anti dnase x  (Thermo Fisher)


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    Name:
    Pierce DNase I
    Description:

    Catalog Number:
    89835
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    Structured Review

    Thermo Fisher anti dnase x
    Both EndoG and bleomycin induce DNase I and <t>DNase</t> X transcription in isolated rat brain cell nuclei. (A, B) In vitro transcription of DNase I and DNase X genes in isolated rat brain nuclei exposed with varying concentrations of recombinant EndoG (recEndoG)

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    anti dnase x - by Bioz Stars, 2020-03
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    1) Product Images from "Regulation of Apoptotic Endonucleases by EndoG"

    Article Title: Regulation of Apoptotic Endonucleases by EndoG

    Journal: DNA and Cell Biology

    doi: 10.1089/dna.2014.2772

    Both EndoG and bleomycin induce DNase I and DNase X transcription in isolated rat brain cell nuclei. (A, B) In vitro transcription of DNase I and DNase X genes in isolated rat brain nuclei exposed with varying concentrations of recombinant EndoG (recEndoG)
    Figure Legend Snippet: Both EndoG and bleomycin induce DNase I and DNase X transcription in isolated rat brain cell nuclei. (A, B) In vitro transcription of DNase I and DNase X genes in isolated rat brain nuclei exposed with varying concentrations of recombinant EndoG (recEndoG)

    Techniques Used: Isolation, In Vitro, Recombinant

    Induction of DNase I-like endonucleases in EndoG-overexpressing cells. (A) Western blotting for DNase I, DNase X (both at 8 h), DNase 1-like 2, DNase γ (both at 12 h), caspase-activated DNase (CAD) (at 8 h post-transfection),
    Figure Legend Snippet: Induction of DNase I-like endonucleases in EndoG-overexpressing cells. (A) Western blotting for DNase I, DNase X (both at 8 h), DNase 1-like 2, DNase γ (both at 12 h), caspase-activated DNase (CAD) (at 8 h post-transfection),

    Techniques Used: Western Blot, Transfection

    Related Articles

    Centrifugation:

    Article Title: Discovery of a novel amino acid racemase through exploration of natural variation in Arabidopsis thaliana
    Article Snippet: The soluble extract was collected by centrifugation and applied to Ni-NTA Resin (750 μL resin per 10 mL soluble extract) previously equilibrated with lysis buffer. .. Protein extraction and purification reagents including HisPur Ni-NTA Resin, Pierce Zeba 7-kDa, 10-mL desalting column, Pierce DNaseI (protein extraction grade), Pierce EDTA-free protease inhibitor mixture, Pierce protein-stabilizing mixture, and Pierce 20-kDa cutoff spin concentrator were all purchased from Thermo Scientific.

    Article Title: Glycosaminoglycans from Alzheimer’s disease hippocampus have altered capacities to bind and regulate growth factors activities and to bind tau
    Article Snippet: Then, peptides were eliminated by precipitation with trifluoroacetic acid (TCA, final 10%) at 4°C followed by centrifugation (13 000 g, 20 min). .. Supernatants were washed with chloroform (x2) to clear TCA and lipids, followed by dialysis to eliminate residual peptides from PK digestion, oligonucleotides from DNAse digestion, and many other small molecules (Slide-A-Lyzer Mini Dialysis Units 3 500 MWCO; Pierce); dialysis was carried against the buffer and then against water.

    Article Title: p53 is active in murine stem cells and alters the transcriptome in a manner that is reminiscent of mutant p53
    Article Snippet: Sucrose gradient centrifugation Cells were washed twice with ice-cold PBS, scraped into PBS and collected by centrifugation. .. Cells were suspended in (50 mM Tris pH 7.4, 20 mM NaCl, 10 mM MgCl2 , 0.5% NP40, 5 mM ATP, 1 mM DTT, 1 mM PMSF, 40 U/ml DNAse (Universal Nuclease for cell lysis; Pierce), 10 mM N-ethylmaleimide, 10 mM 1,10-phenanthtroline and 1 × Phosphostop), pushed three times through a 26G needle and incubated on ice for 30 min.

    Article Title: Artificial covalent linkage of bacterial acyl carrier proteins for fatty acid production
    Article Snippet: After 4 hours, the cells were harvested by centrifugation at 4 °C and 11000 × g on a Sorvall Lynx 4000 Centrifuge using a Fiberlite™ F14-14 × 50cy Fixed-Angle Rotor (Thermo). .. Pellets were resuspended in lysis buffer (20 mM Tris, 500 mM NaCl, 1 mM DTT, 20% glycerol, pH 7.8) in the presence of lysozyme (10 mg/ml), DNAse (1 mg/ml), 2X protease inhibitor cocktail (Pierce) and sonicated.

    Transferring:

    Article Title: Regulation of Apoptotic Endonucleases by EndoG
    Article Snippet: The total protein extract from cells (10–100 μg) was dissolved in 50 mM Tris-HCl, pH 6.8, 1% sodium dodecyl sulfate, 2 mM EDTA, 1% 2-mercaptoethanol, 7.5% glycerol, and denatured by heating at 100°C for 10 min. Electrophoresis was performed at 100 V for 2 h. Proteins were transferred onto the nitrocellulose membrane in NuPAGE® transferring buffer (Invitrogen) at 40 V for 3 h. The membranes were stained with Ponseau S (Sigma-Aldrich) to control equal protein load as described elsewhere (Hofnagel et al. , ). .. Primary antibodies, anti-DNase I, anti-CAD, and anti-GAPDH were detected with anti-rabbit IgG-horseradish peroxidase (HRP) while anti-DNase X, anti-DNase I-like 2, and anti-DNase γ were detected with donkey anti-goat IgG-HRP using SuperSignal chemiluminescent kit (Pierce Biotechnology).

    BIA-KA:

    Article Title: Human Papillomavirus Episome Stability Is Reduced by Aphidicolin and Controlled by DNA Damage Response Pathways
    Article Snippet: Lysates were incubated with 150 U/ml DNase I (ThermoScientific; catalog no. 89835) for 30 min at room temperature with mixing. .. Protein concentrations were determined by a bicinchoninic acid (BCA) assay (ThermoScientific; catalog no. 23227), and 50 μg of protein was subjected to electrophoresis in Tris-glycine (4% to 20%) gels (NuPAGE).

    Article Title: DNA Damage Repair Genes Controlling Human Papillomavirus (HPV) Episome Levels under Conditions of Stability and Extreme Instability
    Article Snippet: Lysates were incubated with 150 U/mL DNAse I (Thermoscientific, catalog no. 89835) for 30 minutes at room temperature with mixing. .. Lysates were incubated with 150 U/mL DNAse I (Thermoscientific, catalog no. 89835) for 30 minutes at room temperature with mixing.

    Blocking Assay:

    Article Title: Regulation of Apoptotic Endonucleases by EndoG
    Article Snippet: After soaking in the blocking solution overnight at 4°C, the membrane was incubated with polyclonal anti-DNase I antibody (Rockland, Gilbertsville, PA) diluted 1:1000, polyclonal anti-CAD antibody (Abbiotec, San Diego, CA) diluted 1:500, polyclonal anti-glyceraldehyde-3-phosphate dehydrogenase (GAPDH). (Abcam, Cambridge, MA) antibody diluted 1:1000, or polyclonal anti-DNase X, anti-DNase I-like 2, or anti-DNase γ antibodies (Santa Cruz Biotechnology, Santa Cruz, CA) diluted 1:500, then washed in Tris-buffered saline, pH 7.6. .. Primary antibodies, anti-DNase I, anti-CAD, and anti-GAPDH were detected with anti-rabbit IgG-horseradish peroxidase (HRP) while anti-DNase X, anti-DNase I-like 2, and anti-DNase γ were detected with donkey anti-goat IgG-HRP using SuperSignal chemiluminescent kit (Pierce Biotechnology).

    SYBR Green Assay:

    Article Title: Molecular basis of CENP-C association with the CENP-A nucleosome at yeast centromeres
    Article Snippet: The nucleosomes were then digested with 1 U of DNase I (Thermo Scientific, catalog no. 89835) for 80 sec at 23°C. .. The reaction products were resolved on a 1.3% native agarose gel, bands containing the free and Mif2c dimer-bound nucleosomes were visualized by SYBR Green staining and excised from the gel, and DNA was recovered from the gel slices and resolved on an 8% DNA sequencing gel (National Diagnostics, catalog no. EC-833).

