scRNA-seq analysis of ETP-ALL isolated from the spleen and the bone marrow (BM) after ABT-199 treatment. (A) Overview of the experimental workflow. The bioluminescence was recorded after injection of luciferin on days 0, 8, and 11 in vehicle-treated and ABT-199–treated mice. Each column with pictures represents one individual mouse. At day 11, BM and spleen of vehicle- and ABT-199–treated mice were dissociated to obtain a single-cell suspension, barcoded using 10x Genomics and sequenced on an Illumina sequencer. (B) Clustering of LOUCY cells isolated from vehicle- and ABT-199–treated mice spleen with dimensional reduction by UMAP. (C) Clustering of LOUCY cells isolated from vehicle- and ABT-199–treated mice BM with dimensional reduction by UMAP. Pie charts representing number of LOUCY cells in each cluster (in percentage) for vehicle- and ABT-199–treated spleen (D) and BM (E). (F) DE genes regulated in LOUCY cells after ABT-199 treatment (219 genes; 132 genes downregulated and 87 genes upregulated) and, respectively, in the spleen (54 genes downregulated; 63 genes upregulated) and BM (97 genes downregulated and 69 upregulated) niche. (G) Venn diagram illustrating the intersections among genes differentially upregulated in LOUCY cells isolated from the spleen and BM niche in vehicle- and ABT-199–treated mice.