Repositories: Human Cell Atlas Data Portal

The Human Cell Atlas (HCA) is an ambitious project to map the location, function and molecular signature of every cell type in the human body. As well as being an extremely important resource in its own right, it aims to be a healthy reference dataset that many researchers can use to supplement their own research data.

Raw, curated data that is part of the Human Cell Atlas is coordinated and made available through the HCA Data Portal. It contains a variety of directly contributed and manually curated datasets from various sources. Much of the data is openly available with both raw data files and expression matrices. Studies with controlled access requirements provide an expression matrix with raw data files available by applying through the normal data access process for either dbGaP or EGA depending on where the study was submitted. The majority of datasets are single-cell sequencing experiments, largely generated from 10x and SmartSeq experiments. Data can be explored via the UI or through APIs. All data in the portal adheres to the HCA Metadata Standard which is comprehensive and explained in detail on the portal.

HCA data can also be explored via a number of other portals including:

• Cambridge Cell Atlas - A portal generated by the Gene Expression Atlas team from EBI that offers cross project gene searching and visualisation of datasets via annotated tsne and umap plots
• The UCSC Cell Browser - A portal generated by the University of California Santa Cruz to visualise annotated cell types through UMAP plots
• The Single Cell Portal - A portal generated by the Broad Institute to visualise expression data and download summary information
• The covid19 cell atlas - https://www.covid19cellatlas.org/
• The EBI HCA Project Catalogue - A curated catalogue of cellular resolution projects with pointers to publications and where data is stored
• https://cellxgene.cziscience.com/ - data can be explored visually in cell x gene and also with a gene expression matrix

The HCA is open to submission for any cellular resolution research data that can contribute to building a healthy atlas of human cells. Further information about how to contribute data can be found via the data portal. Studies that are yet to be archived can be brokered to EBI repositories (BioStudies, BioSamples and ENA) by the HCA team.

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