Study Information

Last updated: Feb 1st, 2021
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This site is a data portal to help scientists, researchers, and clinicians mine the human gene expression changes that occur in response to SARS-CoV-2 infection, the pathogenic agent of COVID-19, as well as to provide resources for use of RNA-seq data from clinical cohorts.


Nasopharyngeal swab transcriptome are from the first batch of 735 patient samples (n=216 COVID-19 positive and 519 COVID-19 negative by RT-PCR) described in more detail in our paper here.

Shotgun Transcriptome and Spatial Omics Profiling of SARS-CoV-2 Infection Reveals Host Dysregulation and Isothermal Detection

Nature Communications, 2021


Tissue autopsy data are from 39 patients analyzed in collaboration of Schwartz lab and Mason lab. We used a shotgun metatranscriptomics platform (total-RNA-seq) for comprehensive host and viral profiling on 39 patients who died from COVID-19, as well as spatial transcriptomics data (GeoMx) data and RNA-seq on 190 organs (heart, liver, lung, kidney, and lymph nodes) from the autopsies of those patients. We compared and contrasted these in-depth spatial and tissue-specific transcriptome data with a replication cohort of nasopharyngeal (NP) swabs from 216 COVID-19+ patients and 430 COVID-19- controls.

Systemic Tissue and Cellular Disruption from SARS-CoV-2 Infection revealed in COVID-19 Autopsies and Spatial Omics Tissue Maps

Pre-print in biorxiv



This work is generously supported by Citadel, WorldQuant, the Vallee Foundation, the National Center for Advancing Translational Sciences of the National Institutes of Health (UL1TR000457), the Core Facilities at Weill Cornell Medicine, the Scientific Computing Unit (SCU) of the ICB, XSEDE Supercomputing Resources, and the National Science Foundation (1840275).


You can download the pre-print version of Supplementary Table 3 & 4 from here. Results are subject to change.

Download (26mb)



The gene descriptions, aliases, and protein product synonyms available on this website were extracted from public information provided by the National Center for Biotechnology Information (NCBI). Disease association information was derived from publicly available abstracts on PubMed.

Website by Cem Meydan

Gene metadata and disease association by Ciaran Hassan & Michael Chau

Unless otherwise noted, all site content is copyrighted by Mason Lab and Weill Cornell Medicine.

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