mnase Worthington Biochemical Search Results


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  • 99
    Worthington Biochemical nuclease micrococcal
    Nuclease Micrococcal, supplied by Worthington Biochemical, used in various techniques. Bioz Stars score: 99/100, based on 106 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    Millipore phosphodiesterase ii
    Phosphodiesterase Ii, supplied by Millipore, used in various techniques. Bioz Stars score: 96/100, based on 82 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Worthington Biochemical dnase i
    Summary of the nucleosomal organization of the active and inactive HPRT ) (vertical rectangles, their binding sites); bent arrow, position of the two major transcription initiation sites on the HPRT promoter; white box, first exon of the HPRT gene; ATG, position of the translation initiation site; thick vertical arrows, approximate positions and relative intensities of the major MNase cleavage sites in the HPRT promoter; clusters of thin triangular dashed arrows and barbed arrows, positions of the high-resolution <t>DNase</t> I cleavage ladders suggestive of rotationally positioned nucleosomes on the active and inactive HPRT promoters, respectively, in permeabilized cells (the slightly longer arrows on the lower strand in the inactive allele indicate that this ladder was unusually prominent); hatched bars, approximate locations of the DNase I-hypersensitive sites on the active HPRT promoter in permeabilized cells; All position numbers are relative to the translation initiation site.
    Dnase I, supplied by Worthington Biochemical, used in various techniques. Bioz Stars score: 99/100, based on 4059 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Worthington Biochemical spleen phosphodiesterase
    Summary of the nucleosomal organization of the active and inactive HPRT ) (vertical rectangles, their binding sites); bent arrow, position of the two major transcription initiation sites on the HPRT promoter; white box, first exon of the HPRT gene; ATG, position of the translation initiation site; thick vertical arrows, approximate positions and relative intensities of the major MNase cleavage sites in the HPRT promoter; clusters of thin triangular dashed arrows and barbed arrows, positions of the high-resolution <t>DNase</t> I cleavage ladders suggestive of rotationally positioned nucleosomes on the active and inactive HPRT promoters, respectively, in permeabilized cells (the slightly longer arrows on the lower strand in the inactive allele indicate that this ladder was unusually prominent); hatched bars, approximate locations of the DNase I-hypersensitive sites on the active HPRT promoter in permeabilized cells; All position numbers are relative to the translation initiation site.
    Spleen Phosphodiesterase, supplied by Worthington Biochemical, used in various techniques. Bioz Stars score: 93/100, based on 30 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Worthington Biochemical calf thymus dna
    Summary of the nucleosomal organization of the active and inactive HPRT ) (vertical rectangles, their binding sites); bent arrow, position of the two major transcription initiation sites on the HPRT promoter; white box, first exon of the HPRT gene; ATG, position of the translation initiation site; thick vertical arrows, approximate positions and relative intensities of the major MNase cleavage sites in the HPRT promoter; clusters of thin triangular dashed arrows and barbed arrows, positions of the high-resolution <t>DNase</t> I cleavage ladders suggestive of rotationally positioned nucleosomes on the active and inactive HPRT promoters, respectively, in permeabilized cells (the slightly longer arrows on the lower strand in the inactive allele indicate that this ladder was unusually prominent); hatched bars, approximate locations of the DNase I-hypersensitive sites on the active HPRT promoter in permeabilized cells; All position numbers are relative to the translation initiation site.
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    Millipore micrococcal nuclease
    Summary of the nucleosomal organization of the active and inactive HPRT ) (vertical rectangles, their binding sites); bent arrow, position of the two major transcription initiation sites on the HPRT promoter; white box, first exon of the HPRT gene; ATG, position of the translation initiation site; thick vertical arrows, approximate positions and relative intensities of the major MNase cleavage sites in the HPRT promoter; clusters of thin triangular dashed arrows and barbed arrows, positions of the high-resolution <t>DNase</t> I cleavage ladders suggestive of rotationally positioned nucleosomes on the active and inactive HPRT promoters, respectively, in permeabilized cells (the slightly longer arrows on the lower strand in the inactive allele indicate that this ladder was unusually prominent); hatched bars, approximate locations of the DNase I-hypersensitive sites on the active HPRT promoter in permeabilized cells; All position numbers are relative to the translation initiation site.
    Micrococcal Nuclease, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 1897 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore potato apyrase
