<p align="center"> <a href="#dataset-list">Dataset list</a>&nbsp;&nbsp;&nbsp;&nbsp; <a href="#datasets-in-details">Datasets in details</a>&nbsp;&nbsp;&nbsp;&nbsp; <a href="contributing.md">Contribution guide</a>&nbsp;&nbsp;&nbsp;&nbsp; <a href="https://twitter.com/immunomind">Twitter updates</a>&nbsp;&nbsp;&nbsp;&nbsp; </p>

COVID19 dataset list

🦠 To accelerate the COVID-19 research and vaccine development we collected a list of publicly available datasets with single-cell (scRNAseq) and immune repertoire (AIRR / RepSeq / immunosequencing) data. The data comes from confirmed COVID-19 patients or from human cell lines infected with SARS-CoV-2. The repository is regularly updated with community’s help and is managed by the ImmunoMind team.

:star: The contribution to the project is warmly welcome. To add a new publicly available dataset, request or ask something please create a new issue according to our Contribution guide.

🧬 We recommend to use Immunarch to analyse the T-cell / antibody immune repertoire data or the scVI package and Seurat to analyse the scRNAseq gene expression data.

Dataset list

| Public availability of data | Data type | Publication title | |:------------------------------|:----------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| | :heavy_check_mark: Available | scRNAseq + AIRR | <a name="11_short"></a>:arrow_right: A molecular cell atlas of the human lung from single cell RNA sequencing | | :heavy_check_mark: Available | scRNAseq | <a name="12_short"></a>:arrow_right: Bulk and single-cell gene expression profiling of SARS-CoV-2 infected human cell lines identifies molecular targets for therapeutic intervention | | :heavy_check_mark: Available | AIRR | <a name="0_short"></a>:arrow_right: B cell clonal expansion and convergent antibody responses to SARS-CoV-2 | | :heavy_check_mark: Available | AIRR | <a name="7_short"></a>:arrow_right: Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T cell memory formation after mild COVID-19 infection | | :heavy_check_mark: Available | AIRR | <a name="1_short"></a>:arrow_right: The landscape of lung bronchoalveolar immune cells in COVID-19 revealed by single-cell RNA sequencing | | :email: Upon request | scRNAseq + AIRR | <a name="10_short"></a>:arrow_right: Tocilizumab treatment in severe COVID-19 patients attenuates the inflammatory storm incited by monocyte centric immune interactions revealed by single-cell analysis | | :question: Pending | scRNAseq + AIRR | <a name="4_short"></a>:arrow_right: Blood single cell immune profiling reveals the interferon-MAPK pathway mediated adaptive immune response for COVID-19 | | :question: Pending | scRNAseq + AIRR | <a name="2_short"></a>:arrow_right: Immune cell profiling of COVID-19 patients in the recovery stage by single-cell sequencing | | :question: Pending | scRNAseq + AIRR | <a name="8_short"></a>:arrow_right: Potent neutralizing antibodies against SARS-CoV-2 identified by high-throughput single-cell sequencing of convalescent patients’ B cells | | :question: Pending | scRNAseq | <a name="14_short"></a>:arrow_right: Identification of Candidate COVID-19 Therapeutics using hPSC-derived Lung Organoids | | :question: Pending | scRNAseq | <a name="5_short"></a>:arrow_right: New Single-Cell Technologies Help Scientists Understand COVID-19 Disease Progression | | :question: Pending | scRNAseq | <a name="6_short"></a>:arrow_right: SARS‐CoV‐2 receptor ACE2 and TMPRSS2 are primarily expressed in bronchial transient secretory cells | | :question: Pending | scRNAseq | <a name="9_short"></a>:arrow_right: Single-cell longitudinal analysis of SARS-CoV-2 infection in human bronchial epithelial cells | | :question: Pending | AIRR | <a name="13_short"></a>:arrow_right: Immunologic perturbations in severe COVID-19/SARS-CoV-2 infection | | :question: Pending | AIRR | <a name="3_short"></a>:arrow_right: Microsoft and Adaptive Biotechnologies are studying how the human immune system reacts to the coronavirus: MSNBC |

Datasets in details

• <a name="11_long"></a>:arrow_left: Back to the list

• A molecular cell atlas of the human lung from single cell RNA sequencing

  • Public availability of data: :heavy_check_mark: Available
  • Data type: scRNAseq + AIRR
  • Source type: Publication
  • Publication DOI: https://doi.org/10.1101/742320
  • Publication abstract/Press release: Although single cell RNA sequencing studies have begun providing compendia of cell expression profiles, it has proven more difficult to systematically identify and localize all molecular cell types in individual organs to create a full molecular cell atlas. Here we describe droplet- and plate-based single cell RNA sequencing applied to ∼75,000 human lung and blood cells, combined with a multi-pronged cell annotation approach, which have allowed us to define the gene expression profiles and anatomical locations of 58 cell populations in the human lung, including 41 of 45 previously known cell types or subtypes and 14 new ones. This comprehensive molecular atlas elucidates the biochemical functions of lung cell types and the cell-selective transcription factors and optimal markers for making and monitoring them; defines the cell targets of circulating hormones and predicts local signaling interactions including sources and targets of chemokines in immune cell trafficking and expression changes on lung homing; and identifies the cell types directly affected by lung disease genes and respiratory viruses. Comparison to mouse identified 17 molecular types that appear to have been gained or lost during lung evolution and others whose expression profiles have been substantially altered, revealing extensive plasticity of cell types and cell-type-specific gene expression during organ evolution including expression switches between cell types. This atlas provides the molecular foundation for investigating how lung cell identities, functions, and interactions are achieved in development and tissue engineering and altered in disease and evolution.
  • Dataset link: https://www.synapse.org/#!Synapse:syn21041850/
  • Sharing statement: Counts/UMI tables, cellular metadata, Seurat objects, and scanpy objects are available on Synapse (accession syn21041850). The data can be explored in a browser using cellxgene at https://hlca.ds.czbiohub.org/. Code for demultiplexing counts/UMI tables, clustering, annotation, and other downstream analyses are available on GitHub (https://github.com/krasnowlab/HLCA). Human sequencing data will be available by data access agreement on the European Genome-phenome Archive (EGA) upon publication of this manuscript. Mouse sequencing data will be available on the National Institute of Health’s Sequence Read Archive (SRA) also upon publication of this manuscript. <br/>

• <a name="12_long"></a>:arrow_left: Back to the list

• Bulk and single-cell gene expression profiling of SARS-CoV-2 infected human cell lines identifies molecular targets for therapeutic intervention

  • Public availability of data: :heavy_check_mark: Available
  • Data type: scRNAseq
  • Source type: Publication
  • Publication DOI: https://doi.org/10.1101/2020.05.05.079194
  • Publication abstract/Press release: The coronavirus disease 2019 (COVID-19) pandemic, caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is an ongoing global health threat with more than two million infected people since its emergence in late 2019. Detailed knowledge of the molecular biology of the infection is indispensable for understanding of the viral replication, host responses, and disease progression. We provide gene expression profiles of SARS-CoV and SARS-CoV-2 infections in three human cell lines (H1299, Caco-2 and Calu-3 cells), using bulk and single-