Fig. 1 | Nature Communications

Fig. 1

From: A non-canonical BRD9-containing BAF chromatin remodeling complex regulates naive pluripotency in mouse embryonic stem cells

Fig. 1

BRD9 is part of the ESC pluripotency transcriptional regulatory network. a Time course experiment assessing mouse ES cell number after treatment with DMSO or I-BRD9 at either 1.11 or 3.33 µM. Error bars represent one standard deviation from the mean of biological replicates, n = 9. Two-tailed t-test was performed to obtain the p values. *p < 0.05, **p < 0.01, ***p < 0.001. b As in a, but for ESCs treated with DMSO or BI-9564 at either 300 nM or 1 µM; n = 6. c As in a, but for ESCs transduced with shRNA against a scrambled control or Brd9; n = 3 for each shBrd9 experiment. d Scatterplot of average log2 fragments per kilobase of transcript per million mapped reads (FPKM) mRNA expression level in DMSO-treated ESCs against log2 fold change (FC) in expression after 24 or 48 h of 10 µM I-BRD9 treatment in serum/LIF conditions. Red and blue indicate differential expression increased or decreased by 1.5-fold or more (Benjamin-Hochberg FDR < 0.05), respectively, from two independent biological replicates. e Venn diagram of differentially expressed genes (DEGs) in the 24 and 48 h I-BRD9 RNA-Seq datasets. f Significance of the I-BRD9 DEG enrichment in each gene ontology process. FDR values were calculated according to Benjamin-Hochberg multiple testing (GSEA). g GSEA enrichment plots of either the significantly downregulated (left) or upregulated (right) I-BRD9 DEGs using the shcontrol and shBrd9 RNA-Seq dataset. NES normalized enrichment score, FWER p value familywise error rate calculated using single tail tests on the positive or negative side of the null distribution. h Box plot of the log2 FC in expression upon shBrd9 knockdown, grouped into quintiles according to the genes’ log2 FC upon I-BRD9 addition. Shades of blue and red correspond to the degree of log2 FC down- or upregulation in I-BRD9/DMSO. Black bars indicate the mean per quintile. i As in g, GSEA enrichment plot of BRG1-dependent genes in ESCs using the I-BRD9 RNA-Seq dataset. Source data for ac are provided as Source Data file