Additional file 1 of A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues
Creators: name: Halstead, Michelle M.
name: Kern, Colin
name: Saelao, Perot
name: Wang, Ying
name: Chanthavixay, Ganrea
name: Medrano, Juan F.
name: Van Eenennaam, Alison L.
name: Korf, Ian
name: Tuggle, Christopher K.
name: Ernst, Catherine W.
name: Zhou, Huaijun
name: Ross, Pablo J.
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1 Figure S1. Correlation of ATAC-seq signal in select technical replicates ATAC-seqlibraries. A) Pearson correlation of genome-wide signal (RPKM) in 500 bp windows. B) PCA of Cortex A technical replicate libraries alongside all biological replicates. C) PCA of pig technical replicate libraries alongside all biological replicates. D) Signal of cattle cortex technical and biological replicates at the STMN4 locus. E) Signal of pig cerebellum and hypothalamus technical and biological replicates at the STMN4 locus. Figure S2. Correlation of ATAC-seq signal in biological replicates. Scatterplots showing Pearson correlation of normalized genome-wide signal in 500 bp windows between biological replicates for cattle and pig tissues. Figure S3. ATAC-seq signal at TSS. Heatmaps depicting normalized ATAC-seq signal in the proximity of TSS, including 2 kb upstream and downstream, with TSS sorted by signal intensity. Figure S4. PCA of normalized ATAC-seq signal in consensus open chromatin identified in pig and cattle tissues tissues. Principal components 1, 2 and 3 are included to better visualize clustering of tissues. Figure S5. Mouse open chromatin localization and differential accessibility. A) Distribution of mouse consensus open chromatin relative to the Ensembl gene annotation (v96). B) Distribution of consensus peak activity, ranging from tissue-specific (accessible in only one tissue) to ubiquitous (accessible in all sampled tissues). Consensus peaks that were accessible in a single tissue were further broken down by tissue. Figure S6. Conservation of open chromatin in individual tissues. Titles above bar plots indicate the species that consensus peaks were identified in, followed by the species to which the consensus peak coordinates were projected to evaluate accessibility conservation in the corresponding tissue. Figure S7. Characterization of conserved open chromatin. Proportion of all consensus peaks, promoter consensus peaks (within 2 kb upstream and 50 bp downstream of TSS), and intergenic consensus peaks that were identified in (A) cattle or (B) pig that demonstrated both conserved sequence and accessibility in the other two species. Number of tissues in which consensus peaks demonstrated conserved accessibility in (C) all three species or (D) only in cattle and pig. E) Distribution of consensus peaks with conserved accessibility in cattle, pig, and mouse, relative to the mouse gene annotation (Ensembl v96). Figure S8. Positional conservation of chromatin accessibility at the FOXG1 locus. For each species, consensus peaks, consensus peaks with conserved sequence (that could be mapped to all three species), and consensus peaks with conserved accessibility are shown. Tracks show normalized ATAC-seq signal for each sample. Conserved promoter open chromatin is highlighted in green. Consensus peaks that appear to be syntenically conserved, relative to FOXG1, but which could not be mapped between species, are highlighted in grey. Figure S9. Bioanalyzer traces of cattle ATAC-seq libraries prior to size selection. Bioanalyzer traces were used to check for nucleosomal laddering. Size selection removed excess primer and fragments &gt; 250 bp. Figure S10. Bioanalyzer traces of pig ATAC-seq libraries prior to size selection. Bioanalyzer traces were used to check for nucleosomal laddering. Size selection removed excess primer and fragments &gt; 250 bp. Table S1. ATAC-seq library construction details. For each library constructed, rounds of PCR amplification, number of cells used as input, and concentration in the 150–250 bp range prior to size selection are indicated. Table S2. Functional annotation clustering of genes with conserved and global TSS accessibility. Genes with accessible TSS (± 50 bp) in all profiled tissues in all species were subjected to functional annotation clustering to identify enriched cellular functions. Top four clusters reported. Table S3. Functional annotation clustering of genes near conserved intergenic open chromatin. Genes that were closest (within 100 kb) to intergenic open chromatin that was conserved in all three species were subjected to functional annotation clustering to identify enriched cellular functions. Top four clusters reported. Table S4. ATAC-seq oligos used for PCR. Sequences have been previously described by Buenrostro et al., 2013. Primers 2A-2X contain variable barcodes which permit library pooling prior to sequencing, and which were used to demultiplex sequencing data.