Publicly available COVID-19 AIRR-seq data sets

The AIRR Community (www.airr-community.org), in response to the AIRR Community’s call to share COVID-19 AIRR-seq data, has created this page to provide a central location for finding and tracking research that is producing (or planning on producing) COVID-19 AIRR-seq data sets. The page provides links to the papers/projects and the sources for the sequence data (SRA, ENA, etc.). If annotated AIRR-seq data are available, links to the sources for those data sets are also available (e.g. iReceptor, ImmunoAccess, Observer Antibody Space, etc.). If you know of papers or research groups that have such data sets, please add them to this list.

There are three sections that can be found below:

  • Papers that have publicly available AIRR-seq data
  • Papers that are published and are expected to have publicly available AIRR-seq data
  • Papers that are in pre-print and have committed to providing publicly available AIRR-seq data

Papers/projects that have publicly available AIRR-seq data:

  1. Liao, M. et al. The landscape of lung bronchoalveolar immune cells in COVID-19 revealed by single-cell RNA sequencing. medrxiv.
  2. Minervina, A. et al. Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T cell memory formation after mild COVID-19 infection. bioRxiv (Preprint).
  3. Nielsen, S. et al. B cell clonal expansion and convergent antibody responses to SARS-CoV-2. Research Square (Preprint).
  4. Raybould, M. et al. CoV-AbDab: the Coronavirus Antibody Database (Preprint).

Papers/projects that are published and are expected to have publicly available AIRR-seq data:
Stay tuned!

Papers that are in pre-print and/or projects that have stated that they will be providing publicly available AIRR-seq data:

  1. Galson, J. et al. Deep sequencing of B cell receptor repertoires from COVID-19 patients reveals strong convergent immune signatures. bioRxiv (Preprint).
    • Paper DOI
    • Data availability: COVID-19 BCR sequence data will be made available upon publication.
    • Species: Homo Sapiens
    • BioProject Accession: NA
    • Annotated sequences: NA
  2. Huang, L. et al. Blood single cell immune profiling reveals the interferon-MAPK pathway mediated adaptive immune response for COVID-19, medrxiz
  3. Microsoft and Adaptive Biotechnologies are studying how the human immune system reacts to the coronavirus: MSNBC
  4. Wen, W. et al. Immune cell profiling of COVID-19 patients in the recovery stage by single-cell sequencing. Cell Discov 6, 31 (2020).
3 Likes

It looks like we have a winner… The BioProject does not directly link to the paper, but the authors of the paper are the same as the creators of the BioProject, so I am assuming these are the same…

1 Like

Boyd-Lab at Stanford has a preprint out on AIRRseq data!

Thank JP, added it above

Hi, guys!

Check out (and add to the post?) our TCRalpha and TCRbeta longitudinal dataset from Minervina et. al 2020 (preprint: https://www.biorxiv.org/content/10.1101/2020.05.18.100545v1)
Github with COVID-19 associated TCR tables (pogorely/Minervina_COVID).
Raw data:
PRJNA633317
UMI-clustered and mixcr processed data (complete dataset):
https://zenodo.org/record/3835956

Thanks!

We’ll release our (VH) BCR sequencing data from 19 UK COVID-19 patients upon journal publication

As part of the study we compared to the data from Nielsen et al. - if anyone wants this processed data (fully AIRR community compliant) please get in touch at opig[at]stats.ox.ac.uk

Hi @mraybould I have contacted you (OPIG) separately about sharing the Nielsen et al paper (and your data when it is available) in an AIRR Covid-19 repository…

Brian