exoiii buffer Search Results


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  • 99
    New England Biolabs i iiic
    C-technology application and preliminary assessment in Hi-C. ( A ) DNA library (572 ng) linear noise elimination for C-technologies, after proximal-ligation. M (left), 1 kb DNA ladder; 1: LRL, LRL used for linear noise elimination. 2: LRC, LRC used for linear noise elimination; 3: <t>LIC,</t> LIC used for linear noise elimination; 4: <t>I+IIIC,</t> I+IIIC used for linear noise elimination; C: Co, without exonucleases digestion; M (right): 100 bp DNA ladder. ( B ) The yield ratio of remaining DNA after four linear elimination treatments, which was consistent to (A). The remaining ratio (gray) and eliminated ratio (purple) are shown together in the bar chart. ( C ) A 40 ng library was given four exonuclease treatment combinations, along with addition of plasmid chaperon carrier, as indicated. M: 1 kb + 100 bp DNA ladder. 1′: LRLP1, LRL with P1 chaperon used for linear noise elimination; 2′: LRC with P1 chaperon used for linear noise elimination; 3′: LICP1, LIC with P1 chaperon used for linear noise elimination; 4′: I+IIICP1, I+IIIC with P1 chaperon used for linear noise elimination; C’: P1 chaperon added, without exonucleases digestion. ( D ) The yield ratio of remaining DNA, after four linear DNA elimination treatments, which was consistent to ( C ). ( E ) HiC-Pro filtering results of Hi-C with exonuclease elimination LIC, compared with standard Hi-C in Figure 1B . LIC-Hi-C had three experimental replicates (LIC-Hi-C 1; LIC-Hi-C 2; and LIC-Hi-C 3). HiC-Pro terms are as indicated in Supplemental S.3.
    I Iiic, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher s1 nuclease digestion
    C-technology application and preliminary assessment in Hi-C. ( A ) DNA library (572 ng) linear noise elimination for C-technologies, after proximal-ligation. M (left), 1 kb DNA ladder; 1: LRL, LRL used for linear noise elimination. 2: LRC, LRC used for linear noise elimination; 3: <t>LIC,</t> LIC used for linear noise elimination; 4: <t>I+IIIC,</t> I+IIIC used for linear noise elimination; C: Co, without exonucleases digestion; M (right): 100 bp DNA ladder. ( B ) The yield ratio of remaining DNA after four linear elimination treatments, which was consistent to (A). The remaining ratio (gray) and eliminated ratio (purple) are shown together in the bar chart. ( C ) A 40 ng library was given four exonuclease treatment combinations, along with addition of plasmid chaperon carrier, as indicated. M: 1 kb + 100 bp DNA ladder. 1′: LRLP1, LRL with P1 chaperon used for linear noise elimination; 2′: LRC with P1 chaperon used for linear noise elimination; 3′: LICP1, LIC with P1 chaperon used for linear noise elimination; 4′: I+IIICP1, I+IIIC with P1 chaperon used for linear noise elimination; C’: P1 chaperon added, without exonucleases digestion. ( D ) The yield ratio of remaining DNA, after four linear DNA elimination treatments, which was consistent to ( C ). ( E ) HiC-Pro filtering results of Hi-C with exonuclease elimination LIC, compared with standard Hi-C in Figure 1B . LIC-Hi-C had three experimental replicates (LIC-Hi-C 1; LIC-Hi-C 2; and LIC-Hi-C 3). HiC-Pro terms are as indicated in Supplemental S.3.
    S1 Nuclease Digestion, supplied by Thermo Fisher, 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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    80
    Promega erase abase kit
    C-technology application and preliminary assessment in Hi-C. ( A ) DNA library (572 ng) linear noise elimination for C-technologies, after proximal-ligation. M (left), 1 kb DNA ladder; 1: LRL, LRL used for linear noise elimination. 2: LRC, LRC used for linear noise elimination; 3: <t>LIC,</t> LIC used for linear noise elimination; 4: <t>I+IIIC,</t> I+IIIC used for linear noise elimination; C: Co, without exonucleases digestion; M (right): 100 bp DNA ladder. ( B ) The yield ratio of remaining DNA after four linear elimination treatments, which was consistent to (A). The remaining ratio (gray) and eliminated ratio (purple) are shown together in the bar chart. ( C ) A 40 ng library was given four exonuclease treatment combinations, along with addition of plasmid chaperon carrier, as indicated. M: 1 kb + 100 bp DNA ladder. 1′: LRLP1, LRL with P1 chaperon used for linear noise elimination; 2′: LRC with P1 chaperon used for linear noise elimination; 3′: LICP1, LIC with P1 chaperon used for linear noise elimination; 4′: I+IIICP1, I+IIIC with P1 chaperon used for linear noise elimination; C’: P1 chaperon added, without exonucleases digestion. ( D ) The yield ratio of remaining DNA, after four linear DNA elimination treatments, which was consistent to ( C ). ( E ) HiC-Pro filtering results of Hi-C with exonuclease elimination LIC, compared with standard Hi-C in Figure 1B . LIC-Hi-C had three experimental replicates (LIC-Hi-C 1; LIC-Hi-C 2; and LIC-Hi-C 3). HiC-Pro terms are as indicated in Supplemental S.3.
