunter	 	 

[Second Amended and Restated Registration Rights Agreement of BioTrove, Inc.]

 

 

	 	 	 	 	 
	 	INVESTORS:

CHTP/BTRV ASSOCIATES, LLC

 	 
	 	By:  	CATALYST HEALTH AND TECHNOLOGY
PARTNERS, LLC, Its Manager
 	 
	 	 	 	 
	 	 	 
	 	By:  	                     /s/ Joshua S. Phillips
 	 
	 	 	Name:  	Joshua S. Phillips 	 
	 	 	Title:  	Manager 	 
	 

[Second Amended and Restated Registration Rights Agreement of BioTrove, Inc.]

 

 

	 	 	 	 	 
	 	CB HEALTHCARE FUND II, L.P.
 	 
	 	 	 
	 	By:  	                     CB HEALTH VENTURES II, L.L.C.
 	 
	 	 	 
	 	By:  	                     /s/ Enrico Petrillo
 	 
	 	 	Name:  	 	 
	 	 	Title:  	 	 
	 

	 	 	 	 	 
	 	CB-AH PARALLEL FUND II, L.P.

 	 
	 	By:  	                     CB HEALTH VENTURES II, L.L.C.
 	 
	 	 	 	 
	 	By:  	                     /s/ Enrico Petrillo
 	 
	 	 	Name:  	Enrico Petrillo,  MD 	 
	 	 	Title:  	Partner 	 
	 

[Second Amended and Restated Registration Rights Agreement of BioTrove, Inc.]

 

 

	 	 	 	 	 
	 	VOX EQUITY PARTNERS, L.P., successor by merger to ZERO STAGE CAPITAL SBIC VII, L.P.

 	 
	 	By:  	
VOX EQUITY ASSOCIATES, L.L.C., Its General Partner
 	 
	 	 	 	 
	 
	 	By:  	              /s/ Matthew Kelley
 	 
	 	 	Name:  	Matthew Kelley 	 
	 	 	Title:  	MGP 	 
	 

	 	 	 	 	 
	 	VOX EQUITY PARTNERS II, LP, successor-in-interest to ZERO

STAGE CAPITAL VII, L.P. and ZERO STAGE CAPITAL (CAYMAN) VII,
L.P.

 	 
	 	By:  	 	 

	 	 	 	 	 
	 	 	 
	 	By:  	
 	 
	 	 	Name:  	 	 
	 	 	Title:  	 	 
	 

[Second Amended and Restated Registration Rights Agreement of BioTrove, Inc.]

 

 

	 	 	 	 	 
	 	FLETCHER SPAGHT VENTURES, L.P.

 	 
	 	By:  	FLETCHER SPAGHT ASSOCIATES, LLC
 	 
	 	 	 
	 	By:  	                    /s/ Linda Tufts
 	 
	 	 	Name:  	 	 
	 	 	Title:  	 	 
	 

	 	 	 	 	 
	 	FLETCHER SPAGHT VENTURE PARTNERS, LLC

 	 
	 	By:  	/s/ Linda Tufts
 	 
	 	 	Name:  	Linda Tufts 	 
	 	 	Title:  	 	 
	 

[Second Amended and Restated Registration Rights Agreement of BioTrove, Inc.]

 

 

	 	 	 	 	 
	 	ECHELON VENTURES LP

 	 
	 	By:  	ECHELON VENTURES, LLC, 
Its General Partner
 	 
	 	 	 
	 	By:  	                    /s/ Alfred S. Woodworth, Jr.
 	 
	 	 	Name:  	Alfred S. Woodworth, Jr. 	 
	 	 	Title:  	Manager 	 
	 

	 	 	 	 	 
	 	ECHELON VENTURES SPECIAL LIMITED PARTNERS I, LP

 	 
	 	By:  	

ECHELON VENTURES, LLC,
Its General Partner
 	 
	 	 	 
	 	By:  	                    /s/ Alfred S. Woodworth, Jr.
 	 
	 	 	Name:  	Alfred S. Woodworth, Jr. 	 
	 	 	Title:  	Manager 	 
	 

	 	 	 	 	 
	 	ECHELON VENTURES II, L.P.

