Fig. 2: Bcl11b broadly constrains cell fate changes.
a, Patterns of the gene signature score composed of 150 genes enriched in C1 and C2 on the diffusion map. The graph integrates the 30,146 preprocessed cells of two biological replicates that were run in one sequencing experiment. b, Statistical over-representation assays conducted with PantherDB on the gene signature. c, Patterns of Thy1 and Bcl11b transcript levels on the diffusion map. d, Western blot for Bcl11b in MEFs, Thy1low and Thy1high cells after 5 d of reprogramming and transformation. e, Top, experimental design. Bottom, pictures of soft agar colonies, representative of four independent experiments. f, Colony quantification (n = 4 independent experiments). g, Top, experimental design. Bottom, pictures of iPS colonies stained for AP. Dox, doxycycline. h, Colony quantification (n = 3 independent experiments). i, Pou5f1+ colony quantification (n = 3 independent experiments). j, Pictures depicting the histological analysis of teratomas. Two independent teratomas were analysed per cell line. Scale bars, 1 mm. k, Top, experimental design. Bottom, pictures depicting mouse T cells and iPS cells obtained following reprogramming. cKO, conditional knockout; Tamox, tamoxifen. Scale bars, 120 µm. l, Colony quantification (n = 2 independent experiments). m, Top, experimental design. Bottom, pictures of MAP2+ neural progenitors. Scale bars, 100 µm. n, MAP2+ cell quantification (n = 2 independent experiments). o, Venn diagram showing the numbers of differentially expressed genes in control versus Bcl11b KD MEFs (orange) and control versus Bcl11b OE MEFs (blue) (log2[FC] < −0.5 or >0.5; adjusted P value < 0.05). p, Distribution of endogenous Bcl11b peaks in relation to genes. UTR, untranslated region. q, Distribution of Bcl11b peaks in relation to the TSS. kb, kilobases. TSS, transcription start site. r, Most enriched DNA-binding motifs associated with Bcl11b derived from a de novo motif analysis (MEME). s, Graph presenting the distribution of Bcl11b peaks on genes deregulated by Bcl11b modulation in MEFs (differentially expressed genes in Bcl11b KD and Bcl11b OE versus control MEFs. t, Western blot depicting Bcl11b and ERK1/2 levels in Control and Bcl11b KD MEFs. In f, h and i, the data represent means ± s.d. Statistical significance was determined by Fisher’s exact two-sided test (b) or two-tailed Student’s t-test (f, h and i).