    Summary of the nucleosomal organization of the active and inactive HPRT ) (vertical rectangles, their binding sites); bent arrow, position of the two major transcription initiation sites on the HPRT promoter; white box, first exon of the HPRT gene; ATG, position of the translation initiation site; thick vertical arrows, approximate positions and relative intensities of the major MNase cleavage sites in the HPRT promoter; clusters of thin triangular dashed arrows and barbed arrows, positions of the high-resolution <t>DNase</t> I cleavage ladders suggestive of rotationally positioned nucleosomes on the active and inactive HPRT promoters, respectively, in permeabilized cells (the slightly longer arrows on the lower strand in the inactive allele indicate that this ladder was unusually prominent); hatched bars, approximate locations of the DNase I-hypersensitive sites on the active HPRT promoter in permeabilized cells; All position numbers are relative to the translation initiation site.
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    Qiagen rnase a
    Summary of the nucleosomal organization of the active and inactive HPRT ) (vertical rectangles, their binding sites); bent arrow, position of the two major transcription initiation sites on the HPRT promoter; white box, first exon of the HPRT gene; ATG, position of the translation initiation site; thick vertical arrows, approximate positions and relative intensities of the major MNase cleavage sites in the HPRT promoter; clusters of thin triangular dashed arrows and barbed arrows, positions of the high-resolution <t>DNase</t> I cleavage ladders suggestive of rotationally positioned nucleosomes on the active and inactive HPRT promoters, respectively, in permeabilized cells (the slightly longer arrows on the lower strand in the inactive allele indicate that this ladder was unusually prominent); hatched bars, approximate locations of the DNase I-hypersensitive sites on the active HPRT promoter in permeabilized cells; All position numbers are relative to the translation initiation site.
    Rnase A, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 10710 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    BioSpec glass beads
    Summary of the nucleosomal organization of the active and inactive HPRT ) (vertical rectangles, their binding sites); bent arrow, position of the two major transcription initiation sites on the HPRT promoter; white box, first exon of the HPRT gene; ATG, position of the translation initiation site; thick vertical arrows, approximate positions and relative intensities of the major MNase cleavage sites in the HPRT promoter; clusters of thin triangular dashed arrows and barbed arrows, positions of the high-resolution <t>DNase</t> I cleavage ladders suggestive of rotationally positioned nucleosomes on the active and inactive HPRT promoters, respectively, in permeabilized cells (the slightly longer arrows on the lower strand in the inactive allele indicate that this ladder was unusually prominent); hatched bars, approximate locations of the DNase I-hypersensitive sites on the active HPRT promoter in permeabilized cells; All position numbers are relative to the translation initiation site.
    Glass Beads, supplied by BioSpec, used in various techniques. Bioz Stars score: 93/100, based on 5095 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Bio-Rad acrylamide solution
    Summary of the nucleosomal organization of the active and inactive HPRT ) (vertical rectangles, their binding sites); bent arrow, position of the two major transcription initiation sites on the HPRT promoter; white box, first exon of the HPRT gene; ATG, position of the translation initiation site; thick vertical arrows, approximate positions and relative intensities of the major MNase cleavage sites in the HPRT promoter; clusters of thin triangular dashed arrows and barbed arrows, positions of the high-resolution <t>DNase</t> I cleavage ladders suggestive of rotationally positioned nucleosomes on the active and inactive HPRT promoters, respectively, in permeabilized cells (the slightly longer arrows on the lower strand in the inactive allele indicate that this ladder was unusually prominent); hatched bars, approximate locations of the DNase I-hypersensitive sites on the active HPRT promoter in permeabilized cells; All position numbers are relative to the translation initiation site.
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    Millipore alkaline phosphatase
    Summary of the nucleosomal organization of the active and inactive HPRT ) (vertical rectangles, their binding sites); bent arrow, position of the two major transcription initiation sites on the HPRT promoter; white box, first exon of the HPRT gene; ATG, position of the translation initiation site; thick vertical arrows, approximate positions and relative intensities of the major MNase cleavage sites in the HPRT promoter; clusters of thin triangular dashed arrows and barbed arrows, positions of the high-resolution <t>DNase</t> I cleavage ladders suggestive of rotationally positioned nucleosomes on the active and inactive HPRT promoters, respectively, in permeabilized cells (the slightly longer arrows on the lower strand in the inactive allele indicate that this ladder was unusually prominent); hatched bars, approximate locations of the DNase I-hypersensitive sites on the active HPRT promoter in permeabilized cells; All position numbers are relative to the translation initiation site.
