Data and Code Availability
In Table S9 , we provide a guide to all datasets analyzed in this paper as well as links to each individual dataset for download with the main landing page here: https://singlecell.broadinstitute.org/single_cell?scpbr=the-alexandria-project. To download the data from the portal, follow the link to the visualization page, sign in a free account in the portal using a Google apps enabled email address, and select the ‘Download’ tab in the study. Downloadable datasets include both raw and normalized cell x gene matrices, as well as relevant metadata. These datasets are additionally available here to facilitate downloading: https://drive.google.com/drive/folders/1bxCIqNeZ7wLuVOT16gphwj98_cc9KhrV?usp=sharing. We have also posted these cell x gene matrices to Chan Zuckerberg Initiative cellxgene (https://chanzuckerberg.github.io/cellxgene/posts/cellxgene_cziscience_com) and the Broad Institute Single Cell COVID-19 portal (https://singlecell.broadinstitute.org/single_cell/covid19) as leading community efforts. FASTQ files and cell x gene matrices for NHP and murine datasets, and cell x gene matrices for human datasets, are available at GEO: GSE148829.
In this same table, we further highlight four access types. 1. published datasets where everything is available (1 study); 2. unpublished datasets where everything is available (2 studies, 19,670 new cells for download), 3. unpublished datasets where ACE2+ cell subsets, and the necessary subsets to contextualize those cells (i.e., epithelial cells for type II pneumocytes) are fully available (5 studies, 17,986 new cells for download); and, 4. those unpublished datasets where expression is shared for ACE2/TMPRSS2 (2 studies, 9,112 new cells). For those unpublished datasets where only specific subsets of cells or genes are available, full expression matrices are available upon request for COVID-19 related questions.
All data included in the present study can be visualized using the following web viewer:
https://singlecell.broadinstitute.org/single_cell?scpbr=the-alexandria-project.
As we gain further insight and feedback from our own groups, collaborators, and investigators, we will continue to provide updates on our resource websites, including the utility of in vitro systems, such as organoids (Mead et al., 2018), for the study of SARS-CoV-2: http://shaleklab.com/resource/covid-19-resources/ and www.ordovasmontaneslab.com/covid-19-resources/. We also note that there are several ongoing efforts unified together through the HCA Lung Biological Network group that we will reference and to which we will link as they become available.
No custom code was used to analyze these data and all methods and packages used are cited in the Method Details section.