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chip dna binding buffer  (Zymo Research)


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    Structured Review

    Zymo Research chip dna binding buffer
    Chip Dna Binding Buffer, supplied by Zymo Research, used in various techniques. Bioz Stars score: 93/100, based on 17 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/oligonucleotide+microarray+experiments/ChIP+DNA+Binding+Buffer/pmc07052505-67-5-4
    Average 93 stars, based on 17 article reviews
    chip dna binding buffer - by Bioz Stars, 2026-10
    93/100 stars

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    Related Articles

    Incubation:

    Article Title: Enhanced oligonucleotides for inhibiting RTEL1 expression
    Article Snippet: Samples were thawed at 37° C. and 1 μl of Proteinase K (cat no. AM25448 @ Ambion biosciences, 20 mg/mL Stock) was added to each well of the 96-well plate and samples were incubated at 56° C. for 30 minutes. .. After incubation, 3 volumes of ChIP DNA binding buffer from ZYMO Research Genomic DNA Clean & Concentrator kit (ZymoResearch, cat no. D4067) were added and DNA was purified following the manufacturer's protocol. ..

    Chromatin Immunoprecipitation:

    Article Title: Enhanced oligonucleotides for inhibiting RTEL1 expression
    Article Snippet: Samples were thawed at 37° C. and 1 μl of Proteinase K (cat no. AM25448 @ Ambion biosciences, 20 mg/mL Stock) was added to each well of the 96-well plate and samples were incubated at 56° C. for 30 minutes. .. After incubation, 3 volumes of ChIP DNA binding buffer from ZYMO Research Genomic DNA Clean & Concentrator kit (ZymoResearch, cat no. D4067) were added and DNA was purified following the manufacturer's protocol. ..

    Article Title: Precise modulation of transcription factor levels identifies features underlying dosage sensitivity
    Article Snippet: .. ChIP and input samples were purified by Zymo DNA Clean & Concentrator Kit with ChIP DNA binding buffer. .. For library preparation, samples were quantified by Qubit dsDNA HS assay kit, and 10–50 ng of ChIP DNA was used for library preparation with end repair, A-tailing and adaptor ligation (NEB).

    Article Title: High-throughput library transgenesis in Caenorhabditis elegans via Transgenic Arrays Resulting in Diversity of Integrated Sequences (TARDIS)
    Article Snippet: .. ChIP DNA binding buffer (Zymo, CA) was added in a 2:1 ratio and gently inverted to mix. .. Samples were then purified with Zymo- Spin IIC- XLR columns following the manufacturer’s protocol.

    Article Title: High-throughput library transgenesis in Caenorhabditis elegans via Transgenic Arrays Resulting in Diversity of Integrated Sequences (TARDIS)
    Article Snippet: Each sample was then digested with 10 mg/ml RNase A (Thermo Fisher Scientific, MA, Cat# EN0531) at 42°C for 2 hr. .. Genomic DNA was then reisolated by adding a 2:1 ratio of ChIP DNA binding buffer and purifying with Zymo- Spin IIC- XLR columns. ..

    Article Title: Restriction Endonuclease-Based Modification-Dependent Enrichment (REMoDE) of DNA for Metagenomic Sequencing.
    Article Snippet: For the experiment in Fig. 3B, the same protocol was followed as in Fig. 3A except after the EcoRII incubation, 8 mL of NEB purple loading dye was added and the samples were loaded into a 1% agarose gel and run for 45 min at 120 V. The high-molecular-weight bands were excised with a razor and dissolved in 3 volumes of Zymo agarose dissolving buffer (Zymo D4001) at 50°C. .. They were then processed January 2023 Volume 89 Issue 1 10.1128/aem.01670-22 12 D ow nl oa de d fr om h ttp s: //j ou rn al s. as m .o rg /jo ur na l/a em o n 19 J ul y 20 23 b y 2a 0d :6 fc 0: 89 b: ae 00 :e d1 c: 28 2f :f 10 0: a6 72 . through the Zymo genomic clean and concentrate kit as in Fig. 3A excluding the step of the addition of chromatin immunoprecipitation (ChIP) DNA binding buffer. ..

    Binding Assay:

    Article Title: Enhanced oligonucleotides for inhibiting RTEL1 expression
    Article Snippet: Samples were thawed at 37° C. and 1 μl of Proteinase K (cat no. AM25448 @ Ambion biosciences, 20 mg/mL Stock) was added to each well of the 96-well plate and samples were incubated at 56° C. for 30 minutes. .. After incubation, 3 volumes of ChIP DNA binding buffer from ZYMO Research Genomic DNA Clean & Concentrator kit (ZymoResearch, cat no. D4067) were added and DNA was purified following the manufacturer's protocol. ..