    Alkaline Phosphatase, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 8519 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Thermo Fisher anti rabbit igg magnetic beads
    Summary of the nucleosomal organization of the active and inactive HPRT ) (vertical rectangles, their binding sites); bent arrow, position of the two major transcription initiation sites on the HPRT promoter; white box, first exon of the HPRT gene; ATG, position of the translation initiation site; thick vertical arrows, approximate positions and relative intensities of the major MNase cleavage sites in the HPRT promoter; clusters of thin triangular dashed arrows and barbed arrows, positions of the high-resolution <t>DNase</t> I cleavage ladders suggestive of rotationally positioned nucleosomes on the active and inactive HPRT promoters, respectively, in permeabilized cells (the slightly longer arrows on the lower strand in the inactive allele indicate that this ladder was unusually prominent); hatched bars, approximate locations of the DNase I-hypersensitive sites on the active HPRT promoter in permeabilized cells; All position numbers are relative to the translation initiation site.
    Anti Rabbit Igg Magnetic Beads, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 107 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher anti mouse igg
    Summary of the nucleosomal organization of the active and inactive HPRT ) (vertical rectangles, their binding sites); bent arrow, position of the two major transcription initiation sites on the HPRT promoter; white box, first exon of the HPRT gene; ATG, position of the translation initiation site; thick vertical arrows, approximate positions and relative intensities of the major MNase cleavage sites in the HPRT promoter; clusters of thin triangular dashed arrows and barbed arrows, positions of the high-resolution <t>DNase</t> I cleavage ladders suggestive of rotationally positioned nucleosomes on the active and inactive HPRT promoters, respectively, in permeabilized cells (the slightly longer arrows on the lower strand in the inactive allele indicate that this ladder was unusually prominent); hatched bars, approximate locations of the DNase I-hypersensitive sites on the active HPRT promoter in permeabilized cells; All position numbers are relative to the translation initiation site.
    Anti Mouse Igg, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 6123 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher anti v5 tag
    Summary of the nucleosomal organization of the active and inactive HPRT ) (vertical rectangles, their binding sites); bent arrow, position of the two major transcription initiation sites on the HPRT promoter; white box, first exon of the HPRT gene; ATG, position of the translation initiation site; thick vertical arrows, approximate positions and relative intensities of the major MNase cleavage sites in the HPRT promoter; clusters of thin triangular dashed arrows and barbed arrows, positions of the high-resolution <t>DNase</t> I cleavage ladders suggestive of rotationally positioned nucleosomes on the active and inactive HPRT promoters, respectively, in permeabilized cells (the slightly longer arrows on the lower strand in the inactive allele indicate that this ladder was unusually prominent); hatched bars, approximate locations of the DNase I-hypersensitive sites on the active HPRT promoter in permeabilized cells; All position numbers are relative to the translation initiation site.
    Anti V5 Tag, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 126 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore deoxyguanosine
    (A) LC separation of a mixture of authentic standards of 2′-deoxynucleosides 2′-deoxycytidine, 2′-deoxythymidine, <t>2′-deoxyguanosine,</t> 2′-deoxyadenosine and N 6 -methyl-2′-deoxyadenosine plus dideoxyinosine (dC, dG, dT, dA, N 6 -medA and ddI respectively). (B) N 6 -methyl-2′-deoxyadenosine detected by LC/ESI(+)-MS/MS SRM mode at transition 266 > 150, and (C) putative DNA adduct VII detected by LC/ESI(+)-MS/MS SRM mode at transition 266 > 150. The peak that was detected at 9.75 min occurred due to the abundantly detected sodiated ion of 2′-deoxythymidine which was detected at SRM transition 265 > 149. LC/ESI (+)-MS/MS, liquid chromatography electrospray ionization-tandem mass spectrometry in positive ionization mode; SRM, single reaction monitoring.
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    Millipore bacterial alkaline phosphatase type iii
    (A) LC separation of a mixture of authentic standards of 2′-deoxynucleosides 2′-deoxycytidine, 2′-deoxythymidine, <t>2′-deoxyguanosine,</t> 2′-deoxyadenosine and N 6 -methyl-2′-deoxyadenosine plus dideoxyinosine (dC, dG, dT, dA, N 6 -medA and ddI respectively). (B) N 6 -methyl-2′-deoxyadenosine detected by LC/ESI(+)-MS/MS SRM mode at transition 266 > 150, and (C) putative DNA adduct VII detected by LC/ESI(+)-MS/MS SRM mode at transition 266 > 150. The peak that was detected at 9.75 min occurred due to the abundantly detected sodiated ion of 2′-deoxythymidine which was detected at SRM transition 265 > 149. LC/ESI (+)-MS/MS, liquid chromatography electrospray ionization-tandem mass spectrometry in positive ionization mode; SRM, single reaction monitoring.
    Bacterial Alkaline Phosphatase Type Iii, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Branson Ultrasonics branson 250d sonifier
