Exhibit 10.1



 Exhibit 10.1 

AMENDMENT AGREEMENT NO. 2 TO REGISTRATION RIGHTS AGREEMENT 

This Amendment Agreement No. 2 to the Registration Rights Agreement (as defined below) (this “Second Amendment
Agreement”) is entered into as of February 29, 2016, by and between Great Basin Scientific, Inc., a Delaware corporation (the “Company”), and the undersigned holder (the “Holder”) which is one of the
investors listed on the Schedule of Buyers (“Schedule of Buyers”) attached to that certain Securities Purchase Agreement between the Company and all of the investors listed on the Schedule of Buyers (the “Buyers”)
dated December 28, 2015 (the “SPA”) with reference to the following facts: 
 A. On December 28, 2015, the
Company and the Buyers (as defined in the Registration Rights Agreement) entered into the SPA in relation to the issuance and sale by the Company and purchase by the Holders of: (i) that aggregate principal amount of senior secured convertible
notes of the Company, in substantially the form attached to the SPA as Exhibit A (the “Notes”), set forth opposite such Buyer’s name in column (3) on the Schedule of Buyers (which aggregate principal amount of Notes
for all Buyers was $22,100,000) and (ii) related Series D Warrants, in substantially the form attached to the SPA as Exhibit B (the “Warrants”), representing the right to acquire that number of shares of common stock of
the Company, par value $0.0001 (“Common Stock”), set forth opposite such Buyer’s name in column (4) on the Schedule of Buyers (as exercised, collectively, the “Warrant Shares”), which totaled in the
aggregate 3,503,116 Warrant Shares. 
 B. The issuance of the Notes and the Warrants occurred at a closing on December 30, 2015 (the
“Closing Date”). 
 C. In accordance with the terms of the SPA, the Company agreed to provide certain registration rights
under the United States Securities Act of 1933, as amended and the rules and regulations thereunder pursuant to the Registration Rights Agreement by and between the Company and each of the Buyers (the “Original Registration Rights
Agreement”) entered into December 30, 2015. 
 D. On February 16, 2016, the Company and certain of the Buyers holding
enough of the Notes and Warrants to constitute the Required Holders under Section 9 (e) of the SPA and Section 10 of the Registration Rights Agreement entered into Amendment Agreement No.1 to the Original Registration Rights Agreement
(the “First Amendment Agreement” and the Original Registration Rights Agreement as amended by the First Amendment Agreement, the “Registration Rights Agreement”), whereby the Company and the Buyers agreed to, among
other things, to redefine the term “Initial Filing Deadline” as “February 29, 2016”. 
 E. The Company
desires to further amend the definition of “Initial Filing Deadline” in the Registration Rights Agreement as to permit the Company to file its Annual Report on Form 10-K for the year ended December 31, 2015 including, once
prepared, the Company’s audited annual financial statements for that period before the filing of the Initial Registration Statement (as defined in the Registration Rights Agreement). 







 F. In compliance with Section 10 of the Registration Rights Agreement, this Second Amendment
Agreement shall only be effective upon the execution and delivery of this Second Amendment Agreement and agreements in form and substance identical to this Second Amendment Agreement (the “Other Second Amendment Agreements”) by
other holders of Registrable Securities (as defined in the SPA) (each an “Other Holder”) representing on the Closing Date at least fifty-one percent (51%) of the aggregate number of Registrable Securities issued or issuable
under the Cash Notes and Cash Warrants issued on the Closing Date and shall include Hudson Bay so long as Hudson Bay and/or any of its affiliates collectively hold at least five percent (5%) of the Registrable Securities, in the aggregate (the
“Required Holders”) (such time, the “Effective Time”). 
 NOW, THEREFORE, in consideration of the premises
set forth above, and other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the parties hereto hereby agree as follows: 

