mnase Millipore Search Results


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  • 99
    New England Biolabs micrococcal nuclease
    Micrococcal Nuclease, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 2706 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher subcellular protein fractionation kit
    Subcellular Protein Fractionation Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 3652 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore micrococcal nuclease
    shRNA-mediated inactivation of ATRX does not alter subtelomeric chromatin accessibility to <t>MNase.</t> (A) Chromatin isolated from 8-MG-BA glioma cells in which ATRX had been inactivated (shATRX) or not (shscrambled [shSCR]) was digested with MNase for the indicated times. (Left gel) Ethidium bromide (EtBr) staining of bulk chromatin. (Right gel) Southern blot with subtelomeric probe. (Far right) Quantification of the data. The signals obtained for mononucleosomes were normalized to the total signals measured for each time point (EtBr or Southern blot). (B) Chromatin samples from shATRX or shSCR 8-MG-BA cells were digested for 5 min with the indicated amounts of MNase (milliunits per microgram of DNA). (Far right) Quantification of the data.
    Micrococcal Nuclease, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 1991 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore rnase a
    Consensus GGUG-containing RNA oligonucleotide promotes the inhibitory effect of TLS on CBP/p300 HAT activities a , Co-immunoprecipitation (IP) of p300 and TLS from RNase A-treated HeLa cells. b, P300 HAT activity was measured using micrococcal nuclease (MNase) or DNase I pre-treated GST and GST-TLS in the presence of GGUG- or CCUC-oligonucleotide. * p
    Rnase A, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 29486 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore mgcl2
    Consensus GGUG-containing RNA oligonucleotide promotes the inhibitory effect of TLS on CBP/p300 HAT activities a , Co-immunoprecipitation (IP) of p300 and TLS from RNase A-treated HeLa cells. b, P300 HAT activity was measured using micrococcal nuclease (MNase) or DNase I pre-treated GST and GST-TLS in the presence of GGUG- or CCUC-oligonucleotide. * p
    Mgcl2, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 50653 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore pmsf
    Consensus GGUG-containing RNA oligonucleotide promotes the inhibitory effect of TLS on CBP/p300 HAT activities a , Co-immunoprecipitation (IP) of p300 and TLS from RNase A-treated HeLa cells. b, P300 HAT activity was measured using micrococcal nuclease (MNase) or DNase I pre-treated GST and GST-TLS in the presence of GGUG- or CCUC-oligonucleotide. * p
    Pmsf, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 32146 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore edta
    Consensus GGUG-containing RNA oligonucleotide promotes the inhibitory effect of TLS on CBP/p300 HAT activities a , Co-immunoprecipitation (IP) of p300 and TLS from RNase A-treated HeLa cells. b, P300 HAT activity was measured using micrococcal nuclease (MNase) or DNase I pre-treated GST and GST-TLS in the presence of GGUG- or CCUC-oligonucleotide. * p
    Edta, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 32373 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore lysis buffer
    Consensus GGUG-containing RNA oligonucleotide promotes the inhibitory effect of TLS on CBP/p300 HAT activities a , Co-immunoprecipitation (IP) of p300 and TLS from RNase A-treated HeLa cells. b, P300 HAT activity was measured using micrococcal nuclease (MNase) or DNase I pre-treated GST and GST-TLS in the presence of GGUG- or CCUC-oligonucleotide. * p
    Lysis Buffer, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 96097 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore buffer a
    PHF20 binds to DNA and transcriptionally up-regulates p53. A, association of PHF20 with chromatin. Cells were resuspended in <t>buffer</t> A with Nonidet P-40 (0.1%). Nuclei were collected by low speed centrifugation. Insoluble chromatin pellet (P3) was collected by centrifugation and resuspended in SDS-loading buffer. Release of chromatin-bound PHF20 proteins was detected following treatment of the cell nuclei with micrococcal nuclease ( MNase ). B, electrophoretic mobility shift assay was performed as described under “Experimental Procedures.” C, PHF20 possesses transcription factor activity. Three repeats of PHF20-binding consensus binding sequence were cloned to pGL3-basic vector ( 3 × PBCS-Luc ), which was co-transfected into MCF7 cells with indicated plasmids. Following incubation for 36 h, luciferase activity was measured and normalized to β-galactosidase. Results are the mean ± S.E. of three independent experiments performed in triplicate. D and E, PHF20 induces p53. MCF7/Tet-Off inducible PHF20 cells were cultured in the media without doxycycline ( Dox ) for the indicated time and then were immunoblotted with indicated antibodies ( D ) and were subjected to Northern blot analysis probed with p53 and β-actin ( E ). F, knockdown of PHF20 reduces p53 expression. MCF7 and HCT116 were transfected with PHF20 siRNA or control siRNA and subjected to immunoblotting ( left ) and Northern blot ( right ) analysis. G, PHF20 induces p53 promoter activity. Luciferase report assay was performed as described in C in MCF7 cells that were transfected with indicated plasmids. H, ChIP assay shows that PHF20 directly binds to p53 promoter in vivo . ChIP assay was performed with PHF20 antibody in HCT116 cells, and PCR was carried out using the primers spanning two PHF20-binding sites in the p53 promoter. IP , immunoprecipitation.
    Buffer A, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 12743 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore benzonase