    (A) LC separation of a mixture of authentic standards of 2′-deoxynucleosides 2′-deoxycytidine, 2′-deoxythymidine, <t>2′-deoxyguanosine,</t> 2′-deoxyadenosine and N 6 -methyl-2′-deoxyadenosine plus dideoxyinosine (dC, dG, dT, dA, N 6 -medA and ddI respectively). (B) N 6 -methyl-2′-deoxyadenosine detected by LC/ESI(+)-MS/MS SRM mode at transition 266 > 150, and (C) putative DNA adduct VII detected by LC/ESI(+)-MS/MS SRM mode at transition 266 > 150. The peak that was detected at 9.75 min occurred due to the abundantly detected sodiated ion of 2′-deoxythymidine which was detected at SRM transition 265 > 149. LC/ESI (+)-MS/MS, liquid chromatography electrospray ionization-tandem mass spectrometry in positive ionization mode; SRM, single reaction monitoring.
    Branson 250d Sonifier, supplied by Branson Ultrasonics, used in various techniques. Bioz Stars score: 90/100, based on 21 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore buffer a
    (A) LC separation of a mixture of authentic standards of 2′-deoxynucleosides 2′-deoxycytidine, 2′-deoxythymidine, <t>2′-deoxyguanosine,</t> 2′-deoxyadenosine and N 6 -methyl-2′-deoxyadenosine plus dideoxyinosine (dC, dG, dT, dA, N 6 -medA and ddI respectively). (B) N 6 -methyl-2′-deoxyadenosine detected by LC/ESI(+)-MS/MS SRM mode at transition 266 > 150, and (C) putative DNA adduct VII detected by LC/ESI(+)-MS/MS SRM mode at transition 266 > 150. The peak that was detected at 9.75 min occurred due to the abundantly detected sodiated ion of 2′-deoxythymidine which was detected at SRM transition 265 > 149. LC/ESI (+)-MS/MS, liquid chromatography electrospray ionization-tandem mass spectrometry in positive ionization mode; SRM, single reaction monitoring.
    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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    Fisher Scientific sodium carbonate
    (A) LC separation of a mixture of authentic standards of 2′-deoxynucleosides 2′-deoxycytidine, 2′-deoxythymidine, <t>2′-deoxyguanosine,</t> 2′-deoxyadenosine and N 6 -methyl-2′-deoxyadenosine plus dideoxyinosine (dC, dG, dT, dA, N 6 -medA and ddI respectively). (B) N 6 -methyl-2′-deoxyadenosine detected by LC/ESI(+)-MS/MS SRM mode at transition 266 > 150, and (C) putative DNA adduct VII detected by LC/ESI(+)-MS/MS SRM mode at transition 266 > 150. The peak that was detected at 9.75 min occurred due to the abundantly detected sodiated ion of 2′-deoxythymidine which was detected at SRM transition 265 > 149. LC/ESI (+)-MS/MS, liquid chromatography electrospray ionization-tandem mass spectrometry in positive ionization mode; SRM, single reaction monitoring.
    Sodium Carbonate, supplied by Fisher Scientific, used in various techniques. Bioz Stars score: 93/100, based on 157 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Bio-Rad tetramethylethylenediamine temed
    (A) LC separation of a mixture of authentic standards of 2′-deoxynucleosides 2′-deoxycytidine, 2′-deoxythymidine, <t>2′-deoxyguanosine,</t> 2′-deoxyadenosine and N 6 -methyl-2′-deoxyadenosine plus dideoxyinosine (dC, dG, dT, dA, N 6 -medA and ddI respectively). (B) N 6 -methyl-2′-deoxyadenosine detected by LC/ESI(+)-MS/MS SRM mode at transition 266 > 150, and (C) putative DNA adduct VII detected by LC/ESI(+)-MS/MS SRM mode at transition 266 > 150. The peak that was detected at 9.75 min occurred due to the abundantly detected sodiated ion of 2′-deoxythymidine which was detected at SRM transition 265 > 149. LC/ESI (+)-MS/MS, liquid chromatography electrospray ionization-tandem mass spectrometry in positive ionization mode; SRM, single reaction monitoring.
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    Millipore sodium tetraborate decahydrate
    (A) LC separation of a mixture of authentic standards of 2′-deoxynucleosides 2′-deoxycytidine, 2′-deoxythymidine, <t>2′-deoxyguanosine,</t> 2′-deoxyadenosine and N 6 -methyl-2′-deoxyadenosine plus dideoxyinosine (dC, dG, dT, dA, N 6 -medA and ddI respectively). (B) N 6 -methyl-2′-deoxyadenosine detected by LC/ESI(+)-MS/MS SRM mode at transition 266 > 150, and (C) putative DNA adduct VII detected by LC/ESI(+)-MS/MS SRM mode at transition 266 > 150. The peak that was detected at 9.75 min occurred due to the abundantly detected sodiated ion of 2′-deoxythymidine which was detected at SRM transition 265 > 149. LC/ESI (+)-MS/MS, liquid chromatography electrospray ionization-tandem mass spectrometry in positive ionization mode; SRM, single reaction monitoring.
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    Thermo Fisher bis tris mes
    (A) LC separation of a mixture of authentic standards of 2′-deoxynucleosides 2′-deoxycytidine, 2′-deoxythymidine, <t>2′-deoxyguanosine,</t> 2′-deoxyadenosine and N 6 -methyl-2′-deoxyadenosine plus dideoxyinosine (dC, dG, dT, dA, N 6 -medA and ddI respectively). (B) N 6 -methyl-2′-deoxyadenosine detected by LC/ESI(+)-MS/MS SRM mode at transition 266 > 150, and (C) putative DNA adduct VII detected by LC/ESI(+)-MS/MS SRM mode at transition 266 > 150. The peak that was detected at 9.75 min occurred due to the abundantly detected sodiated ion of 2′-deoxythymidine which was detected at SRM transition 265 > 149. LC/ESI (+)-MS/MS, liquid chromatography electrospray ionization-tandem mass spectrometry in positive ionization mode; SRM, single reaction monitoring.
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    Image Search Results


