Fig. 5
From: Nanogrid single-nucleus RNA sequencing reveals phenotypic diversity in breast cancer
Single-nuclei sequencing of a TNBC. a Clustered heat map of single nuclei RNA copy number profiles isolated from tumor tissue or normal breast tissue. Green arrows indicate five stromal cells from the tumor with diploid copy number profiles. Bar-plot shows increase in tumor purity after image selection of larger nuclei. b Enrichment of tumor cells using nanogrid SNRS from 41 to 99%. c t-SNE projection of single nuclei in high-dimensional space with SNN clustering of three subpopulations a, b, c indicated by color. d Clustered heat map of single nuclei RNA expression profiles using differentially expressed genes. Cancer genes are highlighted in red and the three major clusters are indicated by color. e Violin plots of single cells expression levels of individual genes across the three tumor subpopulations. f GSVA scores for a subset of oncogenic phenotypes with single nuclei sorted by each row independently with header bars indicating their identities of the predicted subpopulations. g Clustered heat map of cell cycle signature scores for single nuclei with subpopulation indicated in the header. h Subtype signature classifications for single tumor nuclei predicted by PAM50 for the five breast cancer subtypes (left) and for the six TNBC subtypes (right)