    PHF20 binds to DNA and transcriptionally up-regulates p53. A, association of PHF20 with chromatin. Cells were resuspended in <t>buffer</t> A with Nonidet P-40 (0.1%). Nuclei were collected by low speed centrifugation. Insoluble chromatin pellet (P3) was collected by centrifugation and resuspended in SDS-loading buffer. Release of chromatin-bound PHF20 proteins was detected following treatment of the cell nuclei with micrococcal nuclease ( MNase ). B, electrophoretic mobility shift assay was performed as described under “Experimental Procedures.” C, PHF20 possesses transcription factor activity. Three repeats of PHF20-binding consensus binding sequence were cloned to pGL3-basic vector ( 3 × PBCS-Luc ), which was co-transfected into MCF7 cells with indicated plasmids. Following incubation for 36 h, luciferase activity was measured and normalized to β-galactosidase. Results are the mean ± S.E. of three independent experiments performed in triplicate. D and E, PHF20 induces p53. MCF7/Tet-Off inducible PHF20 cells were cultured in the media without doxycycline ( Dox ) for the indicated time and then were immunoblotted with indicated antibodies ( D ) and were subjected to Northern blot analysis probed with p53 and β-actin ( E ). F, knockdown of PHF20 reduces p53 expression. MCF7 and HCT116 were transfected with PHF20 siRNA or control siRNA and subjected to immunoblotting ( left ) and Northern blot ( right ) analysis. G, PHF20 induces p53 promoter activity. Luciferase report assay was performed as described in C in MCF7 cells that were transfected with indicated plasmids. H, ChIP assay shows that PHF20 directly binds to p53 promoter in vivo . ChIP assay was performed with PHF20 antibody in HCT116 cells, and PCR was carried out using the primers spanning two PHF20-binding sites in the p53 promoter. IP , immunoprecipitation.
    Benzonase, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 18516 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore protease inhibitor cocktail
    PHF20 binds to DNA and transcriptionally up-regulates p53. A, association of PHF20 with chromatin. Cells were resuspended in <t>buffer</t> A with Nonidet P-40 (0.1%). Nuclei were collected by low speed centrifugation. Insoluble chromatin pellet (P3) was collected by centrifugation and resuspended in SDS-loading buffer. Release of chromatin-bound PHF20 proteins was detected following treatment of the cell nuclei with micrococcal nuclease ( MNase ). B, electrophoretic mobility shift assay was performed as described under “Experimental Procedures.” C, PHF20 possesses transcription factor activity. Three repeats of PHF20-binding consensus binding sequence were cloned to pGL3-basic vector ( 3 × PBCS-Luc ), which was co-transfected into MCF7 cells with indicated plasmids. Following incubation for 36 h, luciferase activity was measured and normalized to β-galactosidase. Results are the mean ± S.E. of three independent experiments performed in triplicate. D and E, PHF20 induces p53. MCF7/Tet-Off inducible PHF20 cells were cultured in the media without doxycycline ( Dox ) for the indicated time and then were immunoblotted with indicated antibodies ( D ) and were subjected to Northern blot analysis probed with p53 and β-actin ( E ). F, knockdown of PHF20 reduces p53 expression. MCF7 and HCT116 were transfected with PHF20 siRNA or control siRNA and subjected to immunoblotting ( left ) and Northern blot ( right ) analysis. G, PHF20 induces p53 promoter activity. Luciferase report assay was performed as described in C in MCF7 cells that were transfected with indicated plasmids. H, ChIP assay shows that PHF20 directly binds to p53 promoter in vivo . ChIP assay was performed with PHF20 antibody in HCT116 cells, and PCR was carried out using the primers spanning two PHF20-binding sites in the p53 promoter. IP , immunoprecipitation.
    Protease Inhibitor Cocktail, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 134786 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore dnase i
    Deoxyribonuclease (DNase) I treatment abolished neutrophil extracellular traps (NETs) formation and ameliorated atherosclerotic burden. WT and peptidylarginine deiminase 4 (PAD4) KO mice were fed on high-fat chow (HFC) for 6 weeks, starting at 3-week HFC, 400 U of <t>DNase</t> I or vehicle control (PBS) was intravenously administered three times weekly until the end of experiments. (A) Representative confocal immunofluorescence microscopy images of aortic root sections stained for DAPI (blue), MPO (green), Ly-6G (red), and Cit-H3 (cyan). Data are representative of five mice in each group. (B) Quantification of NETs from (A) ( n = 5/group). (C) Representative images of aortic root sections stained for lipid (Oil Red O, red) and hematoxylin ( n = 5/group). (D) mRNA levels of IL-1β, TNF-α, CCL2, CXCL1, and CXCL2 in the aorta from WT and PAD4 KO mice placed on HFC for 6 weeks and administered with DNase I or vehicle control (PBS). mRNA levels were normalized to the GAPDH and expressed relative to levels measured in one of the vehicle control-treated WT mice ( n = 5/group). * p
    Dnase I, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 33878 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore dna samples
    Deoxyribonuclease (DNase) I treatment abolished neutrophil extracellular traps (NETs) formation and ameliorated atherosclerotic burden. WT and peptidylarginine deiminase 4 (PAD4) KO mice were fed on high-fat chow (HFC) for 6 weeks, starting at 3-week HFC, 400 U of <t>DNase</t> I or vehicle control (PBS) was intravenously administered three times weekly until the end of experiments. (A) Representative confocal immunofluorescence microscopy images of aortic root sections stained for DAPI (blue), MPO (green), Ly-6G (red), and Cit-H3 (cyan). Data are representative of five mice in each group. (B) Quantification of NETs from (A) ( n = 5/group). (C) Representative images of aortic root sections stained for lipid (Oil Red O, red) and hematoxylin ( n = 5/group). (D) mRNA levels of IL-1β, TNF-α, CCL2, CXCL1, and CXCL2 in the aorta from WT and PAD4 KO mice placed on HFC for 6 weeks and administered with DNase I or vehicle control (PBS). mRNA levels were normalized to the GAPDH and expressed relative to levels measured in one of the vehicle control-treated WT mice ( n = 5/group). * p
    Dna Samples, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 188 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore proteinase k
