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The Illumina Billion Cell Atlas is here

The world’s largest genome‑wide genetic perturbation data set built to accelerate drug discovery and AI models

> 150,000,000 single cells sequenced to date
3.1 petabytes of data generated

Unlocking hyperscale biology

The Illumina Billion Cell Atlas uses CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) technology to switch on and off 20,000 genes across 250 disease-relevant human cell types. The result will be the most comprehensive map of disease biology to date.

20,000 genes × 2 directions × 250 cell types = 107 total perturbations

Illumina billion cell atlas

CRISPR-cas9 expression in IPSC (induced pluripotent stem cell)-derived contracting cardiomyocytes.

Access the breakthrough Illumina Billion Cell Atlas

Illumina is broadening access to the Illumina Billion Cell Atlas and maximizing its value through strategic partnerships and services. To access this breakthrough data set and learn more about collaboration opportunities, email Illumina using the address below.

BusinessDevelopment@illumina.com

Building frontiers with pharmaceutical partners using AI and human genomics

The Illumina Billion Cell atlas will be the world’s largest genome-wide genetic perturbation dataset, built to accelerate drug discovery through AI across the pharmaceutical ecosystem. Under an alliance framework with AstraZeneca, Merck, and Eli Lilly and Company leading as founding participants, the Atlas unleashes a new era of capabilities that can:

Characterize mechanisms of action for drugs and diseases

Explore new indication expansion opportunities

Train AI models at unprecedented scale

Validate functional target candidates

By harnessing advanced genomic patient datasets, Merck scientists are building and leveraging AI models grounded in real biological variation—not just literature text—and translating those insights into novel targets and precision biomarkers that matter for patients. Through our close collaboration with Illumina, we’re establishing a scalable bridge from genomic insight to therapeutic impact, accelerating the path from discovery to the clinic and enabling a deeper understanding of complex disease biology with unprecedented confidence and speed.

Iya Khalil Vice President and Head of Data, A.I. & Genome Sciences Merck

Cell types and disease models

Coverage spans areas historically hard-to-decode such as cardiometabolic disease, neurological disease, immune disorders, rare genetic diseases, and cancer.

Tissue type (origin of the cells)
  • Bladder
  • Blood
  • Bone
  • Breast
  • Central Nervous System
  • Cervix
  • Colorectal
  • Connective Tissue
  • Embryo
  • Esophagus
  • Gastric
  • Kidney
  • Liver
  • Lung
  • Lymphocyte
  • Muscle
  • Ovary
  • Pancreas
  • Plasma
  • Prostate

Powering the atlas with Illumina solutions and workflows

Information from 1 billion cells creates large, perturbation‑rich data sets that are pushing the technological boundaries to understand cell‑state annotation, perturbation prediction, and drug‑response modeling. This unprecedented scale of single-cell data generation creates new opportunities to connect human genetics and functional genomics to therapeutic mechanisms. Illumina BioInsight powers the next generation of drug discovery with advanced, foundational AI technologies and data sets for deeper biological insights. With secure access to multiomic data sets and interconnected, advanced analytical tools, BioInsight enables teams to move more quickly from raw data to meaningful biological interpretation, supporting everything from early‑stage drug discovery to large national genomics initiatives using proven expertise from Illumina.

Learn more about BioInsight

Illumina Single Cell 3' RNA Prep

The Illumina Billion Cell Atlas is enabled by Illumina Single Cell 3′ RNA Prep, a microfluidics-free workflow that captures millions of single cells in a single experiment.

DRAGEN Single Cell RNA

The workflow optimizes single-cell RNA sequencing analysis on DRAGEN software using hardware acceleration that is hosted on the Illumina Connected Analytics for secure, scalable analysis.

Partner with us and get access to the Illumina Billion Cell Atlas

Unlock groundbreaking and unique insights into human biology with the Illumina Billion Cell Atlas. This initiative provides partners with secure access to one of the world’s largest multiomic data sets, powering target discovery, biomarker validation, and precision medicine development.

BusinessDevelopment@illumina.com