    Article Title: A Multicenter Study To Evaluate the Performance of High-Throughput Sequencing for Virus Detection
    Article Snippet: Virus stock mixed with lysis buffer was sent to Norgen for RNA or DNA extraction and reverse transcription-quantitative PCR (RT-qPCR) using SYBR green I. .. For accurate determination of encapsidated virus genomes in the PCV1 virus stock, virus was treated with DNase I (catalogue number 89835; Pierce, Milwaukee, WI) at 37°C for 1 h, followed by heat inactivation at 65°C for 10 min prior to ultracentrifugation (Optima RL ultracentrifuge, TLA 45 rotor; Beckman, Palo Alto, CA) at 45,000 rpm for 3 h at 4°C.

    Incubation:

    Article Title: p53 is active in murine stem cells and alters the transcriptome in a manner that is reminiscent of mutant p53
    Article Snippet: .. For DNAse treatment, DNAse (Pierce Universal Nuclease for Cell lysis, Thermo Fisher Scientific, Bonn, Germany) was added to the nuclear lysate and incubated for 1 h on ice. .. Immunofluorescence staining ES cells were grown on gelatinised cover slips.

    Article Title: Quantitative Proteomics Analysis Reveals the Min System of Escherichia coli Modulates Reversible Protein Association with the Inner Membrane *
    Article Snippet: Isolation of Inner Membrane Fraction One liter of cells cultured to the optical density (OD) of 0.6 at 600 nm was harvested, resuspended in 13 ml 10 mm Tris-Cl, pH8.0, 1 mm EDTA, 0.75 m sucrose, and incubated at room temperature for 10 min. Twenty-six milliliters of 10 mm Tris-Cl, pH8.0, 1 mm EDTA were added to dilute the sucrose. .. The cell suspension was then treated with 2 mg/ml lysozyme, 1 protease inhibitor tablet (Cat. 04 693 132 001, Roche, Basel, Switzerland), and 30 units DNase I (Cat. 89835, Thermo Fisher Scientific, Inc., MA, USA) at room temperature for 30 min.

    Article Title: Molecular basis of CENP-C association with the CENP-A nucleosome at yeast centromeres
    Article Snippet: Purified Mif2c dimer (3 pM) was added to 6 pmol of end-labeled nucleosomes in the nucleosome reconstitution buffer (see above), and the volume was adjusted to 40–60 µL and incubated for 40 min at room temperature. .. The nucleosomes were then digested with 1 U of DNase I (Thermo Scientific, catalog no. 89835) for 80 sec at 23°C.

    Article Title: p53 is active in murine stem cells and alters the transcriptome in a manner that is reminiscent of mutant p53
    Article Snippet: Immunoprecipitation Cells were washed twice with ice-cold PBS and lysed in Co-IP lysis buffer (10 mM HEPES, pH 7.4, 50 mM NaCl, 0.5 M sucrose, 0.5%Triton x-100, 1 mM PMSF, 1 × Phosphostop (Roche, Mannheim, Germany), 200 U/ml DNAse (Universal Nuclease for cell lysis; Pierce). .. After 2 h incubation on a rotating wheel at 4 °C, the precipitates were washed three times with Co-IP wash buffer (50 mM Tris, pH 7.5, 1 mM EDTA, 100 mM NaCl, 0.1% Triton x-100, 5% glycerol).

    Article Title: Human Papillomavirus Episome Stability Is Reduced by Aphidicolin and Controlled by DNA Damage Response Pathways
    Article Snippet: .. Lysates were incubated with 150 U/ml DNase I (ThermoScientific; catalog no. 89835) for 30 min at room temperature with mixing. .. Protein concentrations were determined by a bicinchoninic acid (BCA) assay (ThermoScientific; catalog no. 23227), and 50 μg of protein was subjected to electrophoresis in Tris-glycine (4% to 20%) gels (NuPAGE).

    Article Title: DNA Damage Repair Genes Controlling Human Papillomavirus (HPV) Episome Levels under Conditions of Stability and Extreme Instability
    Article Snippet: .. Lysates were incubated with 150 U/mL DNAse I (Thermoscientific, catalog no. 89835) for 30 minutes at room temperature with mixing. .. Protein concentration was determined by BCA Assay (Thermoscientific, catalog no. 23227) and 50 µg protein separated on Tris-Glycine 4−20% gels (NuPAGE).

    Article Title: Discovery of a novel amino acid racemase through exploration of natural variation in Arabidopsis thaliana
    Article Snippet: After a 30-min incubation at 4 °C with occasional mixing, the resin was washed several times with Wash Buffer [50 mM Tris, 500 mM NaCl, 20 mM imidazole, 10% (vol/vol) glycerol, 10 mM β-mercaptoethanol, pH 8]. .. Protein extraction and purification reagents including HisPur Ni-NTA Resin, Pierce Zeba 7-kDa, 10-mL desalting column, Pierce DNaseI (protein extraction grade), Pierce EDTA-free protease inhibitor mixture, Pierce protein-stabilizing mixture, and Pierce 20-kDa cutoff spin concentrator were all purchased from Thermo Scientific.

    Article Title: Regulation of Apoptotic Endonucleases by EndoG
    Article Snippet: After soaking in the blocking solution overnight at 4°C, the membrane was incubated with polyclonal anti-DNase I antibody (Rockland, Gilbertsville, PA) diluted 1:1000, polyclonal anti-CAD antibody (Abbiotec, San Diego, CA) diluted 1:500, polyclonal anti-glyceraldehyde-3-phosphate dehydrogenase (GAPDH). (Abcam, Cambridge, MA) antibody diluted 1:1000, or polyclonal anti-DNase X, anti-DNase I-like 2, or anti-DNase γ antibodies (Santa Cruz Biotechnology, Santa Cruz, CA) diluted 1:500, then washed in Tris-buffered saline, pH 7.6. .. Primary antibodies, anti-DNase I, anti-CAD, and anti-GAPDH were detected with anti-rabbit IgG-horseradish peroxidase (HRP) while anti-DNase X, anti-DNase I-like 2, and anti-DNase γ were detected with donkey anti-goat IgG-HRP using SuperSignal chemiluminescent kit (Pierce Biotechnology).

    Article Title: Single-cell mass cytometry reveals intracellular survival/proliferative signaling in FLT3-ITD-mutated AML stem/progenitor cells
    Article Snippet: .. The cells were incubated in the same medium supplemented with heparin (Cat. 9041-08-1; Alfa Aesar, Ward Hill, MA), DNase I (Cat. 89835; Thermo Scientific, Waltham, MA) and MgSO4 at 37°C for 15 minutes, washed once and filtered to remove debris. ..

    Article Title: Glycosaminoglycans from Alzheimer’s disease hippocampus have altered capacities to bind and regulate growth factors activities and to bind tau
    Article Snippet: Samples were then treated with proteinase K to digest proteins (5 μg/mL; Merck) at 56°C overnight followed by heat-inactivation at 90°C for 30 min. DNAse (7.5 mU/mL; Qiagen) was added to samples to digest DNA and samples were incubated overnight at 37°C. .. Supernatants were washed with chloroform (x2) to clear TCA and lipids, followed by dialysis to eliminate residual peptides from PK digestion, oligonucleotides from DNAse digestion, and many other small molecules (Slide-A-Lyzer Mini Dialysis Units 3 500 MWCO; Pierce); dialysis was carried against the buffer and then against water.

    Article Title: p53 is active in murine stem cells and alters the transcriptome in a manner that is reminiscent of mutant p53
    Article Snippet: .. Cells were suspended in (50 mM Tris pH 7.4, 20 mM NaCl, 10 mM MgCl2 , 0.5% NP40, 5 mM ATP, 1 mM DTT, 1 mM PMSF, 40 U/ml DNAse (Universal Nuclease for cell lysis; Pierce), 10 mM N-ethylmaleimide, 10 mM 1,10-phenanthtroline and 1 × Phosphostop), pushed three times through a 26G needle and incubated on ice for 30 min. .. The protein extract was cleared by centrifugation at 16 000 × g at 4 °C for 15 min, loaded onto a 10–40% sucrose gradient and centrifuged at 100 000 × g at 4 °C for 18 h. Fractions were collected and analysed by western blotting.

    Expressing:

    Article Title: Discovery of a novel amino acid racemase through exploration of natural variation in Arabidopsis thaliana
    Article Snippet: Paragraph title: Recombinant Protein Expression and Purification. ... Protein extraction and purification reagents including HisPur Ni-NTA Resin, Pierce Zeba 7-kDa, 10-mL desalting column, Pierce DNaseI (protein extraction grade), Pierce EDTA-free protease inhibitor mixture, Pierce protein-stabilizing mixture, and Pierce 20-kDa cutoff spin concentrator were all purchased from Thermo Scientific.