    Reverse splicing of the Ll.ltrB intron into the E1E2 DNA substrate. ( A ) Reverse splicing reactions with internally labeled DNA substrate. RNP particles (0.025 OD 260 unit) from cells grown at 37°C were incubated with the 129-bp 32 P-labeled E1E2 DNA substrate (150,000 cpm, ∼125 fmoles). The products were denatured with glyoxal and analyzed in a 1% agarose gel. (Lane 1 ) DNA substrate incubated in the absence of RNP particles; (lane 2 ) DNA substrate incubated with RNP particles from cells expressing pLI1; (lanes 3–6 ) reverse spliced products of pLI1 RNP particles treated with RNase A, alkali, S1 nuclease, or DNase I; (lanes 7,8 ) pLI1 RNP particles pretreated with RNase A or <t>proteinase</t> K prior to reverse splicing (see Materials and Methods); (lanes 9–11 ) DNA substrate incubated with RNP particles from cells containing pET-11a, pLI1–FS, and pLI1P, respectively. ( B ) Reverse splicing reaction with E1E2 DNA substrates labeled separately at each of the four termini. pLI1 RNP particles were incubated with 5′- or 3′-end-labeled DNA substrates (150,000 cpm; ∼250 fmoles of 5′-end-labeled substrates and ∼200 fmoles of 3′-end-labeled substrates), and the products were analyzed as above. Numbers to the left indicate DNA size markers (kb).
    Proteinase K, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 26156 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore anti flag m2 affinity gel
    Anticipated Results from ORGANIC profiling (A) Robust ORGANIC profiling across a range of input cell numbers and immunoprecipitation epitopes in yeast. Example ~50 kb window showing comparison of ORGANIC profiles of the ATPase Mot1 generated using different input cell numbers and epitopes: 250 mL starting culture with <t>FLAG-tagged</t> Mot1 (black track); 25, 50, and 100 mL starting cultures with FRB-GFP-tagged Mot1 and immunoprecipitated with FRB <t>antibody</t> (blue tracks); and 25, 50, and 100 mL starting cultures with FRB-GFP-tagged Mot1 and immunoprecipitated with GFP antibody (green tracks). (B) High resolution mapping of Trl with ORGANIC in Drosophila S2 cells. An example Trl-bound site revealed by X-ChIP-seq (black track) is resolved to a ~40bp segment by ORGANIC (brown track).
    Anti Flag M2 Affinity Gel, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 27094 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore formaldehyde
    Anticipated Results from ORGANIC profiling (A) Robust ORGANIC profiling across a range of input cell numbers and immunoprecipitation epitopes in yeast. Example ~50 kb window showing comparison of ORGANIC profiles of the ATPase Mot1 generated using different input cell numbers and epitopes: 250 mL starting culture with <t>FLAG-tagged</t> Mot1 (black track); 25, 50, and 100 mL starting cultures with FRB-GFP-tagged Mot1 and immunoprecipitated with FRB <t>antibody</t> (blue tracks); and 25, 50, and 100 mL starting cultures with FRB-GFP-tagged Mot1 and immunoprecipitated with GFP antibody (green tracks). (B) High resolution mapping of Trl with ORGANIC in Drosophila S2 cells. An example Trl-bound site revealed by X-ChIP-seq (black track) is resolved to a ~40bp segment by ORGANIC (brown track).
    Formaldehyde, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 15340 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore dtt
    Anticipated Results from ORGANIC profiling (A) Robust ORGANIC profiling across a range of input cell numbers and immunoprecipitation epitopes in yeast. Example ~50 kb window showing comparison of ORGANIC profiles of the ATPase Mot1 generated using different input cell numbers and epitopes: 250 mL starting culture with <t>FLAG-tagged</t> Mot1 (black track); 25, 50, and 100 mL starting cultures with FRB-GFP-tagged Mot1 and immunoprecipitated with FRB <t>antibody</t> (blue tracks); and 25, 50, and 100 mL starting cultures with FRB-GFP-tagged Mot1 and immunoprecipitated with GFP antibody (green tracks). (B) High resolution mapping of Trl with ORGANIC in Drosophila S2 cells. An example Trl-bound site revealed by X-ChIP-seq (black track) is resolved to a ~40bp segment by ORGANIC (brown track).
    Dtt, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 36382 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore staphylococcus aureus
    Anticipated Results from ORGANIC profiling (A) Robust ORGANIC profiling across a range of input cell numbers and immunoprecipitation epitopes in yeast. Example ~50 kb window showing comparison of ORGANIC profiles of the ATPase Mot1 generated using different input cell numbers and epitopes: 250 mL starting culture with <t>FLAG-tagged</t> Mot1 (black track); 25, 50, and 100 mL starting cultures with FRB-GFP-tagged Mot1 and immunoprecipitated with FRB <t>antibody</t> (blue tracks); and 25, 50, and 100 mL starting cultures with FRB-GFP-tagged Mot1 and immunoprecipitated with GFP antibody (green tracks). (B) High resolution mapping of Trl with ORGANIC in Drosophila S2 cells. An example Trl-bound site revealed by X-ChIP-seq (black track) is resolved to a ~40bp segment by ORGANIC (brown track).
    Staphylococcus Aureus, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 1321 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore protease inhibitors
    Anticipated Results from ORGANIC profiling (A) Robust ORGANIC profiling across a range of input cell numbers and immunoprecipitation epitopes in yeast. Example ~50 kb window showing comparison of ORGANIC profiles of the ATPase Mot1 generated using different input cell numbers and epitopes: 250 mL starting culture with <t>FLAG-tagged</t> Mot1 (black track); 25, 50, and 100 mL starting cultures with FRB-GFP-tagged Mot1 and immunoprecipitated with FRB <t>antibody</t> (blue tracks); and 25, 50, and 100 mL starting cultures with FRB-GFP-tagged Mot1 and immunoprecipitated with GFP antibody (green tracks). (B) High resolution mapping of Trl with ORGANIC in Drosophila S2 cells. An example Trl-bound site revealed by X-ChIP-seq (black track) is resolved to a ~40bp segment by ORGANIC (brown track).
    Protease Inhibitors, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 34531 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    shRNA-mediated inactivation of ATRX does not alter subtelomeric chromatin accessibility to MNase. (A) Chromatin isolated from 8-MG-BA glioma cells in which ATRX had been inactivated (shATRX) or not (shscrambled [shSCR]) was digested with MNase for the indicated times. (Left gel) Ethidium bromide (EtBr) staining of bulk chromatin. (Right gel) Southern blot with subtelomeric probe. (Far right) Quantification of the data. The signals obtained for mononucleosomes were normalized to the total signals measured for each time point (EtBr or Southern blot). (B) Chromatin samples from shATRX or shSCR 8-MG-BA cells were digested for 5 min with the indicated amounts of MNase (milliunits per microgram of DNA). (Far right) Quantification of the data.

