Figure S4.
Single-cell analysis of Arid1a homozygous tumor.(A) Representative immunofluorescence image of ARID1A and CD44 costaining of Arid1a homozygous tumors at 20 wk shows both ARID1A+ CD44+ (white arrowhead) and ARID1A− CD44+ (yellow arrowhead) cells (n = 3). Scale bar, 100 µm. (B) Immunofluorescence image of ARID1A staining of epithelial cells isolated from Arid1a homozygous tumors in preparation for scRNA-seq; the white arrowhead denotes the ARID1A− cells, and yellow arrowheads denote the ARID1A+ cells (n = 3). Scale bar, 100 µm. (C) GO term analysis of clustering markers of epithelial cells in Arid1a homozygous tumors. (D) Analysis of GO terms related to p53 signaling and apoptosis displays increased enrichment in clusters 2 and 3 compared with the other clusters. (E) Feature plots of the scRNA-seq data shows enriched expression of Trp53 in clusters 2 and 3 (dotted line). (F) Representative images of TUNEL staining in Arid1a homozygous gastric tumors at 10 and 20 wk (n = 4 and 7, respectively). Scale bar, 100 µm. (G) Quantification of TUNEL+ cells in Arid1a homozygous gastric tumors at 10 and 20 wk (*, P = 0.01, unpaired t test). Bars represent mean ± SD. (H) Number of H3K27ac peaks per replicate in normal Cre− stomach, Arid1a intact, Arid1a heterozygous, and Arid1a homozygous tumors. (I) Representative images of TUNEL fluorescence staining in Arid1a heterozygous and homozygous gastric tumors at 10 wk (n = 3 and 4, respectively). Scale bar, 100 µm. (J) Quantification of TUNEL+ cells in Arid1a heterozygous and homozygous gastric tumors at 10 wk (unpaired t test). Bars represent mean ± SD. (K) Expression of Arid1b in wild-type stomachs (n = 3), Arid1a intact tumors (n = 3), and Arid1a heterozygous tumors (n = 3) from RNA-seq (unpaired t test). (L) Violin plots of Arid1a and Arid1b expression from scRNA-seq of Arid1a homozygous tumors. (M) Representative images of ARID1A and ARID1B antibody staining in serial sections of 20-wk-old Arid1a homozygous tumors shows expression of ARID1B in both ARID1A− and ARID1A+ regions (n = 4). Scale bars, 100 μm.

Single-cell analysis of Arid1a homozygous tumor. (A) Representative immunofluorescence image of ARID1A and CD44 costaining of Arid1a homozygous tumors at 20 wk shows both ARID1A+ CD44+ (white arrowhead) and ARID1A− CD44+ (yellow arrowhead) cells (n = 3). Scale bar, 100 µm. (B) Immunofluorescence image of ARID1A staining of epithelial cells isolated from Arid1a homozygous tumors in preparation for scRNA-seq; the white arrowhead denotes the ARID1A− cells, and yellow arrowheads denote the ARID1A+ cells (n = 3). Scale bar, 100 µm. (C) GO term analysis of clustering markers of epithelial cells in Arid1a homozygous tumors. (D) Analysis of GO terms related to p53 signaling and apoptosis displays increased enrichment in clusters 2 and 3 compared with the other clusters. (E) Feature plots of the scRNA-seq data shows enriched expression of Trp53 in clusters 2 and 3 (dotted line). (F) Representative images of TUNEL staining in Arid1a homozygous gastric tumors at 10 and 20 wk (n = 4 and 7, respectively). Scale bar, 100 µm. (G) Quantification of TUNEL+ cells in Arid1a homozygous gastric tumors at 10 and 20 wk (*, P = 0.01, unpaired t test). Bars represent mean ± SD. (H) Number of H3K27ac peaks per replicate in normal Cre− stomach, Arid1a intact, Arid1a heterozygous, and Arid1a homozygous tumors. (I) Representative images of TUNEL fluorescence staining in Arid1a heterozygous and homozygous gastric tumors at 10 wk (n = 3 and 4, respectively). Scale bar, 100 µm. (J) Quantification of TUNEL+ cells in Arid1a heterozygous and homozygous gastric tumors at 10 wk (unpaired t test). Bars represent mean ± SD. (K) Expression of Arid1b in wild-type stomachs (n = 3), Arid1a intact tumors (n = 3), and Arid1a heterozygous tumors (n = 3) from RNA-seq (unpaired t test). (L) Violin plots of Arid1a and Arid1b expression from scRNA-seq of Arid1a homozygous tumors. (M) Representative images of ARID1A and ARID1B antibody staining in serial sections of 20-wk-old Arid1a homozygous tumors shows expression of ARID1B in both ARID1A− and ARID1A+ regions (n = 4). Scale bars, 100 μm.

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