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chip dna clean & concentrator  (Zymo Research)


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    Structured Review

    Zymo Research chip dna clean & concentrator
    Chip Dna Clean & Concentrator, supplied by Zymo Research, used in various techniques. Bioz Stars score: 99/100, based on 1600 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/chip+dna+clean+and+concentrator/ChIP+DNA+Clean+%26+Concentrator/custom%40d5201%4042791404
    Average 99 stars, based on 1600 article reviews
    chip dna clean & concentrator - by Bioz Stars, 2026-10
    99/100 stars

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    Related Articles

    Isolation:

    Article Title: Stage-specific epigenetic priming amplifies gene activation during lineage commitment.
    Article Snippet: .. DNA was isolated using Zymo ChIP DNA Clean and Concentrator (Zymo Research) according to the manufacturer’s instructions. .. The cells were then counterstained with Hoechst 33342 (Invitrogen) and subsequently mounted with Fluoromount (Invitrogen).

    Article Title: Stage-specific epigenetic priming amplifies gene activation during lineage commitment
    Article Snippet: .. DNA was isolated using Zymo ChIP DNA Clean and Concentrator (Zymo Research) according to the manufacturer’s instructions. .. CUT&RUN Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (Illumina), with minor modifications, as the end prep step was extended to 30 min at 20°C and 60 min at 50°C.

    Chromatin Immunoprecipitation:

    Article Title: Stage-specific epigenetic priming amplifies gene activation during lineage commitment.
    Article Snippet: .. DNA was isolated using Zymo ChIP DNA Clean and Concentrator (Zymo Research) according to the manufacturer’s instructions. .. The cells were then counterstained with Hoechst 33342 (Invitrogen) and subsequently mounted with Fluoromount (Invitrogen).

    Article Title: H3.1K27M-induced misregulation of the TONSOKU-H3.1 pathway causes genomic instability
    Article Snippet: .. After uncrosslinking, samples were treated with proteinase K and purified using ChIP DNA Clean and Concentrator (Zymo Research, Irvine, CA). .. ChIP sequencing libraries were prepared at the YCGA with a TruSeq Library Prep Kit (Illumina, San Diego, CA).

    Article Title: H3.1K27M-induced misregulation of the TONSOKU-H3.1 pathway causes genomic instability.
    Article Snippet: .. After uncrosslinking, samples were treated with proteinase K and purified using ChIP DNA Clean and Concentrator (Zymo Research, Irvine, CA). .. ChIP sequencing libraries were prepared at the YCGA with a TruSeq Library Prep Kit (Illumina, San Diego, CA).

    Article Title: The DLX/Notch axis is necessary for spatiotemporal regulation of neural cell fate
    Article Snippet: Eluted fragments were incubated with 0.01M EDTA, 0.04M Tri-HCl, pH 7.4, 0.1 mg/mL Proteinase K (Promega Cat# MC5008) at 50°C for 2 hours for crosslinking reversal. .. The eluted DNA fragments were purified using the ChIP DNA Clean and Concentrator (Zymo Research Cat# D5205) according to the manufacturer’s instructions. ..

    Article Title: Stage-specific epigenetic priming amplifies gene activation during lineage commitment
    Article Snippet: Transposition was carried out in 50 μl of transposition mix [25 μl of 2× TD buffer (Illumina), 2.5 μl of transposase (Illumina), 16.5 μl of 1× PBS, 0.5 μl of 1% digitonin, 0.5 μl of 10% Tween 20, and 5 μl of water) at 37°C for 30 min in a thermomixer with shaking at 1000 rpm. .. Transposed DNA was collected using the Zymo ChIP DNA Clean and Concentrator (Zymo Research) according to the manufacturer’s instructions and added to the PCR mix containing 25 μl of 2× NEBNext Master Mix (NEB) and 2.5 μl of Index adapters (Illumina). .. Transposition was carried out in 50 μl of transposition mix [25 μl of 2× TD buffer (Illumina), 2.5 μl of transposase (Illumina), 16.5 μl of 1× PBS, 0.5 μl of 1% digitonin, 0.5 μl of 10% Tween 20, and 5 μl of water) at 37°C for 30 min in a thermomixer with shaking at 1000 rpm.

    Article Title: Stage-specific epigenetic priming amplifies gene activation during lineage commitment
    Article Snippet: .. DNA was isolated using Zymo ChIP DNA Clean and Concentrator (Zymo Research) according to the manufacturer’s instructions. .. CUT&RUN Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (Illumina), with minor modifications, as the end prep step was extended to 30 min at 20°C and 60 min at 50°C.