    Article Title: High-Throughput Library Transgenesis in Caenorhabditis elegans via Transgenic Arrays Resulting in Diversity of Integrated Sequences (TARDIS)
    Article Snippet: Each sample was then digested with 10mg/ml RNase A (ThermoFisher Scientific Massachussets, USA, Cat. No. EN0531) at 42C° for 2 hours. .. Genomic DNA was then reisolated by adding a 2:1 ratio of Chip DNA binding buffer and purifying with Zymo-Spin IIC-XLR columns. ..

    Article Title: High-Throughput Library Transgenesis in Caenorhabditis elegans via Transgenic Arrays Resulting in Diversity of Integrated Sequences (TARDIS)
    Article Snippet: .. Chip DNA binding buffer (Zymo, California, USA) was added in a 2:1 ratio and gently inverted to mix. .. Samples were then purified with Zymo-Spin IIC-XLR columns following manufacture protocol.

    Article Title: Precise modulation of transcription factor levels identifies features underlying dosage sensitivity
    Article Snippet: .. ChIP and input samples were purified by Zymo DNA Clean & Concentrator Kit with ChIP DNA binding buffer. .. For library preparation, samples were quantified by Qubit dsDNA HS assay kit, and 10–50 ng of ChIP DNA was used for library preparation with end repair, A-tailing and adaptor ligation (NEB).

    Article Title: High-throughput library transgenesis in Caenorhabditis elegans via Transgenic Arrays Resulting in Diversity of Integrated Sequences (TARDIS)
    Article Snippet: .. ChIP DNA binding buffer (Zymo, CA) was added in a 2:1 ratio and gently inverted to mix. .. Samples were then purified with Zymo- Spin IIC- XLR columns following the manufacturer’s protocol.

    Article Title: High-throughput library transgenesis in Caenorhabditis elegans via Transgenic Arrays Resulting in Diversity of Integrated Sequences (TARDIS)
    Article Snippet: Each sample was then digested with 10 mg/ml RNase A (Thermo Fisher Scientific, MA, Cat# EN0531) at 42°C for 2 hr. .. Genomic DNA was then reisolated by adding a 2:1 ratio of ChIP DNA binding buffer and purifying with Zymo- Spin IIC- XLR columns. ..

    Article Title: Restriction Endonuclease-Based Modification-Dependent Enrichment (REMoDE) of DNA for Metagenomic Sequencing.
    Article Snippet: For the experiment in Fig. 3B, the same protocol was followed as in Fig. 3A except after the EcoRII incubation, 8 mL of NEB purple loading dye was added and the samples were loaded into a 1% agarose gel and run for 45 min at 120 V. The high-molecular-weight bands were excised with a razor and dissolved in 3 volumes of Zymo agarose dissolving buffer (Zymo D4001) at 50°C. .. They were then processed January 2023 Volume 89 Issue 1 10.1128/aem.01670-22 12 D ow nl oa de d fr om h ttp s: //j ou rn al s. as m .o rg /jo ur na l/a em o n 19 J ul y 20 23 b y 2a 0d :6 fc 0: 89 b: ae 00 :e d1 c: 28 2f :f 10 0: a6 72 . through the Zymo genomic clean and concentrate kit as in Fig. 3A excluding the step of the addition of chromatin immunoprecipitation (ChIP) DNA binding buffer. ..

    Purification:

    Article Title: Enhanced oligonucleotides for inhibiting RTEL1 expression
    Article Snippet: Samples were thawed at 37° C. and 1 μl of Proteinase K (cat no. AM25448 @ Ambion biosciences, 20 mg/mL Stock) was added to each well of the 96-well plate and samples were incubated at 56° C. for 30 minutes. .. After incubation, 3 volumes of ChIP DNA binding buffer from ZYMO Research Genomic DNA Clean & Concentrator kit (ZymoResearch, cat no. D4067) were added and DNA was purified following the manufacturer's protocol. ..

    Article Title: Precise modulation of transcription factor levels identifies features underlying dosage sensitivity
    Article Snippet: .. ChIP and input samples were purified by Zymo DNA Clean & Concentrator Kit with ChIP DNA binding buffer. .. For library preparation, samples were quantified by Qubit dsDNA HS assay kit, and 10–50 ng of ChIP DNA was used for library preparation with end repair, A-tailing and adaptor ligation (NEB).