    Erase Abase Kit, supplied by Promega, used in various techniques. Bioz Stars score: 80/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Thermo Fisher exoiii
    C-technology application and preliminary assessment in Hi-C. ( A ) DNA library (572 ng) linear noise elimination for C-technologies, after proximal-ligation. M (left), 1 kb DNA ladder; 1: LRL, LRL used for linear noise elimination. 2: LRC, LRC used for linear noise elimination; 3: <t>LIC,</t> LIC used for linear noise elimination; 4: <t>I+IIIC,</t> I+IIIC used for linear noise elimination; C: Co, without exonucleases digestion; M (right): 100 bp DNA ladder. ( B ) The yield ratio of remaining DNA after four linear elimination treatments, which was consistent to (A). The remaining ratio (gray) and eliminated ratio (purple) are shown together in the bar chart. ( C ) A 40 ng library was given four exonuclease treatment combinations, along with addition of plasmid chaperon carrier, as indicated. M: 1 kb + 100 bp DNA ladder. 1′: LRLP1, LRL with P1 chaperon used for linear noise elimination; 2′: LRC with P1 chaperon used for linear noise elimination; 3′: LICP1, LIC with P1 chaperon used for linear noise elimination; 4′: I+IIICP1, I+IIIC with P1 chaperon used for linear noise elimination; C’: P1 chaperon added, without exonucleases digestion. ( D ) The yield ratio of remaining DNA, after four linear DNA elimination treatments, which was consistent to ( C ). ( E ) HiC-Pro filtering results of Hi-C with exonuclease elimination LIC, compared with standard Hi-C in Figure 1B . LIC-Hi-C had three experimental replicates (LIC-Hi-C 1; LIC-Hi-C 2; and LIC-Hi-C 3). HiC-Pro terms are as indicated in Supplemental S.3.
    Exoiii, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 65 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Roche exonuclease iii exoiii
    C-technology application and preliminary assessment in Hi-C. ( A ) DNA library (572 ng) linear noise elimination for C-technologies, after proximal-ligation. M (left), 1 kb DNA ladder; 1: LRL, LRL used for linear noise elimination. 2: LRC, LRC used for linear noise elimination; 3: <t>LIC,</t> LIC used for linear noise elimination; 4: <t>I+IIIC,</t> I+IIIC used for linear noise elimination; C: Co, without exonucleases digestion; M (right): 100 bp DNA ladder. ( B ) The yield ratio of remaining DNA after four linear elimination treatments, which was consistent to (A). The remaining ratio (gray) and eliminated ratio (purple) are shown together in the bar chart. ( C ) A 40 ng library was given four exonuclease treatment combinations, along with addition of plasmid chaperon carrier, as indicated. M: 1 kb + 100 bp DNA ladder. 1′: LRLP1, LRL with P1 chaperon used for linear noise elimination; 2′: LRC with P1 chaperon used for linear noise elimination; 3′: LICP1, LIC with P1 chaperon used for linear noise elimination; 4′: I+IIICP1, I+IIIC with P1 chaperon used for linear noise elimination; C’: P1 chaperon added, without exonucleases digestion. ( D ) The yield ratio of remaining DNA, after four linear DNA elimination treatments, which was consistent to ( C ). ( E ) HiC-Pro filtering results of Hi-C with exonuclease elimination LIC, compared with standard Hi-C in Figure 1B . LIC-Hi-C had three experimental replicates (LIC-Hi-C 1; LIC-Hi-C 2; and LIC-Hi-C 3). HiC-Pro terms are as indicated in Supplemental S.3.
    Exonuclease Iii Exoiii, supplied by Roche, used in various techniques. Bioz Stars score: 88/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Promega exoiii
    C-technology application and preliminary assessment in Hi-C. ( A ) DNA library (572 ng) linear noise elimination for C-technologies, after proximal-ligation. M (left), 1 kb DNA ladder; 1: LRL, LRL used for linear noise elimination. 2: LRC, LRC used for linear noise elimination; 3: <t>LIC,</t> LIC used for linear noise elimination; 4: <t>I+IIIC,</t> I+IIIC used for linear noise elimination; C: Co, without exonucleases digestion; M (right): 100 bp DNA ladder. ( B ) The yield ratio of remaining DNA after four linear elimination treatments, which was consistent to (A). The remaining ratio (gray) and eliminated ratio (purple) are shown together in the bar chart. ( C ) A 40 ng library was given four exonuclease treatment combinations, along with addition of plasmid chaperon carrier, as indicated. M: 1 kb + 100 bp DNA ladder. 1′: LRLP1, LRL with P1 chaperon used for linear noise elimination; 2′: LRC with P1 chaperon used for linear noise elimination; 3′: LICP1, LIC with P1 chaperon used for linear noise elimination; 4′: I+IIICP1, I+IIIC with P1 chaperon used for linear noise elimination; C’: P1 chaperon added, without exonucleases digestion. ( D ) The yield ratio of remaining DNA, after four linear DNA elimination treatments, which was consistent to ( C ). ( E ) HiC-Pro filtering results of Hi-C with exonuclease elimination LIC, compared with standard Hi-C in Figure 1B . LIC-Hi-C had three experimental replicates (LIC-Hi-C 1; LIC-Hi-C 2; and LIC-Hi-C 3). HiC-Pro terms are as indicated in Supplemental S.3.