 	 
	 	By:  	ECHELON VENTURES, LLC,
Its General Partner
 	 
	 	 	 
	 	By:  	                    /s/ Alfred S. Woodworth, Jr.
 	 
	 	 	Name:  	Alfred S. Woodworth, Jr. 	 
	 	 	Title:  	Manager 	 
	 

	 	 	 	 	 
	 	LEWIS WHARF PARTNERS

 	 
	 	By:  	/s/ Alfred S. Woodworth, Jr.
 	 
	 	 	Name:  	Alfred S. Woodworth, Jr. 	 
	 	 	Title:  	Managing General Partner 	 
	 

[Second Amended and Restated Registration Rights Agreement of BioTrove, Inc.]

 

 

	 	 	 	 	 
	 	BIOFRONTIER GLOBAL INVESTMENT PARTNERSHIP, A Japanese Civil Law Partnership

 	 
	 	By:  	

BIOFRONTIER PARTNERS CO., LTD.
Its General Partner
 	 
	 	 	 
	 	By:  	

 	 
	 	 	Name:  	 	 
	 	 	Title:  	 	 
	 

[Second Amended and Restated Registration Rights Agreement of BioTrove, Inc.]

 

 

	 	 	 	 	 
	 	BOSCOLO INTERVEST LIMITED

 	 
	 	By:  	/s/ Jaime J. Montealegre
 	 
	 	 	Name:  	Jaime J. Montealegre 	 
	 	 	Title:  	Attorney-in-fact 	 
	 

[Second Amended and Restated Registration Rights Agreement of BioTrove, Inc.]

 

 

	 	 	 	 	 
	 	BIOTECHONOMY VENTURES, LLC

 	 
	 	By:  	/s/ Caleb Winder
 	 
	 	 	Name:  	Caleb M. Winder 	 
	 	 	Title:  	Principal 	 
	 

	 	 	 	 	 
	 	 	 
	 	  Juan Enriquez
 	 
	 	 	 
	 
	 	                                      /s/ Caleb Winder
 	 
	 	Caleb Winder 	 
	 	 	 
	 

[Second Amended and Restated Registration Rights Agreement of BioTrove, Inc.]

 

 

	 	 	 	 	 
	 	 	 
	 	                                      /s/ Colin Brenan
 	 
	 	Colin Brenan 	 
	 	 	 
	 
	 	 	 
	 	                                      /s/ Edward L. Erickson
 	 
	 	Edward L. Erickson 	 
	 
	 	 	 
	 	                                      /s/ D. Gideon Searle
 	 
	 	D. Gideon Searle 	 
	 	 	 
	 

[Second Amended and Restated Registration Rights Agreement of BioTrove, Inc.]

 

 

Exhibit A

STOCKHOLDERS

Name

Colin Brenan

c/o Biotrove, Inc.

12 Gill Street, Suite 4000

Woburn, Massachusetts 01801

Ian Hunter

6 Oak Dale Lane

Lincoln, MA 01773

Tanya Kanigan

c/o Biotrove, Inc.

12 Gill Street, Suite 4000

Woburn, Massachusetts 01801

Serge LeFontaine

6 Mill St. Ext.

Lincoln, MA 01773

Lynette Jones

6 Oak Dale Lane

Lincoln, MA 01773

 

 

Exhibit B

INVESTORS

     Name

CHTP/BTRV Associates, LLC

c/o Catalyst Health and Technology

Partners, LLC

One Gateway Center, Suite 312

Newton, MA 02458

Attention: Joshua S. Phillips

Facsimilie: 617-964-8887

CB HealthCare Fund II, L.P.

c/o CB Health Ventures II, L.L.C.

Prudential Tower, Suite 800

800 Boylston Street

Boston, MA 02199

Attention: Enrico Petrillo, MD

Facsimilie: 617-450-9749

CB-AH Parallel Fund II, L.P.

c/o CB Health Ventures II, L.L.C.