    Article Title: Artificial covalent linkage of bacterial acyl carrier proteins for fatty acid production
    Article Snippet: Paragraph title: Protein expression and purification ... Pellets were resuspended in lysis buffer (20 mM Tris, 500 mM NaCl, 1 mM DTT, 20% glycerol, pH 7.8) in the presence of lysozyme (10 mg/ml), DNAse (1 mg/ml), 2X protease inhibitor cocktail (Pierce) and sonicated.

    Cell Fractionation:

    Article Title: p53 is active in murine stem cells and alters the transcriptome in a manner that is reminiscent of mutant p53
    Article Snippet: For cell fractionation, the cellular pellet was suspended in 4 packed cell volumes lysis buffer (10 mM HEPES pH7.4, 50 mM NaCl, 0.5 M sucrose, 0.5% Triton x-100, 1 mM PMSF), incubated for 5 min on ice and centrifuged at 1000 r.p.m. for 10 min. .. For DNAse treatment, DNAse (Pierce Universal Nuclease for Cell lysis, Thermo Fisher Scientific, Bonn, Germany) was added to the nuclear lysate and incubated for 1 h on ice.

    Western Blot:

    Article Title: p53 is active in murine stem cells and alters the transcriptome in a manner that is reminiscent of mutant p53
    Article Snippet: Paragraph title: Cell lysis and western blotting ... For DNAse treatment, DNAse (Pierce Universal Nuclease for Cell lysis, Thermo Fisher Scientific, Bonn, Germany) was added to the nuclear lysate and incubated for 1 h on ice.

    Article Title: Human Papillomavirus Episome Stability Is Reduced by Aphidicolin and Controlled by DNA Damage Response Pathways
    Article Snippet: Paragraph title: Western blotting. ... Lysates were incubated with 150 U/ml DNase I (ThermoScientific; catalog no. 89835) for 30 min at room temperature with mixing.

    Article Title: DNA Damage Repair Genes Controlling Human Papillomavirus (HPV) Episome Levels under Conditions of Stability and Extreme Instability
    Article Snippet: Paragraph title: Western Blotting ... Lysates were incubated with 150 U/mL DNAse I (Thermoscientific, catalog no. 89835) for 30 minutes at room temperature with mixing.

    Article Title: Regulation of Apoptotic Endonucleases by EndoG
    Article Snippet: Paragraph title: Western blotting ... Primary antibodies, anti-DNase I, anti-CAD, and anti-GAPDH were detected with anti-rabbit IgG-horseradish peroxidase (HRP) while anti-DNase X, anti-DNase I-like 2, and anti-DNase γ were detected with donkey anti-goat IgG-HRP using SuperSignal chemiluminescent kit (Pierce Biotechnology).

    Article Title: p53 is active in murine stem cells and alters the transcriptome in a manner that is reminiscent of mutant p53
    Article Snippet: Cells were suspended in (50 mM Tris pH 7.4, 20 mM NaCl, 10 mM MgCl2 , 0.5% NP40, 5 mM ATP, 1 mM DTT, 1 mM PMSF, 40 U/ml DNAse (Universal Nuclease for cell lysis; Pierce), 10 mM N-ethylmaleimide, 10 mM 1,10-phenanthtroline and 1 × Phosphostop), pushed three times through a 26G needle and incubated on ice for 30 min. .. The protein extract was cleared by centrifugation at 16 000 × g at 4 °C for 15 min, loaded onto a 10–40% sucrose gradient and centrifuged at 100 000 × g at 4 °C for 18 h. Fractions were collected and analysed by western blotting.

    Transformation Assay:

    Article Title: Artificial covalent linkage of bacterial acyl carrier proteins for fatty acid production
    Article Snippet: Protein expression and purification E . coli BL21(DE3) - Codon Plus RIL cells (Invitrogen) were transformed with each plasmid and grown in liquid Luria-Bertani medium supplemented with 0.4% glycerol, 1% glucose, which contained kanamycin (100 mg/L) and chloramphenicol (25 mg/ L). .. Pellets were resuspended in lysis buffer (20 mM Tris, 500 mM NaCl, 1 mM DTT, 20% glycerol, pH 7.8) in the presence of lysozyme (10 mg/ml), DNAse (1 mg/ml), 2X protease inhibitor cocktail (Pierce) and sonicated.

    Immunoprecipitation:

    Article Title: p53 is active in murine stem cells and alters the transcriptome in a manner that is reminiscent of mutant p53
    Article Snippet: .. Immunoprecipitation Cells were washed twice with ice-cold PBS and lysed in Co-IP lysis buffer (10 mM HEPES, pH 7.4, 50 mM NaCl, 0.5 M sucrose, 0.5%Triton x-100, 1 mM PMSF, 1 × Phosphostop (Roche, Mannheim, Germany), 200 U/ml DNAse (Universal Nuclease for cell lysis; Pierce). .. One milligram of protein was added to protein A-agarose (Pierce) pre-coupled with the anti-p53 antibody 1C12.

    Protease Inhibitor:

    Article Title: Quantitative Proteomics Analysis Reveals the Min System of Escherichia coli Modulates Reversible Protein Association with the Inner Membrane *
    Article Snippet: .. The cell suspension was then treated with 2 mg/ml lysozyme, 1 protease inhibitor tablet (Cat. 04 693 132 001, Roche, Basel, Switzerland), and 30 units DNase I (Cat. 89835, Thermo Fisher Scientific, Inc., MA, USA) at room temperature for 30 min. .. The concentration of KCl was brought to 150 mm before passing the suspension through a high-pressure cell disruption system (TS Series Cabinet, Constant System Ltd., Northants, UK) under 8,000 psi for three passages.

    Article Title: Discovery of a novel amino acid racemase through exploration of natural variation in Arabidopsis thaliana
    Article Snippet: .. Protein extraction and purification reagents including HisPur Ni-NTA Resin, Pierce Zeba 7-kDa, 10-mL desalting column, Pierce DNaseI (protein extraction grade), Pierce EDTA-free protease inhibitor mixture, Pierce protein-stabilizing mixture, and Pierce 20-kDa cutoff spin concentrator were all purchased from Thermo Scientific. .. The identity of the expressed fusion protein was confirmed by Western blot.

    Article Title: Artificial covalent linkage of bacterial acyl carrier proteins for fatty acid production
    Article Snippet: .. Pellets were resuspended in lysis buffer (20 mM Tris, 500 mM NaCl, 1 mM DTT, 20% glycerol, pH 7.8) in the presence of lysozyme (10 mg/ml), DNAse (1 mg/ml), 2X protease inhibitor cocktail (Pierce) and sonicated. ..

    Footprinting:

    Article Title: Molecular basis of CENP-C association with the CENP-A nucleosome at yeast centromeres
    Article Snippet: Paragraph title: DNase I footprinting ... The nucleosomes were then digested with 1 U of DNase I (Thermo Scientific, catalog no. 89835) for 80 sec at 23°C.

    Cell Culture:

    Article Title: Quantitative Proteomics Analysis Reveals the Min System of Escherichia coli Modulates Reversible Protein Association with the Inner Membrane *
    Article Snippet: Isolation of Inner Membrane Fraction One liter of cells cultured to the optical density (OD) of 0.6 at 600 nm was harvested, resuspended in 13 ml 10 mm Tris-Cl, pH8.0, 1 mm EDTA, 0.75 m sucrose, and incubated at room temperature for 10 min. Twenty-six milliliters of 10 mm Tris-Cl, pH8.0, 1 mm EDTA were added to dilute the sucrose. .. The cell suspension was then treated with 2 mg/ml lysozyme, 1 protease inhibitor tablet (Cat. 04 693 132 001, Roche, Basel, Switzerland), and 30 units DNase I (Cat. 89835, Thermo Fisher Scientific, Inc., MA, USA) at room temperature for 30 min.

    Generated:

    Article Title: Glycosaminoglycans from Alzheimer’s disease hippocampus have altered capacities to bind and regulate growth factors activities and to bind tau
    Article Snippet: Samples were brought to 2 M NaCl to avoid interaction between peptides, generated by PK digestion, with the sulfated GAGs. .. Supernatants were washed with chloroform (x2) to clear TCA and lipids, followed by dialysis to eliminate residual peptides from PK digestion, oligonucleotides from DNAse digestion, and many other small molecules (Slide-A-Lyzer Mini Dialysis Units 3 500 MWCO; Pierce); dialysis was carried against the buffer and then against water.

    DNA Sequencing:

    Article Title: Molecular basis of CENP-C association with the CENP-A nucleosome at yeast centromeres
    Article Snippet: The nucleosomes were then digested with 1 U of DNase I (Thermo Scientific, catalog no. 89835) for 80 sec at 23°C. .. The reaction products were resolved on a 1.3% native agarose gel, bands containing the free and Mif2c dimer-bound nucleosomes were visualized by SYBR Green staining and excised from the gel, and DNA was recovered from the gel slices and resolved on an 8% DNA sequencing gel (National Diagnostics, catalog no. EC-833).