    Exoiii, supplied by Promega, used in various techniques. Bioz Stars score: 90/100, based on 85 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    New England Biolabs exonuclease iii exoiii
    C-technology application and preliminary assessment in Hi-C. ( A ) DNA library (572 ng) linear noise elimination for C-technologies, after proximal-ligation. M (left), 1 kb DNA ladder; 1: LRL, LRL used for linear noise elimination. 2: LRC, LRC used for linear noise elimination; 3: <t>LIC,</t> LIC used for linear noise elimination; 4: <t>I+IIIC,</t> I+IIIC used for linear noise elimination; C: Co, without exonucleases digestion; M (right): 100 bp DNA ladder. ( B ) The yield ratio of remaining DNA after four linear elimination treatments, which was consistent to (A). The remaining ratio (gray) and eliminated ratio (purple) are shown together in the bar chart. ( C ) A 40 ng library was given four exonuclease treatment combinations, along with addition of plasmid chaperon carrier, as indicated. M: 1 kb + 100 bp DNA ladder. 1′: LRLP1, LRL with P1 chaperon used for linear noise elimination; 2′: LRC with P1 chaperon used for linear noise elimination; 3′: LICP1, LIC with P1 chaperon used for linear noise elimination; 4′: I+IIICP1, I+IIIC with P1 chaperon used for linear noise elimination; C’: P1 chaperon added, without exonucleases digestion. ( D ) The yield ratio of remaining DNA, after four linear DNA elimination treatments, which was consistent to ( C ). ( E ) HiC-Pro filtering results of Hi-C with exonuclease elimination LIC, compared with standard Hi-C in Figure 1B . LIC-Hi-C had three experimental replicates (LIC-Hi-C 1; LIC-Hi-C 2; and LIC-Hi-C 3). HiC-Pro terms are as indicated in Supplemental S.3.
    Exonuclease Iii Exoiii, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 130 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Thermo Fisher exoiii s1 kit
    C-technology application and preliminary assessment in Hi-C. ( A ) DNA library (572 ng) linear noise elimination for C-technologies, after proximal-ligation. M (left), 1 kb DNA ladder; 1: LRL, LRL used for linear noise elimination. 2: LRC, LRC used for linear noise elimination; 3: <t>LIC,</t> LIC used for linear noise elimination; 4: <t>I+IIIC,</t> I+IIIC used for linear noise elimination; C: Co, without exonucleases digestion; M (right): 100 bp DNA ladder. ( B ) The yield ratio of remaining DNA after four linear elimination treatments, which was consistent to (A). The remaining ratio (gray) and eliminated ratio (purple) are shown together in the bar chart. ( C ) A 40 ng library was given four exonuclease treatment combinations, along with addition of plasmid chaperon carrier, as indicated. M: 1 kb + 100 bp DNA ladder. 1′: LRLP1, LRL with P1 chaperon used for linear noise elimination; 2′: LRC with P1 chaperon used for linear noise elimination; 3′: LICP1, LIC with P1 chaperon used for linear noise elimination; 4′: I+IIICP1, I+IIIC with P1 chaperon used for linear noise elimination; C’: P1 chaperon added, without exonucleases digestion. ( D ) The yield ratio of remaining DNA, after four linear DNA elimination treatments, which was consistent to ( C ). ( E ) HiC-Pro filtering results of Hi-C with exonuclease elimination LIC, compared with standard Hi-C in Figure 1B . LIC-Hi-C had three experimental replicates (LIC-Hi-C 1; LIC-Hi-C 2; and LIC-Hi-C 3). HiC-Pro terms are as indicated in Supplemental S.3.
    Exoiii S1 Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Promega proprietary buffer
    C-technology application and preliminary assessment in Hi-C. ( A ) DNA library (572 ng) linear noise elimination for C-technologies, after proximal-ligation. M (left), 1 kb DNA ladder; 1: LRL, LRL used for linear noise elimination. 2: LRC, LRC used for linear noise elimination; 3: <t>LIC,</t> LIC used for linear noise elimination; 4: <t>I+IIIC,</t> I+IIIC used for linear noise elimination; C: Co, without exonucleases digestion; M (right): 100 bp DNA ladder. ( B ) The yield ratio of remaining DNA after four linear elimination treatments, which was consistent to (A). The remaining ratio (gray) and eliminated ratio (purple) are shown together in the bar chart. ( C ) A 40 ng library was given four exonuclease treatment combinations, along with addition of plasmid chaperon carrier, as indicated. M: 1 kb + 100 bp DNA ladder. 1′: LRLP1, LRL with P1 chaperon used for linear noise elimination; 2′: LRC with P1 chaperon used for linear noise elimination; 3′: LICP1, LIC with P1 chaperon used for linear noise elimination; 4′: I+IIICP1, I+IIIC with P1 chaperon used for linear noise elimination; C’: P1 chaperon added, without exonucleases digestion. ( D ) The yield ratio of remaining DNA, after four linear DNA elimination treatments, which was consistent to ( C ). ( E ) HiC-Pro filtering results of Hi-C with exonuclease elimination LIC, compared with standard Hi-C in Figure 1B . LIC-Hi-C had three experimental replicates (LIC-Hi-C 1; LIC-Hi-C 2; and LIC-Hi-C 3). HiC-Pro terms are as indicated in Supplemental S.3.