Prudential Tower, Suite 800

800 Boylston Street

Boston, MA 02199

Attention: Enrico Petrillo, MD

Facsimilie: 617-450-9749

Biofrontier Global Investment Partnership,

     a Japanese Civil Law Partnership

c/o Biofrontier Partners

K.I. Kousan Building, 3rd Floor

2-3-14 Yaesu, Chuo-ku

Tokyo, Japan 104-0028

Attention: Yoshihiro Ohtaki, Ph.D.

Facsimilie: 011813-5204-7009

Vox Equity Partners, L.P.

4 Canal Park, Suite 706

Cambridge, MA 02141

Attention: Matthew Kelley

Vox Equity Partners II, L.P.

4 Canal Park, Suite 706

Cambridge, MA 02141

Attention: Matthew Kelley

 

 

Fletcher Spaght Ventures, L.P.

Attention: Linda Tufts

222 Berkeley Street

Boston, MA 02116

Facsimile: 617-247-7757

Fletcher Spaght Venture Partners, L.L.C.

Attention: Linda Tufts

222 Berkeley Street

Boston, MA 02116

Facsimile: 617-247-7757

Echelon Ventures, L.P.

c/o Echelon Ventures LLC

300 Fifth Avenue, 3rd Floor

Waltham, MA 02451

Attention: Alfred S. Woodworth, Jr.

Facsimile: 781-419-9851

Echelon Ventures II, L.P.

c/o Echelon Ventures LLC

300 Fifth Avenue, 3rd Floor

Waltham, MA 02451

Attention: Alfred S. Woodworth, Jr.

Facsimile: 781-419-9851

Echelon Ventures Special Limited Partners I, L.P.

c/o Echelon Ventures LLC

300 Fifth Avenue, 3rd Floor

Waltham, MA 02451

Attention: Alfred S. Woodworth, Jr.

Facsimile: 781-419-9851

Lewis Wharf Partners

c/o Echelon Ventures LLC

300 Fifth Avenue, 3rd Floor

Waltham, MA 02451

Attention: Alfred S. Woodworth, Jr.

Facsimile: 781-419-9851

Boscolo Intervest Limited

Residencial Acrópolis

Calle Jaboncillo

De Apartamentos Terranova 600 mts. S.O. y 200 Este

Escazú, Costa Rica

Attention.: Jaime J. Montealegre

Facsimile: 011-506-288-0310

With a copy to:

Fox Horan & Camerini LLP

825 Third Avenue, 12th Floor

New York, NY 10022

Attention: Rafael Urquia II, Esq.

Facsimile: 212-709-0248

 

 

D. Gideon Searle

750 Green Bay Road

Winnetka, IL 60093

Facsimile: 847-446-7414

Edward L. Erickson

c/o Biotrove, Inc.

12 Gill Street, Suite 4000

Woburn, Massachusetts 01801

Biotechonomy Ventures, LLC

800 Boylston Street, Suite 1585

Boston, MA 02199

Attention: Juan Enriquez

Caleb M. Winder

800 Boylston Street, Suite 1585

Boston, MA 02199

Juan Enriquez

800 Boylston Street, Suite 1585

Boston, MA 02199

Colin Brenan

c/o Biotrove, Inc.

12 Gill Street, Suite 4000

Woburn, Massachusetts 01801

 

 

Attachment I

Counterpart Signature Page for Common Stockholders

     The undersigned hereby agrees to join, become a party to and be bound by the Second Amended
and Restated Registration Rights Agreement (the “Agreement”) entered into as of December
10, 2007, by and among: (i) BioTrove, Inc., a Delaware corporation (together with any predecessors
or successors thereto, the “Company”), (ii) certain holders of the Company’s outstanding
Common Stock listed on Exhibit A thereto, and (iii) certain holders of the Company’s Series
B Preferred Stock and/or Series C Preferred Stock listed on Exhibit B thereto.

