Extended Data Fig. 6: T-cell phenotypes persist after they are harvested from matrices.
T cells were first cultured on plates or in fast relaxing or slow relaxing collagen matrices, after which they were harvested and subsequently cultured in suspension with or without dynabead restimulation. a–e. T cell phenotyping without dynabead restimulation. a. Expansion fold (left) and viability (right) of T cells cultured in suspension after they were harvested from their indicated matrices. Data are mean ± s.e.m. n = 3 biological replicates. b. Umap plots of phenotyped T cells. c-d. K-means clustering was performed on pooled T cells from all experimental conditions. c. Heat map plot showing characteristic markers for each cluster. Heat map is z-scored by column. Legend for colour scale is shown. d. Heat map plot showing the frequencies of cells per condition for each cluster. Heat map is z-scored by row. Legend for colour scale is shown. e. PCA plot showing relative similarities between the different conditions. Data for b-d show pooled samples for n = 3 replicates. f–j. Similar analyses as a-e but for T cells cultured with dynabead restimulation. Data are mean ± s.e.m. n = 3 biological replicates.
