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    Zymo Research zymo dna clean
    ( A ) Workflow of <t>DNA</t> O-MAP integrated with sample multiplexing quantitative proteomics. ( B ) Schematic of the three DNA loci examined in the TMT16plex experiment: pericentromeric alpha satellites, telomeres, and mitochondrial genomes. ( C ) Co-localization of DNA fluorescent in situ hybridization (FISH) and the streptavidin staining of the proteins biotinylated by DNA O-MAP targeting the pericentromeric alpha satellites, telomeres, and mitochondrial genomes. Scale bar: 5 µm. ( D ) Principal component analysis of scaled intensities of proteins enriched by the pan-alpha probe, telomere probe, mitochondrial <t>genome</t> <t>oligo</t> pool, and no-primary-probe control. ( E ) Unsupervised hierarchical clustering of scaled intensities of proteins enriched by the pan-alpha probe, telomere probe, mitochondrial genome oligo pool, and no-primary-probe control. ( F ) Log 2 fold change of proteins compared to no-primary-probe control, grouped by HPA subcellular location. Significance calculated based on Welch’s t -test for pairwise comparisons (****p-value <0.0001). Log 2 fold change of proteins compared to mitochondrial probe enriched proteins for the RNA Polymerases ( G ), mtDNA nucleoid packaging proteins ( H ), Shelterin ( I ), and CENP-A nucleosomal complexes ( J ). Significance calculated based on Welch’s t -test for pairwise comparisons (p-value: *<0.05, **<0.01, ***<0.001, ****<0.0001).
    Zymo Dna Clean, supplied by Zymo Research, used in various techniques. Bioz Stars score: 95/100, based on 172 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/dna+clean+concentrator+100/DNA+Clean+%26+Concentrator-100/pmc13056364-243-7-7
    Average 95 stars, based on 172 article reviews
    zymo dna clean - by Bioz Stars, 2026-11
    95/100 stars

    Images

    1) Product Images from "DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci"

    Article Title: DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci

    Journal: eLife

    doi: 10.7554/eLife.102489

    ( A ) Workflow of DNA O-MAP integrated with sample multiplexing quantitative proteomics. ( B ) Schematic of the three DNA loci examined in the TMT16plex experiment: pericentromeric alpha satellites, telomeres, and mitochondrial genomes. ( C ) Co-localization of DNA fluorescent in situ hybridization (FISH) and the streptavidin staining of the proteins biotinylated by DNA O-MAP targeting the pericentromeric alpha satellites, telomeres, and mitochondrial genomes. Scale bar: 5 µm. ( D ) Principal component analysis of scaled intensities of proteins enriched by the pan-alpha probe, telomere probe, mitochondrial genome oligo pool, and no-primary-probe control. ( E ) Unsupervised hierarchical clustering of scaled intensities of proteins enriched by the pan-alpha probe, telomere probe, mitochondrial genome oligo pool, and no-primary-probe control. ( F ) Log 2 fold change of proteins compared to no-primary-probe control, grouped by HPA subcellular location. Significance calculated based on Welch’s t -test for pairwise comparisons (****p-value <0.0001). Log 2 fold change of proteins compared to mitochondrial probe enriched proteins for the RNA Polymerases ( G ), mtDNA nucleoid packaging proteins ( H ), Shelterin ( I ), and CENP-A nucleosomal complexes ( J ). Significance calculated based on Welch’s t -test for pairwise comparisons (p-value: *<0.05, **<0.01, ***<0.001, ****<0.0001).
    Figure Legend Snippet: ( A ) Workflow of DNA O-MAP integrated with sample multiplexing quantitative proteomics. ( B ) Schematic of the three DNA loci examined in the TMT16plex experiment: pericentromeric alpha satellites, telomeres, and mitochondrial genomes. ( C ) Co-localization of DNA fluorescent in situ hybridization (FISH) and the streptavidin staining of the proteins biotinylated by DNA O-MAP targeting the pericentromeric alpha satellites, telomeres, and mitochondrial genomes. Scale bar: 5 µm. ( D ) Principal component analysis of scaled intensities of proteins enriched by the pan-alpha probe, telomere probe, mitochondrial genome oligo pool, and no-primary-probe control. ( E ) Unsupervised hierarchical clustering of scaled intensities of proteins enriched by the pan-alpha probe, telomere probe, mitochondrial genome oligo pool, and no-primary-probe control. ( F ) Log 2 fold change of proteins compared to no-primary-probe control, grouped by HPA subcellular location. Significance calculated based on Welch’s t -test for pairwise comparisons (****p-value <0.0001). Log 2 fold change of proteins compared to mitochondrial probe enriched proteins for the RNA Polymerases ( G ), mtDNA nucleoid packaging proteins ( H ), Shelterin ( I ), and CENP-A nucleosomal complexes ( J ). Significance calculated based on Welch’s t -test for pairwise comparisons (p-value: *<0.05, **<0.01, ***<0.001, ****<0.0001).

