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Data availability and use guidelines

What is the Human Cell Atlas?

The HCA is a collaborative effort by an international group of scientists to create a comprehensive reference map of all the cells in the human body. The HCA Data Portal and Data Coordination Platform are built by scientists and technologists at EMBL-EBI, the Broad Institute, UC Santa Cruz, and the Chan Zuckerberg Initiative. Learn more about the HCA project here.

What kind of data is in the HCA?

The HCA data will eventually accept all types of single-cell data, but it currently contains single-cell RNA-sequencing data from Smart-seq2 and 10X v2 assays. While we are focused on curating a collection of data from healthy human specimens, as we grow we are accepting data from a number of sources, including model organisms and organoids, and both healthy and diseased samples. Stay tuned, the HCA is constantly evolving!

Currently, both Smart-seq2 and 10X v2 processed data can be downloaded as expression matrices from individual cell data using the CLI. The matrices for 10x data are per channel.

In addition, an expression matrix containing the combined Smart-Seq2 data from all the cells of a particular project can also be obtained by requesting an expression matrix in the Data Browser.

Note that these matrices contain Gencode IDs, rather than gene name symbols. Please contact us if you need help converting Gencode IDs to gene names.

How do I get more details about projects, like protcols or publications?

You can learn more about each project by visiting the Projects tab in the Explore section of the Data Portal. We encourage all contributing projects to provide a detailed description of their protocol and post their protocol details at Publication information, where available, is also visible on the Projects page.

Can I use this data for a publication?

Yes, data from the HCA can be used for publication. Learn more about our data use agreement.

How do I cite HCA data?

The URL for the HCA DCP Data Portal,, can be used as the citation for data obtained from the HCA. Alternatively, you can cite: Regev A., et al. 2017. The Human Cell Atlas. Elife. Dec 5;6. pii: e27041. doi: 10.7554/eLife.27041.

Data access, analysis, and development help

How do I access the data in the HCA?

The user guides in the Intro section of the data portal contain detailed information about how to access the data. We have also created a series of data consumer vignettes, which give examples of how others have accessed and used the data from the HCA.

How do I visualize or analyze the data in the HCA?

Single-cell sequencing analysis methods are constantly changing, and there are many tools for visualizing or analyzing the data in the HCA. Popular tools for analyzing single-cell RNA-seq data include Seurat (R) and ScanPy (Python),though many other excellent tools exist. We offer a list of community-built analysis applications in the Analyze section on the Data Portal.

How do I make my tool compatible with HCA data and add it to the HCA Data Portal?

We encourage scientists and developers to contribute their own analysis and visualization applications and data processing pipelines to the HCA. You can learn more about how to do this in the Intro section of the Data Portal.

How can I get involved with the HCA?

Visit the Contact page to learn how to collaborate with us and to reach us with your feedback.

How can I reuse parts of the DCP?

One of our goals is to make the HCA data coordination platform code open and reusable to the community. For now, contact us at with questions about reusing our code. Stay tuned for more information about reusing code in the Intro section of the Data Portal.

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