    Journal: Molecular and Cellular Biology

    Article Title: Genetic Inactivation of ATRX Leads to a Decrease in the Amount of Telomeric Cohesin and Level of Telomere Transcription in Human Glioma Cells

    doi: 10.1128/MCB.01317-14

    Figure Lengend Snippet: shRNA-mediated inactivation of ATRX does not alter subtelomeric chromatin accessibility to MNase. (A) Chromatin isolated from 8-MG-BA glioma cells in which ATRX had been inactivated (shATRX) or not (shscrambled [shSCR]) was digested with MNase for the indicated times. (Left gel) Ethidium bromide (EtBr) staining of bulk chromatin. (Right gel) Southern blot with subtelomeric probe. (Far right) Quantification of the data. The signals obtained for mononucleosomes were normalized to the total signals measured for each time point (EtBr or Southern blot). (B) Chromatin samples from shATRX or shSCR 8-MG-BA cells were digested for 5 min with the indicated amounts of MNase (milliunits per microgram of DNA). (Far right) Quantification of the data.

    Article Snippet: Nuclei isolated from 107 cells were digested with 8 mU of micrococcal nuclease (MNase) (Sigma)/μg DNA at 37°C for the indicated times, as described previously ( ).

    Techniques: shRNA, Isolation, Staining, Southern Blot

    Consensus GGUG-containing RNA oligonucleotide promotes the inhibitory effect of TLS on CBP/p300 HAT activities a , Co-immunoprecipitation (IP) of p300 and TLS from RNase A-treated HeLa cells. b, P300 HAT activity was measured using micrococcal nuclease (MNase) or DNase I pre-treated GST and GST-TLS in the presence of GGUG- or CCUC-oligonucleotide. * p

    Journal: Nature

    Article Title: Induced ncRNAs Allosterically Modify RNA Binding Proteins in cis to Inhibit Transcription

    doi: 10.1038/nature06992

    Figure Lengend Snippet: Consensus GGUG-containing RNA oligonucleotide promotes the inhibitory effect of TLS on CBP/p300 HAT activities a , Co-immunoprecipitation (IP) of p300 and TLS from RNase A-treated HeLa cells. b, P300 HAT activity was measured using micrococcal nuclease (MNase) or DNase I pre-treated GST and GST-TLS in the presence of GGUG- or CCUC-oligonucleotide. * p

    Article Snippet: RNase A, micrococcal nuclease (MNase), DNase I, RNase H and RNase T1 treatment Whole cell extracts of GST proteins were treated with RNase A (25 μg/50 μl, Sigma), and incubated on ice for 20 min. GST-TLS in whole cell extracts was sequentially treated with 10 μg of micrococcal nuclease (Roche) in 100 mM sodium glycine (pH 8.6) and 10 mM CaCl2 at 37 °C for 4 min, 0 °C for 1 min, and room temperature for 20 min, and terminated by addition of 10 mM EGTA, followed with or without incubation of 100 pmol/20 μl of RNA oligonucleotides.

