UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 8-K

CURRENT REPORT

Pursuant to Section 13 or 15(d)

of the Securities Exchange Act of 1934

Date of Report (Date of earliest event reported): June 29, 2016

GREAT BASIN SCIENTIFIC, INC.

(Exact name of registrant as specified in its charter)

420 E. South Temple, Suite 520, Salt Lake City, Utah

(Address of principal executive offices)

84111

(Zip code)

(801) 990-1055

(Registrant’s telephone number, including area code)

N/A

(Former name or former address, if changed since last report.)

Check the appropriate box below if the Form 8-K filing is intended to simultaneously satisfy the filing obligation of the registrant under any of the following provisions (see General Instruction A.2 below):

Securities Purchase Agreement

On June 29, 2016, Great Basin Scientific, Inc. (the “Company”) entered into a Securities Purchase Agreement dated June 29, 2016 (the “SPA”) with certain investors named on the Schedule of Buyers attached to the SPA (each a “Buyer”) pursuant to which the Company has agreed to issue $75 million in principal face amount of senior secured convertible notes of the Company (the “Notes”) and related Series H common stock purchase warrants (the “Warrants”). The Buyers will purchase Notes and related Series H Warrants through payment of cash at a discount by paying $906.67 for each $1,000 in principal face amount of Notes and related Warrants.

The Notes will not bear any ordinary interest. The Company will receive total gross proceeds of $68 million, assuming all conditions for subsequent funding are met and no events of default occur, each as described below.

The SPA provides that each Buyer shall pay for the Notes and the Warrants to be issued and sold to such Buyer at the closing (1) 8.8235% (approximately $6 million) of its applicable aggregate cash purchase price to the Company by wire transfer of immediately available funds and (2) 91.1765% (approximately $62 million) of its applicable aggregate cash purchase price (“Restricted Cash”) to an account of the Company established for such Buyer (a “Master Restricted Account”) by wire transfer of immediately available funds, such purchase price to be held and in accordance with and pursuant to the terms and conditions of an account control agreement between the Buyer and the bank (a “Master Control Account Agreement”).

Subject to obtaining the Stockholder Approval (as defined below) and certain other equity conditions as described below, the Restricted Cash will become unrestricted and released to the Company as follows: (i) $6 million on the fifth trading day after January 30, 2017 (such date, the “First Amortization Date”)), (ii) $8 million after the fifth trading day after the last business day of the calendar month following the First Amortization Date and (iii) $3,692,308 on the 75th trading day after the initial date the shares of common stock underlying the Notes are eligible to be resold pursuant to Rule 144 of the Securities Act of 1933, as amended (the “144 Date”) and each 30th calendar day thereafter until all Restricted Cash has become unrestricted and released.

Release of the remaining cash purchase price will be subject to certain equity conditions including, but not limited to:

Under the SPA, the Company has agreed to call a meeting of its stockholders within 65 days of closing, solicit proxies at such meeting and use its reasonable best efforts to obtain the approval of its stockholders for purposes of complying with NASDAQ Listing Rule 5635(d) for the issuance of shares of common stock underlying the Notes without giving effect to the exchange cap in the Notes in an amount that may be equal to or exceed 20% of our common stock outstanding before the issuance of the Notes and the issuance of shares of common stock under the Warrants without giving effect to the exercise floor price set forth in the Warrants (the “Stockholder Approval”).

The SPA contains customary representations and warranties of the Buyers and the Company regarding the purchase and offer and sell, respectively, of the Notes and Warrants. Under the SPA, the Company makes certain covenants including, but not limited to:

The closing of the transactions contemplated by the SPA is expected to occur on or about June 30, 2016 and is subject to certain customary closing conditions and deliverables as set forth in the SPA, including but not limited to, the execution of certain subordination agreements for the Company’s outstanding indebtedness to Spring Forth Investments LLC and the Utah Autism Foundation. If the transactions in the SPA do not close in accordance with the terms of the SPA within 5 business days of the execution of the SPA, then any non-breaching party may terminate the SPA.

