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. 2023 Jul 20;14:4400. doi: 10.1038/s41467-023-39985-2

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 4 — A Uncorrected GeneVector UMAPs showing stimulated condition (left) and cell type annotation (right) on 10k PBMCs with control and interferon beta stimulated cells. B GeneVector batch corrected UMAPs showing stimulated condition (left) and cell type annotation (right) indicated stronger interferon-beta stimulated response in myeloid cells. C Harmony batch correction applied to normalized expression eliminates all variation related to interferon beta stimulation. D Most similar genes by cosine similarity to IFIT1 includes genes found in Reactome interferon related pathways. E Gene embedding UMAP highlighting an ISG (interferon stimulated genes) metagene that includes genes most similar to IFIT1. F Scaled log-normalized expression of ISG (interferon stimulated gene) metagene shows increased expression across stimulated cells without cell type specific effects. G PCA embedding colored by cell type (left) and stimulation (right). H Top genes by contribution to variance indicates PC1 defines cell type. I Top genes by contribution to PC2 defined by ISG stimulation colored by scaled normalized, log-transformed gene expression scaled by variable. J, K Scaled normalized, log-transformed expression scaled by variable of ISG related loadings from PCA (left) and LDVAE (right) includes cell type specific markers intermixed with ISGs. Source data provided as a Source Data file.