HCA Data Portal
  • Contributing Data to the Human Cell Atlas
  • Submitting Count Matrices and Tier 1 Metadata to CELLxGENE Discover
  • Submitting FASTQs and Tier 2 metadata to the HCA Data Repository
  • Submitting Cell Annotation Metadata to the Cell Annotation Platform (CAP)

Submitting FASTQs and Tier 2 metadata to the HCA Data Repository

File format

Data contributors are required to submit FASTQ files to the HCA Data Repository.

Tier 2 metadata fields

Tier 2 metadata fields are tailored to each Biological Network to ensure vital network-specific information is captured (e.g. for lung, it is important to have information about lung function, whereas for gut it is important to have information on dietary factors). The lists of fields are currently being defined by members of the Biological Networks. Completed field lists will appear below once finalised.

  • Adipose
  • Breast
  • Development
  • Eye
  • Genetic diversity
  • Gut
  • Heart
  • Immune
  • Kidney
  • Liver
  • Lung
  • Musculoskeletal
  • Nervous system
  • Oral and craniofacial
  • Organoid
  • Pancreas
  • Reproduction
  • Skin

Submission process

To submit raw data (FASTQ files) and Tier 2 metadata, please follow the process for submission:

  1. All data contributors will be emailed to complete two tasks:

    • Check the type of consent and data protection measures the data requires

    • Reply to the email with the names and email addresses of:

      i. An institutional representative who is authorised to sign legal agreements for your institution

      ii. The PI responsible for the dataset.

    They will be required to sign the Data Contributor Agreement HCA will send.

  2. Signatories are requested to sign the Data Contributor Agreement that will be sent through Docusign.

  3. Data contributors will then be sent a metadata template to complete and credentials to securely upload the Tier 2 metadata and FASTQ files to the HCA Data Repository.

If a contributor wishes to publish their embargoed dataset at an earlier date they can do so by contacting the wrangling team at wrangler-team@data.humancellatlas.org.