Figure 3

Figure 3

General Dyes Enhance Hematopoietic Cell Type Segregation in FACS Space to Allow HSPC Purification with GateID

(A) Left panel: PCA of zebrafish WKM TD2 (stained, BD FACSJazz). Each point represents a single cell, and single cells are colored based on cell type identification from scRNA-seq. The ellipses represent normal contour lines that contain 50% of the data points for each cell type. Right panel: PC1 and PC2 loadings. Each point represents a FACS channel measured by the BD FACSJazz.

(B) Barplots and t-SNE map showing the outcome of GateID enrichments of eosinophils (WKM 4) on BD FACSJazz. Gates were predicted on stained TD2.

(C) Contour plots of stained WKM cells showing experimental sorting gates for HSPCs for the WKM 10 experiment (representative example for WKM 5, 10, and 15 HSPC enrichment experiments) on BD FACSJazz. Sorted cells passed through gate 1 and gate 2. Percentages of events within each gate are indicated.

(D) Projection of the sorted GateID HSPCs for WKM 10 in FSC height versus SSC height (representative example for WKM 5, 10, and 15 HSPC enrichment experiments).

(E) t-SNE map of zebrafish WKM TD2, where HSPCs inside and outside of GateID gates are colored red and blue, respectively.

(F–H) Barplots and t-SNE maps showing the outcome of HSPC enrichments for (F) WKM 5, (G) WKM 10, and (H) WKM 15 on BD FACSJazz.

See also Figures S3 and S4 and Table S1.