	 	 	 	 	 
	 	 	 
	   Name of Common Stockholder
 	 	 
	 	 	 
	By:  	
 	 	 
	 	(if applicable) 	 	 
	 	 	 	 
	 
	 	 	 
	By:  	
 	 	 
	 	Name:  	 	 	 
	 	Title:  	 	 	 
	 

Dated:
__________ ___, 200___

	 	 	 
	Address of Stockholder for notices:

	 	 
	 
	 	 
	 

	 	 
	 
	 	 
	 

	 	 
	 
	 	 
	 

	 	 

 

 

Attachment II

Counterpart Signature Page for Investors

     The undersigned hereby agrees to join, become a party to and be bound by the Second Amended
and Restated Registration Rights Agreement (the “Agreement”) entered into as of December
10, 2007, by and among: (i) BioTrove, Inc., a Delaware corporation (together with any predecessors
or successors thereto, the “Company”), (ii) certain holders of the Company’s outstanding
Common Stock listed on Exhibit A thereto, and (iii) certain holders of the Company’s Series
B Preferred Stock and/or Series C Preferred Stock listed on Exhibit B thereto.

	 	 	 	 	 
	 	 	 
	 Name of Investor
 	 	 
	 	 	 
	By:  	
 	 	 
	 	(if applicable) 	 	 
	 	 	 	 
	 	 	 
	By:  	
 	 	 
	 	Name:  	 	 	 
	 	Title:  	 	 	 
	 

Dated:
__________ ___, 200___

	 	 	 
	Address of Investor for notices:exv4w3

 

Exhibit 4.3

NEITHER THIS WARRANT NOR THE SECURITIES ISSUABLE UPON THE EXERCISE OF THIS WARRANT HAVE BEEN
REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED, OR ANY STATE SECURITIES LAW. NEITHER THIS
WARRANT NOR THE SECURITIES ISSUABLE UPON THE EXERCISE OF THIS WARRANT MAY BE SOLD OR TRANSFERRED IN
THE ABSENCE OF SUCH REGISTRATION UNLESS THE COMPANY RECEIVES AN OPINION OF COUNSEL REASONABLY
ACCEPTABLE TO IT STATING THAT SUCH SALE OR TRANSFER IS EXEMPT FROM REGISTRATION UNDER THE ACT.

THIS WARRANT AND ANY SECURITIES ACQUIRED UPON THE EXERCISE OF THIS WARRANT ARE SUBJECT TO
AGREEMENTS, COVENANTS AND RESTRICTIONS PROVIDED IN THE AMENDED AND RESTATED STOCKHOLDERS’
AGREEMENT, DATED AS OF DECEMBER 30, 2003, AS AMENDED FROM TIME TO TIME, BY AND AMONG THE COMPANY
AND THE PERSONS NAMED THEREIN. A COPY OF SUCH AGREEMENT WILL BE PROVIDED TO AT NO COST TO THE
HOLDER HEREOF UPON WRITTEN REQUEST TO THE COMPANY.

WARRANT

to Purchase Common Stock of

BIOTROVE, INC.

			
	 	 	 
	Date of Issuance: _____, 2005
	 	Certificate No. BW-[___]

THIS WARRANT IS TO CERTIFY THAT [________] (“Holder”), is entitled to purchase from
BioTrove, Inc., a Delaware corporation (the “Company”), [_______] shares of the Company’s
Common Stock, par value $0.01 per share (“Common Stock”), at a price per share of $0.01
(the “Exercise Price”). Terms used but not defined herein shall have the meanings set
forth in the Series B Convertible Participating Preferred Stock Purchase Agreement of even date
herewith, among the Company and the Investors named therein (as amended from time to time, the
“Purchase Agreement”).

          Section 1. Certain Definitions. As used in this Warrant, unless the context
otherwise requires:

          “Change of Control” shall mean (a) a merger or consolidation of the Company with or
into any other company or companies in which the stockholders of the Company immediately prior to
the merger or consolidation do not own more than fifty percent (50%) of the outstanding voting
power (assuming conversion of all convertible securities and the exercise of all outstanding
options) of the surviving company or (b) the sale, lease, licensing, transfer or other disposition
of all or substantially all the assets of the Company.

          “Date of Issuance” shall mean the date hereof.

          “Stockholders’ Agreement” shall mean that certain Amended and Restated Stockholders
Agreement, dated as of December 30, 2003, among the Company and Stockholders and Institutional
Investors listed therein, as amended from time to time.