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    Image Search Results


    A) The stacked bar chart represents a summary of total upregulated (red) and downregulated (green) genes representing 22 important signaling and disease pathways in AD subjects compared to controls. The output core analysis, reflecting the differential gene expressions obtained from the microarrays (gene sets with≥2-fold change, t -test, p < 0.05). B) Ingenuity Pathway Analysis (IPA)-derived Amyloid Processing network of differentially expressed genes derived from microarray analysis. IPA analysis identified a group of genes expression status and their potential interactive links in the context of Amyloid Processing, Neuronal Death. We noted activation of Gamma Secretase, Beta Secretase, upregulation of ERK1/2 CK1/2 P38MAPK, PKA, PRKCE, CDK5 , and CDK5R1 and downregulation of MAPT , and GSK3B .

    Journal: Journal of Alzheimer's Disease Reports

    Article Title: Transcriptomic Analysis of Alzheimer’s Disease Pathways in a Pakistani Population 1

    doi: 10.3233/ADR-230146

    Figure Lengend Snippet: A) The stacked bar chart represents a summary of total upregulated (red) and downregulated (green) genes representing 22 important signaling and disease pathways in AD subjects compared to controls. The output core analysis, reflecting the differential gene expressions obtained from the microarrays (gene sets with≥2-fold change, t -test, p < 0.05). B) Ingenuity Pathway Analysis (IPA)-derived Amyloid Processing network of differentially expressed genes derived from microarray analysis. IPA analysis identified a group of genes expression status and their potential interactive links in the context of Amyloid Processing, Neuronal Death. We noted activation of Gamma Secretase, Beta Secretase, upregulation of ERK1/2 CK1/2 P38MAPK, PKA, PRKCE, CDK5 , and CDK5R1 and downregulation of MAPT , and GSK3B .

    Article Snippet: The oligonucleotide microarray experiments were conducted by EpigenDx (Boston, MA) using the Affymetrix U133 Plus 2.0 Array platform, which has comprehensive coverage of the whole transcribed human genome on a single array.

    Techniques: Derivative Assay, Microarray, Expressing, Activation Assay

    Comparison of transcript quantification by Affymetrix microarray with real time RT-PCR. A 200 ng aliquot total RNA from dDAVP- and vehicle-exposed mpkCCD cells was used for quantification of transcript abundances with real time RT-PCR. *, statistically significant versus no change i.e. log2(dDAVP/vehicle) = 0 (p < 0.05, n = 3). The RefSeq accession numbers are: Akap12, NM_031185; Aqp2, NM_009699; Asap2, NM_001004364; C3, NM_009778; Clmn, NM_001040682; Cpt1a, NM_013495; Fth1, NM_010239; Gsdmc1, NM_031378; Gsdmc2, NM_177912; Gsdmc4, XM_001474104; Gstt3, NM_133994; Idh1, NM_001111320; Mon2, NM_153395; Osbpl1a, NM_207530; Spnb3, NM_021287; and Trip11, XM_001001171.

    Journal: Molecular & Cellular Proteomics : MCP

    Article Title: Quantitative Protein and mRNA Profiling Shows Selective Post-Transcriptional Control of Protein Expression by Vasopressin in Kidney Cells *

    doi: 10.1074/mcp.M110.004036

    Figure Lengend Snippet: Comparison of transcript quantification by Affymetrix microarray with real time RT-PCR. A 200 ng aliquot total RNA from dDAVP- and vehicle-exposed mpkCCD cells was used for quantification of transcript abundances with real time RT-PCR. *, statistically significant versus no change i.e. log2(dDAVP/vehicle) = 0 (p < 0.05, n = 3). The RefSeq accession numbers are: Akap12, NM_031185; Aqp2, NM_009699; Asap2, NM_001004364; C3, NM_009778; Clmn, NM_001040682; Cpt1a, NM_013495; Fth1, NM_010239; Gsdmc1, NM_031378; Gsdmc2, NM_177912; Gsdmc4, XM_001474104; Gstt3, NM_133994; Idh1, NM_001111320; Mon2, NM_153395; Osbpl1a, NM_207530; Spnb3, NM_021287; and Trip11, XM_001001171.

    Article Snippet: To address whether changes in protein abundance measured by SILAC LC-MS/MS are generally because of corresponding changes in mRNA levels, we carried out oligonucleotide microarray experiments (Affymetrix) in mpkCCD cells treated in the same manner (0.1 n m dDAVP or vehicle for 5 days).

    Techniques: Microarray, Quantitative RT-PCR