Extended Data Fig. 3: Lineage-specific chromatin signatures.
From: Epigenetic programming defines haematopoietic stem cell fate restriction
a) Heatmap of promoter accessibility signatures specific for MkPs (Meg signature), CFU-Es (Ery), NMPs (Myl) and proB/DN3 cells (Lym). Each signature contains the top 1500 features identified as selectively accessible in each of the 4 cell populations/combined cell populations using DESeq2 (Padj<0.05 and |log2(fold change)| >1). N = 3 biological replicates for all populations. Scale shows row z-score of transformed gene expression levels. b) Heatmap of URE accessibility signatures specific for MkPs (Meg signature), CFU-Es (Ery), NMPs (Myl) and proB/DN3 cells (Lym). Each signature contains the top 1500 features identified as selectively accessible in each of the 4 cell populations/combined cell populations using DESeq2 (Padj<0.05 and |log2(fold change)| >1). N = 3 biological replicates for all populations. Scale shows row z-score of transformed chromatin accessibility levels. c) Enrichment of TF motifs differentially accessible in HSC subtypes (from Fig. 3a) in lymphoid-specific promoter peaks calculated using PWMEnrich-based sequence analysis. These values are those plotted along the Fig. 4a x-axis. d) Enrichment analysis of HSC-subtype TF motifs (from Fig. 2a) in Lym URE peaks calculated using PWMEnrich, corresponding to Fig. 4a y-axis.
