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. 2020 Jun 3;10:9047. doi: 10.1038/s41598-020-65939-5

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© The Author(s) 2020

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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Genome coverage of positive-sense DENV-1 mapped transcripts identified by 5′ capture scRNAseq. (A) Heatmap representation of positive-sense DENV-1 genomic sequence recovery in individual cells analyzed by 5′ capture scRNAseq from DENV-1 infected cultures (blue), DENV-1 infected sorted NS1^pos cultures (red), and DENV-1 infected sorted NS1^pos cultures supplemented with a DENV-specific cDNA synthesis primer (orange). Color intensity indicates sequence coverage/depth at that genomic location, vertical axis contains a single cell per line. Cells are ranked by total DENV-1 genomic coverage. Cells with > =1 DENV-1 mapped UMI are included in the visualization. (B) Positive-sense DENV-1 genomic localization of individual UMIs obtained from the top 10 cells in each analysis condition with the most DENV-1 coverage as assessed by 5′ capture scRNAseq analysis. UMIs are ranked by genomic location 5′ to 3′, and the vertical axis contains a single DENV-1 mapped UMI per line. (C) Aggregated positive-sense DENV-1 genomic coverage and sequence depth of all in vitro infected samples as assessed by 5′ capture scRNAseq.