    Summary of the nucleosomal organization of the active and inactive HPRT ) (vertical rectangles, their binding sites); bent arrow, position of the two major transcription initiation sites on the HPRT promoter; white box, first exon of the HPRT gene; ATG, position of the translation initiation site; thick vertical arrows, approximate positions and relative intensities of the major MNase cleavage sites in the HPRT promoter; clusters of thin triangular dashed arrows and barbed arrows, positions of the high-resolution DNase I cleavage ladders suggestive of rotationally positioned nucleosomes on the active and inactive HPRT promoters, respectively, in permeabilized cells (the slightly longer arrows on the lower strand in the inactive allele indicate that this ladder was unusually prominent); hatched bars, approximate locations of the DNase I-hypersensitive sites on the active HPRT promoter in permeabilized cells; All position numbers are relative to the translation initiation site.

    Journal: Molecular and Cellular Biology

    Article Title: Nucleosomes Are Translationally Positioned on the Active Allele and Rotationally Positioned on the Inactive Allele of the HPRT Promoter

    doi: 10.1128/MCB.21.22.7682-7695.2001

    Figure Lengend Snippet: Summary of the nucleosomal organization of the active and inactive HPRT ) (vertical rectangles, their binding sites); bent arrow, position of the two major transcription initiation sites on the HPRT promoter; white box, first exon of the HPRT gene; ATG, position of the translation initiation site; thick vertical arrows, approximate positions and relative intensities of the major MNase cleavage sites in the HPRT promoter; clusters of thin triangular dashed arrows and barbed arrows, positions of the high-resolution DNase I cleavage ladders suggestive of rotationally positioned nucleosomes on the active and inactive HPRT promoters, respectively, in permeabilized cells (the slightly longer arrows on the lower strand in the inactive allele indicate that this ladder was unusually prominent); hatched bars, approximate locations of the DNase I-hypersensitive sites on the active HPRT promoter in permeabilized cells; All position numbers are relative to the translation initiation site.

    Article Snippet: This similarity to naked DNA, when coupled with the increased accessibility to MNase and the hypersensitivity to DNase I observed in the active promoter, strongly suggests that the functional promoter on the active X chromosome is devoid of nucleosomes.

    Techniques: Binding Assay

    Locations of probes and primers for analysis of the HPRT promoter region. Horizontal line bounded by Bcl I sites, 4.3-kb Bcl I fragment containing the HPRT promoter; gray box, potential AP-2 site; five black boxes, cluster of GC boxes in the HPRT promoter; white box, first exon of the HPRT gene including the region of multiple transcription initiation sites in the promoter; ATG, translation initiation site; Bam HI, position of a reference Bam HI site in the first intron 100 bp downstream of the translation initiation site; hatched box, position of the 400-bp hybridization probe used to map DNase I and MNase cleavage sites in the HPRT promoter by indirect end labeling; black rectangles above and below the line, positions of the LMPCR primer sets used to map the high-resolution DNase I cleavage pattern of the HPRT minimal promoter; arrows extending from the black boxes, strand and region analyzed with each primer set.