          “Warrant” shall mean this Warrant and all additional or new warrants issued upon
division or combination of, or in substitution for, this Warrant.

 

 

          “Warrantholder” shall mean the Holder, as the initial holder of this Warrant, and its
nominees, successors or assigns, including any subsequent holder of this Warrant to whom it has
been legally transferred.

          “Warrant Stock” shall mean the shares of the Company’s Common Stock purchasable by the
holder of this Warrant upon the exercise of such Warrant.

          Section 2. Exercise of Warrant.

               
(a) After the date hereof but prior to July 1, 2015, the Warrantholder may at any time and
from time to time exercise this Warrant, in whole or in part.

       (b) (i) The Warrantholder shall exercise this Warrant by means of delivering to the
Company at its office identified in Section 10 hereof (1) a written notice of exercise,
including the Warrant Stock to be delivered pursuant to such exercise, (2) this Warrant and
(3) payment equal to the Exercise Price in accordance with Section 2(b)(ii). In the event
that any exercise shall not be for all of the Warrant Stock purchasable hereunder, a new
Warrant registered in the name of the Warrantholder, of like tenor to this Warrant and for
the remaining Warrant Stock purchasable hereunder, shall be delivered to the Warrantholder
within five (5) days of any such exercise. Such notice of exercise shall be in the
Subscription Form attached hereto as Exhibit A (the “Subscription Form”).

            (ii) The Warrantholder may elect to pay the Exercise Price to the Company either (1) by
cash, certified check or wire transfer, (2) by converting the Warrant into Warrant Stock
(“Cashless Exercise”) or (3) any combination of the foregoing, and specifying such
election(s) in the Subscription Form. If the Warrantholder elects to pay the Exercise Price
through Cashless Exercise, upon the exercise hereof the Warrantholder shall specify in the
Subscription Form that the Company is authorized to withhold from issuance that number of
Warrant Stock which, when multiplied by the fair market value (as determined in good faith
by the Board of Directors of the Company) per share of the Warrant Stock, is equal to the
aggregate Exercise Price (and such withheld shares shall no longer be issuable under this
Warrant).

               (c) Upon exercise of this Warrant and delivery of the Subscription Form with proper payment
relating thereto, the Company shall cause to be executed and delivered to the Warrantholder a
certificate or certificates representing the aggregate number of fully paid and nonassessable
shares of Warrant Stock issuable upon such exercise.

               (d) The stock certificate or certificates for Warrant Stock to be delivered in accordance with
this Section 2 shall be in such denominations as may be specified in said notice of exercise and
shall be registered in the name of the Warrantholder or such other name or names as shall be
designated in said notice. Such certificate or certificates shall be deemed to have been issued
and the Warrantholder or any other person so designated to be named therein shall be deemed to have
become the holder of record of such shares, including to the extent permitted by law the right to
vote such shares or to consent or to receive notice as a stockholder of the Company, as of the time
said notice is delivered to the Company as aforesaid.

               (e) The Company shall pay all expenses payable in connection with the preparation, issue and
delivery of stock certificates under this Section 2, including any transfer taxes resulting from
the exercise of the Warrant and the issuance of Warrant Stock hereunder.

-2-

 

               (f) All of the Warrant Stock issuable upon the exercise of this Warrant in accordance with the
terms hereof shall be validly issued, fully paid and nonassessable, and free from all liens and
other encumbrances thereon, other than liens or other encumbrances created by the Warrantholder.

               (g) The Company shall not be required upon the exercise of this Warrant to issue any
fractional shares, and shall round any fractional shares to the next highest whole number of
shares.

          Section 3. Adjustments.

               (a) Adjustment for Stock Splits and Combinations. If the Company shall at any time or
from time to time after the Date of Issuance effect a subdivision of the outstanding Common Stock,
the number of Warrant Stock then in effect immediately before that subdivision shall be
proportionately increased. If the Company shall at any time or from time to time after the Date of
Issuance combine the outstanding shares of Common Stock, the number of Warrant Stock shall be
proportionately decreased. Any adjustment under this paragraph shall become effective at the close
of business on the date the subdivision or combination becomes effective.