    Techniques Used: Multiplexing, Quantitative Proteomics, In Situ Hybridization, Staining, Control

    Related Articles

    Polymerase Chain Reaction:

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    Article Snippet: In brief Zhao et al. uncovered a nuclear-restricted acetyl-CoA regulatory mechanism where nucleus-localized pyruvate dehydrogenase complex (nPDC) is constitutively bound and repressed by nuclear protein ELMSAN1.. Pharmacological disruption of the ELMSAN1-nPDC interaction derepresses nPDC activity, synergizes with HDAC1/2 inhibitors, and therapeutically reprograms diverse cancer types to durably lose proliferation, stemness, and cell-of-origin identity.. Pyruvate

    Article Title: Differentiation stage-specific use of cap-independent and cap-dependent translation initiation in hematopoiesis
    Article Snippet: Genomic DNA was isolated using NucleoSpin Blood Maxi kit (Macherey-Nagel, 740950). .. Next, sgRNA target regions were PCR amplified with Illumina adaptors and indexes using Ultra II Q5 (NEB Biolabs, M0544X) and products were purified with DNA Clean & Concentrator-100 (Zymo Research, D4030). sgRNA target regions (260-280bp) were further enriched by gel extraction (Qiagen, 28704) after running agarose gel. .. Purified PCR products were measured by Qubit and analyzed by TapeStation before sending for next-generation sequencing on Illumina NextSeq 2000.

    Amplification:

    Article Title: Derepressing nuclear pyruvate dehydrogenase induces therapeutic cancer cell reprogramming.
    Article Snippet: In brief Zhao et al. uncovered a nuclear-restricted acetyl-CoA regulatory mechanism where nucleus-localized pyruvate dehydrogenase complex (nPDC) is constitutively bound and repressed by nuclear protein ELMSAN1.. Pharmacological disruption of the ELMSAN1-nPDC interaction derepresses nPDC activity, synergizes with HDAC1/2 inhibitors, and therapeutically reprograms diverse cancer types to durably lose proliferation, stemness, and cell-of-origin identity.. Pyruvate

    Article Title: Differentiation stage-specific use of cap-independent and cap-dependent translation initiation in hematopoiesis
    Article Snippet: Genomic DNA was isolated using NucleoSpin Blood Maxi kit (Macherey-Nagel, 740950). .. Next, sgRNA target regions were PCR amplified with Illumina adaptors and indexes using Ultra II Q5 (NEB Biolabs, M0544X) and products were purified with DNA Clean & Concentrator-100 (Zymo Research, D4030). sgRNA target regions (260-280bp) were further enriched by gel extraction (Qiagen, 28704) after running agarose gel. .. Purified PCR products were measured by Qubit and analyzed by TapeStation before sending for next-generation sequencing on Illumina NextSeq 2000.

    Purification:

    Article Title: Derepressing nuclear pyruvate dehydrogenase induces therapeutic cancer cell reprogramming.
    Article Snippet: In brief Zhao et al. uncovered a nuclear-restricted acetyl-CoA regulatory mechanism where nucleus-localized pyruvate dehydrogenase complex (nPDC) is constitutively bound and repressed by nuclear protein ELMSAN1.. Pharmacological disruption of the ELMSAN1-nPDC interaction derepresses nPDC activity, synergizes with HDAC1/2 inhibitors, and therapeutically reprograms diverse cancer types to durably lose proliferation, stemness, and cell-of-origin identity.. Pyruvate

    Article Title: Differentiation stage-specific use of cap-independent and cap-dependent translation initiation in hematopoiesis
    Article Snippet: Genomic DNA was isolated using NucleoSpin Blood Maxi kit (Macherey-Nagel, 740950). .. Next, sgRNA target regions were PCR amplified with Illumina adaptors and indexes using Ultra II Q5 (NEB Biolabs, M0544X) and products were purified with DNA Clean & Concentrator-100 (Zymo Research, D4030). sgRNA target regions (260-280bp) were further enriched by gel extraction (Qiagen, 28704) after running agarose gel. .. Purified PCR products were measured by Qubit and analyzed by TapeStation before sending for next-generation sequencing on Illumina NextSeq 2000.

