SIXTH AMENDMENT TO LEASE

Exhibit 10.1

SIXTH AMENDMENT TO LEASE

THIS SIXTH AMENDMENT TO LEASE (this “Sixth Amendment”) is made as of December 8, 2015, by and between ARE-SAN FRANCISCO NO. 17, LLC, a Delaware limited liability company (“Landlord”), and FLUIDIGM CORPORATION, a Delaware corporation (“Tenant”).

RECITALS

A. Landlord and Tenant are now parties to that certain Lease Agreement dated as of September 14, 2010, as amended by that certain First Amendment to Lease dated as of September 22, 2010, as further amended by that certain letter agreement dated August 2, 2012, as further amended by that certain Second Amendment to Lease dated as of April 9, 2013 (“Second Amendment”), as further amended by that certain Third Amendment to Lease dated as of June 25, 2013 (“Third Amendment”), as further amended by that certain Fourth Amendment to Lease dated as of June 4, 2014, and as further amended by that certain Fifth Amendment to Lease dated as of September 15, 2014 (as amended, the “Lease”). Pursuant to the Lease, Tenant leases certain premises consisting of approximately 70,696 rentable square feet (“Current Premises”) in a building located at 7000 Shoreline Court, South San Francisco, California. The Current Premises are more particularly described in the Lease. Capitalized terms used herein without definition shall have the meanings defined for such terms in the Lease.

B. Landlord and Tenant desire, subject to the terms and conditions set forth below, to amend the Lease to, among other things, expand the size of the Current Premises by adding approximately 24,039 rentable square feet of space on the second floor of the Building, as set forth on Exhibit A attached to this Sixth Amendment (collectively, the “Fourth Expansion Premises”).

NOW, THEREFORE, in consideration of the foregoing Recitals, which are incorporated herein by this reference, the mutual promises and conditions contained herein, and for other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, Landlord and Tenant hereby agree as follows:

The “Fourth Expansion Premises Commencement Date” shall be the date Landlord Delivers the Fourth Expansion Premises to Tenant; provided, however, that in no event shall the Fourth Expansion Premises Commencement Date occur prior to April 1, 2016, unless the Fourth Expansion Premises become available for Delivery by Landlord and Tenant agrees in writing to accept Delivery prior to such date. The “Fourth Expansion Premises Rent Commencement

Date” shall be the date that is 2 months after the Fourth Expansion Premises Commencement Date. Upon request of Landlord, Tenant shall execute and deliver a written acknowledgment of the Fourth Expansion Premises Commencement Date in substantially the form of the “Acknowledgement of Commencement Date” attached to the Second Amendment as Exhibit B; provided, however, Tenant’s failure to execute and deliver such acknowledgment shall not affect Landlord’s rights hereunder.

For the period of 60 consecutive days after the Fourth Expansion Premises Commencement Date, Landlord shall, at its sole cost and expense (which shall not constitute an Operating Expense), be responsible for any repairs that are required to be made to the Building Systems serving the Fourth Expansion Premises, unless Tenant or any Tenant Party was responsible for the cause of such repair, in which case Tenant shall pay the cost.

If the following “Early Access Conditions” are satisfied: (i) the tenant occupying the Fourth Expansion Premises as of the date of this Sixth Amendment (the “Existing Tenant”) surrenders the Fourth Expansion Premises prior to March 31, 2016, and (ii) the Existing Tenant enters into an agreement with Landlord, acceptable to Landlord in its sole and absolute discretion, that would allow Tenant to access the Fourth Expansion Premises prior to March 31, 2016 (including a lease termination agreement), then Landlord shall permit Tenant access to the Fourth Expansion Premises commencing 1 business day after the Early Access Conditions are satisfied for the purposes of preparing the Fourth Expansion Premises for Tenant’s occupancy (collectively, “Fourth Expansion Premises Preparation”), provided that such Fourth Expansion Premises Preparation is coordinated with Landlord, and Tenant complies with the Lease and all other reasonable restrictions and conditions Landlord may impose during the Fourth Expansion Premises Preparation. All such access shall be during normal business hours. Landlord shall have no liability whatsoever to Tenant relating to or arising from the failure of the Early Access Conditions to be satisfied. Any access to the Fourth Expansion Premises by Tenant before the Fourth Expansion Premises Commencement Date shall be subject to all of the terms and conditions of the Lease, excluding the obligation to pay Base Rent or Operating Expenses.