    Proprietary Buffer, supplied by Promega, used in various techniques. Bioz Stars score: 91/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Kaneka Corp saci buffer
    <t>pL102</t> presentation and shortening description. pL102 is composed of a 13.5-kb DNA fragment (▪) inserted in the pUC19 vector (□).The mclC structural gene, the mclI immunity gene, and the mclA and mclB export genes constitute the MccL genetic system. The restriction sites used for the insert shortening were <t>XbaI/SacI</t> on one side and HindIII/PauI on the other side. The HindIII-PauI fragment was deleted. The dotted arrows indicate the start points and the direction of the shortening.
    Saci Buffer, supplied by Kaneka Corp, used in various techniques. Bioz Stars score: 85/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Pacific Biosciences pacbio exoiii
    <t>pL102</t> presentation and shortening description. pL102 is composed of a 13.5-kb DNA fragment (▪) inserted in the pUC19 vector (□).The mclC structural gene, the mclI immunity gene, and the mclA and mclB export genes constitute the MccL genetic system. The restriction sites used for the insert shortening were <t>XbaI/SacI</t> on one side and HindIII/PauI on the other side. The HindIII-PauI fragment was deleted. The dotted arrows indicate the start points and the direction of the shortening.
    Pacbio Exoiii, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 92/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs buffer 1
    <t>pL102</t> presentation and shortening description. pL102 is composed of a 13.5-kb DNA fragment (▪) inserted in the pUC19 vector (□).The mclC structural gene, the mclI immunity gene, and the mclA and mclB export genes constitute the MccL genetic system. The restriction sites used for the insert shortening were <t>XbaI/SacI</t> on one side and HindIII/PauI on the other side. The HindIII-PauI fragment was deleted. The dotted arrows indicate the start points and the direction of the shortening.
    Buffer 1, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 60 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    New England Biolabs exoiii
    <t>ExoIII</t> analysis of flap-out and flap-in 154-bp 5 S nucleosome substrates. <t>Nucleosomes</t> were purified and digested with ExoIII as described in the text, and cleavage products were analyzed by sequencing gels and phosphorimagery. Shown are lanes corresponding
    Exoiii, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 90/100, based on 161 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Enzymatics exoiii
    <t>ExoIII</t> analysis of flap-out and flap-in 154-bp 5 S nucleosome substrates. <t>Nucleosomes</t> were purified and digested with ExoIII as described in the text, and cleavage products were analyzed by sequencing gels and phosphorimagery. Shown are lanes corresponding
    Exoiii, supplied by Enzymatics, used in various techniques. Bioz Stars score: 90/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs exoiii enzyme
    RSC1 and RSC2 slide Widom 601 H3 R40A mononucleosomes similarly. (A) Comparative sliding of RSC1 and RSC2 complexes (10 nM) on H3 R40A 205 bp Widom 601 yeast mononucleosomes (20 nM). The nucleosomal Start (green), Slid (blue), and free DNA (grey) bands were quantified and reported as a percent of the total signal. (B) Mapping the positions of the wild-type and H3 R40A 205 bp Widom 601 yeast mononucleosomes by <t>ExoIII</t> and S1 treatment as in Figure 3 -figure supplement 3. Partially unwrapped nucleosome fragments (≤120 bp) are depicted in blue. More fully wrapped nucleosome fragments (≥128 bp) are in black. Averages from two technical replicates. Figure 4 - figure supplement 5B - Source Data 1. 205 bp Widom 601 nucleosome mapping.
    Exoiii Enzyme, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 84/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs ne buffer 1
    RSC1 and RSC2 slide Widom 601 H3 R40A mononucleosomes similarly. (A) Comparative sliding of RSC1 and RSC2 complexes (10 nM) on H3 R40A 205 bp Widom 601 yeast mononucleosomes (20 nM). The nucleosomal Start (green), Slid (blue), and free DNA (grey) bands were quantified and reported as a percent of the total signal. (B) Mapping the positions of the wild-type and H3 R40A 205 bp Widom 601 yeast mononucleosomes by <t>ExoIII</t> and S1 treatment as in Figure 3 -figure supplement 3. Partially unwrapped nucleosome fragments (≤120 bp) are depicted in blue. More fully wrapped nucleosome fragments (≥128 bp) are in black. Averages from two technical replicates. Figure 4 - figure supplement 5B - Source Data 1. 205 bp Widom 601 nucleosome mapping.
