Fig. 3: Image-seq analysis of calvarium bone marrow using the 10x Genomics Chromium platform.
From: Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging
a, scRNA-seq workflow. For the experiments in this fig., step 5a was chosen as the final step. Scale bar, 50 µm. b,c, UMAP embedding of joint alignment of all Image-seq data (b) and WCBM data (c), color coded by the major cell populations. B, B cell; DC, dendritic cell; DP, diverse progenitors; GP, granulocyte progenitor; MP, monocyte progenitor; Pre/Pro, Pre- and Pro-B cell; Mono, monocyte. d, Heatmap showing Spearman correlation coefficients of gene average expression level between WCBM and Image-seq for each cell type. e, Dot plots showing selected marker gene expression across major cell populations for the combined Image-seq and WCBM data. The color represents scaled average expression of marker genes in each cell type, and the dot size indicates the proportion of cells expressing the individual marker gene. f, Violin plots comparing the number of expressed genes and total unique molecular identifiers (UMIs) per cell between WCBM and Image-seq samples. Statistical significance was determined using a two-sided Wilcoxon rank sum test. g, Tiled, maximum intensity projection image of leukemic bone marrow at day 10 after transplantation; examples of high-burden (HB) and low-burden (LB) regions marked by white squares and shown in the inset. Green, AML-GFP; gray, bone SHG. Scale bars: main image, 1 mm; insets, 50 μm. Also included is a distribution of GFP expression in UMAP embeddings of scRNA-seq data obtained from HB and LB regions. Tilescans were obtained from n = 5 independent mice. A total of n = 4 biological replicates of cell extraction from HB and n = 4 biological replicates of cell extraction from LB regions were performed in six independent mice. A total of four HB and LB cell extractions were performed in the same mice from which we also obtained tilescans. Sequencing was performed on one LB and one HB sample. h, UMAP embeddings of HB and LB samples color coded by cell type, and using the annotations given in b.
