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Additional file 3: Figure S3. Lineage specific, HSC-primed peaks were marked by H3K4me1 and not H3K27Ac. A) About one in three (21,085 peaks out of 71,072) of our ATAC-seq non-promoter peaks in the master peak-list overlapped with peaks designated as probable enhancers based on H3K4me1 and H3K27Ac ChIP data (Lara-Astiaso et al.). B) About one in three (32.5%) of all HSC-primed peaks for the five unipotent lineage cell types were also marked by the histone modification H3K4me1, and 2.8% were marked by H3K27Ac. C) HSC-primed peaks for each unipotent lineage were primarily marked by H3K4me1 and not H3K27Ac. Results in panel B represent the aggregate of the results shown in panel C.

Additional file 2: Figure S2. Erythroid-selective accessibility of the β-globin cluster. ATAC-seq signal tracks of the six cell types in this study at the β-globin cluster (chr7: 103,792,027–103,879,340; mm10). The adult globin genes β-major (ßmaj) and β-minor (ßmin), as well as the hypersensitive sites (HS1-4,6) of the Locus Control Region (LCR) that regulates expression of the genes in this locus, displayed accessibility in EPs. HS2, but not the other HSs, and the β-major promoter were also accessible in HSCs, possibly indicating a “permissive” chromatin state. Accessibility of HS2 and HS4 in MkPs may relate to a closer relationship to HSCs and/or EPs (Fig. 1). As expected, no accessibility was observed at the fetal-specific epsilon Y globin (Ey), β-h1 (ßh1), β-h2 (ßh2) genes, or HS5. Likewise, GMs, B and T cells, that do not express β-globin genes, did not display accessibility of any of the regulatory elements in the locus.

Additional file 1: Figure S1. Library fragment distributions for ATAC-seq samples. The library size distribution after deep-sequencing, mapping, and filtering to unique reads is shown of both replicates for A) HSCs B) EPs C) MkPs D) GMs E) B cells, and F) T cells.

Hematopoiesis is arguably one of the best understood stem cell systems; however, significant challenges remain to reach a consensus understanding of the lineage potential, heterogeneity, and relationships of hematopoietic stem and progenitor cell populations. To gain new insights, we performed quantitative analyses of mature cell production from hematopoietic stem cells (HSCs) and multiple hematopoietic progenitor populations. Assessment of the absolute numbers of mature cell types produced by each progenitor cell revealed a striking erythroid dominance of all myeloid-competent progenitors assessed, accompanied by strong platelet reconstitution. All populations with myeloid potential also produced robust numbers of red blood cells and platelets invivo. Clonal analysis by single-cell transplantation and by spleen colony assays revealed that a significant fraction of HSCs and multipotent progenitors have multilineage potential at the single-cell level. These new insights prompt an erythroid-focused model of hematopoietic differentiation.

We measure many-body interactions in isolated quantum dot states using double-quantum multidimensional coherent spectroscopy. Few states are probed in a diffraction limited spot, which is enabled by a novel collinear scheme in which radiated four-wave-mixing signals are measured with phase resolution. Many-body interactions are enhanced by an additional prepulse tuned to the delocalized quasi-continuum states. We propose this effect as a method for controlling coupling between quantum states.