    Ne Buffer 1, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 25 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs neb buffer 2
    RSC1 and RSC2 slide Widom 601 H3 R40A mononucleosomes similarly. (A) Comparative sliding of RSC1 and RSC2 complexes (10 nM) on H3 R40A 205 bp Widom 601 yeast mononucleosomes (20 nM). The nucleosomal Start (green), Slid (blue), and free DNA (grey) bands were quantified and reported as a percent of the total signal. (B) Mapping the positions of the wild-type and H3 R40A 205 bp Widom 601 yeast mononucleosomes by <t>ExoIII</t> and S1 treatment as in Figure 3 -figure supplement 3. Partially unwrapped nucleosome fragments (≤120 bp) are depicted in blue. More fully wrapped nucleosome fragments (≥128 bp) are in black. Averages from two technical replicates. Figure 4 - figure supplement 5B - Source Data 1. 205 bp Widom 601 nucleosome mapping.
    Neb Buffer 2, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1495 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs nb bbvci
    RSC1 and RSC2 slide Widom 601 H3 R40A mononucleosomes similarly. (A) Comparative sliding of RSC1 and RSC2 complexes (10 nM) on H3 R40A 205 bp Widom 601 yeast mononucleosomes (20 nM). The nucleosomal Start (green), Slid (blue), and free DNA (grey) bands were quantified and reported as a percent of the total signal. (B) Mapping the positions of the wild-type and H3 R40A 205 bp Widom 601 yeast mononucleosomes by <t>ExoIII</t> and S1 treatment as in Figure 3 -figure supplement 3. Partially unwrapped nucleosome fragments (≤120 bp) are depicted in blue. More fully wrapped nucleosome fragments (≥128 bp) are in black. Averages from two technical replicates. Figure 4 - figure supplement 5B - Source Data 1. 205 bp Widom 601 nucleosome mapping.
    Nb Bbvci, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 97/100, based on 230 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher t4 dna ligase
    RSC1 and RSC2 slide Widom 601 H3 R40A mononucleosomes similarly. (A) Comparative sliding of RSC1 and RSC2 complexes (10 nM) on H3 R40A 205 bp Widom 601 yeast mononucleosomes (20 nM). The nucleosomal Start (green), Slid (blue), and free DNA (grey) bands were quantified and reported as a percent of the total signal. (B) Mapping the positions of the wild-type and H3 R40A 205 bp Widom 601 yeast mononucleosomes by <t>ExoIII</t> and S1 treatment as in Figure 3 -figure supplement 3. Partially unwrapped nucleosome fragments (≤120 bp) are depicted in blue. More fully wrapped nucleosome fragments (≥128 bp) are in black. Averages from two technical replicates. Figure 4 - figure supplement 5B - Source Data 1. 205 bp Widom 601 nucleosome mapping.
    T4 Dna Ligase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 25057 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs dpni
    RSC1 and RSC2 slide Widom 601 H3 R40A mononucleosomes similarly. (A) Comparative sliding of RSC1 and RSC2 complexes (10 nM) on H3 R40A 205 bp Widom 601 yeast mononucleosomes (20 nM). The nucleosomal Start (green), Slid (blue), and free DNA (grey) bands were quantified and reported as a percent of the total signal. (B) Mapping the positions of the wild-type and H3 R40A 205 bp Widom 601 yeast mononucleosomes by <t>ExoIII</t> and S1 treatment as in Figure 3 -figure supplement 3. Partially unwrapped nucleosome fragments (≤120 bp) are depicted in blue. More fully wrapped nucleosome fragments (≥128 bp) are in black. Averages from two technical replicates. Figure 4 - figure supplement 5B - Source Data 1. 205 bp Widom 601 nucleosome mapping.
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    TaKaRa e coli exonuclease iii
    RSC1 and RSC2 slide Widom 601 H3 R40A mononucleosomes similarly. (A) Comparative sliding of RSC1 and RSC2 complexes (10 nM) on H3 R40A 205 bp Widom 601 yeast mononucleosomes (20 nM). The nucleosomal Start (green), Slid (blue), and free DNA (grey) bands were quantified and reported as a percent of the total signal. (B) Mapping the positions of the wild-type and H3 R40A 205 bp Widom 601 yeast mononucleosomes by <t>ExoIII</t> and S1 treatment as in Figure 3 -figure supplement 3. Partially unwrapped nucleosome fragments (≤120 bp) are depicted in blue. More fully wrapped nucleosome fragments (≥128 bp) are in black. Averages from two technical replicates. Figure 4 - figure supplement 5B - Source Data 1. 205 bp Widom 601 nucleosome mapping.
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    Image Search Results


