Host, Viral, and Environmental Transcriptome Profiles of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

Daniel J Butler; Christopher Mozsary; Cem Meydan; David C Danko; Jonathan Foox; Joel Rosiene; Alon Shaiber; Ebrahim Afshinnekoo; Matthew MacKay; Fritz J Sedlazeck; Nikolay A Ivanov; Maria A Sierra; Diana Pohle; Michael Zeitz; Vijendra Ramlall; Undina Gisladottir; Craig D Westover; Krista Ryon; Benjamin Young; Chandrima Bhattacharya; Phyllis Ruggiero; Bradley W Langhorst; Nathan A Tanner; Justyn Gawrys; Dmitry Meleshko; Dong Xu; Jenny Xiang; Angelika Iftner; Daniela Bezdan; John Sipley; Lin Cong; Arryn Craney; Priya Velu; Ari Melnick; Iman A Hajirasouliha; Thomas Iftner; Mirella Salvatore; Massimo Loda; Lars F Westblade; Shawn Levy; Melissa Cushing; Nicholas P Tatonetti; Marcin Imielinski; Hanna Rennert; Christopher Mason

The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.20.048066 doi: bioRxiv preprint Supplemental Figure 9 . Cellular sub-type deconvolution from nasopharyngeal (NP) swabs. The Bisque algorithm (https://github.com/cozygene/bisque) was used to separate the cellular sub-type gene expression signatures present in the total RNA-seq data from the NP swabs. (a) The fraction of cells estimated for each cell type (y-axis) was calculated for the samples that tested positive by RT-qPCR (P, positive on the right) as well as negative by RT-qPCR (N, negative on the left), with proportions shown for goblet cells (blue), ciliated cells (green), basal cells (red), dendritic cells (purple), ionocytes (orange), club cells (yellow), luminal macrophages (brown), neutrophils (pink), and B-cells (grey). (b) The same data is in (a) shown as the square root for visibility of low incidence cell types.