Figure 2
From: Extensive reprogramming of the nascent transcriptome during iPSC to hepatocyte differentiation
Identification of differentially expressed pri-miRNA transcripts and alternative TSS usage at pri-miRNA loci. (A) UCSC Genome browser shot image depicting normalized GRO-seq taq counts for the miR-302–367 cluster pri-miRNAs. (B) A pri-miRNA network of 29 hub miRNAs identified through miRNET tool, which was used to construct liver-specific miRNA target networks connecting miRNA to genes that had been validated by CLIP-studies. (C) A heatmap representation of the 29 hub miRNAs. Scale bar represents log2 fold change of M1-HLC/M2-HLC/PHH vs iPSC. (D) GO analysis of the hub miRNA target genes. (E) Quantification of differential transcription start site (TSS) activity at intergenic pri-miRNA loci with multiple TSSs. The differential TSS activity is calculated based on the GRO-seq signal difference between adjacent elements (TV FPKM = TV − TV + 1 FPKM). Pri-miRNAs were clustered using pairwise average linkage with un-centered correlation distance. (F) GRO-seq signal across the four cell types at the miR-221 locus, where two distinct TVs were identified. TV = transcript variant. See also Supplementary Fig. S2.