    Journal: Molecular and Cellular Biology

    Article Title: Nucleosomes Are Translationally Positioned on the Active Allele and Rotationally Positioned on the Inactive Allele of the HPRT Promoter

    doi: 10.1128/MCB.21.22.7682-7695.2001

    Figure Lengend Snippet: Locations of probes and primers for analysis of the HPRT promoter region. Horizontal line bounded by Bcl I sites, 4.3-kb Bcl I fragment containing the HPRT promoter; gray box, potential AP-2 site; five black boxes, cluster of GC boxes in the HPRT promoter; white box, first exon of the HPRT gene including the region of multiple transcription initiation sites in the promoter; ATG, translation initiation site; Bam HI, position of a reference Bam HI site in the first intron 100 bp downstream of the translation initiation site; hatched box, position of the 400-bp hybridization probe used to map DNase I and MNase cleavage sites in the HPRT promoter by indirect end labeling; black rectangles above and below the line, positions of the LMPCR primer sets used to map the high-resolution DNase I cleavage pattern of the HPRT minimal promoter; arrows extending from the black boxes, strand and region analyzed with each primer set.

    Article Snippet: This similarity to naked DNA, when coupled with the increased accessibility to MNase and the hypersensitivity to DNase I observed in the active promoter, strongly suggests that the functional promoter on the active X chromosome is devoid of nucleosomes.

    Techniques: Hybridization, End Labeling

    DNase I in vivo footprint analysis of the human HPRT promoter. Active, samples from cells containing an active HPRT gene on the active human X chromosome; inactive, samples from cells containing an inactive HPRT gene on the inactive human X chromosome; DNA , naked DNA treated with DNase I; cells, DNA from permeabilized cells treated with DNase I; GC boxes, position of a DNase I in vivo footprint over the five GC boxes in the human HPRT promoter; AP-2, position of a DNase I in vivo footprint over a putative consensus AP-2 site in the human HPRT promoter. All position numbers (left and right) are relative to the translation initiation site of the HPRT gene. (A) DNase I in vivo footprint analysis of the upper strand of the HPRT promoter using LMPCR primer set E. Ladder of arrows, apparent 10-bp ladder of DNase I cleavages in permeabilized cells consistent with rotationally positioned nucleosomes on the inactive HPRT promoter. (B) DNase I in vivo footprinting analysis of the lower strand of the HPRT promoter using LMPCR primer set A. All designations and symbols are as described above. This analysis identifies footprints over both a cluster of five GC boxes and a putative AP-2 site in the active HPRT promoter. (C) DNase I in vivo footprinting analysis of the upper strand using LMPCR primer set C. All designations and symbols are as described above. This analysis identifies a DNase in vivo footprint over a putative AP-2 site on the active HPRT promoter.

    Journal: Molecular and Cellular Biology

    Article Title: Nucleosomes Are Translationally Positioned on the Active Allele and Rotationally Positioned on the Inactive Allele of the HPRT Promoter

    doi: 10.1128/MCB.21.22.7682-7695.2001

    Figure Lengend Snippet: DNase I in vivo footprint analysis of the human HPRT promoter. Active, samples from cells containing an active HPRT gene on the active human X chromosome; inactive, samples from cells containing an inactive HPRT gene on the inactive human X chromosome; DNA , naked DNA treated with DNase I; cells, DNA from permeabilized cells treated with DNase I; GC boxes, position of a DNase I in vivo footprint over the five GC boxes in the human HPRT promoter; AP-2, position of a DNase I in vivo footprint over a putative consensus AP-2 site in the human HPRT promoter. All position numbers (left and right) are relative to the translation initiation site of the HPRT gene. (A) DNase I in vivo footprint analysis of the upper strand of the HPRT promoter using LMPCR primer set E. Ladder of arrows, apparent 10-bp ladder of DNase I cleavages in permeabilized cells consistent with rotationally positioned nucleosomes on the inactive HPRT promoter. (B) DNase I in vivo footprinting analysis of the lower strand of the HPRT promoter using LMPCR primer set A. All designations and symbols are as described above. This analysis identifies footprints over both a cluster of five GC boxes and a putative AP-2 site in the active HPRT promoter. (C) DNase I in vivo footprinting analysis of the upper strand using LMPCR primer set C. All designations and symbols are as described above. This analysis identifies a DNase in vivo footprint over a putative AP-2 site on the active HPRT promoter.

    Article Snippet: This similarity to naked DNA, when coupled with the increased accessibility to MNase and the hypersensitivity to DNase I observed in the active promoter, strongly suggests that the functional promoter on the active X chromosome is devoid of nucleosomes.

