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

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

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

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

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

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

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

Quantitative Study on the Influence of Bromide Ions toward the Reduction Kinetics for Size-Tunable Palladium Nanocubes

During the preparation of nanocrystals, regulating the dosage of key additives in the reaction system and the reaction temperature commonly affects the sizes and morphologies of the products. Despite the fact that bromide ions play a pivotal role in the synthesis of palladium nanocubes (Pd NCs), there is still a lack of quantitative and in-depth research on how the ions affect the reduction kinetics of Pd precursors and further on products. In this work, Pd NCs with different sizes have been prepared under various reaction conditions coupled to a systematic mechanism study. Quantitative measurements demonstrate that the reduction processes could be considered quasi-first-order reactions, and the corresponding kinetic parameters have been obtained. Furthermore, a linear relationship is discovered between k and the average size (d) of Pd NCs. The investigation on the growth patterns of four chosen systems reveals that given reaction conditions lead to certain results with unique growth patterns