Clonal multi-omics reveals Bcor as a negative regulator of emergency dendritic cell development

•Clonal multi-omics assesses daughters from one founder cell for different features•SIS-seq identifies the genes that control clonal fate•SIS-skew how perturbation affects fate•Bcor is identified as a novel regulator of dendritic subset development Despite advances in single-cell multi-omics, single stem or progenitor can only be tested once. We developed which clone act surrogates founder, thereby allowing multiple independent assays per clone. With SIS-seq, siblings parallel “sister” are examined either gene expression by RNA sequencing (RNA-seq) fate culture. identified, and then validated using CRISPR, controlled bias (DC) subtypes. This included Bcor suppressor plasmacytoid DC (pDC) conventional type 2 (cDC2) numbers during Flt3 ligand-mediated emergency development. SIS-skew to examine wild-type Bcor-deficient same parallel. found restricted expansion, especially cDC2s, suppressed potential, pDCs. Therefore, SIS-seq reveal molecular cellular mechanisms governing fate. 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To visualize sample samples, whether represented dots ternary plots 1D), sample’s composition (percentage total DCs) shown its position relative labeled outcomes: pDC, cDC1, cDC2. pDCs, dot apex pDC. If contained subtypes, positioned center. As control, background) establish baseline distribution seen left Figure 1D, centrally positioned, corresponding relatively reproducible output HSPCs. indicated grown proportions. When assessed, spread plot, many apices an ensemble recapitulate average, aggregated. resulting pseudopopulation right orange dot) indistinguishable bona fide plot), providing assurance reflective system. single-cell-derived visualized concordance plots, they position. short connecting lines too plot). By cosine similarity statistical readout sisters, 98/105 compared variable randomized panel). few interest (because represent asymmetric excluded initial goals SIS-seq. sensitive distance-based measures, also classification threshold ? 25% subtype. 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