Human Cell Atlas

Human Cell Atlas

A comprehensive mapping of the types of cell, their interrelationships in 3D and the systems they form in biology.

The Human Cell Atlas (HCA) is an international collaborative effort, established in 2016, to map all the cells in the human body and their relationships to each other. The human body is estimated to have 37 trillion cells. Each cell type in the atlas would have a unique ID card, a three-dimensional map for how cell types fit together forming tissues.

The aims of the project would be to define all human cell types in terms of distinctive molecular profiles (e.g., gene expression) and connect this information with classical cellular descriptions (e.g., location and morphology). A comprehensive reference map of the molecular state of cells in healthy human tissues would advance the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, as well as provide a framework for human disease.

The HCA will build upon previous consortia such as the Human Genome Project and link with efforts to characterize related elements such as functional genomics (ENCODE), epigenetics (IHEC, BLUPRINT), transcriptomics (GTEx) and proteomics (the Human Protein Alas). Some of the participating networks include the Immune Cell Atlas (ICA), the Developmental Cell Atlas (DCA), and the Skin Cell Atlas (SCA).

The first phase of the HCA will profile 30-100 million cells both isolated and also in their tissue context. The cells will come from major tissues and systems of healthy participants of both genders. Dissociated cells will be profiled at the single cell level and frozen samples will have single-nucleus profiling with spatial analysis in relation to tissues.

The first single-cell sequencing datasets became available to the research community in April 2018. Information from more than 500,000 cells was collected by research teams at the Broad Institute and the Wellcome Trust Center. Products from 10x Genomics were used to collect the data. The data includes a type of RNA sequencing called RNA-seq (whole transcriptome shotgun sequencing) profiles for approximately 530,000 human immune cells from adult bone marrow and newborn umbilical cord, about 200,000 human spleen cells and 6,635 lymph node and tumor cells from a mouse model for melanoma.

Scientist working on the Human Cell Atlas projects are sharing their detailed research methods and discuss sequencing processes, tissue handling, and computational workflows in the Human Cell Atlas Method Development Community on which is a free and open-access group.

Wellcome Trust is funding projects at six UK research institutes which will be part of the HCA. The Medical Research Council provided a funding opportunity for UK-based researchers to contribute to the HCA using single-cell gene expression and imaging analysis. The Helmsley Charitable Trust and the Chan Zuckerberg Initiative (CZI) are partnering to provide funding for research towards the HCA.

The HCA is led by Aviv Regev at the Broad Institute (MIT and Harvard) and Sarah Teichmann at UK Wellcome Trust Sanger Institute. Regev launched Celsius Therapeutics in spring 2018 to help her research findings move more quickly to drug development for cancer and autoimmune disease. The HCA meeting in San Francisco in Autumn 2018 was sponsored by the biomedical research center, Chan Zuckerberg BioHub. BioHub’s co-president Stephen Quake is an HCA organizer.




Aviv Regev

Organizing committe co-chair

Sarah Teichmann

Organizing committe co-chair

Further reading


The Human Cell Atlas

Aviv Regev, Sarah A Teichmann, Eric S Lander, Ido Amit, Christophe Benoist, Ewan Birney, Bernd Bodenmiller, Peter Campbell, Piero Carninci, Menna Clatworthy, Hans Clevers, Bart Deplancke, Ian Dunham, James Eberwine, Roland Eils, Wolfgang Enard, Andrew Farmer, Lars Fugger, Berthold Gottgens, Nir Hacohen, Muzlifah Haniffa, Martin Hemberg, Seung K Kim, Paul Klenerman, Nir Yosef

Academic paper

The Human Cell Atlas Is Biologists' Latest Grand Project



The Human Cell Atlas: from vision to reality

Orit Rozenblatt-Rosen et al.

Documentaries, videos and podcasts





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