               (b) Adjustments for Other Dividends and Distributions. In the event the Company at
any time or from time to time after the Date of Issuance shall make or issue, or fix a record date
for the determination of holders of Common Stock entitled to receive, a dividend or other
distribution payable in securities of the Company or in cash or other property, then and in each
such event provision shall be made so that the Warrantholder shall receive upon exercise hereof, in
addition to the number of shares of Common Stock issuable hereunder, the kind and amount of
securities of the Company and/or cash and other property which the Warrantholder would have been
entitled to receive had this Warrant been exercised on the date of such event and had the Holder
thereafter, during the period from the date of such event to and including the date of exercise,
retained any such securities receivable, giving application to all adjustments called for during
such period under this Section 3 with respect to the rights of the Warrantholder.

               (c) Adjustment for Mergers or Reorganizations, etc. If there shall occur any
reorganization, recapitalization, consolidation or merger involving the Company in which the Common
Stock is converted into or exchanged for securities, cash or other property (other than a
transaction covered by subsection 3(a) above), then, following any such reorganization,
recapitalization, consolidation or merger, the Warrantholder shall receive upon exercise hereof the
kind and amount of securities, cash or other property which the Warrantholder would have been
entitled to receive if, immediately prior to such reorganization, recapitalization, consolidation
or merger, the Warrantholder had held the number of shares of Common Stock subject to this Warrant.

               (d) Certificate as to Adjustments. Upon the occurrence of any event requiring
adjustments of the number of shares subject to this Warrant pursuant to Section 3, the Company
shall mail to the Warrantholder (by registered or certified mail, postage prepaid) a certificate
signed by an officer of the Company, setting forth in reasonable detail the events requiring the
adjustment and the method by which such proposed adjustment was calculated, specifying the adjusted
number of shares subject to this Warrant after giving effect to the proposed adjustment and the
Warrant Stock to be issued pursuant to Section 3 hereof.

-3-

 

          Section 4. Requirements for Transfer; Purchase Entirely for Own Account.

               (a) This Warrant and the Warrant Stock shall be deemed “Shares” under the Stockholders’
Agreement and shall not be transferred except in compliance with the Stockholders’ Agreement.

               (b) Each certificate representing Warrant Stock shall bear a legend substantially in the
following form:

THE SECURITIES REPRESENTED BY THIS CERTIFICATE HAVE NOT BEEN REGISTERED
UNDER THE SECURITIES ACT OF 1933, AS AMENDED, NOR PURSUANT TO THE SECURITIES
OR “BLUE SKY” LAWS OF ANY STATE. SUCH SECURITIES MAY NOT BE OFFERED, SOLD,
TRANSFERRED, PLEDGED, HYPOTHECATED OR OTHERWISE ASSIGNED, EXCEPT (I)
PURSUANT TO A REGISTRATION STATEMENT WITH RESPECT TO SUCH SECURITIES WHICH
IS EFFECTIVE UNDER SUCH ACT, (II) PURSUANT TO RULE 144 UNDER SUCH ACT, OR
(III) UPON THE FURNISHING OF AN OPINION OF COUNSEL (OR OTHER EVIDENCE)
REASONABLY SATISFACTORY TO THE COMPANY THAT SUCH TRANSACTION IS NOT REQUIRED
TO BE REGISTERED UNDER SUCH ACT OR ANY APPLICABLE “BLUE SKY” LAWS.

“THE SECURITIES REPRESENTED BY THIS CERTIFICATE ARE SUBJECT TO
AGREEMENTS, COVENANTS AND RESTRICTIONS PROVIDED IN THE AMENDED AND RESTATED
STOCKHOLDERS’ AGREEMENT, DATED AS OF DECEMBER 30, 2003, AS AMENDED FROM TIME
TO TIME, BY AND AMONG THE COMPANY AND THE PERSONS NAMED THEREIN. A COPY OF
SUCH AGREEMENT WILL BE PROVIDED TO AT NO COST TO THE HOLDER HEREOF UPON
WRITTEN REQUEST TO THE COMPANY.”

