Supplementary Figure 2: Gate settings used for index sorting of hematopoietic progenitors. | Nature Methods

Supplementary Figure 2: Gate settings used for index sorting of hematopoietic progenitors.

From: FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data

Supplementary Figure 2

Two different sorting schemes were used. In a first experiment with n = 2 mice (sorting scheme 1), we purified 384 Lineage (Lin) KithiSca-1hi (LSK) cells with high surface expression of Kit and Sca-1 (encoded by Ly6a), a permissive sorting strategy to sample the pool of HSCs and multipotent progenitors. In addition, we sorted 768 lymphoid-primed multipotent progenitors (LMPP) as Flt3+ LSK cells, and 384 LinKitloSca-1lo as well as 192 LinKitloSca-1lo/−Flt3hi common lymphoid progenitors (CLP) in order to enrich for the lymphoid branch. We deliberately did not gate on Il7r to comprehensively sample CLPs1–3. In order to capture more mature and potentially underrepresented progenitor states of all hematopoietic lineages we subsequently applied a second sorting strategy (sorting scheme 2). Here, we sequenced 1,152 cells from 16 adjacent windows spanning different ranges of Kit and Sca-1 expression and being either Flt3+ or Flt3. Cells in (a) and (b) were sorted from n = 2 mice each in another independent experiment. Flow cytometry data are from one experiment with n = 1 mouse.

1. Inlay, M. A. et al. Ly6d marks the earliest stage of B-cell specification and identifies the branchpoint between B-cell and T-cell development. Genes Dev. 23, 2376–81 (2009).

2. Mansson, R. et al. Single-cell analysis of the common lymphoid progenitor compartment reveals functional and molecular heterogeneity. Blood 115, 2601–2609 (2010).

3. Tsapogas, P. et al. IL-7 mediates Ebf-1-dependent lineage restriction in early lymphoid progenitors. Blood 118, 1283–1290 (2011).

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