MOESM5 of Profiling of chromatin accessibility and identification of general cis-regulatory mechanisms that control two ocular lens differentiation pathways

Additional file 5: Table S3. Number of peaks inside unique and shared clusters

MOESM9 of Profiling of chromatin accessibility and identification of general cis-regulatory mechanisms that control two ocular lens differentiation pathways

Additional file 9: Fig. S6. ATAC-seq peaks at previously described Prox1 binding regions at Lctl, Fgfr3, Fgfrl1, and Crybb1

MOESM8 of Profiling of chromatin accessibility and identification of general cis-regulatory mechanisms that control two ocular lens differentiation pathways

Additional file 8: Fig. S5. Hierarchical clustering of transcription factors predicted for lens fiber cell differentiation and lens epithelium maturation paths. a. 27 TFs showed higher expression in Path1. b. 51 TFs showed higher expression in Path2

MOESM6 of Profiling of chromatin accessibility and identification of general cis-regulatory mechanisms that control two ocular lens differentiation pathways

Additional file 6: Fig. S3. Analysis of unique or shared clusters of open chromatin regions and their corresponding gene expression levels. a. b. Heatmaps show ATAC-seq signals and corresponding gene expression for unique and shared peak groups

MOESM2 of Profiling of chromatin accessibility and identification of general cis-regulatory mechanisms that control two ocular lens differentiation pathways

Additional file 2: Fig. S1. Quality controls of ATAC-seq data. a. Distributions of insert sizes from 8 ATAC-seq libraries. b. Heatmap shows Pearson correlation coefficients among samples, computed from reads mapped to peaks. c. Scatterplots of mean normalized counts (mean read counts inside peaks from biological replicates normalized by the total read numbers for all peaks) between pairwise spatial and temporal comparisons

MOESM1 of Profiling of chromatin accessibility and identification of general cis-regulatory mechanisms that control two ocular lens differentiation pathways

Additional file 1: Table S1. Summary for the ATAC-seq data

MOESM10 of Profiling of chromatin accessibility and identification of general cis-regulatory mechanisms that control two ocular lens differentiation pathways

Additional file 10: Fig. S7. Potential enhancers at key transcription factors and structural proteins in lens. a. b. Examples of putative enhancers for lens transcription factors (a) and structural proteins (b) based on ATAC-seq enrichment. The evolutionary conservation (cons) tracks are shown in green. ATAC-seq data are from mouse E14.5 lens epithelium, lens fibers, forebrain, liver, and ESCs

MOESM7 of Profiling of chromatin accessibility and identification of general cis-regulatory mechanisms that control two ocular lens differentiation pathways

Additional file 7: Fig. S4. Correlation of DARs and DEGs. a. Pie charts show the percentages of differentially expressed genes (DEGs, dark blue), reversely differentially expressed genes (DEGs reverse, light blue) and not differentially expressed genes (not DEGs, red) associated with each group of differentially accessible regions (DARs). b. Bar plots show the percentages of DEGs and DEGs reverse in each group of DARs mapped genes divided by the number of peaks annotated to the genes

MOESM11 of Profiling of chromatin accessibility and identification of general cis-regulatory mechanisms that control two ocular lens differentiation pathways

Additional file 11: Fig. S8. Pax6 binding sites at open and closed chromatin play distinct roles for gene expression. a. Examples of P1 lens Pax6 peaks at open chromatin regions in Prox1 (left) and closed chromatin regions in Hivep2 (right). b. Table shows the number of Pax6 peaks detected at open and closed chromatin regions in mouse ATAC-seq atlas. c. Venn diagram shows the overlaps of genes with lens Pax6 peaks at open and closed chromatin regions and the differentially expressed genes in Pax6 KO vs WT. d. Venn diagram shows the overlap of Pax6 peaks at E12.5 forebrain and P300 peaks (E11.5 forebrain)

MOESM4 of Profiling of chromatin accessibility and identification of general cis-regulatory mechanisms that control two ocular lens differentiation pathways

Additional file 4: Fig. S2. Overlaps between DARs from 8 comparison groups