Extended Data Fig. 1: Effects of SMARCA4 degradation on BAF complex members.

a, Western blot analysis of HAP1 ARID2^KOSMARCA4^dTAG cells after treatment for different times with 700 nM dTAG47, dTAG13, dTAG7 or DMSO as control (cropped images). b, Semi-quantitative analysis of SMARCA4 protein levels based on whole-cell extract western blot data normalized to α-Tubulin (shown in Fig. 1b) and based on nuclear-extract proteomics data (shown in Fig. 1d). Cropped western blot images of dTAG47 time-course in SMARCA4^dTAG cells. c, Western blot analysis of HAP1 SMARCA4^dTAG cells after treatment for different times with 300 nM dTAG47 or DMSO as control in various cellular fractions. Staining for SMARCA4, SMARCA2 and SMARCC1 as well as α-Tubulin and RCC1 as control. Cropped images, WCE=whole cell extract. Semi-quantitative analysis of SMARCA4 protein levels based on nucleoplasm and chromatin fraction western blot data normalized to RCC1. RCC1 run on a separate plot from the same experiment and was processed in parallel. d, Western blot analyses of BAF subunit members after SMARCA4 degradation (dTAG) induced with 300 nM dTAG47 for 24 h compared to control (DMSO) in different cellular compartments of HAP1 SMARCA4^dTAG cells (cropped images). e, SMARCC1 immunoprecipitation in different cellular compartments of HAP1 SMARCA4^dTAG cells treated with 300 nM dTAG47 or DMSO for 24 h. Western blot analysis for SMARCA4 (cropped images). f, HA immunoprecipitation in different cellular compartments of HAP1 ARID2^KOSMARCA4^dTAG cells treated with 300 nM dTAG47 or DMSO for 24 h. Western blot analysis for various BAF subunits and HDAC2 (cropped images). g, Heatmap showing mean log₂ SMARCC1-normalized abundance values of mass spectrometry results of Fig. 1f. 0, protein abundance below quantification threshold.