    Article Title: High-throughput transcriptomic screening reveals entrectinib as a repositioning opportunity in 19q12 autism spectrum disorder.
    Article Snippet: Using an Echo 650 Liquid Handler (Beckman Coulter), barcoded RT primers were dispensed into each well. .. Plates were incubated at 42 °C for 2 h. Following RT, each well was pooled into a single tube and purified using DNA Clean & Concentrator-100 (Zymo Research) followed by concentration with Agencourt RNAClean XP beads (Beckman Coulter). .. Single-stranded DNA was removed by incubating cDNA with Exonuclease I (New England Biolabs) followed by pre-amplification of the cDNA with DRUG-seq PCR primers. cDNA was fragmented and tagged with Illumina sequencing adapters using Tagmentation DNA Enzyme (TDE1).

    Article Title: Methods for treating neurodevelopmental disorders via administration of organic tricyclic compounds
    Article Snippet: .. Following RT, each well was pooled into a single tube and purified using DNA Clean & Concentrator-100 (Zymo Research) followed by concentration with Agencourt RNAClean XP beads (Beckman Coulter). .. Single-stranded DNA was removed by incubating cDNA with Exonuclease I (New England Biolabs) followed by pre-amplification of the cDNA with DRUG-seq PCR primers. cDNA was fragmented and tagged with Illumina sequencing adapters using Tagmentation DNA Enzyme (TDE1).

    Article Title: High-throughput transcriptomic screening reveals entrectinib as a repositioning opportunity in 19q12 autism spectrum disorder
    Article Snippet: Using an Echo 650 Liquid Handler (Beckman Coulter), barcoded RT primers were dispensed into each well. .. Plates were incubated at 42 °C for 2 h. Following RT, each well was pooled into a single tube and purified using DNA Clean & Concentrator-100 (Zymo Research) followed by concentration with Agencourt RNAClean XP beads (Beckman Coulter). .. Single-stranded DNA was removed by incubating cDNA with Exonuclease I (New England Biolabs) followed by pre-amplification of the cDNA with DRUG-seq PCR primers. cDNA was fragmented and tagged with Illumina sequencing adapters using Tagmentation DNA Enzyme (TDE1).

    Article Title: Lineage-determining transcription factors constrain cohesin to drive multi-enhancer oncogene regulation
    Article Snippet: Reverse transcription was performed with maxima RT-H (Thermo, cat. no. EP0751) at 50 °C with universal forward primer for 2.5 h, and EDTA/NaOH was added to remove RNA at 92 °C for 10 min. .. Finally, ssDNA was purified with Zymo DNA Clean & Concentrator-100 (cat. no. D4030), SpeedVac dried and resuspended in molecular grade water to 50 μM. .. The 40-mm round, glass coverslips (Bioptechs, cat. no. 10200–064) were coated with 0.01% poly-L-lysine (Sigma-Aldrich, cat. no. P4832) for 15 min at room temperature.

    Gel Extraction:

    Article Title: Derepressing nuclear pyruvate dehydrogenase induces therapeutic cancer cell reprogramming.
    Article Snippet: In brief Zhao et al. uncovered a nuclear-restricted acetyl-CoA regulatory mechanism where nucleus-localized pyruvate dehydrogenase complex (nPDC) is constitutively bound and repressed by nuclear protein ELMSAN1.. Pharmacological disruption of the ELMSAN1-nPDC interaction derepresses nPDC activity, synergizes with HDAC1/2 inhibitors, and therapeutically reprograms diverse cancer types to durably lose proliferation, stemness, and cell-of-origin identity.. Pyruvate

    Article Title: Differentiation stage-specific use of cap-independent and cap-dependent translation initiation in hematopoiesis
    Article Snippet: Genomic DNA was isolated using NucleoSpin Blood Maxi kit (Macherey-Nagel, 740950). .. Next, sgRNA target regions were PCR amplified with Illumina adaptors and indexes using Ultra II Q5 (NEB Biolabs, M0544X) and products were purified with DNA Clean & Concentrator-100 (Zymo Research, D4030). sgRNA target regions (260-280bp) were further enriched by gel extraction (Qiagen, 28704) after running agarose gel. .. Purified PCR products were measured by Qubit and analyzed by TapeStation before sending for next-generation sequencing on Illumina NextSeq 2000.