    Protein Concentration:

    Article Title: DNA Damage Repair Genes Controlling Human Papillomavirus (HPV) Episome Levels under Conditions of Stability and Extreme Instability
    Article Snippet: Lysates were incubated with 150 U/mL DNAse I (Thermoscientific, catalog no. 89835) for 30 minutes at room temperature with mixing. .. Lysates were incubated with 150 U/mL DNAse I (Thermoscientific, catalog no. 89835) for 30 minutes at room temperature with mixing.

    Sequencing:

    Article Title: Molecular basis of CENP-C association with the CENP-A nucleosome at yeast centromeres
    Article Snippet: The nucleosomes were then digested with 1 U of DNase I (Thermo Scientific, catalog no. 89835) for 80 sec at 23°C. .. DNA mobility markers were G+A and C+T sequencing reactions of the same 33 P-labeled DNA fragments performed as described (Molecular Cloning, Cold Spring Harbor Laboratory).

    Sonication:

    Article Title: p53 is active in murine stem cells and alters the transcriptome in a manner that is reminiscent of mutant p53
    Article Snippet: The pellet was washed twice with cold PBS, suspended in the same volume lysis buffer as the cells at the beginning of the procedure and disrupted by sonication. .. For DNAse treatment, DNAse (Pierce Universal Nuclease for Cell lysis, Thermo Fisher Scientific, Bonn, Germany) was added to the nuclear lysate and incubated for 1 h on ice.

    Article Title: Artificial covalent linkage of bacterial acyl carrier proteins for fatty acid production
    Article Snippet: .. Pellets were resuspended in lysis buffer (20 mM Tris, 500 mM NaCl, 1 mM DTT, 20% glycerol, pH 7.8) in the presence of lysozyme (10 mg/ml), DNAse (1 mg/ml), 2X protease inhibitor cocktail (Pierce) and sonicated. ..

    Binding Assay:

    Article Title: Molecular basis of CENP-C association with the CENP-A nucleosome at yeast centromeres
    Article Snippet: To determine the site of Mif2 binding on Cse4 nucleosomal DNA, nucleosomes were reconstituted with DNA fragments end-labeled at 3′ with 33 P-dTTP for the top strand and 33 P-dATP for the bottom strand using Klenow polymerase. .. The nucleosomes were then digested with 1 U of DNase I (Thermo Scientific, catalog no. 89835) for 80 sec at 23°C.

    Article Title: Single-cell mass cytometry reveals intracellular survival/proliferative signaling in FLT3-ITD-mutated AML stem/progenitor cells
    Article Snippet: The cells were incubated in the same medium supplemented with heparin (Cat. 9041-08-1; Alfa Aesar, Ward Hill, MA), DNase I (Cat. 89835; Thermo Scientific, Waltham, MA) and MgSO4 at 37°C for 15 minutes, washed once and filtered to remove debris. .. For surface marker staining, cells were blocked with human Fc receptor binding inhibitor (Cat.14-9161-73; eBioscience, San Diego, CA) for 15 minutes at 4°C and stained with a cocktail of Ab comprising CD34-APC, CD38-PE-Cy7, CD45-APC-Cy7, CD123-PerCP-Cy5.5, and CD99-FITC for 30 minutes at room temperature.

    DNA Extraction:

    Article Title: A Multicenter Study To Evaluate the Performance of High-Throughput Sequencing for Virus Detection
    Article Snippet: Virus stock mixed with lysis buffer was sent to Norgen for RNA or DNA extraction and reverse transcription-quantitative PCR (RT-qPCR) using SYBR green I. .. For accurate determination of encapsidated virus genomes in the PCV1 virus stock, virus was treated with DNase I (catalogue number 89835; Pierce, Milwaukee, WI) at 37°C for 1 h, followed by heat inactivation at 65°C for 10 min prior to ultracentrifugation (Optima RL ultracentrifuge, TLA 45 rotor; Beckman, Palo Alto, CA) at 45,000 rpm for 3 h at 4°C.

    Molecular Cloning:

    Article Title: Molecular basis of CENP-C association with the CENP-A nucleosome at yeast centromeres
    Article Snippet: The nucleosomes were then digested with 1 U of DNase I (Thermo Scientific, catalog no. 89835) for 80 sec at 23°C. .. DNA mobility markers were G+A and C+T sequencing reactions of the same 33 P-labeled DNA fragments performed as described (Molecular Cloning, Cold Spring Harbor Laboratory).

    Isolation:

    Article Title: Quantitative Proteomics Analysis Reveals the Min System of Escherichia coli Modulates Reversible Protein Association with the Inner Membrane *
    Article Snippet: Paragraph title: Isolation of Inner Membrane Fraction ... The cell suspension was then treated with 2 mg/ml lysozyme, 1 protease inhibitor tablet (Cat. 04 693 132 001, Roche, Basel, Switzerland), and 30 units DNase I (Cat. 89835, Thermo Fisher Scientific, Inc., MA, USA) at room temperature for 30 min.

    Size-exclusion Chromatography:

    Article Title: Molecular basis of CENP-C association with the CENP-A nucleosome at yeast centromeres
    Article Snippet: .. The nucleosomes were then digested with 1 U of DNase I (Thermo Scientific, catalog no. 89835) for 80 sec at 23°C. .. The reaction products were resolved on a 1.3% native agarose gel, bands containing the free and Mif2c dimer-bound nucleosomes were visualized by SYBR Green staining and excised from the gel, and DNA was recovered from the gel slices and resolved on an 8% DNA sequencing gel (National Diagnostics, catalog no. EC-833).

    Purification:

    Article Title: Molecular basis of CENP-C association with the CENP-A nucleosome at yeast centromeres
    Article Snippet: Purified Mif2c dimer (3 pM) was added to 6 pmol of end-labeled nucleosomes in the nucleosome reconstitution buffer (see above), and the volume was adjusted to 40–60 µL and incubated for 40 min at room temperature. .. The nucleosomes were then digested with 1 U of DNase I (Thermo Scientific, catalog no. 89835) for 80 sec at 23°C.

    Article Title: Discovery of a novel amino acid racemase through exploration of natural variation in Arabidopsis thaliana
    Article Snippet: .. Protein extraction and purification reagents including HisPur Ni-NTA Resin, Pierce Zeba 7-kDa, 10-mL desalting column, Pierce DNaseI (protein extraction grade), Pierce EDTA-free protease inhibitor mixture, Pierce protein-stabilizing mixture, and Pierce 20-kDa cutoff spin concentrator were all purchased from Thermo Scientific. .. The identity of the expressed fusion protein was confirmed by Western blot.

    Article Title: Artificial covalent linkage of bacterial acyl carrier proteins for fatty acid production
    Article Snippet: Paragraph title: Protein expression and purification ... Pellets were resuspended in lysis buffer (20 mM Tris, 500 mM NaCl, 1 mM DTT, 20% glycerol, pH 7.8) in the presence of lysozyme (10 mg/ml), DNAse (1 mg/ml), 2X protease inhibitor cocktail (Pierce) and sonicated.

    Polymerase Chain Reaction:

    Article Title: A Multicenter Study To Evaluate the Performance of High-Throughput Sequencing for Virus Detection
    Article Snippet: Virus stock mixed with lysis buffer was sent to Norgen for RNA or DNA extraction and reverse transcription-quantitative PCR (RT-qPCR) using SYBR green I. .. For accurate determination of encapsidated virus genomes in the PCV1 virus stock, virus was treated with DNase I (catalogue number 89835; Pierce, Milwaukee, WI) at 37°C for 1 h, followed by heat inactivation at 65°C for 10 min prior to ultracentrifugation (Optima RL ultracentrifuge, TLA 45 rotor; Beckman, Palo Alto, CA) at 45,000 rpm for 3 h at 4°C.

    Protein Extraction:

    Article Title: Discovery of a novel amino acid racemase through exploration of natural variation in Arabidopsis thaliana
    Article Snippet: .. Protein extraction and purification reagents including HisPur Ni-NTA Resin, Pierce Zeba 7-kDa, 10-mL desalting column, Pierce DNaseI (protein extraction grade), Pierce EDTA-free protease inhibitor mixture, Pierce protein-stabilizing mixture, and Pierce 20-kDa cutoff spin concentrator were all purchased from Thermo Scientific. .. The identity of the expressed fusion protein was confirmed by Western blot.

