Figure 2
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- ZDB-FIG-191230-896
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- Baron et al., 2019 - Cell Type Purification by Single-Cell Transcriptome-Trained Sorting
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Proof of Principle: Enrichment of Zebrafish Eosinophils Using GateID (A) GateID-predicted gates to isolate eosinophils from unstained WKM on BD FACSJazz. Gates were predicted on unstained WKM TD1. Red points show desired cells (eosinophils) present in TD1, and blue points show undesired cells present in the other gate. A blue undesired cell in a gate denotes an impure cell that will be sorted. (B) Contour plots of unstained WKM cells showing experimental sorting gates for eosinophils for the WKM 2 experiment (representative example for WKM 1–3 eosinophil enrichment experiments) on BD FACSJazz. Gates in black represent GateID-predicted gates prior to normalization, whereas red gates show GateID-normalized sorting gates. Sorted cells passed through normalized gate 1 and gate 2. Percentages of events within each gate are indicated. (C) t-SNE map of the complete zebrafish WKM dataset (all WKM TDs and enrichment experiment datasets of this study, n = 15,984 cells). Single cells are colored based on cell type. (D) Barplots and t-SNE maps showing the outcome of GateID eosinophil enrichments for three independent experiments (WKM 1–3) on BD FACSJazz. Gates were predicted on unstained TD1. In the barplots, numbers within the bars indicate the percentage of eosinophils in the corresponding library, and numbers above the bars indicate the cell type fold enrichment between the unenriched and GateID enriched library. On the t-SNE maps, gray points represent all cells from the WKM dataset. For each experiment, black dots represent single cells in the unenriched library for a given experiment, whereas colored dots represent single cells in the GateID-enriched library for the same experiment. (E) Left panel: principal-component analysis (PCA) of zebrafish WKM TD1 (unstained, 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. (F) Curves showing the trade-off between yield and purity of GateID solutions for HSPCs, lymphocytes, monocytes, and eosinophils on stained (solid line) and unstained (dashed line) cells from the same zebrafish WKM (WKM 7). See also |
Reprinted from Cell, 179, Baron, C.S., Barve, A., Muraro, M.J., van der Linden, R., Dharmadhikari, G., Lyubimova, A., de Koning, E.J.P., van Oudenaarden, A., Cell Type Purification by Single-Cell Transcriptome-Trained Sorting, 527-542.e19, Copyright (2019) with permission from Elsevier. Full text @ Cell