Extended Data Fig. 7: Niche-dependent changes in HSCs chromatin accessibility and transcriptome.

a, ATAC signal ±3 Kb around the center of the peak. b, Motifs identified in clusters with lost and gained accessibility in HSCs from Ebf1^+/+Prx1^Cre and Ebf1^fl/flPrx1^Cre mice. c, Heatmaps showing footprinted motif co-occurrence enrichment clustering. d, GSEA plot showing enrichments of myeloid cells differentiation signature in HSCs derived from wild-type niche. The Normalized Enrichment Score (NES) was computed using a Kolmogorov–Smirnov statistic. Significance was assessed using a two-tailed t-test comparing to a null distribution computed via 1000 gene-set permutations. Correction for multiple testing was performed using FDR adjustment, n=183. e, Representative tracks showing differential merged ATAC signal in HSCs from Ebf1^+/+Prx1^Cre and Ebf1^fl/flPrx1^Cre mice correlated with genes differentially expressed between cluster 2 and 3 (Fig 6e). Region on chromosome 8 with Pcm1 and Asah1 serves as a control without differential ATAC signal. The scale in the y-axis represents RPKM.