MOESM2 of Retinal-input-induced epigenetic dynamics in the developing mouse dorsal lateral geniculate nucleus
Creators: name: Jianlin He
name: Xiguang Xu
name: Aboozar Monavarfeshani
name: Sharmi Banerjee
name: Fox, Michael
name: Hehuang Xie
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Physiology
subject: Pharmacology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology

description: Additional file 2: Fig. S1. Distribution of read depth for CpG sites determined in four dLGN WGBS libraries. Fig. S2. Distribution of CpG methylation levels determined for four dLGN WGBS libraries. Fig. S3. Venn diagram of DMS lists identified from four pairwise comparisons. Fig. S4. Relationships between mCH and gene expression. The mCH profiles for (A) P6 WT, (B) P6 Math5KO, (C) P23 WT and (D) P23 Math5KO. Red line denote the group of genes with the top one-third expression; green line denote the group of genes with the median one-third expression; blue line denote the group of genes with the bottom one-third expression; and black line show the group of genes not expressed. The average expression levels at P3 and P7 were shown for P6. Fig. S5. Pairwise comparisons identified common sets of 463 upregulated (A) and 554 downregulated (B) genes from P3 to P23 were identified in both WT and Math5KO. No gene was identified to be overlapped for upregulated (C) or downregulated (D) in Math5KO in pairwise comparisons between WT and Math5KO dLGN across all four time points. Fig. S6. The mCH profiles for 463 upregulated (Green) and 554 downregulated (Red) genes from P3 to P23 in P7 WT (A), P7 Math5KO (B), P23 WT (C) and P23 Math5KO methylomes. Fig. S7. Heat map (A) and scatter plot (B) for gene expression profiles of 61 genes which promoters overlapped with DMRs showing methylation increased in P23 Math5KO. Heat map was generated using RNAseq data from four time points with color bar showing log (1 + TPM), and scatter plot was generated with RNAseq data at P23 for WT and Math5KO with X- and Y-axis showing log (1 + TPM). Fig. S8. Methylation profiles of DMRs during mouse brain development. Fig. S9. DNA Methylation for DMRs and gene expression profiles for Lhx2 and CACNA1E loci. Fig. S10. WGCNA clustering and motif enrichment analysis for DMS sites identified in the comparison between P6 WT and P23 WT. (A) WGCNA clustering. (B) Methylation profiles of different clusters. (C) Top TFs with motifs significantly enriched in each cluster predicted by HOMER. Fig. S11. WGCNA clustering and motif enrichment analysis for DMS sites identified in the comparison between P6 Math5KO and P23 Math5KO. (A) WGCNA clustering. (B) Methylation profiles of different clusters. (C) Top TFs with motifs significantly enriched in each cluster predicted by HOMER. Fig. S12. WGCNA clustering and motif enrichment analysis for DMS sites identified in the comparison between P6 WT and P6 Math5KO. (A) WGCNA clustering. (B) Methylation profiles of different clusters. (C) Top TFs with motifs significantly enriched in each cluster predicted by HOMER. Fig. S13. WGCNA clustering and motif enrichment analysis for DMS sites identified in the comparison between P23 WT and P23 Math5KO. (A) WGCNA clustering. (B) Methylation profiles of different clusters. (C) Top TFs with motifs significantly enriched in each cluster predicted by HOMER.