Additional file 1 of Early-life undernutrition induces enhancer RNA remodeling in mice liver

Additional file 1: Figures S1–S10. Figure S1. Overview of GRO-seq library construction. A, C Isolated liver nuclei stained with DAPI. B, D Amplified DNA library range from 200–500 bp. Figure S2. Agarose gel extraction for cDNA fragment from 150nt-500nt in GRO-seq library construction. Figure S3. Impact of maternal PRD on total transcripts. Differentially expressed genes between the offspring of the dams fed the PRD and NCD at the age of 4 weeks (A) and 7 weeks (B) in RNA-seq were analyzed by Kyoto Encyclopedia of Genes and Genomes (KEGG). Fold Change > 1.5, p 1.5, p < 0.05. Figure S5. High confidence enhancers identification. Overlap of enhancers identified in the mouse liver GRO-seq from two independent replicates prepared from 4 and 7 weeks, respectively. Figure S6. Correlation of RNA transcriptional abundance in gene body regions associated with up- (PRD1) and down- (PRD2) regulated enhancers for the closest and other active genes. Figure S7. Examination of serum lipids profiles for 7-week-old PRD mice. Figure S8. Validation results for the change of enhancers-induced metabolic genes. A Q-PCR detection for 10 randomly selected genes in total RNA of NCD1 vs PRD1, and NCD2 vs PRD2 mice livers. B Heatmap of 10 randomly chosen eRNA expression results generated by IMAGE based on their transcription in PRD1 and PRD2 (weighted p < 0.05). Figure S9. Visualization of enhancer induced metabolic gene transcription in PRD. IGV snapshot of sequencing data, identified novel enhancer, H3K27ac peaks, and RNA-seq data of Nudt7, Serpina4-ps1 and Cyp2b10. These novel enhancers (chr8: 114091772–114095641; chr12: 104066247–104069323; chr7: 25890844–25894913) contribute to altered expression of their closest genes in PRD. Figure S10. Correlation between different replications of GRO-seq (A) and RNA-seq (B) libraries, respectively.