Within five (5) business days following the Fourth Expansion Premises Commencement Date, Tenant shall notify Landlord in writing (“Furniture Removal Notice”) of the items of furniture present in the Fourth Expansion Premises that Tenant does not want to use (“Landlord’s Furniture”). Landlord shall cause such item(s) of Landlord’s Furniture identified in the Furniture Removal Notice to be removed within five (5) business days after receipt of such notice. The cost of the removal of such item(s) of Landlord’s Furniture shall be the responsibility of Landlord. Any furniture located in the Fourth Expansion Premises on the Fourth Expansion Premises Commencement Date not identified for removal in the Furniture Removal Notice (“Existing Furniture”) shall become the property of Tenant as of the date the Furniture Removal Notice is provided to Landlord.

Except as set forth in the Lease or this Sixth Amendment: (i) tenant shall accept the Fourth Expansion Premises and the Existing Furniture in their condition as of the Fourth Expansion Premises Commencement Date, subject to all applicable Legal Requirements; (ii) Landlord shall have no obligation for any defects in the Fourth Expansion Premises or the Existing Furniture; and (iii) Tenant’s taking possession of the Fourth Expansion Premises and the Existing Furniture shall be conclusive evidence that Tenant accepts the Fourth Expansion Premises and the Existing Furniture, and that the Fourth Expansion Premises and the Existing Furniture were in good condition at the time possession was taken.

Tenant agrees and acknowledges that, except as otherwise expressly set forth in this Sixth Amendment or in the Lease, neither Landlord nor any agent of Landlord has made any representation or warranty with respect to the condition of all or any portion of the Fourth Expansion Premises or the Existing Furniture, and/or the suitability of the Fourth Expansion Premises or Existing Furniture for the conduct of Tenant’s business, and Tenant waives any implied warranty that the Fourth Expansion Premises or the Existing Furniture are suitable for the Permitted Use.

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“Premises: That portion of the Project, containing approximately 94,735 rentable square feet (“RSF”), consisting of (i) approximately 29,228 rentable square feet (the “Original Premises”), (ii) approximately 19,177 rentable square feet (“Expansion Premises”), (iii) approximately 13,388 rentable square feet (“Second Expansion Premises”), (iv) approximately 8,903 rentable square feet (“Third Expansion Premises”), and (v) approximately 24,039 rentable square feet (“Fourth Expansion Premises”), all as determined by Landlord, as shown on Exhibit A.”

As of the Fourth Expansion Premises Commencement Date, Exhibit A to the Lease is amended to include Exhibit A attached to this Sixth Amendment.

a. Current Premises. Tenant shall continue to pay Base Rent for the Current Premises as provided for in the Lease through April 30, 2020.

b. Fourth Expansion Premises. Commencing on the Fourth Expansion Premises Rent Commencement Date, Base Rent for the Fourth Expansion Premises shall be equal to $3.20 per rentable square foot of the Fourth Expansion Premises per month. Base Rent payable with respect to the Fourth Expansion Premises shall be increased, commencing on the later of (i) the first anniversary of the Fourth Expansion Premises Rent Commencement Date, or (ii) May 1, 2017, and on each subsequent anniversary of such date during the Base Term each, a “Fourth Expansion Premises Adjustment Date”) by multiplying the Base Rent payable with respect to the Fourth Expansion Premises immediately before such Fourth Expansion Premises Adjustment Date by 3% and adding the resulting amount to the Base Rent payable with respect to the Fourth Expansion Premises immediately before such Fourth Expansion Premises Adjustment Date.

