Figure 1.
Transcriptomic and chromatin accessibility profiling of P2 cells shows a clear split in cell fate between P2/CD23+and P2/CD23–cells. (A) VPD-labeled NBCs were differentiated using a 2-step cell culture process that gave rise to 3 different cell populations (referred to as P1, P2, and P3) according to the VPD450 dilution and the CD38 expression on day 5 (D5) and D6.24 Active caspase-3–negative (Casp3a–) P2 cells split into CD23+ and CD23– subsets, and the P1 population arose from the latter.25 Representative cell morphologies during in vitro differentiation for each population are shown after Cytospin preparation and May-Grünwald-Giemsa staining (scale bar, 20 µm). (B) PCA of RNA-seq data from the D4lo, P2/CD23+, P2/CD23–, and P1 cell populations. P2/CD23+ and P2/CD23– clearly show different transcriptomic signatures and different differentiation abilities. (C) PCA of RNA-seq data from the D4lo, P2/CD23+, P2/CD23–, and P1 populations indicating the positions of samples (colored circles, with the mean shown by colored diamonds) and genes (gray dots). The position of selected B-cell identity genes (red dots), PC identity genes (green dots), and IL-4–dependent genes (orange dots) are indicated. (D) Ranking of genes according to their rPC1 weights; genes known to be related to PC identity are shown in green, and those known to be related to B-cell identity are shown in red. Note that both sets of genes are aggregated at opposite ends of the rPC1 axis. (E) GSEA for a signature (GSE22886) comparing NBCs with PCs collected from blood; “up” indicates genes specific for NBCs (left) and “down” indicates genes specific for PCs (right). (F) GSEAs for an IRE1-mediated unfolded protein response (UPR) Gene Ontology (GO) signature (left) and an endoplasmic reticulum (ER) stress response GO signature (right). (G) GSEA of signatures upregulated in activated B cells from Irf4-KO (left) and Prdm1-KO (right) mice for an RNA-seq comparison between P2 populations (P2/CD23+ vs P2/CD23–). het, heterozygous littermates; NES, normalized enrichment score.

Transcriptomic and chromatin accessibility profiling of P2 cells shows a clear split in cell fate between P2/CD23+and P2/CD23–cells. (A) VPD-labeled NBCs were differentiated using a 2-step cell culture process that gave rise to 3 different cell populations (referred to as P1, P2, and P3) according to the VPD450 dilution and the CD38 expression on day 5 (D5) and D6.24  Active caspase-3–negative (Casp3a–) P2 cells split into CD23+ and CD23– subsets, and the P1 population arose from the latter.25  Representative cell morphologies during in vitro differentiation for each population are shown after Cytospin preparation and May-Grünwald-Giemsa staining (scale bar, 20 µm). (B) PCA of RNA-seq data from the D4lo, P2/CD23+, P2/CD23–, and P1 cell populations. P2/CD23+ and P2/CD23– clearly show different transcriptomic signatures and different differentiation abilities. (C) PCA of RNA-seq data from the D4lo, P2/CD23+, P2/CD23–, and P1 populations indicating the positions of samples (colored circles, with the mean shown by colored diamonds) and genes (gray dots). The position of selected B-cell identity genes (red dots), PC identity genes (green dots), and IL-4–dependent genes (orange dots) are indicated. (D) Ranking of genes according to their rPC1 weights; genes known to be related to PC identity are shown in green, and those known to be related to B-cell identity are shown in red. Note that both sets of genes are aggregated at opposite ends of the rPC1 axis. (E) GSEA for a signature (GSE22886) comparing NBCs with PCs collected from blood; “up” indicates genes specific for NBCs (left) and “down” indicates genes specific for PCs (right). (F) GSEAs for an IRE1-mediated unfolded protein response (UPR) Gene Ontology (GO) signature (left) and an endoplasmic reticulum (ER) stress response GO signature (right). (G) GSEA of signatures upregulated in activated B cells from Irf4-KO (left) and Prdm1-KO (right) mice for an RNA-seq comparison between P2 populations (P2/CD23+ vs P2/CD23–). het, heterozygous littermates; NES, normalized enrichment score.

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