          The foregoing legend shall be removed from the certificates representing any Warrant Stock, at
the request of the holder thereof, at such time as they become eligible for resale pursuant to Rule
144(k) under the Act.

          (c) The Warrant is acquired and the Warrant Stock issuable upon the exercise hereof will be
acquired for investment for the Warrantholder’s own account and not with a view to the distribution
of any part thereof. The Warrantholder does not have any contract, undertaking, agreement or
arrangement with any person or entity to sell, transfer, or grant participations to such person or
entity or to any third party, with respect to this Warrant and the Warrant Stock.

          Section 5. No Impairment. The Company will not, by amendment of its certificate or
articles of incorporation, by-laws or other constitutional documents or through reorganization,
transfer of assets, consolidation, merger, dissolution, issue or sale of securities 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 of this Warrant against impairment.

          Section 6. Notices of Record Date, etc. In the event:

               (a) the Company shall take a record of the holders of its Common Stock (or other stock or
securities at the time deliverable upon the exercise of this Warrant) for the purpose of entitling
or enabling them to receive any dividend or other distribution, or to receive any right to
subscribe for or purchase any shares of stock of any class or any other securities, or to receive
any other right; or

               (b) of any capital reorganization of the Company, any reclassification of the Common Stock of
the Company, any consolidation or merger of the Company with or into another

-4-

 

corporation (other than a consolidation or merger in which the Company is the surviving entity
and its capital stock is not converted into or exchanged for any other securities or property), or
any transfer of all or substantially all of the assets of the Company; or

               (c) of the voluntary or involuntary dissolution, liquidation or winding-up of the Company; or

               (d) the Company or any stockholders of the Company shall enter into any agreement
contemplating a Change of Control,

then, and in each such case, the Company will mail or cause to be mailed to the Warrantholder a
notice specifying, as the case may be, (i) the record date for such dividend, distribution or
right, and the amount and character of such dividend, distribution or right, or (ii) the effective
date on which such reorganization, reclassification, consolidation, merger, transfer, dissolution,
liquidation, winding-up or Change of Control is to take place, and the time, if any is to be fixed,
as of which the holders of record of Common Stock (or such other stock or securities at the time
deliverable upon the exercise of this Warrant) shall be entitled to exchange their shares of Common
Stock (or such other stock or securities) for securities or other property deliverable upon such
reorganization, reclassification, consolidation, merger, transfer, dissolution, liquidation or
winding-up. Such notice shall be mailed at least three (3) days prior to the record date or
effective date for the event specified in such notice.

          Section 7. Reservation of Stock. The Company will reserve for issuance and delivery
upon the exercise of this Warrant, such number of Warrant Stock and other securities, cash and/or
property, as from time to time shall be issuable upon the exercise of this Warrant no later than
immediately prior to the exercise of this Warrant.

          Section 8. Replacement of Warrants. Upon receipt of evidence reasonably satisfactory
to the Company of the loss, theft, destruction or mutilation of this Warrant and (in the case of
loss, theft or destruction) upon delivery of an indemnity agreement (with surety if reasonably
required) in an amount reasonably satisfactory to the Company, or (in the case of mutilation) upon
surrender and cancellation of this Warrant, the Company will issue, in lieu thereof, a new Warrant
of like tenor.

          Section 9. Warrant Register. The Company will maintain a register containing the
name and address of the holder of this Warrant. The Warrantholder may change its address as shown
on the warrant register by written notice to the Company requesting such change.

          Section 10. Mailing of Notices, etc. All notices and other communications from the
Company to the Holder shall be mailed by first-class certified or registered mail, postage prepaid,
to the address last furnished to the Company in writing by the Holder. All notices and other
communications from the Holder or in connection herewith to the Company shall be mailed by
first-class certified or registered mail, postage prepaid, to the Company at its principal office
set forth below:

BioTrove, Inc.