    Agarose Gel Electrophoresis:

    Article Title: Derepressing nuclear pyruvate dehydrogenase induces therapeutic cancer cell reprogramming.
    Article Snippet: In brief Zhao et al. uncovered a nuclear-restricted acetyl-CoA regulatory mechanism where nucleus-localized pyruvate dehydrogenase complex (nPDC) is constitutively bound and repressed by nuclear protein ELMSAN1.. Pharmacological disruption of the ELMSAN1-nPDC interaction derepresses nPDC activity, synergizes with HDAC1/2 inhibitors, and therapeutically reprograms diverse cancer types to durably lose proliferation, stemness, and cell-of-origin identity.. Pyruvate

    Article Title: Differentiation stage-specific use of cap-independent and cap-dependent translation initiation in hematopoiesis
    Article Snippet: Genomic DNA was isolated using NucleoSpin Blood Maxi kit (Macherey-Nagel, 740950). .. Next, sgRNA target regions were PCR amplified with Illumina adaptors and indexes using Ultra II Q5 (NEB Biolabs, M0544X) and products were purified with DNA Clean & Concentrator-100 (Zymo Research, D4030). sgRNA target regions (260-280bp) were further enriched by gel extraction (Qiagen, 28704) after running agarose gel. .. Purified PCR products were measured by Qubit and analyzed by TapeStation before sending for next-generation sequencing on Illumina NextSeq 2000.

    Incubation:

    Article Title: High-throughput transcriptomic screening reveals entrectinib as a repositioning opportunity in 19q12 autism spectrum disorder.
    Article Snippet: Using an Echo 650 Liquid Handler (Beckman Coulter), barcoded RT primers were dispensed into each well. .. Plates were incubated at 42 °C for 2 h. Following RT, each well was pooled into a single tube and purified using DNA Clean & Concentrator-100 (Zymo Research) followed by concentration with Agencourt RNAClean XP beads (Beckman Coulter). .. Single-stranded DNA was removed by incubating cDNA with Exonuclease I (New England Biolabs) followed by pre-amplification of the cDNA with DRUG-seq PCR primers. cDNA was fragmented and tagged with Illumina sequencing adapters using Tagmentation DNA Enzyme (TDE1).

    Article Title: High-throughput transcriptomic screening reveals entrectinib as a repositioning opportunity in 19q12 autism spectrum disorder
    Article Snippet: Using an Echo 650 Liquid Handler (Beckman Coulter), barcoded RT primers were dispensed into each well. .. Plates were incubated at 42 °C for 2 h. Following RT, each well was pooled into a single tube and purified using DNA Clean & Concentrator-100 (Zymo Research) followed by concentration with Agencourt RNAClean XP beads (Beckman Coulter). .. Single-stranded DNA was removed by incubating cDNA with Exonuclease I (New England Biolabs) followed by pre-amplification of the cDNA with DRUG-seq PCR primers. cDNA was fragmented and tagged with Illumina sequencing adapters using Tagmentation DNA Enzyme (TDE1).

    Concentration Assay:

    Article Title: High-throughput transcriptomic screening reveals entrectinib as a repositioning opportunity in 19q12 autism spectrum disorder.
    Article Snippet: Using an Echo 650 Liquid Handler (Beckman Coulter), barcoded RT primers were dispensed into each well. .. Plates were incubated at 42 °C for 2 h. Following RT, each well was pooled into a single tube and purified using DNA Clean & Concentrator-100 (Zymo Research) followed by concentration with Agencourt RNAClean XP beads (Beckman Coulter). .. Single-stranded DNA was removed by incubating cDNA with Exonuclease I (New England Biolabs) followed by pre-amplification of the cDNA with DRUG-seq PCR primers. cDNA was fragmented and tagged with Illumina sequencing adapters using Tagmentation DNA Enzyme (TDE1).

    Article Title: Methods for treating neurodevelopmental disorders via administration of organic tricyclic compounds
    Article Snippet: .. Following RT, each well was pooled into a single tube and purified using DNA Clean & Concentrator-100 (Zymo Research) followed by concentration with Agencourt RNAClean XP beads (Beckman Coulter). .. Single-stranded DNA was removed by incubating cDNA with Exonuclease I (New England Biolabs) followed by pre-amplification of the cDNA with DRUG-seq PCR primers. cDNA was fragmented and tagged with Illumina sequencing adapters using Tagmentation DNA Enzyme (TDE1).