    C-technology application and preliminary assessment in Hi-C. ( A ) DNA library (572 ng) linear noise elimination for C-technologies, after proximal-ligation. M (left), 1 kb DNA ladder; 1: LRL, LRL used for linear noise elimination. 2: LRC, LRC used for linear noise elimination; 3: LIC, LIC used for linear noise elimination; 4: I+IIIC, I+IIIC used for linear noise elimination; C: Co, without exonucleases digestion; M (right): 100 bp DNA ladder. ( B ) The yield ratio of remaining DNA after four linear elimination treatments, which was consistent to (A). The remaining ratio (gray) and eliminated ratio (purple) are shown together in the bar chart. ( C ) A 40 ng library was given four exonuclease treatment combinations, along with addition of plasmid chaperon carrier, as indicated. M: 1 kb + 100 bp DNA ladder. 1′: LRLP1, LRL with P1 chaperon used for linear noise elimination; 2′: LRC with P1 chaperon used for linear noise elimination; 3′: LICP1, LIC with P1 chaperon used for linear noise elimination; 4′: I+IIICP1, I+IIIC with P1 chaperon used for linear noise elimination; C’: P1 chaperon added, without exonucleases digestion. ( D ) The yield ratio of remaining DNA, after four linear DNA elimination treatments, which was consistent to ( C ). ( E ) HiC-Pro filtering results of Hi-C with exonuclease elimination LIC, compared with standard Hi-C in Figure 1B . LIC-Hi-C had three experimental replicates (LIC-Hi-C 1; LIC-Hi-C 2; and LIC-Hi-C 3). HiC-Pro terms are as indicated in Supplemental S.3.

