Extended Data Fig. 2: scRNA-seq defined neutrophil populations correlated with previously reported neutrophil subpopulations.

a, Correlation of scRNA-seq defined neutrophil populations with the indicated four samples characterized by Olsson et al.²⁵. Shown are the fraction of each indicated scRNA-seq defined cluster in the four samples. The cluster identity of each cell was inferred based on the transcriptomic similarity between this cell and the reference clusters (G0-G5) defined in current study. b, Correlation of scRNA-seq defined neutrophil populations with the neutrophil subtypes reported by Evrard et al.²⁶. Coefficient matrix showing deconvolution results of bulk profiles of indicated neutrophil subpopulations. The 20 highest DEGs per single-cell group (G0-G5) were selected as signatures for deconvolution. Each column is normalized by column sums. (c, d), Correlation of scRNA-seq defined neutrophil populations with the C1 and C2 neutrophil clusters reported by Zhu et al.²⁷. c, Top: t-distributed stochastic neighbor embedding (t-SNE) plot of the C1 and C2 cells characterized by Zhu et al. The raw data was retrieved from GEO website and reanalyzed. Bottom: t-SNE plot of C1 and C2 cells colored based on scRNA-seq defined clusters (G0-G5). The cluster identity of each cell was determined as described in (A). d, Heatmap showing row-scaled expression of the 10 highest DEGs of C1 and C2 in indicated scRNA-seq defined clusters. Signature genes Ly6g, Cebpa and Cebpe were also included in the map. (e-f), Correlation of scRNA-seq defined neutrophil populations with the Stage I and Stage II neutrophils defined by Giladi et al.¹³. e, The Stage I (x-axis) and Stage II (y-axis) score of each single cell in the reference sample of current study (Fig.1b). The scRNA-seq defined neutrophil identity of each cell is indicated. f, Violin plots of Stage I and Stage II score for each scRNA-seq defined neutrophil population. g, Correlation between scRNA-seq-defined neutrophil populations and the neutrophil subpopulations reported by Muench et al.²⁹ Left: The fraction of indicated scRNA-seq defined clusters (G0-G5) in samples characterized by Muench et al. Right: The fraction of indicated scRNA-seq defined clusters (G0-G5) in each neutrophil subtype. Each row is normalized by row sums. The cluster identity of each cell was determined as described in (a). h, Correlation between scRNA-seq-defined neutrophil populations and the neutrophil subpopulations reported by Kwok et al.³⁰ Shown are the fraction of indicated scRNA-seq defined clusters in each neutrophil subtype. Each row is normalized by row sums.