    Quantitative RT-PCR:

    Article Title: A Multicenter Study To Evaluate the Performance of High-Throughput Sequencing for Virus Detection
    Article Snippet: Virus stock mixed with lysis buffer was sent to Norgen for RNA or DNA extraction and reverse transcription-quantitative PCR (RT-qPCR) using SYBR green I. .. For accurate determination of encapsidated virus genomes in the PCV1 virus stock, virus was treated with DNase I (catalogue number 89835; Pierce, Milwaukee, WI) at 37°C for 1 h, followed by heat inactivation at 65°C for 10 min prior to ultracentrifugation (Optima RL ultracentrifuge, TLA 45 rotor; Beckman, Palo Alto, CA) at 45,000 rpm for 3 h at 4°C.

    Bradford Protein Assay:

    Article Title: Regulation of Apoptotic Endonucleases by EndoG
    Article Snippet: Protein content was measured using the Bradford protein assay (Pierce Biotechnology, Rockford, IL). .. Primary antibodies, anti-DNase I, anti-CAD, and anti-GAPDH were detected with anti-rabbit IgG-horseradish peroxidase (HRP) while anti-DNase X, anti-DNase I-like 2, and anti-DNase γ were detected with donkey anti-goat IgG-HRP using SuperSignal chemiluminescent kit (Pierce Biotechnology).

    Lysis:

    Article Title: p53 is active in murine stem cells and alters the transcriptome in a manner that is reminiscent of mutant p53
    Article Snippet: .. For DNAse treatment, DNAse (Pierce Universal Nuclease for Cell lysis, Thermo Fisher Scientific, Bonn, Germany) was added to the nuclear lysate and incubated for 1 h on ice. .. Immunofluorescence staining ES cells were grown on gelatinised cover slips.

    Article Title: p53 is active in murine stem cells and alters the transcriptome in a manner that is reminiscent of mutant p53
    Article Snippet: .. Immunoprecipitation Cells were washed twice with ice-cold PBS and lysed in Co-IP lysis buffer (10 mM HEPES, pH 7.4, 50 mM NaCl, 0.5 M sucrose, 0.5%Triton x-100, 1 mM PMSF, 1 × Phosphostop (Roche, Mannheim, Germany), 200 U/ml DNAse (Universal Nuclease for cell lysis; Pierce). .. One milligram of protein was added to protein A-agarose (Pierce) pre-coupled with the anti-p53 antibody 1C12.

    Article Title: Discovery of a novel amino acid racemase through exploration of natural variation in Arabidopsis thaliana
    Article Snippet: The soluble extract was collected by centrifugation and applied to Ni-NTA Resin (750 μL resin per 10 mL soluble extract) previously equilibrated with lysis buffer. .. Protein extraction and purification reagents including HisPur Ni-NTA Resin, Pierce Zeba 7-kDa, 10-mL desalting column, Pierce DNaseI (protein extraction grade), Pierce EDTA-free protease inhibitor mixture, Pierce protein-stabilizing mixture, and Pierce 20-kDa cutoff spin concentrator were all purchased from Thermo Scientific.

    Article Title: A Multicenter Study To Evaluate the Performance of High-Throughput Sequencing for Virus Detection
    Article Snippet: Virus stock mixed with lysis buffer was sent to Norgen for RNA or DNA extraction and reverse transcription-quantitative PCR (RT-qPCR) using SYBR green I. .. For accurate determination of encapsidated virus genomes in the PCV1 virus stock, virus was treated with DNase I (catalogue number 89835; Pierce, Milwaukee, WI) at 37°C for 1 h, followed by heat inactivation at 65°C for 10 min prior to ultracentrifugation (Optima RL ultracentrifuge, TLA 45 rotor; Beckman, Palo Alto, CA) at 45,000 rpm for 3 h at 4°C.

    Article Title: p53 is active in murine stem cells and alters the transcriptome in a manner that is reminiscent of mutant p53
    Article Snippet: .. Cells were suspended in (50 mM Tris pH 7.4, 20 mM NaCl, 10 mM MgCl2 , 0.5% NP40, 5 mM ATP, 1 mM DTT, 1 mM PMSF, 40 U/ml DNAse (Universal Nuclease for cell lysis; Pierce), 10 mM N-ethylmaleimide, 10 mM 1,10-phenanthtroline and 1 × Phosphostop), pushed three times through a 26G needle and incubated on ice for 30 min. .. The protein extract was cleared by centrifugation at 16 000 × g at 4 °C for 15 min, loaded onto a 10–40% sucrose gradient and centrifuged at 100 000 × g at 4 °C for 18 h. Fractions were collected and analysed by western blotting.

    Article Title: Artificial covalent linkage of bacterial acyl carrier proteins for fatty acid production
    Article Snippet: .. Pellets were resuspended in lysis buffer (20 mM Tris, 500 mM NaCl, 1 mM DTT, 20% glycerol, pH 7.8) in the presence of lysozyme (10 mg/ml), DNAse (1 mg/ml), 2X protease inhibitor cocktail (Pierce) and sonicated. ..

    Chloramphenicol Acetyltransferase Assay:

    Article Title: Single-cell mass cytometry reveals intracellular survival/proliferative signaling in FLT3-ITD-mutated AML stem/progenitor cells
    Article Snippet: The cells were incubated in the same medium supplemented with heparin (Cat. 9041-08-1; Alfa Aesar, Ward Hill, MA), DNase I (Cat. 89835; Thermo Scientific, Waltham, MA) and MgSO4 at 37°C for 15 minutes, washed once and filtered to remove debris. .. For surface marker staining, cells were blocked with human Fc receptor binding inhibitor (Cat.14-9161-73; eBioscience, San Diego, CA) for 15 minutes at 4°C and stained with a cocktail of Ab comprising CD34-APC, CD38-PE-Cy7, CD45-APC-Cy7, CD123-PerCP-Cy5.5, and CD99-FITC for 30 minutes at room temperature.

    SDS Page:

    Article Title: p53 is active in murine stem cells and alters the transcriptome in a manner that is reminiscent of mutant p53
    Article Snippet: Immunoprecipitation Cells were washed twice with ice-cold PBS and lysed in Co-IP lysis buffer (10 mM HEPES, pH 7.4, 50 mM NaCl, 0.5 M sucrose, 0.5%Triton x-100, 1 mM PMSF, 1 × Phosphostop (Roche, Mannheim, Germany), 200 U/ml DNAse (Universal Nuclease for cell lysis; Pierce). .. Thirty microlitres of 2 × SDS sample buffer (4% sodium dodecyl sulphate, 0.16 M Tris pH 6.8, 20% glycerol, 4% β -mercaptoethanol, 0.002% bromphenol blue) were added to the precipitates prior to heat-denaturation and loading onto a 10% SDS-PAGE gel.

    Plasmid Preparation:

    Article Title: Artificial covalent linkage of bacterial acyl carrier proteins for fatty acid production
    Article Snippet: Protein expression and purification E . coli BL21(DE3) - Codon Plus RIL cells (Invitrogen) were transformed with each plasmid and grown in liquid Luria-Bertani medium supplemented with 0.4% glycerol, 1% glucose, which contained kanamycin (100 mg/L) and chloramphenicol (25 mg/ L). .. Pellets were resuspended in lysis buffer (20 mM Tris, 500 mM NaCl, 1 mM DTT, 20% glycerol, pH 7.8) in the presence of lysozyme (10 mg/ml), DNAse (1 mg/ml), 2X protease inhibitor cocktail (Pierce) and sonicated.

    Electrophoresis:

    Article Title: Human Papillomavirus Episome Stability Is Reduced by Aphidicolin and Controlled by DNA Damage Response Pathways
    Article Snippet: Lysates were incubated with 150 U/ml DNase I (ThermoScientific; catalog no. 89835) for 30 min at room temperature with mixing. .. Protein concentrations were determined by a bicinchoninic acid (BCA) assay (ThermoScientific; catalog no. 23227), and 50 μg of protein was subjected to electrophoresis in Tris-glycine (4% to 20%) gels (NuPAGE).

    Article Title: Regulation of Apoptotic Endonucleases by EndoG
    Article Snippet: The total protein extract from cells (10–100 μg) was dissolved in 50 mM Tris-HCl, pH 6.8, 1% sodium dodecyl sulfate, 2 mM EDTA, 1% 2-mercaptoethanol, 7.5% glycerol, and denatured by heating at 100°C for 10 min. Electrophoresis was performed at 100 V for 2 h. Proteins were transferred onto the nitrocellulose membrane in NuPAGE® transferring buffer (Invitrogen) at 40 V for 3 h. The membranes were stained with Ponseau S (Sigma-Aldrich) to control equal protein load as described elsewhere (Hofnagel et al. , ). .. Primary antibodies, anti-DNase I, anti-CAD, and anti-GAPDH were detected with anti-rabbit IgG-horseradish peroxidase (HRP) while anti-DNase X, anti-DNase I-like 2, and anti-DNase γ were detected with donkey anti-goat IgG-HRP using SuperSignal chemiluminescent kit (Pierce Biotechnology).