    Journal: Nucleic Acids Research

    Article Title: Exonuclease combinations reduce noises in 3D genomics technologies

    doi: 10.1093/nar/gkaa106

    Figure Lengend Snippet: C-technology application and preliminary assessment in Hi-C. ( A ) DNA library (572 ng) linear noise elimination for C-technologies, after proximal-ligation. M (left), 1 kb DNA ladder; 1: LRL, LRL used for linear noise elimination. 2: LRC, LRC used for linear noise elimination; 3: LIC, LIC used for linear noise elimination; 4: I+IIIC, I+IIIC used for linear noise elimination; C: Co, without exonucleases digestion; M (right): 100 bp DNA ladder. ( B ) The yield ratio of remaining DNA after four linear elimination treatments, which was consistent to (A). The remaining ratio (gray) and eliminated ratio (purple) are shown together in the bar chart. ( C ) A 40 ng library was given four exonuclease treatment combinations, along with addition of plasmid chaperon carrier, as indicated. M: 1 kb + 100 bp DNA ladder. 1′: LRLP1, LRL with P1 chaperon used for linear noise elimination; 2′: LRC with P1 chaperon used for linear noise elimination; 3′: LICP1, LIC with P1 chaperon used for linear noise elimination; 4′: I+IIICP1, I+IIIC with P1 chaperon used for linear noise elimination; C’: P1 chaperon added, without exonucleases digestion. ( D ) The yield ratio of remaining DNA, after four linear DNA elimination treatments, which was consistent to ( C ). ( E ) HiC-Pro filtering results of Hi-C with exonuclease elimination LIC, compared with standard Hi-C in Figure 1B . LIC-Hi-C had three experimental replicates (LIC-Hi-C 1; LIC-Hi-C 2; and LIC-Hi-C 3). HiC-Pro terms are as indicated in Supplemental S.3.

    Article Snippet: After LRL (Lambda and RecJF within Lambda buffer) (NEB), LRC (Lambda and RecJF within Cutsmart buffer) (NEB), LIC (Lambda and Exonuclease I within Cutsmart buffer) (NEB) and I+IIIC (I+III or IIIIC) (Exonuclease I and Exonuclease III within Cutsmart buffer) (NEB) elimination, qPCR was performed.

    Techniques: Hi-C, Ligation, Plasmid Preparation

    pL102 presentation and shortening description. pL102 is composed of a 13.5-kb DNA fragment (▪) inserted in the pUC19 vector (□).The mclC structural gene, the mclI immunity gene, and the mclA and mclB export genes constitute the MccL genetic system. The restriction sites used for the insert shortening were XbaI/SacI on one side and HindIII/PauI on the other side. The HindIII-PauI fragment was deleted. The dotted arrows indicate the start points and the direction of the shortening.

    Journal: Antimicrobial Agents and Chemotherapy

    Article Title: Mechanism of Bactericidal Activity of Microcin L in Escherichia coli and Salmonella enterica ▿

    doi: 10.1128/AAC.01217-10

    Figure Lengend Snippet: pL102 presentation and shortening description. pL102 is composed of a 13.5-kb DNA fragment (▪) inserted in the pUC19 vector (□).The mclC structural gene, the mclI immunity gene, and the mclA and mclB export genes constitute the MccL genetic system. The restriction sites used for the insert shortening were XbaI/SacI on one side and HindIII/PauI on the other side. The HindIII-PauI fragment was deleted. The dotted arrows indicate the start points and the direction of the shortening.

    Article Snippet: To shorten the 5′ end of the pL102 insert, 10 μg pL102 was digested with 40 U SacI and XbaI in SacI buffer (Eurogentec) at 37°C for 4 h. After the heat inactivation of the restriction enzymes, the linearized plasmid (4.75 μg) was subjected to the ExoIII nuclease according to the ExoIII/S1 kit (Fermentas) at 30°C for 0, 5, 10, 12, 14, 16, and 18 min and then in 1-min increments from 20 to 36 min. After S1 nuclease digestion for 30 min at room temperature, the reaction was stopped and a ligation with T4 DNA ligase was performed according to the ExoIII/S1 kit (Fermentas) protocol.

