Extended Data Fig. 6: Intersecting transcriptional and chromatin accessibility data reveals HSPC sensory and cytokine production deficiencies in the absence of Fli-1.

a, Intersection dot plot of RNA-seq and ATAC-seq in Fli-1^ROSAΔ vs. WT HSPCs. Each dot represents the transcriptional and chromatic accessibility statuses per gene. For gene labeling of few selected dots, thresholds FDR < 0.05 for both RNA- and ATAC-seq, |LogFC | >2.5 for RNA-seq, |LogFC | >0.75 for ATAC-seq, and |Distance to TSS | < 500 parameters were set. b, Gene ontology (GO) categories of biological processes enrichment for significantly downregulated genes in both RNA- and ATAC-seq analyses of Fli-1^ROSAΔ vs. WT HSPCs (lower left quadrant in panel a). Significance by FDR value is indicated. c, d, Heatmaps for selected HSC extra-sensory quiescence (c) and activation (d) elements across RNA-seq replicates of Fli-1^ROSAΔ and WT HSPCs. Scale bar and coloring represent the Z-score scaled by gene for Log counts per 10⁶ normalized by library size (trimmed mean of M-values). e, Frequency of double positive HSPCs for the activation receptors Lifr and Csfr1 in co-culture as determined by flow cytometry on day 4 post 4-OHT induction. Unpaired two tailed t-test was used; n = 5 per WT or Fli-1^ROSAΔ. Data are presented as mean values +/- SEM. f, Representative flow cytometry dot plots of Lifr⁺/Csfr1⁺ double positive HSPCs in WT (upper panel) and Fli-1^ROSAΔ (lower panel) co-cultures. g, h, Mean fluorescent intensity expression of stem markers CD150 (g) and EPCR (h) on LSK HSPCs in co-culture as determined by flow cytometry on day 4 post 4-OHT induction. Unpaired two tailed t-test was used; n = 5 per WT or Fli-1^ROSAΔ. Data are presented as mean values +/- SEM.

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