Senior Secured Convertible Notes

The Notes will be represented by a form of senior secured convertible note attached to the SPA as Exhibit A. In addition to the terms and conditions of the Notes as described above, the Notes provide that the Company will repay the principal amount of Notes in 15 equal installments (each a “Installment Date”) beginning on the First Amortization Date, and thereafter the last business day of each calendar month through to the maturity date.

The price at which the Company will convert the installment amounts is equal to the lowest of (i) the then prevailing conversion price, (ii) 80% of the arithmetic average of the lower of (i) the three lowest daily weighted average prices of the common stock during the twenty (20) consecutive trading day period ending on the trading day immediately preceding the Installment Date and (iii) the weighted average price of the common stock on the trading day immediately preceding the Installment Date, subject in all cases to a floor price of $1.00.

Any holder of a Note may by notice to the Company accelerate up to four future installment payments to any applicable Installment Date, in which case the Company will deliver shares of Common Stock for the conversion of such accelerated payments. The holder of a Note may also by notice to the Company defer any installment payment to a later Installment Date.

At any time after issuance the Notes will be convertible at the election of the holder into shares of common stock of the Company at an initial conversion price equal to $2.00.

Conversion of the note is subject to a blocker provision which prevents any holder from converting into shares of common stock if their beneficial ownership of the common stock would exceed either 4.99% or 9.99% of the Company’s issued and outstanding common stock, as elected by the holder at closing.

Further, prior to the Company receiving the necessary Stockholder Approval, conversion of all Notes is limited to 19.99% of the Company’s issued and outstanding common stock on the date of closing. The conversion price is subject to certain adjustments upon the occurrence of certain dilutive events, including the issuance of certain options or convertible securities, and upon the occurrence of certain corporate events, including stock splits and dividends.

At any time after the date that is nine months from the closing, issue of the Notes, the Company shall have the right to redeem all, but not less than all, of the conversion amount then remaining under the Notes at a price equal to the greater of (x) 125% of the conversion amount being redeemed and (y) the product of (A) the conversion amount

being redeemed and (B) the quotient determined by dividing (I) the greatest closing price of the shares of common stock during the period beginning on the date immediately preceding the Company’s notice of redemption and ending on the Company redemption date, by (II) the lowest conversion price in effect during such period.

Under the Notes, the holders will have certain rights upon an “Event of Default” (as defined in the Notes). Such rights include (i) the remaining principal amount of the Notes bearing interest at a rate of 10% per annum, (ii) during the Event of Default the conversion price being adjusted to the lowest of (a) the conversion price then in effect, (b) 75% of the lowest weighted average price of the Common Stock during the 30 consecutive trading day period ending on the trading day immediately preceding the date of the event of default conversion and (c) 75% of the weighted average price of the Common Stock on the date of the applicable event of default conversion, and (iii) the holder having the right to demand redemption of all or a portion of the Notes.

At any time after the earlier of the holder’s receipt of a notice of an Event of Default and the holder becoming aware of an Event of Default and ending on the 15th trading day after the later of (x) the date such Event of Default is cured and (y) the holder’s receipt of an Event of Default notice, the holder may require the Company to redeem all or any portion of the Note by delivering written notice to the Company. Each portion of this Note subject to redemption shall be redeemed by the Company in cash by wire transfer of immediately available funds at a price equal to the greater of (x) 125% of the conversion amount being redeemed and (y) the product of (A) the conversion amount being redeemed and (B) the quotient determined by dividing (I) the greatest closing price of the shares of Common Stock during the period beginning on the date immediately preceding such Event of Default and ending on the date the holder delivers the redemption notice, by (II) the lowest conversion price in effect during such period.

“Event of Default” includes, but is not limited to (and subject to the ability to cure in certain instances):

The Notes will also provide the holders with certain rights upon the occurrence of a fundamental transaction, including but not limited to assumption rights and redemption rights.