    Techniques: Plasmid Preparation

    ExoIII analysis of flap-out and flap-in 154-bp 5 S nucleosome substrates. Nucleosomes were purified and digested with ExoIII as described in the text, and cleavage products were analyzed by sequencing gels and phosphorimagery. Shown are lanes corresponding

    Journal: The Journal of Biological Chemistry

    Article Title: Activity of FEN1 Endonuclease on Nucleosome Substrates Is Dependent upon DNA Sequence but Not Flap Orientation *

    doi: 10.1074/jbc.M111.229658

    Figure Lengend Snippet: ExoIII analysis of flap-out and flap-in 154-bp 5 S nucleosome substrates. Nucleosomes were purified and digested with ExoIII as described in the text, and cleavage products were analyzed by sequencing gels and phosphorimagery. Shown are lanes corresponding

    Article Snippet: Sucrose gradient-purified flap-out and flap-in nucleosomes and naked DNA were treated with 1 μl of ExoIII (100 units, New England Biolabs).

    Techniques: Purification, Sequencing

    RSC1 and RSC2 slide Widom 601 H3 R40A mononucleosomes similarly. (A) Comparative sliding of RSC1 and RSC2 complexes (10 nM) on H3 R40A 205 bp Widom 601 yeast mononucleosomes (20 nM). The nucleosomal Start (green), Slid (blue), and free DNA (grey) bands were quantified and reported as a percent of the total signal. (B) Mapping the positions of the wild-type and H3 R40A 205 bp Widom 601 yeast mononucleosomes by ExoIII and S1 treatment as in Figure 3 -figure supplement 3. Partially unwrapped nucleosome fragments (≤120 bp) are depicted in blue. More fully wrapped nucleosome fragments (≥128 bp) are in black. Averages from two technical replicates. Figure 4 - figure supplement 5B - Source Data 1. 205 bp Widom 601 nucleosome mapping.

    Journal: bioRxiv

    Article Title: Specialization of the Chromatin Remodeler RSC to Mobilize Partially-Unwrapped Nucleosomes

    doi: 10.1101/799361

    Figure Lengend Snippet: RSC1 and RSC2 slide Widom 601 H3 R40A mononucleosomes similarly. (A) Comparative sliding of RSC1 and RSC2 complexes (10 nM) on H3 R40A 205 bp Widom 601 yeast mononucleosomes (20 nM). The nucleosomal Start (green), Slid (blue), and free DNA (grey) bands were quantified and reported as a percent of the total signal. (B) Mapping the positions of the wild-type and H3 R40A 205 bp Widom 601 yeast mononucleosomes by ExoIII and S1 treatment as in Figure 3 -figure supplement 3. Partially unwrapped nucleosome fragments (≤120 bp) are depicted in blue. More fully wrapped nucleosome fragments (≥128 bp) are in black. Averages from two technical replicates. Figure 4 - figure supplement 5B - Source Data 1. 205 bp Widom 601 nucleosome mapping.

    Article Snippet: Approximately 400-800 fmol of nucleosomes purified from sucrose gradients was digested with a 5-25U titration of ExoIII enzyme (New England Biolabs) for 1, 2, or 3 min at 37°C in ExoIII Buffer (10 mM Tris [pH 8], 50 mM NaCl, 3 mM MgCl2 ).

    Techniques:

    Mapping the positions of the wt and H3 R40A 174 bp sea urchin 5S yeast mononucleosomes. Nucleo- some mapping by ExoIII and S1 treatment followed by paired-end next-generation sequencing. Experiment conducted once. Partially wrapped nucleosome fragments (≤120 bp) are depicted in blue. More fully wrapped nucleosome fragments (≥128 bp) are in black. Figure 3 - figure supplement 5 - Source Data 1. 174 bp 5S nucleosome mapping.

    Journal: bioRxiv

    Article Title: Specialization of the Chromatin Remodeler RSC to Mobilize Partially-Unwrapped Nucleosomes

    doi: 10.1101/799361

    Figure Lengend Snippet: Mapping the positions of the wt and H3 R40A 174 bp sea urchin 5S yeast mononucleosomes. Nucleo- some mapping by ExoIII and S1 treatment followed by paired-end next-generation sequencing. Experiment conducted once. Partially wrapped nucleosome fragments (≤120 bp) are depicted in blue. More fully wrapped nucleosome fragments (≥128 bp) are in black. Figure 3 - figure supplement 5 - Source Data 1. 174 bp 5S nucleosome mapping.

    Article Snippet: Approximately 400-800 fmol of nucleosomes purified from sucrose gradients was digested with a 5-25U titration of ExoIII enzyme (New England Biolabs) for 1, 2, or 3 min at 37°C in ExoIII Buffer (10 mM Tris [pH 8], 50 mM NaCl, 3 mM MgCl2 ).

    Techniques: Next-Generation Sequencing