12 Gill Street, Suite 4000

Woburn, Massachusetts 01801

Attn: Chief Executive Officer

Fax: (781) 721-3601

If the Company should at any time change the location of its principal office to a place other than
as set forth above, it shall give prompt written notice to the Holder and thereafter all references
in this Warrant to the location of its principal office at the particular time shall be as so
specified in such notice.

-5-

 

          Section 11. No Rights as Stockholders. Until the exercise of this Warrant, the
Warrantholder shall not have or exercise any rights by virtue hereof as a stockholder of the
Company.

          Section 12. Change or Waiver. Any term of this Warrant may be amended or waived upon
the written consent of the Company and the Majority Lenders.

          Section 13. Section Headings. The section headings in this Warrant are for the
convenience of the parties and in no way alter, modify, amend, limit or restrict the contractual
obligations of the parties.

          Section 14. Governing Law. This Warrant will be governed by and construed in
accordance with the laws of the Commonwealth of Massachusetts, without giving effect to the
conflict or choice of law provisions thereof that would give rise the application of the domestic
substantive law of any other jurisdiction.

**Signature Page Follows**

-6-

 

     IN WITNESS WHEREOF, the Company has caused this Warrant to be signed in its name by its
President.

Dated:    
             
            
              
                  

	 	 	 	 	 
	 	BIOTROVE, INC.

 	 
	 	By:  	
 	 
	 	 	Name:  	 	 
	 	 	Title:  	 	 

Signature
Page to Warrant

 

	 	 	 	 	 

EXHIBIT A

SUBSCRIPTION FORM

(to
be executed only upon exercise of Warrant)

	 	 	 	 	 
	To:
	 	 	 	 
	 
	 	 	 
	 
	 	
[Choose one or both of the paragraphs, as applicable]

     
The undersigned, pursuant to the provisions set forth in the attached Warrant (No. ___),
hereby irrevocably elects to purchase
          
          
shares of the Warrant Stock covered by such
Warrant and herewith makes payment of $   
          
       , representing the full purchase price for such
shares at the price per share provided for in such Warrant.

     The undersigned, pursuant to the provisions set forth in the attached Warrant (No. ___),
hereby irrevocably elects to exercise the right of cashless exercise represented by the attached
Warrant for ___ shares of Warrant Stock, and as payment therefor hereby directs
       
              
              
      to withhold ___ shares of Warrant Stock that the undersigned would
otherwise be entitled thereunder.

	 	 	 	 	 	 
	 	 	 
	Dated: ________________________ 	Name:  	
 	 	 
	 	 	Signature: 	 	 
	 	 	Address: 	 	 
	 	 	 	 	 

 

 

	 	 	 	 	 

Schedule
of Outstanding Warrant Holders

	 	 	 	 	 	 
	Name of Holder	 	Shares	 	Expiration Date
	CB Healthcare Fund II, L.P.
	 	33,764	 	 	May 26, 2015
	CB-AH Parallel Fund II, L.P.
	 	5,473	 	 	May 26, 2015
	Colin Brenan
	 	92	 	 	May 26, 2015
	Echelon Ventures, L.P.
	 	5,483	 	 	May 26, 2015
	Echelon Ventures Special Limited Partners I, L.P.
	 	3,750	 	 	May 26, 2015
	Fletcher Spaght Ventures, L.P.
	 	9,233	 	 	May 26, 2015
	Vox Equity Partners, L.P.
	 	4,960	 	 	May 26, 2015
	Vox Equity Partners II, L.P.
	 	34,278	 	 	May 26, 2015
	Lewis Wharf Partners
	 	1,437	 	 	July 1, 2015
	CB Healthcare Fund II, L.P.
	 	36,530	 	 	July 1, 2015
	CB-AH Parallel Fund II, L.P.
	 	5,922	 	 	July 1, 2015
	Colin Brenan
	 	16,432	 	 	July 1, 2015
	Echelon Ventures, L.P.
	 	22,278	 	 	July 1, 2015
	Fletcher Spaght Ventures, L.P.
	 	29,918	 	 	July 1, 2015
	Vox Equity Partners, L.P.
	 	10,786	 	 	July 1, 2015
	Vox Equity Partners II, L.P.
	 	74,545	 	 	July 1, 2015

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