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. 2021 Jul 12;23(7):704–717. doi: 10.1038/s41556-021-00707-9

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© The Author(s) 2021

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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Fig. 4 — a, Heat map of the log₂-transformed fold change of all differentially expressed TE families detected in Mda5^−/− HSCs at the indicated time points after 5-FU treatment. TE families that had a significantly enriched or depleted ATAC-seq peak nearby (±1 kb) are highlighted in the right column (A). b, The number of upregulated or downregulated TE families in Mda5^−/− HSCs at the indicated time points after 5-FU treatment. c, t-SNE representation of sorted Mda5^−/− HSCs (LSK/SLAM) at D0 (red) and H16 (dark red) (the number of sequenced cells is indicated in parentheses). d, t-SNE representation showing the expression of differentially expressed TE families between H16 and D0 in Mda5^−/− HSCs. The colour scale represents the log₂-transformed normalized transcript counts. e, The log₂-transformed fold change in expression of the TE families shown in d at D0 or H16 in Mda5^−/− HSCs from c. The box shows the interquartile range, the whiskers show the minimum and maximum values, and the horizontal line shows the median value. Each dot represents a single cell and the shape of the plot represents probability density. n = 648 (D0) and n = 1,185 (H16) Mda5^−/− cells. One independent experiment per time point. P_adj < 0.05. f, Heat map of the expression values (fold change) of TE copies in Mda5^−/− HSCs at the indicated time points compared to D0. Fold change cut-off = 1.5. P_adj < 0.05.