chip dna clean concentrator kit  (Zymo Research)

Journal: bioRxiv

Article Title: Ancestral chromatin state constrains the functional landscape of bivalent domains in mammalian spermatogenesis

doi: 10.64898/2026.04.14.718508

Figure Lengend Snippet: A, Phylogeny of the species used in this study. B, ChromHMM emissions plot and genomic coverage for human round spermatid (RS) chromatin state maps. C, Example genome browser tracks (hg38) of chromatin states defined by the ChromHMM model. D, Quantitative H3K4me3 and H3K27me3 ChIP-seq signal information for individual regions defined by ChromHMM (see Methods). Color represents functional annotation (FA) of the ChromHMM state. E, Total genomic coverage in megabases (Mb) of bivalent regions across species. F, Fraction of promoters (+/- 1kb around TSS) which overlap with a bivalent domain. Total numbers of promoters: human n=86,363, rhesus n=35,419, mouse n=78,296, rat n=32,862, bull n=36,068, opossum n=30,367. G, Expression level (FPKM) of genes with promoters marked by a given chromatin state in human RS. Box shows median and interquartile range; whiskers show range of the distribution. *p < 1e-10, 1-sample t-test performed (alternative=”less”) against the mean expression of all genes (dashed line). H, GC content of individual regions within each FA type. *p < 1e-30, 1-sample t-test performed (alternative=”greater”) against the mean whole-genome GC content (hg38, dashed line). I, Mean phastCons score within individual regions by FA type. *p < 1e-30, 1-sample t-test performed (alternative=”less”) against the mean of a set of re-shuffled regions in the human genome (hg38, dashed line). J, Genomic enrichment (odds ratio) of CpG islands, promoters, and repeat elements (LINE/SINE/LTR) in bivalent elements across species (see Methods). K, Position weight matrix of the ten most frequent enriched DNA motifs found in human bivalent regions near promoters (n=10,000). For each enriched de-novo motif, frequency in the test set (left), motif E-value (-log10) (middle), and number of predicted TFs (right) are shown.

Article Snippet: ChIP DNA was purified using the Zymo ChIP DNA Clean & Concentrator kit (Zymo D5201) following manufacturer’s instructions.

Techniques: ChIP-sequencing, Functional Assay, Expressing

Journal: bioRxiv

Article Title: Ancestral chromatin state constrains the functional landscape of bivalent domains in mammalian spermatogenesis

doi: 10.64898/2026.04.14.718508

Figure Lengend Snippet: A, Frequencies of orthologous chromatin state combinations between ancestral species (bull, opossum; left) and primate species (rhesus, human; right). The most frequent states are shown based on n=19,953 total regions classified. B, Example genome browser tracks of representative examples of evolutionarily dynamic bivalency classes: conserved bivalent (left), ancestrally Polycomb (middle), and ancestrally active (right). C, Numbers of bivalent regions in each set of evolutionary classes defined in the primate lineage. D, GC content of individual human regions within each class of evolutionarily dynamic bivalent regions. Box shows median and interquartile range; whiskers show range of the distribution. Dashed line indicates mean GC content for all bivalent regions. All comparisons significantly different (p < 1e-30, two-sample, two-sided Kolmogorov-Smirnov test) except where indicated as “ns”. E, Quantitative H3K4me3 and H3K27me3 ChIP-seq signal in human bivalent regions color-coded by evolutionary class. Number of elements in each class as shown in (C). F, Genomic enrichment (odds ratio) of promoters, CpG islands, DNase+ H3K4me3 cCRE elements, and repeat elements (LINE/SINE/LTR) in distinct evolutionary classes of human bivalent elements. G, Fraction of human bivalent regions within an evolutionary class that have the indicated chromatin state in hESCs. Total number of elements within each set as shown in (C). *p < 0.05, Fisher’s exact test (alternative=’greater’) for comparison of co-occurrence between states. H, Position weight matrix of the most frequent enriched DNA-motifs found in human bivalent regions according to evolutionary label, with total number of elements as shown in (C), using all evolutionary classified regions as negative background set. For each enriched motif, frequency in the test set (left) and motif E-value (-log10) (right) is shown (Methods). *p < 0.05.

Article Snippet: ChIP DNA was purified using the Zymo ChIP DNA Clean & Concentrator kit (Zymo D5201) following manufacturer’s instructions.

Techniques: ChIP-sequencing, Comparison