    Co-Immunoprecipitation Assay:

    Article Title: p53 is active in murine stem cells and alters the transcriptome in a manner that is reminiscent of mutant p53
    Article Snippet: .. Immunoprecipitation Cells were washed twice with ice-cold PBS and lysed in Co-IP lysis buffer (10 mM HEPES, pH 7.4, 50 mM NaCl, 0.5 M sucrose, 0.5%Triton x-100, 1 mM PMSF, 1 × Phosphostop (Roche, Mannheim, Germany), 200 U/ml DNAse (Universal Nuclease for cell lysis; Pierce). .. One milligram of protein was added to protein A-agarose (Pierce) pre-coupled with the anti-p53 antibody 1C12.

    Recombinant:

    Article Title: Discovery of a novel amino acid racemase through exploration of natural variation in Arabidopsis thaliana
    Article Snippet: Paragraph title: Recombinant Protein Expression and Purification. ... Protein extraction and purification reagents including HisPur Ni-NTA Resin, Pierce Zeba 7-kDa, 10-mL desalting column, Pierce DNaseI (protein extraction grade), Pierce EDTA-free protease inhibitor mixture, Pierce protein-stabilizing mixture, and Pierce 20-kDa cutoff spin concentrator were all purchased from Thermo Scientific.

    Agarose Gel Electrophoresis:

    Article Title: Molecular basis of CENP-C association with the CENP-A nucleosome at yeast centromeres
    Article Snippet: The nucleosomes were then digested with 1 U of DNase I (Thermo Scientific, catalog no. 89835) for 80 sec at 23°C. .. The reaction products were resolved on a 1.3% native agarose gel, bands containing the free and Mif2c dimer-bound nucleosomes were visualized by SYBR Green staining and excised from the gel, and DNA was recovered from the gel slices and resolved on an 8% DNA sequencing gel (National Diagnostics, catalog no. EC-833).

    Radio Immunoprecipitation:

    Article Title: Human Papillomavirus Episome Stability Is Reduced by Aphidicolin and Controlled by DNA Damage Response Pathways
    Article Snippet: Cells were washed with ice-cold phosphate-buffered saline (PBS) and lysed in radioimmunoprecipitation assay (RIPA) buffer (25 mM Tris-HCl [pH 7.5], 150 mM NaCl, 1% NP-40, 2% sodium deoxycholate, 0.1% SDS) supplemented with 2× Halt Protease & Phosphatase Inhibitor Cocktail (ThermoScientific; catalog no. 1861284). .. Lysates were incubated with 150 U/ml DNase I (ThermoScientific; catalog no. 89835) for 30 min at room temperature with mixing.

    Article Title: DNA Damage Repair Genes Controlling Human Papillomavirus (HPV) Episome Levels under Conditions of Stability and Extreme Instability
    Article Snippet: Cells were trypsinized, washed with ice-cold phosphate-buffered saline (PBS), and lysed in radioimmunoprecipitation assay (RIPA) buffer (25 mM Tris-HCL pH 7.5, 150 mM NaCl, 1% NP-40, 2% sodium deoxycholate, 0.1% SDS) supplemented with 2X Halt Protease & Phosphatase Inhibitor Cocktail (Thermoscientific, catalog no. 1861284). .. Lysates were incubated with 150 U/mL DNAse I (Thermoscientific, catalog no. 89835) for 30 minutes at room temperature with mixing.

    Concentration Assay:

    Article Title: Quantitative Proteomics Analysis Reveals the Min System of Escherichia coli Modulates Reversible Protein Association with the Inner Membrane *
    Article Snippet: The cell suspension was then treated with 2 mg/ml lysozyme, 1 protease inhibitor tablet (Cat. 04 693 132 001, Roche, Basel, Switzerland), and 30 units DNase I (Cat. 89835, Thermo Fisher Scientific, Inc., MA, USA) at room temperature for 30 min. .. The concentration of KCl was brought to 150 mm before passing the suspension through a high-pressure cell disruption system (TS Series Cabinet, Constant System Ltd., Northants, UK) under 8,000 psi for three passages.

    Marker:

    Article Title: Single-cell mass cytometry reveals intracellular survival/proliferative signaling in FLT3-ITD-mutated AML stem/progenitor cells
    Article Snippet: The cells were incubated in the same medium supplemented with heparin (Cat. 9041-08-1; Alfa Aesar, Ward Hill, MA), DNase I (Cat. 89835; Thermo Scientific, Waltham, MA) and MgSO4 at 37°C for 15 minutes, washed once and filtered to remove debris. .. For surface marker staining, cells were blocked with human Fc receptor binding inhibitor (Cat.14-9161-73; eBioscience, San Diego, CA) for 15 minutes at 4°C and stained with a cocktail of Ab comprising CD34-APC, CD38-PE-Cy7, CD45-APC-Cy7, CD123-PerCP-Cy5.5, and CD99-FITC for 30 minutes at room temperature.

    Staining:

    Article Title: Molecular basis of CENP-C association with the CENP-A nucleosome at yeast centromeres
    Article Snippet: The nucleosomes were then digested with 1 U of DNase I (Thermo Scientific, catalog no. 89835) for 80 sec at 23°C. .. The reaction products were resolved on a 1.3% native agarose gel, bands containing the free and Mif2c dimer-bound nucleosomes were visualized by SYBR Green staining and excised from the gel, and DNA was recovered from the gel slices and resolved on an 8% DNA sequencing gel (National Diagnostics, catalog no. EC-833).

    Article Title: Regulation of Apoptotic Endonucleases by EndoG
    Article Snippet: The total protein extract from cells (10–100 μg) was dissolved in 50 mM Tris-HCl, pH 6.8, 1% sodium dodecyl sulfate, 2 mM EDTA, 1% 2-mercaptoethanol, 7.5% glycerol, and denatured by heating at 100°C for 10 min. Electrophoresis was performed at 100 V for 2 h. Proteins were transferred onto the nitrocellulose membrane in NuPAGE® transferring buffer (Invitrogen) at 40 V for 3 h. The membranes were stained with Ponseau S (Sigma-Aldrich) to control equal protein load as described elsewhere (Hofnagel et al. , ). .. Primary antibodies, anti-DNase I, anti-CAD, and anti-GAPDH were detected with anti-rabbit IgG-horseradish peroxidase (HRP) while anti-DNase X, anti-DNase I-like 2, and anti-DNase γ were detected with donkey anti-goat IgG-HRP using SuperSignal chemiluminescent kit (Pierce Biotechnology).

    Article Title: Single-cell mass cytometry reveals intracellular survival/proliferative signaling in FLT3-ITD-mutated AML stem/progenitor cells
    Article Snippet: Paragraph title: Surface and intracellular FCM staining ... The cells were incubated in the same medium supplemented with heparin (Cat. 9041-08-1; Alfa Aesar, Ward Hill, MA), DNase I (Cat. 89835; Thermo Scientific, Waltham, MA) and MgSO4 at 37°C for 15 minutes, washed once and filtered to remove debris.

    Gradient Centrifugation:

    Article Title: p53 is active in murine stem cells and alters the transcriptome in a manner that is reminiscent of mutant p53
    Article Snippet: Paragraph title: Sucrose gradient centrifugation ... Cells were suspended in (50 mM Tris pH 7.4, 20 mM NaCl, 10 mM MgCl2 , 0.5% NP40, 5 mM ATP, 1 mM DTT, 1 mM PMSF, 40 U/ml DNAse (Universal Nuclease for cell lysis; Pierce), 10 mM N-ethylmaleimide, 10 mM 1,10-phenanthtroline and 1 × Phosphostop), pushed three times through a 26G needle and incubated on ice for 30 min.

    Dimethylmethylene Blue Assay:

    Article Title: Glycosaminoglycans from Alzheimer’s disease hippocampus have altered capacities to bind and regulate growth factors activities and to bind tau
    Article Snippet: Supernatants were washed with chloroform (x2) to clear TCA and lipids, followed by dialysis to eliminate residual peptides from PK digestion, oligonucleotides from DNAse digestion, and many other small molecules (Slide-A-Lyzer Mini Dialysis Units 3 500 MWCO; Pierce); dialysis was carried against the buffer and then against water. .. Extracted GAGs were quantified with the 1,9-dimethyl-methylene blue (DMMB) assay [ ].

