Extended Data Fig. 2: ChIP-Seq analysis of Glis1 during somatic cell reprogramming.
From: Glis1 facilitates induction of pluripotency via an epigenome–metabolome–epigenome signalling cascade
a, DNA integrity assessment of P10 control-iPSCs and Glis1-iPSCs by comet assay. The experiment were performed twice, and the data are represented as mean ± S.E.M, (Ctrl, n=134; Glis1, n=187 cell nucleus). Group differences are analyzed by the two-tailed Student’s t test. b, RT-qPCR analysis for detecting the expression of endogenous Glis1 during SKO-mediated reprogramming. Data are presented as the mean ± S.D. (n = 3, each group).Group differences are analyzed by the two-tailed Student’s t test. c, RT-qPCR analysis for detecting the Glis1 knockdown efficiency in MEFs relative to shLuc control. Data are presented as the mean ± S.D. (n = 3, each group).Group differences are analyzed by the two-tailed Student’s t test. d, OG2 MEFs were infected with retroviral SKO and shRNAs against Luciferase (shLuc) or Glis1 (shGlis1). GFP+ colonies were counted on day 20. Data are presented as the mean ± S.D. (n = 3, each group).Group differences are analyzed by the two-tailed Student’s t test. e, Schematic maps of Glis1 truncations used in this study; numbers are for amino acids. f, OG2 MEFs were infected with retroviral SKO plus Glis1 wild-type or deletion mutants. GFP+ colonies were counted on day 20. Data are presented as the mean ± S.D. (n = 3, each group).Group differences are analyzed by the two-tailed Student’s t test. g, RT-qPCR analysis for detecting the Glis1 knockdown efficiency in MEFs relative to shLuc control in DOX-inducible knockdown system. Data are presented as the mean ± S.D. (n =4, each group).Group differences are analyzed by the two-tailed Student’s t test. h, OG2 MEFs were infected with retroviral SKO and DOX-inducible knockdown of Glis1. DOX was added immediately after infection until the indicated day or added from indicated day until day 20. The reprogramming efficiencies were compared with DOX-free control. Data are presented as the mean ± S.D. (n = 3, each group).Group differences are analyzed by the two-tailed Student’s t test. i, OG2 MEFs were infected with retroviral SKO and DOX-inducible Glis1. DOX was added immediately after infection until the indicated day or added from indicated day until day 20. The reprogramming efficiencies were compared with DOX-free control. Data are presented as the mean ± S.D. (n = 3, each group).Group differences are analyzed by the two-tailed Student’s t test. j, The Glis1-N-HA-tag enhanced iPSCs generation equally well as non-tag Glis1. GFP+ colonies were determined on day 20. Data are presented as the mean ± S.D. (n = 3, each group).Group differences are analyzed by the two-tailed Student’s t test. k, GO term analysis of Glis1 peak position to nearest genes by ChIP-seq. 1 replicate was used for Go term analysis in Glis1 ChIP-seq assay. n = 2 independent experiments were repeated with similar results (a–c). l, Genome view of Glis1 binding at indicated gene loci by ChIP-seq. Scale bar, 5 kb. n = 2 independent experiments were repeated with similar results (k–j). Pie chart indicating the number of genes upregulated, downregulated or unchanged upon Glis1 overexpression on day 8. 1 replicate was used for RNA-seq analysis. n = 2 independent experiments were repeated with similar results.