The Company will make certain negative covenants in the Notes, pursuant to which the Company agrees not to: (a) incur or guarantee, assume or suffer to exist any indebtedness, other than permitted indebtedness; (b) allow or suffer to exist any mortgage, lien, pledge, charge, security interest or other encumbrance upon or in any property or assets of the Company other than permitted liens; (c) redeem, defease, repurchase, repay or make any payments in respect of, by the payment of cash or cash equivalents all or any portion of any indebtedness other than the Notes in an Event of Default shall have occurred; (d) redeem, defease, repurchase, repay or make any payments in respect of, by the payment of cash or cash equivalents all or any portion of any indebtedness (other than the Notes), prior to the scheduled maturity date of such indebtedness; (e) redeem or repurchase its equity interest or declare or pay any cash dividend or distribution; (f) make, any change in the nature of its business; (g) encumber or allow any liens on, any of its intellectual property other than permitted liens; or (h) enter into, renew, extend or be a party to, any transaction or series of related transactions (including, without limitation, the purchase, sale, lease, transfer or exchange of property or assets of any kind or the rendering of services of any kind) with any affiliate, except in the ordinary course of business.

The Company will make certain affirmative covenants in the Notes, pursuant to which the Company agrees to: (a) maintain and preserve its existence, rights and privileges, and become or remain duly qualified and in good standing in each jurisdiction in which the character of the properties owned or leased by it or in which the transaction of its business makes such qualification necessary, except where failure to do so would not result in a Material Adverse Effect; (b) maintain and preserve all of its properties which are reasonably necessary in the proper conduct of its business in good working order and condition, ordinary wear and tear excepted, and comply at all times with the material provisions of all leases to which it is a party as lessee or under which it occupies property, so as to prevent

any loss or forfeiture thereof or thereunder; (c) maintain insurance with responsible and reputable insurance companies or associations with respect to its properties) and business, in such amounts and covering such risks as is required by any governmental authority having jurisdiction with respect thereto or as is carried generally in accordance with sound business practice by companies in similar businesses similarly situated; and (d) maintain and preserve all of its intellectual property rights which are reasonably necessary in the proper conduct of its business.

Series H Warrants

In connection with the issuance of the Notes under the SPA, the Company will also issue Series H Warrants, in the form attached to the SPA as Exhibit B, in an amount equal to 150% of the sum of the number of shares of common stock acquirable upon conversion of the Notes in full at the conversion price on the closing date (without regard to any limitations on conversions set forth therein).

Each Series H Warrant will be exercisable by the holder beginning six months after the date of issuance and continuing for a period five years thereafter. Each Series H Warrant will be exercisable initially at a price equal to $2.08, subject to adjustments for certain dilutive events and subject to an exercise price floor equal to $1.70.

The Series H Warrants are exercisable on a cashless basis in the event that there is no effective registration statement under the Securities Act covering the resale of the shares of Common Stock issuable upon exercise of the Series H Warrants.

Security Agreement

Pursuant to the SPA and the Notes, the Company will enter into a Pledge and Security Agreement (the “Security Agreement”) with the lead investor, in its capacity as collateral agent (in such capacity, the “Collateral Agent”) for all holders of the Notes. The Security Agreement creates a first priority security interest (second priority interest until the Company’s December 2015 senior secured convertible notes are paid in full) in all of the personal property of the Company of every kind and description, tangible or intangible, whether currently owned and existing or created or acquired in the future (the “Collateral”).

Under the Security Agreement the Company will agree to certain conditions on its maintenance and use of the Collateral, including but not limited to the location of equipment and inventory, the condition of equipment, the payment of taxes and prevention of liens or encumbrances, the maintenance of insurance, the protection of intellectual property rights, and limitations on transfers and sales.

Upon the occurrence of an “Event of Default” under the Security Agreement, the Collateral Agent will have certain rights under the Security Agreement including taking control of the Collateral and, in certain circumstances, selling the Collateral to cover obligations owed to the holders of the Notes pursuant to its terms. “Event of Default” under the Security Agreement means (i) any defined event of default under any one or more of the transaction documents (including the Notes), in each instance, after giving effect to any notice, grace, or cure periods provided for in the applicable document, (ii) the failure by the Company to pay any amounts when due under the Notes or any other transaction document, or (iii) the breach of any representation, warranty or covenant by the Company under the Security Agreement.

