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. Author manuscript; available in PMC: 2022 May 22.
Published in final edited form as: Nat Genet. 2021 May 10;53(6):881–894. doi: 10.1038/s41588-021-00859-2

Extended Data Fig. 9 ∣. Sox2/Klf5 complexes induce IFN activation.

Extended Data Fig. 9 ∣

a, Most enriched pathways from upregulated genes at loci of gained Sox2 binding sites (SCPP vs Normal organoids); nominal p-value from GSEA package. b, Representative ATAC-seq, Sox2 and H3K27ac ChIP-seq tracks, showing increased accessibility, Sox2 binding and H3K27ac level at Tmem173 (Sting), Mavs and Dhx58 (Lgp2) loci in SCPP (versus CPP). c, mRNA expression of Sting and Lgp2 Normal and SCPP by mRNA seq; two biological replicates performed. d, Quantification of binding of Sox2 and Klf5 as assessed by ChIP-PCR at loci of Tmem173 (Sting), Il6ra and Ifih1(Mda5); Three biological replicates. Data are shown as mean ± SD; p-value by two-sided t-tests. e, mRNA expression Mx1, Cxcl10 and Isg15 in CPP and SCPP as assessed by quantitative RT-PCR 24 h after infection with H1N1 flu virus; tree independent biological replicates. Data are shown as mean ± SD, p-value calculated by two-sided unpaired t-tests. f, mRNA expression of Mx1, Cxcl10 and Isg15 in CPP and SCPP as assessed by quantitative RT-PCR 24 h after transfection with 5’ppp-dsRNA (normalized to 5’ppp-dsRNA control); three independent biological replicates. Data are shown as mean ± SD, NS: not significant as calculated by two-sided unpaired t-tests. g, Quantification of J2(dsRNA) and Adar1 staining in CPP and SCPP (Image J software) with signals normalized to cell number and then CPP; three technical replicates per condition. The data are shown as mean ± SD, p-value calculated by two-sided unpaired t-tests. h, Representative double immunofluorescence images for J2(dsRNA; green) and Adar1 (red) and DAPI (blue) in SCPP with Adar1 silencing. Scale bar=40um. (This experiment was repeated once with similar results). i, Quantification of J2(dsRNA) (Left) and Adar1 (Right) in SCPP with CRISPR-mediated Adar1 knockout. The signal of sgAdar1 was normalized to cell number and then sgNT; three technical replicates. The data are shown as mean ± SD, p-value by one-way ANOVA test with Benjamini-Hochberg correction.