Extended Data Fig. 1: Metabolic profile of human BM HSPCs and their downstream progenitors.

a, Experimental design and gating to characterize the targeted metabolomics and transcriptome of human HSPCs and progenitors. The input material per sample, number and type of detected metabolites and genes are indicated. b, Workflow of method and downstream analysis of low input targeted polar metabolomics in human HSPCs and progenitors. c, Venn diagram representing the detected metabolites above threshold with an input material of 1,000, 3,000, or 5,000 HSPCs. Number of metabolites per dataset is shown. n = 6. d, Representative example of metabolomics peaks in HSPCs, progenitors and background levels (Negative Control). Signal intensity was assessed by picking peaks with the same retention times as their respective qualifiers (green and blue lines). AUC, area under the curve. e, Metabolomics Principal component analysis (PCA) of HSPCs and progenitors isolated under different freezing conditions and from various sources as quality control. Conditions included samples with and without prior freezing; sources included commercially available samples (Stem Cell Technology; SCT) or hospital-derived samples. The analysis was based on significantly variable metabolites. n = 7. f, PCA of HSPCs and progenitors RNA-seq samples based on the top 500 most variable genes. n = 4. g, Volcano plot of differentially expressed genes (DEGs) in HSPCs vs progenitors RNA-seq. P-adjusted value. NS, not significant. h, Heatmap representing relative expression of differentially expressed KEGG enzymes in HSPCs vs progenitors (log2FC threshold = 1, p-adjusted < 0.05), classified in their respective metabolic pathways. i, Gene Set Enrichment Analysis (GSEA) of selected Gene Ontology (GO) processes on RNA-seq of HSPCs vs progenitors. P-adjusted value. NES, Normalized Enrichment Score. j, TF activity score estimated by decoupleR in HSPCs vs progenitors RNA-seq. Top 12 differentially activated TFs per condition are shown (p-value < 0.05). (c, e, f) n indicates the number of biological replicates per condition. For (c), 4 independent experiments were performed. For (e), 5 independent experiments were performed.