Additional file 1 of Changes in chromatin accessibility landscape and histone H3 core acetylation during valproic acid-induced differentiation of embryonic stem cells
Creators: name: Baumann, Claudia
name: Zhang, Xiangyu
name: Zhu, Ling
name: Fan, Yuhong
name: De La Fuente, Rabindranath
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. Protein expression levels of H3K56ac and other histone acetylation marks. (A) Immunochemical detection of H3K35ac (green) in control and VPA-treated (2 mM for 48 h) mESCs (DAPI-stained DNA shown in inset) Scale bar of 20 µm. Western blotting of H3K56ac in lysates obtained from control and VPA-treated cultures. Tubulin served as housekeeping control and was used to normalize band intensities for quantitative analysis. P &lt; 0.005. (B) Immunochemical detection of H4K5ac, H4K8ac, and H4K16ac (green) in control and VPA-treated (2 mM for 48 h) mESCs (DAPI-stained DNA shown in inset) Scale bar of 20 µm. Figure S2. ATAC-seq supplemental QC data. (A) Peak tag numbers of merged peak regions. (B) Hierarchical clustering of the two control (Cntl) and two VPA-treated (VPA) samples, respectively. (C) Pearson correlation of peak tag numbers. Correlation analysis between ATAC-seq samples revealed strong correlation between the two replicate samples of each treatment group. (D) A principal component analysis using an orthogonal transformation to convert a set of observations of variables into a set of values of linearly uncorrelated variables (principal components) also showed similar correlation between samples. Scatter plots of raw and normalized peak counts from WT and Cbx2 − / − samples. Pearson correlation of duplicate control (Cntl) (E) and duplicate VPA-treated (VPA) (F) samples. The Pearson correlation coefficients are indicated. Figure S3. Extended ATAC-seq data. (A) Venn diagram of merged regions with peaks from control (Cntl) and VPA-treated (VPA, 2 mM, 48 h) samples. (B) The location of ATAC-seq peaks relative to genomic annotations for control and VPA-treated samples. (C) Comparative analysis of different genomic loci relative to all loci with gained or lost accessibility. (D) The number of changes in loci encoding for non-coding RNAs with gain or loss of chromatin accessibility in response to VPA treatment, respectively. (E) Heatmaps of tag distributions across merged peak regions and genebodies in control and VPA-treated samples. (F) Histograms showing the distance from peak centers at merged peak regions, TSS and genebodies. Figure S4. CUT&amp;RUN validation and genome-wide distribution patterns of H3K56ac. (A) To test the CUT&amp;RUN approach in our hands, control mESCs were used for profiling H3K27me3 genomic distributions according to [55, 101]. IGV browser views of 200 kb of the Hoxd and 35 kb of the Wnt5a loci are shown. H3K27me3 enrichment is in agreement with previously published reports [56–59]. Coherent broad domains of enrichment were identified by SEACR analysis and are denoted as blue bars. (B) SEACR analysis comparison of peak numbers, % peaks reproduced and width of peaks of H3K56ac CUT&amp;RUN assays on control (Cntl) and VPA-treated (2 mM, 48 h) mESCs in two biological replicates (R1, R2). Box pots represent the median value as well as upper and lower quartiles with whiskers representing the minimum and maximum values observed. IGV browser view of 35 kb of the Thy1 locus encoding a cell surface antigen is shown and is in accordance with previously reports [60]. Figure S5. Integrative ATAC-seq/CUT&amp;RUN analysis. (A) List of 11 genes found to show correlative gain in chromatin accessibility and gain in H3K56ac at the TSS. (B) Venn diagram illustrating total overlap between ATAC-seq peak changes and altered H3K56ac enrichment by SEACR analysis. (C) IGV browser view of the Klf4 locus, including E2/E3 enhancer sites. ATAC-seq chromatin accessibility tracks are aligned with H3K56ac CUT&amp;RUN enrichment and differential patterns are indicated in shaded box. Coherent broad domains of H3K56ac enrichment were identified by SEACR analysis and are denoted as blue bars. Table S1. Transcription factor footprinting. List of TFs with high scores in control samples. Table S2. Transcription factor footprinting. List of TFs with high scores in VPA-treated samples.