Genomics software · Single cell immunology

Dropprint Genomics

A San Francisco startup that built computational infrastructure and a database of over a million immune cells to make single cell genomics cheaper to run. It never operated as an independent company for long: Immunai acquired it in March 2021, less than a year after its Y Combinator debut.

A pitch about speeding cars

Dropprint Genomics described its own idea with a traffic metaphor. “It is like a police person trying to identify the speeding car, they won’t find it if they look at all the cars at once, rather they need to look at the speed of each individual car,” the company wrote on its Y Combinator page. “This is the beauty of single cell genomics, we can now identify that speeding car.”

The company’s own tagline was blunter: “The better way to run single cell genomics.”

By the time it presented at Y Combinator’s Winter 2020 demo day in March 2020, Dropprint said it had already turned that pitch into paper commitments. TechCrunch’s roundup of the batch described the company’s software as meant “to reduce the time/financial cost of analyzing individual cell activity to enable better drug discovery,” and reported that Dropprint had “signed over $1 million in LOIs in two months.”

Why cost was the barrier

Single cell RNA sequencing lets researchers read the gene activity of one cell at a time instead of averaging across a whole tissue sample, which is what makes it possible to spot a rare or aberrant cell population, Dropprint’s own version of the speeding car problem. But running a separate sequencing reaction for every patient sample is expensive, and Dropprint said cost and data analysis were “the biggest barrier for entry into the single cell genomics market.” The company said it had cut that cost by tenfold and built the computational infrastructure to process data at scale.

That claim traces back to real academic work. A 2018 Nature Biotechnology paper, “Multiplexed droplet single-cell RNA-sequencing using natural genetic variation,” describes a method called demuxlet that lets researchers pool cells from many individuals into one sequencing run and then sort them back out computationally, using each person’s natural DNA variation as a built in barcode. Multiplexing this way cuts the per sample cost of running many patients through single cell sequencing, which is the same problem Dropprint set out to solve commercially. Both Dropprint co-founders, Meena Subramaniam and Rachel Gate, are listed as authors on that paper, alongside their UCSF advisor Chun Jimmie Ye.

Two scientists from one lab

Dropprint’s founders came out of the Ye lab at the University of California, San Francisco, a group that works on the genetics of the immune system and autoimmune disease. Rachel Gate, PhD, was CEO and co-founder. Meena Subramaniam, PhD, was co-founder. Both hold doctorates and both appear as authors on the 2018 demuxlet paper out of that lab. Subramaniam is also a co-author on a separate, later paper from the same group, a 2022 Science study using single cell RNA sequencing to find cell type specific molecular and genetic associations with lupus; Gate is not listed as an author on that one.

One secondary aggregator profile, Startup Intros, names a third co-founder, Chun Jimmie Ye, the pair’s UCSF advisor. None of the primary sources, including the company’s own Y Combinator page, the acquisition announcements, or Crunchbase, list Ye as a Dropprint co-founder, so that claim is unconfirmed here.

Dropprint said it came “from one of the top single cell genomics labs and were the first to process and analyze millions of immune cells,” and that it had built “a database of over 1 million immune cells spanning healthy, cancerous, and autoimmune immune cells,” growing that database through what it called paid partnerships.

The acquisition

On March 25, 2021, Immunai, a New York and Tel Aviv based biotech, announced it had acquired Dropprint Genomics. The deal came about a month after Immunai closed a $60 million Series A, co-led by Schusterman Family Investments, Duquesne Family Office, Catalio Capital Management and Dexcel Pharma, bringing Immunai’s total funding to $80 million, according to Fierce Biotech and GenomeWeb. Neither company disclosed what Immunai paid for Dropprint.

Immunai said Dropprint’s computational infrastructure and its database of immune cells from autoimmune and cancer cohorts would be folded into AMICA, Immunai’s Annotated Multi-omic Immune Cell Atlas, which Immunai describes as the world’s largest single cell database. Gate and Subramaniam joined Immunai’s Machine Learning and Computational Biology team. The acquisition was announced alongside several other senior hires at Immunai, including Peter Smibert, formerly of the New York Genome Center, as VP of Functional Genomics.

“Dropprint’s team and technology are perfectly aligned with Immunai’s mission,” Gate said in the announcement. “Together, we will work to unlock insights into the functions of the immune system in disease.”

What is proven, and what is still claimed

Read plainly: the acquisition itself is well documented by independent trade press, and the founders’ academic work on multiplexed single cell sequencing is real and peer reviewed. The size of Dropprint’s cell database, its cost reduction figure, and its LOI pipeline are all numbers the company or a reporter relaying the company stated at the time, with no later independent confirmation, deal price, or regulatory record to check them against.

What to watch

• Whether Immunai’s published work on AMICA continues to credit methods that trace back to Dropprint’s founders.
• Both co-founders have since moved on from Immunai. LinkedIn lists Meena Subramaniam as a machine learning scientist at Genentech and Rachel Gate at Xaira Therapeutics.
• Whether Immunai ever discloses what it paid for Dropprint. No SEC filing exists for either the deal or Dropprint itself, since Immunai is a private company.

In their words

Dropprint Genomics funding profile on HVCFHealthcare Venture Capital Fund

Related companies

• CellChorus: Also in Drug Discovery and Delivery. A University of Houston spinout that films immune cells one at a time and scores how well each one kills
• CellType: Also in Drug Discovery and Delivery. A two person Yale spinout that translates single cell biology into a language large models can learn, and is using that model to steer a real cancer drug's next act
• Indee Labs: Also in Drug Discovery and Delivery. A Berkeley company that built a chip the size of a fingernail to push gene editing cargo into immune cells without a virus and without an electric shock
• Biocartesian: Also in Drug Discovery and Delivery. A two person, YC-backed lab service that turns tissue and cell samples into what it calls digital molecular maps

Sources

1. IndependentImmunai acquires single-cell data developer Dropprint Genomics to build out its immune system atlasFierce Biotech, Conor Hale · Mar 25, 2021
2. IndependentImmunai Acquires Dropprint GenomicsGenomeWeb · Mar 25, 2021
3. IndependentImmunai Acquires UCSF Startup Dropprint GenomicsUCSF Innovation Ventures · Mar 26, 2021
4. IndependentAll the companies from Y Combinator's W20 demo day, part IV: healthcare, biotech, fintech and nonprofitsTechCrunch · Mar 17, 2020
5. Public recordMultiplexed droplet single-cell RNA-sequencing using natural genetic variationNature Biotechnology · 2018 (preprint bioRxiv 2017)
6. Public recordSingle-cell RNA-seq reveals cell type specific molecular and genetic associations to lupusScience · Apr 8, 2022
7. Public recordSEC EDGAR full text and company search for “Dropprint”SEC EDGAR · searched Sep 25, 2026, no results
8. CompanyImmunai Acquires Dropprint Genomics and Strengthens Leadership Team with Experts in Immunology to Expand Target Discovery CapabilitiesWebWire, company release · Mar 25, 2021
9. CompanyDropprint Genomics: The better way to run single cell genomicsY Combinator company page · accessed Sep 25, 2026
10. IndependentDropprint Genomics company record, Y Combinator databaseYCDB.co · batch W20, archived Mar 31, 2020
11. IndependentRachel Gate, CEO and Co-Founder at Dropprint GenomicsCrunchbase person profile, via Wayback Machine · archived Mar 26, 2021
12. AggregatorDropprint Genomics: Funding, Team & InvestorsStartup Intros · accessed Sep 25, 2026