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. 2022 Dec 12;13:1092370. doi: 10.3389/fimmu.2022.1092370

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Copyright © 2022 Bishop, Caten, Nakaya and Suhrbier

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Principal component and hierarchical cluster analyses, viral loads, DEGs and scoDEGs. (A) Principal component analysis (PCA) plot (PC1 - Dim1, PC2 - Dim2) for all accessions using all single copy orthologues. (B) Hierarchical cluster analysis using log2 TMM-normalized read counts of the top 500 single copy orthologues ranked by PC1 and PC2 loadings. (C) The number of viral reads in each accession expressed as a percentage of the total number of reads aligning to protein coding genes in the human or mouse genome in the same sample. Cross-bars represent the mean for each group. (D) Histogram showing the number of DEGs and scoDEGs for each group after application of the indicated significance cutoffs (q, FDR).