EX-5.2

Exhibit 5.2

SILICON VALLEY

ANN ARBOR

AUSTIN

BEIJING

BOSTON

LOS ANGELES

NEW YORK

SAN DIEGO

SAN FRANCISCO

SINGAPORE

July 19, 2022

Singular Genomics Systems, Inc.

3010 Science Park Road

San Diego, California 92121

Ladies and Gentlemen:

We have acted as counsel to Singular Genomics Systems, Inc., a Delaware corporation (the “Company”), and you have requested our opinion with respect to certain matters in connection with the offering by the Company of the number of authorized but unissued shares having aggregate sale proceeds of up to $100 million (the “Shares”) of the Company’s common stock, par value $0.0001 (the “Common Stock”), to be issued pursuant to the Registration Statement on Form S-3 filed on the date hereof with the Securities and Exchange Commission (the “Commission”) under the Securities Act of 1933, as amended (the “Act”) (the “Registration Statement”), the related prospectus, included in the Registration Statement (the “Base Prospectus”), and the related at-the-market offering prospectus supplement (the “ATM Prospectus”) and that certain sales agreement, dated July 19, 2022 by and between the Company and Cowen and Company, LLC (the “Sales Agreement”). The Base Prospectus and the ATM Prospectus are collectively referred to as the “Prospectus.” The Shares are to be sold by the Company in accordance with the Sales Agreement, as described in the ATM Prospectus.

In connection with this opinion, we have examined and relied upon the Registration Statement, the Prospectus, the Company’s Amended and Restated Certificate of Incorporation and Amended and Restated Bylaws, as currently in effect, and the originals or copies certified to our satisfaction of such other documents, records, certificates, memoranda and other instruments as in our judgment are necessary or appropriate to enable us to render the opinion expressed below. With your consent, we have relied upon certificates and other assurances of officers of the Company as to factual matters without having independently verified such factual matters. We have assumed the genuineness and authenticity of all documents submitted to us as originals, and the conformity to originals of all documents submitted to us as copies thereof and the due execution and delivery by all parties other than the Company of all documents where due execution and delivery are a prerequisite to the effectiveness thereof.

This opinion is being furnished in connection with the requirements of Item 601(b)(5) of Regulation S-K under the Act, and no opinion is expressed herein as to any matter pertaining to the contents of the Registration Statement or the Prospectus, other than as expressly stated herein with respect to the issue of the Shares. Our opinion is limited to the matters stated herein and no opinion is implied or may be inferred beyond the matters expressly stated. Our opinion herein is expressed solely with respect to the General Corporation Law of the State of Delaware and we express no opinion with respect to any other laws. Our opinion is based on these laws as in effect on the date hereof, and we disclaim any obligation to advise you of facts, circumstances, events or developments which hereafter may be brought to our attention and which may alter, affect or modify the opinion expressed herein.

Subject to the foregoing and the other matters set forth herein, it is our opinion that, as of the date hereof, the Shares have been duly authorized and when issued and paid for in accordance with the terms of the Sales Agreement, such Shares will be validly issued, fully paid and nonassessable.

GUNDERSON DETTMER STOUGH VILLENEUVE FRANKLIN & HACHIGIAN, LLP

3570 Carmel Mountain Road, Suite 200 | San Diego, CA 92130 | gunder.com

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