    Purification:

    Article Title: H3.1K27M-induced misregulation of the TONSOKU-H3.1 pathway causes genomic instability
    Article Snippet: .. After uncrosslinking, samples were treated with proteinase K and purified using ChIP DNA Clean and Concentrator (Zymo Research, Irvine, CA). .. ChIP sequencing libraries were prepared at the YCGA with a TruSeq Library Prep Kit (Illumina, San Diego, CA).

    Article Title: H3.1K27M-induced misregulation of the TONSOKU-H3.1 pathway causes genomic instability.
    Article Snippet: .. After uncrosslinking, samples were treated with proteinase K and purified using ChIP DNA Clean and Concentrator (Zymo Research, Irvine, CA). .. ChIP sequencing libraries were prepared at the YCGA with a TruSeq Library Prep Kit (Illumina, San Diego, CA).

    Article Title: The DLX/Notch axis is necessary for spatiotemporal regulation of neural cell fate
    Article Snippet: Eluted fragments were incubated with 0.01M EDTA, 0.04M Tri-HCl, pH 7.4, 0.1 mg/mL Proteinase K (Promega Cat# MC5008) at 50°C for 2 hours for crosslinking reversal. .. The eluted DNA fragments were purified using the ChIP DNA Clean and Concentrator (Zymo Research Cat# D5205) according to the manufacturer’s instructions. ..

    Incubation:

    Article Title: Conserved HSFA1-dependent chromatin dynamics drive heat stress responses in plants.
    Article Snippet: The nuclei were then pelleted by centrifugation at 1000 × g for 10 min at 4 ◦ C. The sorted nuclei were resuspended in a 50 μL tagmentation reaction mixture consisting of 25 μL of 2x TD buffer, 2.5 μL of TDE1 enzyme (Illumina Tagment DNA TDE1 Enzyme and Buffer Kits), and 22.5 μL of nuclease-free water. .. The reaction was incubated at 37 ◦ C for 30 min, followed by DNA purification with Zymo CHIP DNA Clean and Concentrator (Cat# D5205). .. The eluted DNA was amplified with dual-indexed Nextera primers using NEBNext 2x HiFi PCR Master Mix (New England Biolabs) for library construction.

    DNA Purification:

    Article Title: Conserved HSFA1-dependent chromatin dynamics drive heat stress responses in plants.
    Article Snippet: The nuclei were then pelleted by centrifugation at 1000 × g for 10 min at 4 ◦ C. The sorted nuclei were resuspended in a 50 μL tagmentation reaction mixture consisting of 25 μL of 2x TD buffer, 2.5 μL of TDE1 enzyme (Illumina Tagment DNA TDE1 Enzyme and Buffer Kits), and 22.5 μL of nuclease-free water. .. The reaction was incubated at 37 ◦ C for 30 min, followed by DNA purification with Zymo CHIP DNA Clean and Concentrator (Cat# D5205). .. The eluted DNA was amplified with dual-indexed Nextera primers using NEBNext 2x HiFi PCR Master Mix (New England Biolabs) for library construction.

    other:

    Article Title: Stage-specific epigenetic priming amplifies gene activation during lineage commitment.
    Article Snippet: Two million to 4 million cells were resuspended in 1 ml of lysis buffer [10 mM tris- HCl (pH 8), 10 mM NaCl, and 0.2% Igepal CA- 630], and nuclei were extracted via sonication using a Covaris E220 sonicator (75- W peak incident power, 2% duty factor, 200 cycles per burst, and 45 s).

    Polymerase Chain Reaction:

    Article Title: Stage-specific epigenetic priming amplifies gene activation during lineage commitment
    Article Snippet: Transposition was carried out in 50 μl of transposition mix [25 μl of 2× TD buffer (Illumina), 2.5 μl of transposase (Illumina), 16.5 μl of 1× PBS, 0.5 μl of 1% digitonin, 0.5 μl of 10% Tween 20, and 5 μl of water) at 37°C for 30 min in a thermomixer with shaking at 1000 rpm. .. Transposed DNA was collected using the Zymo ChIP DNA Clean and Concentrator (Zymo Research) according to the manufacturer’s instructions and added to the PCR mix containing 25 μl of 2× NEBNext Master Mix (NEB) and 2.5 μl of Index adapters (Illumina). .. Transposition was carried out in 50 μl of transposition mix [25 μl of 2× TD buffer (Illumina), 2.5 μl of transposase (Illumina), 16.5 μl of 1× PBS, 0.5 μl of 1% digitonin, 0.5 μl of 10% Tween 20, and 5 μl of water) at 37°C for 30 min in a thermomixer with shaking at 1000 rpm.



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    Zymo Research chip dna
    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 <t>ChIP-seq</t> 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 <t>DNA</t> 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.
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    Image Search Results


    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.

    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

    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.

    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