1. Initial Filing Deadline. Section 1(z) of the Registration Rights Agreement is amended such that as of the Effective Time
“Initial Filing Deadline” shall be defined as “March 1, 2016.” 
 2. Acknowledgments. The Company hereby
confirms and agrees that (i) except with respect to the amendment set forth in Section 1 above as of the Effective Time, the Registration Rights Agreement shall continue to be, in full force and effect; (ii) the execution, delivery
and effectiveness of this Second Amendment Agreement shall not operate as an amendment of any right, power or remedy of the Holder except to the extent set forth herein. As of the Effective Time, the Registration Rights Agreement will be deemed to
be fully amended and restated to reflect the amendment set forth in Section 1 above. 
 3. Fees And Expenses. [NTD: HB ONLY: The
Company shall reimburse the Holder for its legal fees and expenses in connection with the preparation and negotiation of this Second Amendment Agreement and transactions contemplated thereby, by paying any such amount to Schulte Roth &
Zabel LLP (the “Holder Counsel Expense”) by wire transfer of immediately available funds in accordance with the written instructions of Schulte Roth & Zabel LLP delivered to the Company. The Holder Counsel Expense shall be
paid by the Company whether or not the transactions contemplated by this Agreement are consummated. Except as otherwise set forth above, each party to this Second Amendment Agreement shall bear its own expenses in connection with the transactions
contemplated hereby.] [NTD: ALL OTHERS: Each party to this Second Amendment Agreement shall bear its own expenses in connection with the transactions contemplated hereby.] 

4. No Material, Nonpublic Information. The Company hereby agrees and acknowledges that the transactions contemplated by this Second
Amendment Agreement do not constitute material, nonpublic information of the Company or any of its Subsidiaries and that any and all confidentiality or similar obligations under any agreement, whether written or oral, between the Company, any of its
Subsidiaries or any of their respective officers, directors, affiliates, employees or agents, on the one hand, and each Holder or any of its affiliates, on the other hand, have terminated prior to the date hereof. The Company shall not, and shall
cause each of its Subsidiaries and its and each of their respective officers, directors, affiliates, 

  
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employees and agents, not to, provide any Holder with any material, nonpublic information regarding the Company or any of its Subsidiaries from and after the date hereof without the express prior
written consent of such Holder. To the extent that the Company, any of its Subsidiaries or any of their respective officers, directors, affiliates employees or agents delivers any material, non-public information to any Holder without such
Holder’s consent, the Company hereby covenants and agrees that such Holder shall not have any duty of confidentiality to the Company, any of its Subsidiaries or any of their respective officers, directors, affiliates, employees or agents with
respect to, or a duty to the Company, any of its Subsidiaries or any of their respective officers, directors, affiliates, employees or agents not to trade on the basis of, such material, non-public information. The Company understands and confirms
that the Holder will rely on the foregoing representations in effecting transactions in securities of the Company. 
 5. Independent
Nature of Holder Obligations and Rights. The obligations of the Holder under this Second Amendment Agreement are several and not joint with the obligations of any Other Holder, and the Holder shall not be responsible in any way for the
performance of the obligations of any Other Holder under any Other Second Amendment Agreement. Nothing contained herein or in any Other Second Amendment Agreement, and no action taken by the Holder pursuant hereto, shall be deemed to constitute the
Holder and Other Holders as a partnership, an association, a joint venture or any other kind of entity, or create a presumption that the Holder and Other Holders are in any way acting in concert or as a group with respect to such obligations or the
transactions contemplated by this Second Amendment Agreement or any Other Second Amendment Agreement and the Company acknowledges that the Holders are not acting in concert or as a group with respect to such obligations or the transactions
contemplated by this Second Amendment Agreement or any Other Second Amendment Agreement. The Company and the Holder confirm that the Holder has independently participated in the negotiation of the transactions contemplated hereby with the advice of
its own counsel and advisors. The Holder shall be entitled to independently protect and enforce its rights, including, without limitation, the rights arising out of this Second Amendment Agreement or, any Other Second Amendment Agreement, and it
shall not be necessary for any Other Holder to be joined as an additional party in any proceeding for such purpose. 
 6. No Third Party
Beneficiaries. This Second Amendment Agreement is intended for the benefit of the parties hereto and their respective permitted successors and assigns, and is not for the benefit of, nor may any provision hereof be enforced by, any other Person.

 7. Counterparts. This Second Amendment Agreement may be executed in any number of counterparts and by different parties hereto in
separate counterparts, each of which when so executed and delivered shall be deemed to be an original and all of which taken together shall constitute but one and the same instrument. In the event that any signature is delivered by facsimile
transmission or by an e-mail which contains a portable document format (.pdf) file of an executed signature page, such signature page shall create a valid and binding obligation of the party executing (or on whose behalf such signature is executed)
with the same force and effect as if such signature page were an original thereof. 

  
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 8. No Strict Construction. The language used in this Second Amendment Agreement will be
deemed to be the language chosen by the parties to express their mutual intent, and no rules of strict construction will be applied against any party. 