    Techniques: In Vivo, Footprinting

    Summary of the 10-base DNase I cleavage ladders of chromatin from the active and inactive HPRT promoters. Boldface letters, protein-coding region of the first exon; lowercase letters, nucleotides within the first intron; partial ovals, approximate positions of the translationally positioned nucleosomes on the active HPRT promoter as determined by MNase cleavage; open boxes, positions of transcription factor (TF) binding sites. From top to bottom, left to right, the TF binding sites are a putative AP-1 site (−271 to −264), five GC boxes (centered at −213, −201, −187, −177, and −166), and a putative initiator element (−94 to −86). Bent arrows, positions of the two major transcription initiation sites identified by Kim et al. (16); line between the nucleotide sequence of the upper and lower strands, region of multiple transcription initiation sites described by Patel et al. (32); black triangles above the sequence, positions of DNase I cleavage sites on the upper strand comprising the 10-bp ladder suggestive of rotationally positioned nucleosomes in the inactive promoter; gray triangles below the sequence, positions of DNase I cleavages on the lower strand comprising the 10-bp ladder suggestive of rotationally positioned nucleosomes in the inactive promoter; white triangles, positions of DNase I cleavages on the lower strand making up the 10-bp ladder, suggestive of rotational positioning of a nucleosome on the active promoter region in permeabilized cells; vertical ovals, positions of three CpG dinucleotides whose methylation is strongly correlated with transcriptional repression of the HPRT ).

    Journal: Molecular and Cellular Biology

    Article Title: Nucleosomes Are Translationally Positioned on the Active Allele and Rotationally Positioned on the Inactive Allele of the HPRT Promoter

    doi: 10.1128/MCB.21.22.7682-7695.2001

    Figure Lengend Snippet: Summary of the 10-base DNase I cleavage ladders of chromatin from the active and inactive HPRT promoters. Boldface letters, protein-coding region of the first exon; lowercase letters, nucleotides within the first intron; partial ovals, approximate positions of the translationally positioned nucleosomes on the active HPRT promoter as determined by MNase cleavage; open boxes, positions of transcription factor (TF) binding sites. From top to bottom, left to right, the TF binding sites are a putative AP-1 site (−271 to −264), five GC boxes (centered at −213, −201, −187, −177, and −166), and a putative initiator element (−94 to −86). Bent arrows, positions of the two major transcription initiation sites identified by Kim et al. (16); line between the nucleotide sequence of the upper and lower strands, region of multiple transcription initiation sites described by Patel et al. (32); black triangles above the sequence, positions of DNase I cleavage sites on the upper strand comprising the 10-bp ladder suggestive of rotationally positioned nucleosomes in the inactive promoter; gray triangles below the sequence, positions of DNase I cleavages on the lower strand comprising the 10-bp ladder suggestive of rotationally positioned nucleosomes in the inactive promoter; white triangles, positions of DNase I cleavages on the lower strand making up the 10-bp ladder, suggestive of rotational positioning of a nucleosome on the active promoter region in permeabilized cells; vertical ovals, positions of three CpG dinucleotides whose methylation is strongly correlated with transcriptional repression of the HPRT ).

    Article Snippet: This similarity to naked DNA, when coupled with the increased accessibility to MNase and the hypersensitivity to DNase I observed in the active promoter, strongly suggests that the functional promoter on the active X chromosome is devoid of nucleosomes.

    Techniques: Binding Assay, Sequencing, Methylation

    Identification of NET-associated proteins. (A) Silver stained SDS-PAGE and (B) immunoblots with samples from NET protein purification procedure. Human neutrophils were stimulated to form NETs. Supernatants from unstimulated (lane 1) and stimulated (lane 2) neutrophils; first wash (lane 3); second wash (lane 4); medium containing DNase-1 incubated with unstimulated neutrophils (lane 5); DNase-1-free medium incubated with washed NETs (lane 6); medium containing DNase-1 incubated with washed NETs (lane 7); medium containing DNase-1 incubated with washed NETs including protease inhibitor cocktail (lane 8).

    Journal: PLoS Pathogens

    Article Title: Neutrophil Extracellular Traps Contain Calprotectin, a Cytosolic Protein Complex Involved in Host Defense against Candida albicans

    doi: 10.1371/journal.ppat.1000639

    Figure Lengend Snippet: Identification of NET-associated proteins. (A) Silver stained SDS-PAGE and (B) immunoblots with samples from NET protein purification procedure. Human neutrophils were stimulated to form NETs. Supernatants from unstimulated (lane 1) and stimulated (lane 2) neutrophils; first wash (lane 3); second wash (lane 4); medium containing DNase-1 incubated with unstimulated neutrophils (lane 5); DNase-1-free medium incubated with washed NETs (lane 6); medium containing DNase-1 incubated with washed NETs (lane 7); medium containing DNase-1 incubated with washed NETs including protease inhibitor cocktail (lane 8).

    Article Snippet: The concentration (F) of Dnase-1, as well as the time of digest (G), was confirmed in a silver-stained SDS-PAGE analysis to be optimal at 10 U/ml and 20 min for a maximal protein yield.

