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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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Extended Data Fig. 1 — a, Schematic of the experimental strategy followed for the RNA-seq and ATAC-seq experiments on WT HSCs. b, Gating strategies for sorting HSCs from the BM of D0 or 5-FU-injected (H2, H6, H16, D3, D10) mice (15 biologically independent samples- representative plots are shown). c, Comparison of our sorting strategy (LSK/SLAM) to the HSCs sorted using EPCR/SLAM (EPCR⁺CD48⁻CD1450⁺) markers. The EPCR/SLAM HSCs are then projected on the LSK/SLAM gating strategy (red color) and the percentage of EPCR/SLAM HSCs that are included in the LSK/SLAM gate is indicated (2 biologically independent samples- representative plots are shown). d, Comparison of the number of cells in the LSK/SLAM gate that are not EPCR/SLAM at D0 and H16 (2 biologically independent samples- representative plots are shown). e, Gene ontology analysis of the genes upregulated at H2, H16 and D10 after 5-FU injection compared to D0 in WT HSCs. X-axis depicts -logP. f, Venn diagrams depicting the overlap of differentially expressed genes (DEGs) in WT HSCs with genes assigned to newly accessible regions-gained ATAC peaks at the indicated time points compared to D0 (-100/+25 kb from TSS, p-values represent hypergeometric test). g, Gene ontology analysis of deregulated genes that also exhibit changes in chromatin accessibility at the indicated time points. X-axis depicts -logP.