9. Headings. The headings of this Second Amendment Agreement are for convenience of reference and shall not form part of, or affect the
interpretation of, this Second Amendment Agreement. 
 10. Severability. If any provision of this Second Amendment Agreement is
prohibited by law or otherwise determined to be invalid or unenforceable by a court of competent jurisdiction, the provision that would otherwise be prohibited, invalid or unenforceable shall be deemed amended to apply to the broadest extent that it
would be valid and enforceable, and the invalidity or unenforceability of such provision shall not affect the validity of the remaining provisions of this Second Amendment Agreement so long as this Second Amendment Agreement as so modified continues
to express, without material change, the original intentions of the parties as to the subject matter hereof and the prohibited nature, invalidity or unenforceability of the provision(s) in question does not substantially impair the respective
expectations or reciprocal obligations of the parties or the practical realization of the benefits that would otherwise be conferred upon the parties. The parties will endeavor in good faith negotiations to replace the prohibited, invalid or
unenforceable provision(s) with a valid provision(s), the effect of which comes as close as possible to that of the prohibited, invalid or unenforceable provision(s). 

11. Amendments. No provision of this Second Amendment Agreement may be amended other than by an instrument in writing signed by the
Company and the Required Holders. 
 12. Further Assurances. Each party shall do and perform, or cause to be done and performed, all
such further acts and things, and shall execute and deliver all such other agreements, certificates, instruments and documents, as the other party may reasonably request in order to carry out the intent and accomplish the purposes of this Second
Amendment Agreement and the consummation of the transactions contemplated hereby. 
 13. Notice. Whenever notice is required to be
given under this Second Amendment Agreement, unless otherwise provided herein, such notice shall be given in accordance with Section 9(f) of the SPA. 

14. Successors and Assigns. This Second Amendment Agreement shall be binding upon and inure to the benefit of the parties and their
respective successors and assigns. 
 15. Capitalized Terms. Capitalized terms used herein and not otherwise defined herein shall
have the respective meaning set forth in the Registration Rights Agreement. 
 16. Governing Law; Jurisdiction; Jury Trial. All
questions concerning the construction, validity, enforcement and interpretation of this Second Amendment Agreement shall be governed by the internal laws of the State of New York, without giving effect to any choice of law or conflict of law
provision or rule (whether of the State of New York or any other jurisdictions) that would cause the application of the laws of any jurisdictions other than the 

  
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State of New York. Each party hereby irrevocably submits to the exclusive jurisdiction of the state and federal courts sitting in The City of New York, Borough of Manhattan, for the adjudication
of any dispute hereunder or in connection herewith or with any transaction contemplated hereby or discussed herein, and hereby irrevocably waives, and agrees not to assert in any suit, action or proceeding, any claim that it is not personally
subject to the jurisdiction of any such court, that such suit, action or proceeding is brought in an inconvenient forum or that the venue of such suit, action or proceeding is improper. Each party hereby irrevocably waives personal service of
process and consents to process being served in any such suit, action or proceeding by mailing a copy thereof to such party at the address for such notices to it under this Second Amendment Agreement and agrees that such service shall constitute
good and sufficient service of process and notice thereof. Nothing contained herein shall be deemed to limit in any way any right to serve process in any manner permitted by law. EACH PARTY HEREBY IRREVOCABLY WAIVES ANY RIGHT IT MAY HAVE, AND
AGREES NOT TO REQUEST, A JURY TRIAL FOR THE ADJUDICATION OF ANY DISPUTE HEREUNDER OR IN CONNECTION WITH OR ARISING OUT OF THIS SECOND AMENDMENT AGREEMENT OR ANY TRANSACTION CONTEMPLATED HEREBY. 

[Signature Pages Follow] 

  
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 IN WITNESS WHEREOF, each Undersigned and the Company have caused their respective signature page to this
Second Amendment Agreement to be duly executed as of the date first written above. 
  

			
	COMPANY:
	
	GREAT BASIN SCIENTIFIC, INC.
		
	By:	 	  

		 	Name: Ryan Ashton
		 	Title: President, CEO


 [Signature Page to Registration Rights Second Amendment Agreement] 







 IN WITNESS WHEREOF, each Undersigned and the Company have caused their respective signature page to this
Second Amendment Agreement to be duly executed as of the date first written above. 
  

			
	HOLDER:
		
	By:	 	  

		 	Name:
		 	Title:


 [Signature Page to Registration Rights Second Amendment Agreement]