The above is a summary of the material terms and conditions of the SPA, the Notes, the Series H Warrants, and the Security Agreement and is qualified in its entirety by the full terms and conditions of such agreements which are attached hereto as Exhibits 10.1 through 10.4 and are hereby incorporated by reference.

Waiver Agreement with Holders of 2015 Convertible Notes

As previously disclosed on the Current Report on Form 8-K filed with the SEC on December 29, 2015, on December 28, 2015, Great Basin Scientific, Inc. (the “Company”) entered into a Securities Purchase Agreement (the “2015 SPA”) in relation to the issuance and sale by the Company to certain buyers as set forth in the Schedule of Buyers attached to the SPA (the “2015 Buyers”) of $22.1 million aggregate principal amount of senior secured convertible notes (the “2015 Notes”) and related Series D common stock purchase warrants (the “Series D Warrants”).

On June 29, 2016, the Company and certain buyers holding enough of the 2015 Notes and Series D Warrants to constitute the required holders under Section 9(e) of the 2015 SPA and Section 19 of the 2015 Notes entered into waiver agreements to waive: (i) the Company’s restriction to incur Indebtedness (as defined in the 2015 Notes) in accordance with Section 17(a) of the 2015 Notes, (ii) the Company’s restriction to incur Liens (as defined in the 2015 Notes) in accordance with Section 17(b) of the 2015 Notes, (iii) the Company’s restriction to incur Indebtedness that ranks pari passu with the 2015 Notes pursuant to Section 16 of the 2015 Notes and (iv) the Company’s restriction in incur Liens (as defined in the 2015 Notes) on certain types of intellectual property in accordance with Section 17(g) of the 2015 Notes, in each case of clauses (i) through (iii), solely with respect to entering into the Notes and related documents thereto and consummating the transactions contemplated thereby (collectively, the “2015 Note Waiver”).

Further the Company and certain buyers holding enough of the 2015 Notes and Series D Warrants to constitute the required holders under Section 10 of the Registration Rights Agreement entered into between the Company and the holders of the 2015 Notes and Series D Warrants entered into waiver agreements to waive: (i) any breach prior to and including June 29, 2016 under Section 2(a) of the Registration Rights Agreement for the Company’s failure to have the initial registration statement brought effective by the initial effectiveness deadline, (ii) any right to Registration Delay Payments (as defined under the Registration Rights Agreement) prior to and including June 29, 2016 for failure to meet its obligations under Section 2(a), and (iii) compliance with the registration requirements of Section 2(a) from and including June 29, 2016, through August 31, 2016.

The foregoing is a summary description of the material terms of the 2015 Note Waiver and is qualified in its entirety by the form of the 2015 Note Waiver, attached as Exhibit 10.5 to this Current Report on Form 8-K and incorporated by reference.

Waiver Agreement with Purchasers in June Unit Offering

On May 26, 2016, the Company entered into subscription agreements (“Subscription Agreements”) with certain investors relating to the sale and issuance by the Company of up to 3,160,000 Units (the “Units”), at a price of $1.90 per Unit, each of which consists of one share of the Company’s common stock and one Series G Warrant (the “Unit Offering”). The Unit Offering closed on June 1, 2016.

On June 29, 2016, the Company and certain investors who executed Subscription Agreements in the Unit Offering representing on the closing date of the Unit Offering at least sixty-seven percent (67%) of the aggregate number of shares of common stock purchased in the Unit Offering pursuant to the Subscription Agreements entered into waiver agreements to waive the lock-up on issuance of securities contained in Section 18 of the Subscription Agreements solely with respect to the Company’s offering and consummation of the Notes and Series H Warrants, the offer and issuance of the placement agent warrants and the offer and issuance of the subordination warrants to be issued in connection with the Notes and Series H Warrants (“Unit Waiver”).

The foregoing is a summary description of the material terms of the Unit Waiver and is qualified in its entirety by the form of the Unit Waiver, attached as Exhibit 10.6 to this Current Report on Form 8-K and incorporated by reference.

Item 3.03 Material Modification to Rights of Security Holders

The information disclosed in Item 1.01 of this Current Report on Form 8-K is incorporated by reference into this Item 3.03.

(d) Exhibits.

SIGNATURE

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned hereunto duly authorized.