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    Thermo Fisher semi automated magmax extraction
    Automation and <t>DNase</t> treatment using <t>MagMax</t> kit. Values plotted in box-plots are raw Cq values. Both mRNA representation ( a ) and miRNA representation ( b ) remained unaffected by semi-automation or DNase treatment step
    Semi Automated Magmax Extraction, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/semi automated magmax extraction/product/Thermo Fisher
    Average 91 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    semi automated magmax extraction - by Bioz Stars, 2020-03
    91/100 stars
      Buy from Supplier

    99
    Thermo Fisher dnase i amplification grade
    NETs contribute to the pathogenesis of myocarditis. (a) Confocal immunofluorescence images of an EMB of patient 6 suffering from PVB19-positive myocarditis (see Table 1 ). Top: Images show staining of <t>H2A-H2B-DNA,</t> MPO, and H3Cit as well as the merged image. Bar, 20 µm. Bottom: Magnification of a selected area of the merged confocal image (box) from the top panel. Arrows indicate NETs. Bar, 10 µm. (b and c) EAM score (b) as well as evaluation of the heart/body weight ratio (c) at day 21 after induction of EAM or sham immunization (sham; mean EAM score, 0.5 ± 0.19; mean heart/body weight ratio, 0.57 ± 0.01). Mice were treated with <t>DNase</t> (EAM + DNase: mean EAM score, 0.8 ± 0.19; mean heart/body weight ratio, 0.62 ± 0.005), Cl-amid (EAM + Cl-amid: mean EAM score, 0.9 ± 0.20; mean heart/body weight ratio, 0.62 ± 0.01), or vehicle as control (EAM + vehicle: mean EAM score, 1.7 ± 0.25; mean heart/body weight ratio, 0.71 ± 0.04) as indicated. n = 8 for sham group; n = 26 for EAM groups. (d) Left: Representative confocal images of cardiac sections of immunized WT mice at day 21 after induction of EAM (EAM + vehicle). Images show staining of DNA, NE, and H3Cit as well as the merged image. Bars, 20 µm. Right: Representative confocal magnified image of NETs. Images show staining of DNA, NE, and H3Cit as well as the merged image, colocalization (coloc) of DNA/NE, and DNA/H3Cit as indicated. Bars, 10 µm. (e) Representative confocal images of cardiac sections of EAM mice at day 21 after induction of EAM and blockade of MK for 21 d. Images show staining of DNA, NE, and H3Cit as well as the merged image. Bars, 20 µm. (f–h) Histological analysis of extravasated PMN into the cardiac tissue at day 21 after induction of EAM without blocking MK (EAM + vehicle) or after application of an anti-N-MK blocking Ab (EAM + anti-N-MK). Diagrams show the number of extravasated PMNs per mm 2 (f: vehicle, 768 ± 55 PMN/mm 2 ; anti-N-MK, 158 ± 86 PMN/mm 2 ), the number of NET + PMNs per mm 2 (g: vehicle, 40 ± 6 NET + PMN; anti-N-MK = 5 ± 2 NET + PMN), and the number of NET + PMNs as a percentage of all extravasated PMNs (h: vehicle, 5.1 ± 0.5 NET + PMN [%]; anti-N-MK, 0.9 ± 0.6 NET + PMN [%]). n = 6 mice. To determine P values, ANOVA on ranks with Dunn’s multiple comparisons test was performed for c and d, and an unpaired Student's t test was used for f–h. For all panels, *, P
    Dnase I Amplification Grade, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dnase i amplification grade/product/Thermo Fisher
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    dnase i amplification grade - by Bioz Stars, 2020-03
    99/100 stars
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    87
    Thermo Fisher dnase treated rna preparation
    Cotranscription analysis of the nmpABCDEF gene cluster. (A) Positions of putative promoters (bent arrows), Rho-independent terminators (hairpin loops), and intragenic and intergenic regions to be amplified by specific primers between the nmpA-nmpB , nmpB-nmpC , nmpC-nmpD , nmpD-nmpE , nmpC-nmpE , and nmpE-nmpF genes. (B to E) Total <t>RNA</t> isolated from Alicycliphilus sp. strain BQ1 cells growing in MM-NMP was reverse transcribed and the cDNA synthesized used as the template for PCRs. (B) Positive and negative controls amplified using the primer set gyrAF-gyrAR, targeting the housekeeping gyrA gene; the templates were genomic DNA (gDNA) from Alicycliphilus sp. strain BQ1, RNA treated <t>(DNase</t> +) or not (DNase −) with RNase-free DNase, and synthesized cDNA. (C) nmpABCDEF intragenic RT-PCR amplifications using the primer sets HydAF-HydAR (lane A), NMHydF-NMHydR (lane B), AaOXiF-AaOXiR (lane C), CupF-CupR (lane D), PucF-PucR (lane E), and SSDHF-SSDHR (lane F). (D and E) Intergenic PCR (D) and RT-PCR (E) amplifications using gDNA and cDNA, respectively, as the templates, with the primers sets HydAF-nmpABR (lanes A-B), nmpBCF/nmpBCR (lanes B-C), AaOXiF/nmpCDR (lanes C-D), CupF/PucR (lanes D-E), AaOXiF/nmpDER (lanes C-E), and nmpEFF/nmpEFR (lanes E-F). Negative-control (C−) reaction mixtures contained no DNA template. M, DNA marker (λ DNA EcoRI + HindIII ladder [Thermo Scientific]).
    Dnase Treated Rna Preparation, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 87/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Automation and DNase treatment using MagMax kit. Values plotted in box-plots are raw Cq values. Both mRNA representation ( a ) and miRNA representation ( b ) remained unaffected by semi-automation or DNase treatment step

    Journal: BMC Research Notes

    Article Title: Simultaneous extraction of mRNA and microRNA from whole blood stabilized in tempus tubes

    doi: 10.1186/s13104-019-4087-5

    Figure Lengend Snippet: Automation and DNase treatment using MagMax kit. Values plotted in box-plots are raw Cq values. Both mRNA representation ( a ) and miRNA representation ( b ) remained unaffected by semi-automation or DNase treatment step

    Article Snippet: For the second phase, the manual MagMax protocol (with and without DNase treatment) was compared to semi-automated MagMax extraction (with and without DNase treatment) per the instructions of the MagMax Express 96 instrument (Thermo Fisher).

    Techniques:

    Automation and DNase treatment using MagMax kit. Values plotted in box-plots are raw Cq values. Both mRNA representation ( a ) and miRNA representation ( b ) remained unaffected by semi-automation or DNase treatment step

    Journal: BMC Research Notes

    Article Title: Simultaneous extraction of mRNA and microRNA from whole blood stabilized in tempus tubes

    doi: 10.1186/s13104-019-4087-5

    Figure Lengend Snippet: Automation and DNase treatment using MagMax kit. Values plotted in box-plots are raw Cq values. Both mRNA representation ( a ) and miRNA representation ( b ) remained unaffected by semi-automation or DNase treatment step

    Article Snippet: For the second phase, the manual MagMax protocol (with and without DNase treatment) was compared to semi-automated MagMax extraction (with and without DNase treatment) per the instructions of the MagMax Express 96 instrument (Thermo Fisher).

    Techniques:

    NETs contribute to the pathogenesis of myocarditis. (a) Confocal immunofluorescence images of an EMB of patient 6 suffering from PVB19-positive myocarditis (see Table 1 ). Top: Images show staining of H2A-H2B-DNA, MPO, and H3Cit as well as the merged image. Bar, 20 µm. Bottom: Magnification of a selected area of the merged confocal image (box) from the top panel. Arrows indicate NETs. Bar, 10 µm. (b and c) EAM score (b) as well as evaluation of the heart/body weight ratio (c) at day 21 after induction of EAM or sham immunization (sham; mean EAM score, 0.5 ± 0.19; mean heart/body weight ratio, 0.57 ± 0.01). Mice were treated with DNase (EAM + DNase: mean EAM score, 0.8 ± 0.19; mean heart/body weight ratio, 0.62 ± 0.005), Cl-amid (EAM + Cl-amid: mean EAM score, 0.9 ± 0.20; mean heart/body weight ratio, 0.62 ± 0.01), or vehicle as control (EAM + vehicle: mean EAM score, 1.7 ± 0.25; mean heart/body weight ratio, 0.71 ± 0.04) as indicated. n = 8 for sham group; n = 26 for EAM groups. (d) Left: Representative confocal images of cardiac sections of immunized WT mice at day 21 after induction of EAM (EAM + vehicle). Images show staining of DNA, NE, and H3Cit as well as the merged image. Bars, 20 µm. Right: Representative confocal magnified image of NETs. Images show staining of DNA, NE, and H3Cit as well as the merged image, colocalization (coloc) of DNA/NE, and DNA/H3Cit as indicated. Bars, 10 µm. (e) Representative confocal images of cardiac sections of EAM mice at day 21 after induction of EAM and blockade of MK for 21 d. Images show staining of DNA, NE, and H3Cit as well as the merged image. Bars, 20 µm. (f–h) Histological analysis of extravasated PMN into the cardiac tissue at day 21 after induction of EAM without blocking MK (EAM + vehicle) or after application of an anti-N-MK blocking Ab (EAM + anti-N-MK). Diagrams show the number of extravasated PMNs per mm 2 (f: vehicle, 768 ± 55 PMN/mm 2 ; anti-N-MK, 158 ± 86 PMN/mm 2 ), the number of NET + PMNs per mm 2 (g: vehicle, 40 ± 6 NET + PMN; anti-N-MK = 5 ± 2 NET + PMN), and the number of NET + PMNs as a percentage of all extravasated PMNs (h: vehicle, 5.1 ± 0.5 NET + PMN [%]; anti-N-MK, 0.9 ± 0.6 NET + PMN [%]). n = 6 mice. To determine P values, ANOVA on ranks with Dunn’s multiple comparisons test was performed for c and d, and an unpaired Student's t test was used for f–h. For all panels, *, P

