Fig 1: CRISPRmap base editing screening enables multimodal phenotyping of cell states.a, Experimental workflow (Methods). Image was made using BioRender. b, Subcellular distribution of six DDR protein stains (top row), five cell cycle regulator stains (middle row), barcode detection (middle row, most right) and transcript detection for six genes (bottom row) for a single cell. Cell and nuclear segmentation are outlined in blue, raw antibody signal and transcript detection in grayscale. Decoded barcodes are shown as false-colored (magenta) spots. Only data under the cell segmentation mask are displayed. Scale bar, 10 μm. c, Quantification of the number of RAD51 foci per cell across cell cycle phases in UNT (n = 1 with 120,253 cells) and IR (n = 1 with 106,116 cells) cells, showing significant foci induction by irradiation and enrichment in the S/G2 phase. Boxes indicate the median and interquartile range (IQR) with whiskers extending 1.5× IQR past the upper and lower quartiles (outliers are omitted). Two-sided Mann–Whitney test, *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001. The P values of (G2/S_UNT, G0_IR, G1_IR and M_IR) versus G2/S_IR are 0.00e + 00, 0.00e + 00, 0.00e + 00 and 2.74 × 10−37, respectively. d, As in c for BRCA1 foci. The P values are 0.00e + 00, 0.00e + 00, 0.00e + 00 and 3.78 × 10−15. e, Correlation between RNA-reporting spots per million spots measured by RNAmap and TPM reads from RNA sequencing. Pearson correlation (r) equals 0.84. f, RNA–protein correlation measured by RNAmap and antibody staining for three RNA–protein pairs (Ccna2-cyclin A2, Ccnb1-cyclin B1 and Cdkn1a-p21), showing significantly enriched RNA-reporting spots in cells with high protein expression. Boxes indicate the median and IQR with whiskers extending 1.5× IQR past the upper and lower quartiles. Two-sided Mann–Whitney test, *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001. The P values (from left to right) are 0.00e + 00, 0.00e + 00 and 0.00e + 00. g, Visualization of the decoded Ccna2-reporting spots (magenta) and cyclin A2 staining (green). Scale bar, 50 μm. h, As in g for Cdkn1a (magenta) and p21 (green). IR, irradiated; UNT, untreated.