CUIMC-NYP_COVID_autopsy_lung

Code for the manuscript

A molecular single-cell lung atlas of lethal COVID-19

Johannes C. Melms, Jana Biermann, Huachao Huang, Yiping Wang, Ajay Nair, Somnath Tagore, Igor Katsyv, André F. Rendeiro, Amit Dipak Amin, Denis Schapiro, Chris J. Frangieh, Adrienne M. Luoma, Aveline Filliol, Yinshan Fang, Hiranmayi Ravichandran, Mariano G. Clausi, George A. Alba, Meri Rogava, Sean W. Chen, Patricia Ho, Daniel T. Montoro, Adam E. Kornberg, Arnold S. Han, Mathieu F. Bakhoum, Niroshana Anandasabapathy, Mayte Suárez-Fariñas, Samuel F. Bakhoum, Yaron Bram, Alain Borczuk, Xinzheng V. Guo, Jay H. Lefkowitch, Charles Marboe, Stephen M. Lagana, Armando Del Portillo, Emmanuel Zorn, Glen S. Markowitz, Robert F. Schwabe, Robert E. Schwartz, Olivier Elemento, Anjali Saqi, Hanina Hibshoosh, Jianwen Que, Benjamin Izar

Overview of code structure and corresponding Figures and Tables can be found in code_overview.csv

Publication

https://doi.org/10.1038/s41586-021-03569-1

GEO data upload (GSE171524)

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE171524

Single Cell Portal data upload

https://singlecell.broadinstitute.org/single_cell/study/SCP1219

Raw data at Broad Data Use and Oversight System

https://duos.broadinstitute.org (study ID DUOS-000130)

Vectra images

https://drive.google.com/drive/folders/1zUtj8HKEoWFA6mS1GPrDQwV3RVKBKjmH?usp=sharing