Extended Data Fig. 2: Single cell RNA-sequencing of Gired-treated, Esr1-WT and mutant mammary epithelia. | Nature Cancer

Extended Data Fig. 2: Single cell RNA-sequencing of Gired-treated, Esr1-WT and mutant mammary epithelia.

From: ERĪ± dysfunction caused by ESR1 mutations and therapeutic pressure promotes lineage plasticity in ER+ breast cancer

Extended Data Fig. 2

(a) Analysis workflow for single-cell RNA-seq (scRNA-seq) data from the Cell Ranger pipeline; see Methods for detailed summary. (b-c) Summary statistics of UMAP clusters. (b, left) Numbers of cells per cluster and (right) proportion of cells in respective clusters across conditions. (c) Marker genes per cluster; see Methods. Unique marker genes are specific to one cluster. (d) UMAP representations, stratified by experimental condition. (e-f) Gene expression analyses; values are normalized expression scores, calculated by merging pipeline. For violin plots, endpoints depict minimum and maximum values; data points are individual cells. (e) Expression of genes encoding the FACS markers, CD49f and CD61. (f) Krt14 and Krt8 gene expression, colored by cluster. (g) Expression of marker genes; markers: Krt14 (basal), Krt8 (luminal), Krt6a and Krt16 (squamous/epidermal); Esr1, Pgr, Foxa1, and Trp63 (transcription factors). In (b, d, e-g), nā€‰=ā€‰4724, 2822, 4088, 3824, 3863, and 1616 single cells in respective clusters C1-C6.

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