Fig. 6: Subcellular resolution CRISPRmap barcode readout and multiplexed phenotyping in vivo.
From: Mapping multimodal phenotypes to perturbations in cells and tissue with CRISPRmap
a, Experimental workflow. Cas9− OE19 cells were transduced with the 364-guide DDR library and selected with puromycin for 2 d, before inoculation in the flanks of nude mice. Tumors were harvested after 17 d of growth and processed for CRISPRmap and immunofluorescence imaging. Image was made using BioRender. b, Quantification of proportion of cells segmented on the E-cadherin stain passing the barcode QC criteria (blue; Methods) and proportion of E-cadherin segmented cells that is part of a clonal region (orange; Methods). Data are presented as mean values ± 95% confidence interval (CI). n = 3 technical replicates. c, Visualization of in vivo barcode detection, showing the guide distribution landscape in a tumor section. Decoded barcodes are shown as spots, false colored according to their guide identity. The region highlighted by a white dashed square is zoomed in on e–h. Scale bar, 200 μm. d, Clonality analysis of barcoded cells in a cell-centric manner based on 10-nearest neighbor graphs (Methods). Scale bar, 50 μm. e, Cell (green) and nuclear (blue) boundaries detected by segmentation of E-cadherin and DAPI, respectively. Subcellular resolution of barcode readout. Decoded barcodes are shown as spots, false colored according to their guide identity. f, Iterative immunofluorescence distinguishes cell types and cellular states in vivo. Protein stains of tenascin C (magenta), mouse CD31 (green) and DAPI (blue) are shown. Antibodies are predicted to recognize epitopes from both human and mouse origins unless otherwise specified. g, As in f for vimentin (magenta) and human p21 (green). h, As in f for N-cadherin (magenta) and E-cadherin (green).