    Article Title: High-throughput transcriptomic screening reveals entrectinib as a repositioning opportunity in 19q12 autism spectrum disorder
    Article Snippet: Using an Echo 650 Liquid Handler (Beckman Coulter), barcoded RT primers were dispensed into each well. .. Plates were incubated at 42 °C for 2 h. Following RT, each well was pooled into a single tube and purified using DNA Clean & Concentrator-100 (Zymo Research) followed by concentration with Agencourt RNAClean XP beads (Beckman Coulter). .. Single-stranded DNA was removed by incubating cDNA with Exonuclease I (New England Biolabs) followed by pre-amplification of the cDNA with DRUG-seq PCR primers. cDNA was fragmented and tagged with Illumina sequencing adapters using Tagmentation DNA Enzyme (TDE1).

    other:

    Article Title: Lineage-determining transcription factors constrain cohesin to drive multi-enhancer oncogene regulation
    Article Snippet: Reverse transcription was performed with maxima RT-H (Thermo cat# EP0751) at 50 °C with universal forward primer for 2.5 hours, and EDTA/NaOH were added to remove RNA at 92 °C for 10 min.

    Article Title: Lineage-determining transcription factors constrain cohesin to drive multi-enhancer oncogene regulation.
    Article Snippet: Multiple enhancers, often separated by vast genomic distances, regulate key genes.. However, how the folding of individual chromatin fibres enables cell-type-restricted multi-enhancer regulation remains unclear.. Here, using acute protein degradation and time-resolved chromatin conformation capture in mantle cell lymphoma, we found that the B cell-lineage-determining factor EBF1 organizes multiple enhancers around sparsely distributed genes essential for B cell identity and oncogenesis.



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    Image Search Results


    ( A ) Workflow of DNA O-MAP integrated with sample multiplexing quantitative proteomics. ( B ) Schematic of the three DNA loci examined in the TMT16plex experiment: pericentromeric alpha satellites, telomeres, and mitochondrial genomes. ( C ) Co-localization of DNA fluorescent in situ hybridization (FISH) and the streptavidin staining of the proteins biotinylated by DNA O-MAP targeting the pericentromeric alpha satellites, telomeres, and mitochondrial genomes. Scale bar: 5 µm. ( D ) Principal component analysis of scaled intensities of proteins enriched by the pan-alpha probe, telomere probe, mitochondrial genome oligo pool, and no-primary-probe control. ( E ) Unsupervised hierarchical clustering of scaled intensities of proteins enriched by the pan-alpha probe, telomere probe, mitochondrial genome oligo pool, and no-primary-probe control. ( F ) Log 2 fold change of proteins compared to no-primary-probe control, grouped by HPA subcellular location. Significance calculated based on Welch’s t -test for pairwise comparisons (****p-value <0.0001). Log 2 fold change of proteins compared to mitochondrial probe enriched proteins for the RNA Polymerases ( G ), mtDNA nucleoid packaging proteins ( H ), Shelterin ( I ), and CENP-A nucleosomal complexes ( J ). Significance calculated based on Welch’s t -test for pairwise comparisons (p-value: *<0.05, **<0.01, ***<0.001, ****<0.0001).

    Journal: eLife

    Article Title: DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci

    doi: 10.7554/eLife.102489

    Figure Lengend Snippet: ( A ) Workflow of DNA O-MAP integrated with sample multiplexing quantitative proteomics. ( B ) Schematic of the three DNA loci examined in the TMT16plex experiment: pericentromeric alpha satellites, telomeres, and mitochondrial genomes. ( C ) Co-localization of DNA fluorescent in situ hybridization (FISH) and the streptavidin staining of the proteins biotinylated by DNA O-MAP targeting the pericentromeric alpha satellites, telomeres, and mitochondrial genomes. Scale bar: 5 µm. ( D ) Principal component analysis of scaled intensities of proteins enriched by the pan-alpha probe, telomere probe, mitochondrial genome oligo pool, and no-primary-probe control. ( E ) Unsupervised hierarchical clustering of scaled intensities of proteins enriched by the pan-alpha probe, telomere probe, mitochondrial genome oligo pool, and no-primary-probe control. ( F ) Log 2 fold change of proteins compared to no-primary-probe control, grouped by HPA subcellular location. Significance calculated based on Welch’s t -test for pairwise comparisons (****p-value <0.0001). Log 2 fold change of proteins compared to mitochondrial probe enriched proteins for the RNA Polymerases ( G ), mtDNA nucleoid packaging proteins ( H ), Shelterin ( I ), and CENP-A nucleosomal complexes ( J ). Significance calculated based on Welch’s t -test for pairwise comparisons (p-value: *<0.05, **<0.01, ***<0.001, ****<0.0001).

    Article Snippet: Final ssDNA probe was purified using a Zymo DNA Clean and Concentrator-100 (DCC-100) kit according to the manufacturer’s protocol for oligo purification.

    Techniques: Multiplexing, Quantitative Proteomics, In Situ Hybridization, Staining, Control