As of September 1, 2015, Tenant’s Share of each earthquake deductible or occurrence of uninsured earthquake damage affecting the Premises shall not exceed $7.00 per rentable square of the Premises (including the Fourth Expansion Premises only once the Fourth Expansion Premises Commencement Date has occurred) (the “Current Cap”). On October 1, 2015, and on the first day of each month thereafter through April 30, 2020, the Current Cap shall be reduced by $0.125 per rentable square foot of the Premises (including the Fourth Expansion Premises only once the Fourth Expansion Premises Commencement Date has occurred). Following earthquake

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damage to the Project during the period between September 1, 2015, and April 30, 2020, Tenant shall pay Tenant’s Share of any such deductible or uninsured damage in equal monthly installments amortized over the balance of the Base Term. For the avoidance of doubt, the caps provided for in this paragraph shall apply from September 1, 2015, through April 30, 2020, and shall thereafter be of no further force or effect.

During the course of design and construction of the Additional Tenant Improvements, Landlord shall reimburse Tenant for the cost of the Additional Tenant Improvements once a month against a draw request in Landlord’s standard form, containing evidence of payment of the applicable costs and such certifications, lien waivers (including a conditional lien release for each progress payment and unconditional lien releases for the prior month’s progress payments), inspection reports and other matters as Landlord customarily and reasonably obtains, to the extent of Landlord’s approval thereof for payment, no later than 30 days following receipt of such draw request. Upon completion of the Additional Tenant Improvements (and prior to any final disbursement of the Fourth Expansion Premises TI Allowance) Tenant shall deliver to Landlord the following items: (i) sworn statements setting forth the names of all contractors and subcontractors who did work on the Additional Tenant Improvements and final lien waivers from all such contractors and subcontractors; and (ii) “as built” plans for the Additional Tenant Improvements. Notwithstanding the foregoing, if the cost of the Additional Tenant Improvements exceeds the Fourth Expansion Premises TI Allowance, Tenant shall be required to pay such excess in full prior to Landlord having any obligation to fund any remaining portion of the Fourth Expansion Premises TI Allowance. The Fourth Expansion Premises TI Allowance shall only be available for use by Tenant for the construction of the Additional Tenant Improvements until the date that is 18 months after the Fourth Expansion Premises Commencement Date (the “Outside Third TI Allowance Date”). Any portion of the Fourth Expansion Premises TI Allowance which has not been properly requested by Tenant from Landlord on or before the Outside Third TI Allowance Date shall be forfeited and shall not be available for use by Tenant.

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a. This Sixth Amendment is the entire agreement between the parties with respect to the subject matter hereof and supersedes all prior and contemporaneous oral and written agreements and discussions. This Sixth Amendment may be amended only by an agreement in writing, signed by the parties hereto.

b. This Sixth Amendment is binding upon and shall inure to the benefit of the parties hereto, their respective successors and assigns.

c. This Sixth Amendment may be executed in any number of counterparts, each of which shall be deemed an original, but all of which when taken together shall constitute one and the same instrument. The signature page of any counterpart may be detached therefrom without impairing the legal effect of the signature(s) thereon provided such signature page is attached to any other counterpart identical thereto except having additional signature pages executed by other parties to this Sixth Amendment attached thereto.

d. Except as amended and/or modified by this Sixth Amendment, the Lease is hereby ratified and confirmed and all other terms of the Lease shall remain in full force and effect, unaltered and unchanged by this Sixth Amendment. In the event of any conflict between the provisions of this Sixth Amendment and the provisions of the Lease, the provisions of this Sixth Amendment shall prevail. Whether or not specifically amended by this Sixth Amendment, all of the terms and provisions of the Lease are hereby amended to the extent necessary to give effect to the purpose and intent of this Sixth Amendment.

[Signatures are on the next page]

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IN WITNESS WHEREOF, the parties hereto have executed this Sixth Amendment as of the day and year first above written.

EXHIBIT A

Fourth Expansion Premises

EXHIBIT B

Proposed Scope of Work for Additional Tenant Improvements