Single cell RNA-sequencing of longitudinal patient samples. (A) Uniform manifold approximation and projection (UMAPs) of the entire scRNA-seq data set (randomly subsampled for display due to the large number of cells) shaded by cell type (left), time point (second from left), response (second from right; Rs in pink vs NRs in blue), and cohort (right). (B) UMAPs showing cells by major cell type at day –28 (left), day +7 (second from left), day +14 (second from right), and IP (right). (C) scRNA-seq analysis of immune cell subset composition, including CAR⁺ and CAR^– CD4 and CD8 cells, over time in Rs (pink) vs NRs (blue). Curves fit by loess smoother. Cells are denoted as CAR⁺ if at least 1 CAR transcript was detected. For a subset of samples from Haradhvala et al¹¹ cohort at day +7, cells were sorted by flow cytometry for the CAR, in which case those designations are used. (D) scRNA-seq analysis of B-cell composition over time in Rs (pink) vs NRs (blue). (E) scRNA-seq analysis of B cells at day –28 (inset, left) and subsetted to naïve B cells (inset, right). NK cell, natural killer cell.