    Techniques: Staining, SDS Page, Western Blot, Protein Purification, Incubation, Protease Inhibitor

    Histones are altered during NET formation. NETs from human neutrophils were washed and digested with DNase-1. (A) The NET-fraction (N) and the remaining pellet after DNase-1 digest (P) were analyzed by immunoblotting at the indicated time points. Unstimulated neutrophils served as controls. All core histones have a reduced molecular mass (2–5 kDa less) in NETs compared to the pellet fraction and the unstimulated control. A representative experiment out of three in total is shown. (B) High-resolution SEM analysis of NETs which consist of smooth fibers (white box) and globular domains (diameter 25–50 nm, arrows), scale bar = 100 nm. (C) High-resolution FESEM analysis of smooth stretch of a singular NET-fiber. Signal intensities were profiled vertically and horizontally showing similar diameters to nucleosomes (depicted as cartoon structure models taken from [41] , with approximate horizontal and vertical diameters of 5 nm and 10 nm, respectively). One experiment out of two is shown.

    Journal: PLoS Pathogens

    Article Title: Neutrophil Extracellular Traps Contain Calprotectin, a Cytosolic Protein Complex Involved in Host Defense against Candida albicans

    doi: 10.1371/journal.ppat.1000639

    Figure Lengend Snippet: Histones are altered during NET formation. NETs from human neutrophils were washed and digested with DNase-1. (A) The NET-fraction (N) and the remaining pellet after DNase-1 digest (P) were analyzed by immunoblotting at the indicated time points. Unstimulated neutrophils served as controls. All core histones have a reduced molecular mass (2–5 kDa less) in NETs compared to the pellet fraction and the unstimulated control. A representative experiment out of three in total is shown. (B) High-resolution SEM analysis of NETs which consist of smooth fibers (white box) and globular domains (diameter 25–50 nm, arrows), scale bar = 100 nm. (C) High-resolution FESEM analysis of smooth stretch of a singular NET-fiber. Signal intensities were profiled vertically and horizontally showing similar diameters to nucleosomes (depicted as cartoon structure models taken from [41] , with approximate horizontal and vertical diameters of 5 nm and 10 nm, respectively). One experiment out of two is shown.

    Article Snippet: The concentration (F) of Dnase-1, as well as the time of digest (G), was confirmed in a silver-stained SDS-PAGE analysis to be optimal at 10 U/ml and 20 min for a maximal protein yield.

    Techniques:

    (A) LC separation of a mixture of authentic standards of 2′-deoxynucleosides 2′-deoxycytidine, 2′-deoxythymidine, 2′-deoxyguanosine, 2′-deoxyadenosine and N 6 -methyl-2′-deoxyadenosine plus dideoxyinosine (dC, dG, dT, dA, N 6 -medA and ddI respectively). (B) N 6 -methyl-2′-deoxyadenosine detected by LC/ESI(+)-MS/MS SRM mode at transition 266 > 150, and (C) putative DNA adduct VII detected by LC/ESI(+)-MS/MS SRM mode at transition 266 > 150. The peak that was detected at 9.75 min occurred due to the abundantly detected sodiated ion of 2′-deoxythymidine which was detected at SRM transition 265 > 149. LC/ESI (+)-MS/MS, liquid chromatography electrospray ionization-tandem mass spectrometry in positive ionization mode; SRM, single reaction monitoring.

    Journal: MicrobiologyOpen

    Article Title: Application of DNA adductomics to soil bacterium Sphingobium sp. strain KK22

    doi: 10.1002/mbo3.283

    Figure Lengend Snippet: (A) LC separation of a mixture of authentic standards of 2′-deoxynucleosides 2′-deoxycytidine, 2′-deoxythymidine, 2′-deoxyguanosine, 2′-deoxyadenosine and N 6 -methyl-2′-deoxyadenosine plus dideoxyinosine (dC, dG, dT, dA, N 6 -medA and ddI respectively). (B) N 6 -methyl-2′-deoxyadenosine detected by LC/ESI(+)-MS/MS SRM mode at transition 266 > 150, and (C) putative DNA adduct VII detected by LC/ESI(+)-MS/MS SRM mode at transition 266 > 150. The peak that was detected at 9.75 min occurred due to the abundantly detected sodiated ion of 2′-deoxythymidine which was detected at SRM transition 265 > 149. LC/ESI (+)-MS/MS, liquid chromatography electrospray ionization-tandem mass spectrometry in positive ionization mode; SRM, single reaction monitoring.

    Article Snippet: Bacterial alkaline phosphatase Type III (Escherichia coli ), 2′-deoxycytidine, 2′-deoxythymidine, 2′-deoxyguanosine, 2′-deoxyadenosine, 2′,3′-dideoxyinosine, and phenanthrene were purchased from Sigma-Aldrich Co. (St. Louis, MO).

    Techniques: Mass Spectrometry, Liquid Chromatography