    Techniques: HAT Assay, Immunoprecipitation, Activity Assay

    PHF20 binds to DNA and transcriptionally up-regulates p53. A, association of PHF20 with chromatin. Cells were resuspended in buffer A with Nonidet P-40 (0.1%). Nuclei were collected by low speed centrifugation. Insoluble chromatin pellet (P3) was collected by centrifugation and resuspended in SDS-loading buffer. Release of chromatin-bound PHF20 proteins was detected following treatment of the cell nuclei with micrococcal nuclease ( MNase ). B, electrophoretic mobility shift assay was performed as described under “Experimental Procedures.” C, PHF20 possesses transcription factor activity. Three repeats of PHF20-binding consensus binding sequence were cloned to pGL3-basic vector ( 3 × PBCS-Luc ), which was co-transfected into MCF7 cells with indicated plasmids. Following incubation for 36 h, luciferase activity was measured and normalized to β-galactosidase. Results are the mean ± S.E. of three independent experiments performed in triplicate. D and E, PHF20 induces p53. MCF7/Tet-Off inducible PHF20 cells were cultured in the media without doxycycline ( Dox ) for the indicated time and then were immunoblotted with indicated antibodies ( D ) and were subjected to Northern blot analysis probed with p53 and β-actin ( E ). F, knockdown of PHF20 reduces p53 expression. MCF7 and HCT116 were transfected with PHF20 siRNA or control siRNA and subjected to immunoblotting ( left ) and Northern blot ( right ) analysis. G, PHF20 induces p53 promoter activity. Luciferase report assay was performed as described in C in MCF7 cells that were transfected with indicated plasmids. H, ChIP assay shows that PHF20 directly binds to p53 promoter in vivo . ChIP assay was performed with PHF20 antibody in HCT116 cells, and PCR was carried out using the primers spanning two PHF20-binding sites in the p53 promoter. IP , immunoprecipitation.

    Journal: The Journal of Biological Chemistry

    Article Title: Identification of Akt Interaction Protein PHF20/TZP That Transcriptionally Regulates p53

    doi: 10.1074/jbc.M111.333922

    Figure Lengend Snippet: PHF20 binds to DNA and transcriptionally up-regulates p53. A, association of PHF20 with chromatin. Cells were resuspended in buffer A with Nonidet P-40 (0.1%). Nuclei were collected by low speed centrifugation. Insoluble chromatin pellet (P3) was collected by centrifugation and resuspended in SDS-loading buffer. Release of chromatin-bound PHF20 proteins was detected following treatment of the cell nuclei with micrococcal nuclease ( MNase ). B, electrophoretic mobility shift assay was performed as described under “Experimental Procedures.” C, PHF20 possesses transcription factor activity. Three repeats of PHF20-binding consensus binding sequence were cloned to pGL3-basic vector ( 3 × PBCS-Luc ), which was co-transfected into MCF7 cells with indicated plasmids. Following incubation for 36 h, luciferase activity was measured and normalized to β-galactosidase. Results are the mean ± S.E. of three independent experiments performed in triplicate. D and E, PHF20 induces p53. MCF7/Tet-Off inducible PHF20 cells were cultured in the media without doxycycline ( Dox ) for the indicated time and then were immunoblotted with indicated antibodies ( D ) and were subjected to Northern blot analysis probed with p53 and β-actin ( E ). F, knockdown of PHF20 reduces p53 expression. MCF7 and HCT116 were transfected with PHF20 siRNA or control siRNA and subjected to immunoblotting ( left ) and Northern blot ( right ) analysis. G, PHF20 induces p53 promoter activity. Luciferase report assay was performed as described in C in MCF7 cells that were transfected with indicated plasmids. H, ChIP assay shows that PHF20 directly binds to p53 promoter in vivo . ChIP assay was performed with PHF20 antibody in HCT116 cells, and PCR was carried out using the primers spanning two PHF20-binding sites in the p53 promoter. IP , immunoprecipitation.

    Article Snippet: To release chromatin-bound proteins by nuclease treatment, cell nuclei were resuspended in prewarmed buffer A plus 1 m m CaCl2 and 0.3 units of micrococcal nuclease (Sigma).

    Techniques: Centrifugation, Electrophoretic Mobility Shift Assay, Activity Assay, Binding Assay, Sequencing, Clone Assay, Plasmid Preparation, Transfection, Incubation, Luciferase, Cell Culture, Northern Blot, Expressing, Chromatin Immunoprecipitation, In Vivo, Polymerase Chain Reaction, Immunoprecipitation

