Extended Data Fig. 6: Fluidigm-based transcriptional analysis of Gfi1R412X/− cells.
From: Mouse models of neutropenia reveal progenitor-stage-specific defects
a, FACS plots of adult mouse bone marrow (left) and representative cytospin of FACS-sorted adult mouse bone marrow (right). The populations sorted for scRNA-seq are indicated in red. b, Schematic summary of the cellHarmony algorithm. c, cellHarmony-assigned ICGS states of combined wild-type and Gfi1R412X/− Fluidigm scRNA-seq data (n = 624 cells, excluding cell-cycle genes). Each tick mark represents data from a single cell. Gene expression clusters were generated in AltAnalyze and the ICGS clusters are annotated (top) (Extended Data Fig. 4c). FACS gates are annotated (right). d, Population distribution of Fluidigm scRNA-seq data from c and Extended Data Fig. 4c. e, cellHarmony heat map of wild-type-aligned Gfi1R412X/− cell gene expression as ordered in c (dotted lines). Each column represents a single cell and each row represents a single gene from Extended Data Fig. 4c. The FACS gates and ICGS clusters are annotated (top) and gene clusters are indicated (left). f, Bar chart of the heat map in e, displaying the incidence and amplitude for selected genes. Arrows indicate differential expression of the adjacent gene, as compared to the wild-type gene. g, Heat map of MarkerFinder cell population-specific genes expression from the Fluidigm scRNA-seq data (n = 191 cells) with enriched pathway associated genes (right) and statistically enriched Gene Ontology biological processes (left). h, i, Heat maps (n = 62 cells) of wild-type-driven genes (same genes as in g) (h) or de novo MarkerFinder genes for cellHarmony classified Gfi1R412X/− cell populations (i) annotated with enriched pathway associated genes (right) and statistically enriched Gene Ontology biological processes (left). j, Representation of the scRNA-seq data from k, displaying the fold change in gene expression in Gfi1R412X/− cells compared to wild-type cells in the indicated clusters, with the number of genes up- or downregulated displayed. Each point represents a single gene. k, Heat map of Fluidigm differentially expressed GFI1-target genes (excluding cell-cycle genes), in which each column represents a single cell and each row represents a single gene, with key genes (right) and enriched biological processes (left) indicated. Cytospin data in a are representative of two biological replicates. Data in a are mean ± s.e.m. ****P < 0.0001, two-tailed t-test in a.
