Extended Data Fig. 7: Characterization of NCP transcriptomes as determined by RNA-seq.

a, Developmental path of NCP1s, NCP2s, NCP3s and NCP4s, as well as HSCs/MPPs, CMPs, PMs, MYs, MMs, BCs, SNs and mature neutrophils (PMN), computationally determined from bulk RNA-seq datasets by using the optimal leaf ordering (OLO) algorithm. b, GO terms enriched by genes associated with the ten gene groups (g1-g10) identified by K-means analysis, as shown in Fig. 4d. The top five GO terms with Benjamini-Hochberg-corrected P values <0.05 (one-sided Fisher’s exact test) are shown for every gene group. ‘Gene ratio’ indicate the fraction of DEGs present in the given GO term. (c), Box plots showing the distribution of mRNA expression levels [as log₂(FPKM + 1)] for genes associated to cell cycle, AG, SG, GG, SV and GM, as well as ROS biosynthetic process, phagocytosis, and chemotaxis. The box plot shows the median with the lower and upper quartiles representing a 25th to 75th percentile range and whiskers extending to 1.5 × interquartile range (IQR). LOESS fitting of the data with relative confidence interval is represented by a blue line with a shadow area. d, PCA biplots based on the DEGs identified by LRT among bulk RNA-seq of NCP1s (orange), NCP2s (green), NCP3s (magenta) and NCP4s (turquiose). The graph lists the ten most relevant genes contributing to sample variations (indicated by vectors) for both PC1 and PC2, under both positive and negative directions. Vector lengths correlate with the weight of the given gene within the components.