    Deoxyribonuclease (DNase) I treatment abolished neutrophil extracellular traps (NETs) formation and ameliorated atherosclerotic burden. WT and peptidylarginine deiminase 4 (PAD4) KO mice were fed on high-fat chow (HFC) for 6 weeks, starting at 3-week HFC, 400 U of DNase I or vehicle control (PBS) was intravenously administered three times weekly until the end of experiments. (A) Representative confocal immunofluorescence microscopy images of aortic root sections stained for DAPI (blue), MPO (green), Ly-6G (red), and Cit-H3 (cyan). Data are representative of five mice in each group. (B) Quantification of NETs from (A) ( n = 5/group). (C) Representative images of aortic root sections stained for lipid (Oil Red O, red) and hematoxylin ( n = 5/group). (D) mRNA levels of IL-1β, TNF-α, CCL2, CXCL1, and CXCL2 in the aorta from WT and PAD4 KO mice placed on HFC for 6 weeks and administered with DNase I or vehicle control (PBS). mRNA levels were normalized to the GAPDH and expressed relative to levels measured in one of the vehicle control-treated WT mice ( n = 5/group). * p

    Journal: Frontiers in Immunology

    Article Title: Myeloid-Specific Deletion of Peptidylarginine Deiminase 4 Mitigates Atherosclerosis

    doi: 10.3389/fimmu.2018.01680

    Figure Lengend Snippet: Deoxyribonuclease (DNase) I treatment abolished neutrophil extracellular traps (NETs) formation and ameliorated atherosclerotic burden. WT and peptidylarginine deiminase 4 (PAD4) KO mice were fed on high-fat chow (HFC) for 6 weeks, starting at 3-week HFC, 400 U of DNase I or vehicle control (PBS) was intravenously administered three times weekly until the end of experiments. (A) Representative confocal immunofluorescence microscopy images of aortic root sections stained for DAPI (blue), MPO (green), Ly-6G (red), and Cit-H3 (cyan). Data are representative of five mice in each group. (B) Quantification of NETs from (A) ( n = 5/group). (C) Representative images of aortic root sections stained for lipid (Oil Red O, red) and hematoxylin ( n = 5/group). (D) mRNA levels of IL-1β, TNF-α, CCL2, CXCL1, and CXCL2 in the aorta from WT and PAD4 KO mice placed on HFC for 6 weeks and administered with DNase I or vehicle control (PBS). mRNA levels were normalized to the GAPDH and expressed relative to levels measured in one of the vehicle control-treated WT mice ( n = 5/group). * p

    Article Snippet: To disrupt NETs, 40 µl DNase I (10,000 U/ml) (Sigma-Aldrich) was added to 500 µl supernatants from both conditions for 3 h at 37°C, as previously described.

    Techniques: Mouse Assay, Immunofluorescence, Microscopy, Staining

    Neutrophil extracellular traps (NETs) present in atherosclerotic lesions stimulate inflammatory responses in arterial macrophages. (A) Bone marrow (BM)-derived neutrophils were stimulated in the absence (UN) or presence (A23187) of A23187 for 4 h. Half the UN-NETs or A23187-NETs were digested by deoxyribonuclease (DNase) I. NETs were quantified by measuring Cit-H3-DNA complexes on ELISA. (B) BM-derived macrophages were stimulated with UN-NETs (BMN-UN), UN-NETs treated with DNase I (BMN-UN-DNase I), A23187-NETs (BMN-A23), or A23187-NETs treated with DNase I (BMN-A23-DNase I) for 4 h. Gene expression levels of IL-1β, CCL2, CXCL1, and CXCL2 were determined. mRNA levels were normalized to GAPDH and expressed relative to levels measured in one of the BMN-UN conditions (C) . WT and peptidylarginine deiminase 4 (PAD4) KO mice were fed high-fat chow (HFC) for 10 weeks, and aortic root sections were stained for indicated markers and observed by confocal immunofluorescence microscopy. Lower panel represents enlarged area of the white squares in upper panels. Blue: DAPI, green: F4/80, red: IL-1β, and magenta: Cit-H3. Data are representative of four mice in two independent experiments. (D) WT and PAD4 KO mice were fed HFC for 10 weeks, and aortic root sections were stained for indicated markers and observed by confocal immunofluorescence microscopy. Lower panel represents enlarged area of the white squares in upper panels. Blue: DAPI, green: F4/80, red: CCL2, and magenta: Cit-H3. Data are representative of four mice in two independent experiments. * p

    Journal: Frontiers in Immunology

    Article Title: Myeloid-Specific Deletion of Peptidylarginine Deiminase 4 Mitigates Atherosclerosis

    doi: 10.3389/fimmu.2018.01680

    Figure Lengend Snippet: Neutrophil extracellular traps (NETs) present in atherosclerotic lesions stimulate inflammatory responses in arterial macrophages. (A) Bone marrow (BM)-derived neutrophils were stimulated in the absence (UN) or presence (A23187) of A23187 for 4 h. Half the UN-NETs or A23187-NETs were digested by deoxyribonuclease (DNase) I. NETs were quantified by measuring Cit-H3-DNA complexes on ELISA. (B) BM-derived macrophages were stimulated with UN-NETs (BMN-UN), UN-NETs treated with DNase I (BMN-UN-DNase I), A23187-NETs (BMN-A23), or A23187-NETs treated with DNase I (BMN-A23-DNase I) for 4 h. Gene expression levels of IL-1β, CCL2, CXCL1, and CXCL2 were determined. mRNA levels were normalized to GAPDH and expressed relative to levels measured in one of the BMN-UN conditions (C) . WT and peptidylarginine deiminase 4 (PAD4) KO mice were fed high-fat chow (HFC) for 10 weeks, and aortic root sections were stained for indicated markers and observed by confocal immunofluorescence microscopy. Lower panel represents enlarged area of the white squares in upper panels. Blue: DAPI, green: F4/80, red: IL-1β, and magenta: Cit-H3. Data are representative of four mice in two independent experiments. (D) WT and PAD4 KO mice were fed HFC for 10 weeks, and aortic root sections were stained for indicated markers and observed by confocal immunofluorescence microscopy. Lower panel represents enlarged area of the white squares in upper panels. Blue: DAPI, green: F4/80, red: CCL2, and magenta: Cit-H3. Data are representative of four mice in two independent experiments. * p

    Article Snippet: To disrupt NETs, 40 µl DNase I (10,000 U/ml) (Sigma-Aldrich) was added to 500 µl supernatants from both conditions for 3 h at 37°C, as previously described.