    Journal: The Journal of Experimental Medicine

    Article Title: Midkine drives cardiac inflammation by promoting neutrophil trafficking and NETosis in myocarditis

    doi: 10.1084/jem.20181102

    Figure Lengend Snippet: NETs contribute to the pathogenesis of myocarditis. (a) Confocal immunofluorescence images of an EMB of patient 6 suffering from PVB19-positive myocarditis (see Table 1 ). Top: Images show staining of H2A-H2B-DNA, MPO, and H3Cit as well as the merged image. Bar, 20 µm. Bottom: Magnification of a selected area of the merged confocal image (box) from the top panel. Arrows indicate NETs. Bar, 10 µm. (b and c) EAM score (b) as well as evaluation of the heart/body weight ratio (c) at day 21 after induction of EAM or sham immunization (sham; mean EAM score, 0.5 ± 0.19; mean heart/body weight ratio, 0.57 ± 0.01). Mice were treated with DNase (EAM + DNase: mean EAM score, 0.8 ± 0.19; mean heart/body weight ratio, 0.62 ± 0.005), Cl-amid (EAM + Cl-amid: mean EAM score, 0.9 ± 0.20; mean heart/body weight ratio, 0.62 ± 0.01), or vehicle as control (EAM + vehicle: mean EAM score, 1.7 ± 0.25; mean heart/body weight ratio, 0.71 ± 0.04) as indicated. n = 8 for sham group; n = 26 for EAM groups. (d) Left: Representative confocal images of cardiac sections of immunized WT mice at day 21 after induction of EAM (EAM + vehicle). Images show staining of DNA, NE, and H3Cit as well as the merged image. Bars, 20 µm. Right: Representative confocal magnified image of NETs. Images show staining of DNA, NE, and H3Cit as well as the merged image, colocalization (coloc) of DNA/NE, and DNA/H3Cit as indicated. Bars, 10 µm. (e) Representative confocal images of cardiac sections of EAM mice at day 21 after induction of EAM and blockade of MK for 21 d. Images show staining of DNA, NE, and H3Cit as well as the merged image. Bars, 20 µm. (f–h) Histological analysis of extravasated PMN into the cardiac tissue at day 21 after induction of EAM without blocking MK (EAM + vehicle) or after application of an anti-N-MK blocking Ab (EAM + anti-N-MK). Diagrams show the number of extravasated PMNs per mm 2 (f: vehicle, 768 ± 55 PMN/mm 2 ; anti-N-MK, 158 ± 86 PMN/mm 2 ), the number of NET + PMNs per mm 2 (g: vehicle, 40 ± 6 NET + PMN; anti-N-MK = 5 ± 2 NET + PMN), and the number of NET + PMNs as a percentage of all extravasated PMNs (h: vehicle, 5.1 ± 0.5 NET + PMN [%]; anti-N-MK, 0.9 ± 0.6 NET + PMN [%]). n = 6 mice. To determine P values, ANOVA on ranks with Dunn’s multiple comparisons test was performed for c and d, and an unpaired Student's t test was used for f–h. For all panels, *, P

    Article Snippet: RNA was isolated using TRIzol (15596026; Thermo Fisher) according to the manufacturer’s protocol, and genomic DNA was digested using the DNase I Amplification Grade kit (18068015; Thermo Fisher).

    Techniques: Immunofluorescence, Staining, Mouse Assay, Blocking Assay

    Cotranscription analysis of the nmpABCDEF gene cluster. (A) Positions of putative promoters (bent arrows), Rho-independent terminators (hairpin loops), and intragenic and intergenic regions to be amplified by specific primers between the nmpA-nmpB , nmpB-nmpC , nmpC-nmpD , nmpD-nmpE , nmpC-nmpE , and nmpE-nmpF genes. (B to E) Total RNA isolated from Alicycliphilus sp. strain BQ1 cells growing in MM-NMP was reverse transcribed and the cDNA synthesized used as the template for PCRs. (B) Positive and negative controls amplified using the primer set gyrAF-gyrAR, targeting the housekeeping gyrA gene; the templates were genomic DNA (gDNA) from Alicycliphilus sp. strain BQ1, RNA treated (DNase +) or not (DNase −) with RNase-free DNase, and synthesized cDNA. (C) nmpABCDEF intragenic RT-PCR amplifications using the primer sets HydAF-HydAR (lane A), NMHydF-NMHydR (lane B), AaOXiF-AaOXiR (lane C), CupF-CupR (lane D), PucF-PucR (lane E), and SSDHF-SSDHR (lane F). (D and E) Intergenic PCR (D) and RT-PCR (E) amplifications using gDNA and cDNA, respectively, as the templates, with the primers sets HydAF-nmpABR (lanes A-B), nmpBCF/nmpBCR (lanes B-C), AaOXiF/nmpCDR (lanes C-D), CupF/PucR (lanes D-E), AaOXiF/nmpDER (lanes C-E), and nmpEFF/nmpEFR (lanes E-F). Negative-control (C−) reaction mixtures contained no DNA template. M, DNA marker (λ DNA EcoRI + HindIII ladder [Thermo Scientific]).

    Journal: Applied and Environmental Microbiology

    Article Title: Novel Metabolic Pathway for N-Methylpyrrolidone Degradation in Alicycliphilus sp. Strain BQ1

    doi: 10.1128/AEM.02136-17

    Figure Lengend Snippet: Cotranscription analysis of the nmpABCDEF gene cluster. (A) Positions of putative promoters (bent arrows), Rho-independent terminators (hairpin loops), and intragenic and intergenic regions to be amplified by specific primers between the nmpA-nmpB , nmpB-nmpC , nmpC-nmpD , nmpD-nmpE , nmpC-nmpE , and nmpE-nmpF genes. (B to E) Total RNA isolated from Alicycliphilus sp. strain BQ1 cells growing in MM-NMP was reverse transcribed and the cDNA synthesized used as the template for PCRs. (B) Positive and negative controls amplified using the primer set gyrAF-gyrAR, targeting the housekeeping gyrA gene; the templates were genomic DNA (gDNA) from Alicycliphilus sp. strain BQ1, RNA treated (DNase +) or not (DNase −) with RNase-free DNase, and synthesized cDNA. (C) nmpABCDEF intragenic RT-PCR amplifications using the primer sets HydAF-HydAR (lane A), NMHydF-NMHydR (lane B), AaOXiF-AaOXiR (lane C), CupF-CupR (lane D), PucF-PucR (lane E), and SSDHF-SSDHR (lane F). (D and E) Intergenic PCR (D) and RT-PCR (E) amplifications using gDNA and cDNA, respectively, as the templates, with the primers sets HydAF-nmpABR (lanes A-B), nmpBCF/nmpBCR (lanes B-C), AaOXiF/nmpCDR (lanes C-D), CupF/PucR (lanes D-E), AaOXiF/nmpDER (lanes C-E), and nmpEFF/nmpEFR (lanes E-F). Negative-control (C−) reaction mixtures contained no DNA template. M, DNA marker (λ DNA EcoRI + HindIII ladder [Thermo Scientific]).

    Article Snippet: Before the synthesis of cDNA, the absence of DNA from the DNase-treated RNA preparation was confirmed by a PCR using the gyrAF-gyrAR primer set, and no amplicon was produced. cDNA was synthesized from total RNA by use of a RevertAid First Strand cDNA synthesis kit (Thermo Scientific) according to the manufacturer's recommendations, using total RNA (2 μg) and a gene-specific primer mix (HydAR, NMHydR, AaOXiR, CupR, PucR, SSDHR, and gyrAR) (20 pmol).

    Techniques: Amplification, Isolation, Synthesized, Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Negative Control, Marker