    Techniques: Derivative Assay, Enzyme-linked Immunosorbent Assay, Expressing, Mouse Assay, Staining, Immunofluorescence, Microscopy

    Reverse splicing of the Ll.ltrB intron into the E1E2 DNA substrate. ( A ) Reverse splicing reactions with internally labeled DNA substrate. RNP particles (0.025 OD 260 unit) from cells grown at 37°C were incubated with the 129-bp 32 P-labeled E1E2 DNA substrate (150,000 cpm, ∼125 fmoles). The products were denatured with glyoxal and analyzed in a 1% agarose gel. (Lane 1 ) DNA substrate incubated in the absence of RNP particles; (lane 2 ) DNA substrate incubated with RNP particles from cells expressing pLI1; (lanes 3–6 ) reverse spliced products of pLI1 RNP particles treated with RNase A, alkali, S1 nuclease, or DNase I; (lanes 7,8 ) pLI1 RNP particles pretreated with RNase A or proteinase K prior to reverse splicing (see Materials and Methods); (lanes 9–11 ) DNA substrate incubated with RNP particles from cells containing pET-11a, pLI1–FS, and pLI1P, respectively. ( B ) Reverse splicing reaction with E1E2 DNA substrates labeled separately at each of the four termini. pLI1 RNP particles were incubated with 5′- or 3′-end-labeled DNA substrates (150,000 cpm; ∼250 fmoles of 5′-end-labeled substrates and ∼200 fmoles of 3′-end-labeled substrates), and the products were analyzed as above. Numbers to the left indicate DNA size markers (kb).

    Journal: Genes & Development

    Article Title: A bacterial group II intron encoding reverse transcriptase, maturase, and DNA endonuclease activities: biochemical demonstration of maturase activity and insertion of new genetic information within the intron

    doi:

    Figure Lengend Snippet: Reverse splicing of the Ll.ltrB intron into the E1E2 DNA substrate. ( A ) Reverse splicing reactions with internally labeled DNA substrate. RNP particles (0.025 OD 260 unit) from cells grown at 37°C were incubated with the 129-bp 32 P-labeled E1E2 DNA substrate (150,000 cpm, ∼125 fmoles). The products were denatured with glyoxal and analyzed in a 1% agarose gel. (Lane 1 ) DNA substrate incubated in the absence of RNP particles; (lane 2 ) DNA substrate incubated with RNP particles from cells expressing pLI1; (lanes 3–6 ) reverse spliced products of pLI1 RNP particles treated with RNase A, alkali, S1 nuclease, or DNase I; (lanes 7,8 ) pLI1 RNP particles pretreated with RNase A or proteinase K prior to reverse splicing (see Materials and Methods); (lanes 9–11 ) DNA substrate incubated with RNP particles from cells containing pET-11a, pLI1–FS, and pLI1P, respectively. ( B ) Reverse splicing reaction with E1E2 DNA substrates labeled separately at each of the four termini. pLI1 RNP particles were incubated with 5′- or 3′-end-labeled DNA substrates (150,000 cpm; ∼250 fmoles of 5′-end-labeled substrates and ∼200 fmoles of 3′-end-labeled substrates), and the products were analyzed as above. Numbers to the left indicate DNA size markers (kb).

    Article Snippet: The products were incubated with proteinase K (Sigma; 1 μg for 5 min at 25°C), extracted with phenol–chloroform–isoamyl alcohol (25:24:1), ethanol precipitated, and analyzed in a denaturing 4% polyacrylamide gel.

    Techniques: Labeling, Incubation, Agarose Gel Electrophoresis, Expressing, Positron Emission Tomography

    Reconstitution of Ll.ltrB intron endonuclease activity. ( A ) Reconstitution and sensitivity to pretreatment with RNase and protease. The endonuclease was reconstituted with spliced pLI2–ΔORF / Bam HI RNA and MNase-digested RNP particles and used for reverse splicing assays with internally labeled E1E2 DNA substrate (∼30 fmoles). (Lane 1 ) DNA substrate incubated without RNP particles; (lane 2 ) DNA substrate incubated with in vitro-spliced pLI2–ΔORF RNA alone; (lane 3 ) DNA substrate incubated with MNase-digested RNP particles alone; (lane 4 ) DNA substrate incubated with endonuclease reconstituted by mixing MNase-digested RNP particles with in vitro spliced pLI2–ΔORF RNA; (lanes 5,6 ) reconstituted endonuclease preincubated with RNase or proteinase K prior to the reverse splicing reaction (see Methods). Reverse-spliced products were denatured with glyoxal and analyzed in a 1% agarose gel. Numbers to the left indicate size markers. ( B ) Reconstitution with full-length and modified intron RNAs. Reverse splicing into the E1E2 DNA substrate (∼60 fmoles) was carried out with endonucleases reconstituted with the following in vitro spliced RNAs: (Lane 1 ) pLI2–ΔORF; (lane 2 ) pLI1; (lane 3 ) pLI2–ΔORF kan R . The products were analyzed as above.

    Journal: Genes & Development

    Article Title: A bacterial group II intron encoding reverse transcriptase, maturase, and DNA endonuclease activities: biochemical demonstration of maturase activity and insertion of new genetic information within the intron

    doi:

    Figure Lengend Snippet: Reconstitution of Ll.ltrB intron endonuclease activity. ( A ) Reconstitution and sensitivity to pretreatment with RNase and protease. The endonuclease was reconstituted with spliced pLI2–ΔORF / Bam HI RNA and MNase-digested RNP particles and used for reverse splicing assays with internally labeled E1E2 DNA substrate (∼30 fmoles). (Lane 1 ) DNA substrate incubated without RNP particles; (lane 2 ) DNA substrate incubated with in vitro-spliced pLI2–ΔORF RNA alone; (lane 3 ) DNA substrate incubated with MNase-digested RNP particles alone; (lane 4 ) DNA substrate incubated with endonuclease reconstituted by mixing MNase-digested RNP particles with in vitro spliced pLI2–ΔORF RNA; (lanes 5,6 ) reconstituted endonuclease preincubated with RNase or proteinase K prior to the reverse splicing reaction (see Methods). Reverse-spliced products were denatured with glyoxal and analyzed in a 1% agarose gel. Numbers to the left indicate size markers. ( B ) Reconstitution with full-length and modified intron RNAs. Reverse splicing into the E1E2 DNA substrate (∼60 fmoles) was carried out with endonucleases reconstituted with the following in vitro spliced RNAs: (Lane 1 ) pLI2–ΔORF; (lane 2 ) pLI1; (lane 3 ) pLI2–ΔORF kan R . The products were analyzed as above.

    Article Snippet: The products were incubated with proteinase K (Sigma; 1 μg for 5 min at 25°C), extracted with phenol–chloroform–isoamyl alcohol (25:24:1), ethanol precipitated, and analyzed in a denaturing 4% polyacrylamide gel.

    Techniques: Activity Assay, Labeling, Incubation, In Vitro, Agarose Gel Electrophoresis, Modification

    Anticipated Results from ORGANIC profiling (A) Robust ORGANIC profiling across a range of input cell numbers and immunoprecipitation epitopes in yeast. Example ~50 kb window showing comparison of ORGANIC profiles of the ATPase Mot1 generated using different input cell numbers and epitopes: 250 mL starting culture with FLAG-tagged Mot1 (black track); 25, 50, and 100 mL starting cultures with FRB-GFP-tagged Mot1 and immunoprecipitated with FRB antibody (blue tracks); and 25, 50, and 100 mL starting cultures with FRB-GFP-tagged Mot1 and immunoprecipitated with GFP antibody (green tracks). (B) High resolution mapping of Trl with ORGANIC in Drosophila S2 cells. An example Trl-bound site revealed by X-ChIP-seq (black track) is resolved to a ~40bp segment by ORGANIC (brown track).

    Journal: Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.]

    Article Title: Mapping regulatory factors by immunoprecipitation from native chromatin

    doi: 10.1002/0471142727.mb2131s110

    Figure Lengend Snippet: Anticipated Results from ORGANIC profiling (A) Robust ORGANIC profiling across a range of input cell numbers and immunoprecipitation epitopes in yeast. Example ~50 kb window showing comparison of ORGANIC profiles of the ATPase Mot1 generated using different input cell numbers and epitopes: 250 mL starting culture with FLAG-tagged Mot1 (black track); 25, 50, and 100 mL starting cultures with FRB-GFP-tagged Mot1 and immunoprecipitated with FRB antibody (blue tracks); and 25, 50, and 100 mL starting cultures with FRB-GFP-tagged Mot1 and immunoprecipitated with GFP antibody (green tracks). (B) High resolution mapping of Trl with ORGANIC in Drosophila S2 cells. An example Trl-bound site revealed by X-ChIP-seq (black track) is resolved to a ~40bp segment by ORGANIC (brown track).

    Article Snippet: - 5 M NaCl - Anti-FLAG M2 magnetic beads (Sigma-Aldrich, Cat. No. A2220) - IP Wash Buffer 10 mM phosphate phosphate buffer, pH 7.5, 0.75 mM EDTA, 70 mM NaCl - RNase A (10 mg/mL, Thermo Scientific, Cat No EN0531) - Proteinase K (20 mg/mL, Life Technologies, Cat. No. AM2542) - Phenol/Chlorophorm/Isoamyl alcohol - Glycogen (20 mg/mL, Life Technologies, Cat. No. 10814-010) - 100% ethanol - 70% ethanol - TE0.1 buffer (see Recipes) - Quant-iT PicoGreen dsDNA assay kit. (Life Technologies, Cat. No. )

    Techniques: Immunoprecipitation, Generated, Chromatin Immunoprecipitation