hincii  (New England Biolabs)


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    HincII
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    HincII 5 000 units
    Catalog Number:
    r0103l
    Price:
    257
    Size:
    5 000 units
    Category:
    Restriction Enzymes
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    New England Biolabs hincii
    HincII
    HincII 5 000 units
    https://www.bioz.com/result/hincii/product/New England Biolabs
    Average 99 stars, based on 671 article reviews
    Price from $9.99 to $1999.99
    hincii - by Bioz Stars, 2020-04
    99/100 stars

    Images

    1) Product Images from "Flexible and scalable genotyping-by-sequencing strategies for population studies"

    Article Title: Flexible and scalable genotyping-by-sequencing strategies for population studies

    Journal: BMC Genomics

    doi: 10.1186/1471-2164-15-979

    Effect of read count on marker dataset size and imputation. Fraction of shared post-filter, pre-imputation genetic markers and fraction of post-imputation shared genome with original sample for subsamplings of A) RsaI F 2 -44 and B) HincII F 2 -23. C) Imputed genomes for each subsample in RsaI F 2 -44 displayed in concentric rings. Sample read count declines from the outermost ring to the innermost. D) Imputed genomes for each subsample in HincII F 2 -23 displayed in concentric circles. Sample read count declines from the outermost ring to the innermost.
    Figure Legend Snippet: Effect of read count on marker dataset size and imputation. Fraction of shared post-filter, pre-imputation genetic markers and fraction of post-imputation shared genome with original sample for subsamplings of A) RsaI F 2 -44 and B) HincII F 2 -23. C) Imputed genomes for each subsample in RsaI F 2 -44 displayed in concentric rings. Sample read count declines from the outermost ring to the innermost. D) Imputed genomes for each subsample in HincII F 2 -23 displayed in concentric circles. Sample read count declines from the outermost ring to the innermost.

    Techniques Used: Marker

    Trait mapping for yellowy ( y1 ) and sugary ( su1 ) in an F 2 admixture population. A green line in the plots annotates the locations of both genes. Pre-imputation markers are shown in black and grey. Markers, post-imputation and error correction are shown in color. A) RsaI GBS dataset, su1 map. B) RsaI GBS dataset, y1 map. C) HincII GBS dataset, su1 map. D) RsaI GBS dataset, y1 map.
    Figure Legend Snippet: Trait mapping for yellowy ( y1 ) and sugary ( su1 ) in an F 2 admixture population. A green line in the plots annotates the locations of both genes. Pre-imputation markers are shown in black and grey. Markers, post-imputation and error correction are shown in color. A) RsaI GBS dataset, su1 map. B) RsaI GBS dataset, y1 map. C) HincII GBS dataset, su1 map. D) RsaI GBS dataset, y1 map.

    Techniques Used:

    Fraction of predicted sites covered in samples from a F 2 admixture population. Reads from each F 2 sample were aligned to predicted sites, then predicted sites were placed in 2 bp bins, with the fraction covered in each bin indicated by the heatmap. A) The RsaI dataset, aligned against total predicted sites. B) RsaI dataset, aligned against the subset of predicted sites with sequencing coverage in the original RsaI B73 GBS experiment. C) HincII dataset, aligned against total predicted sites. D) HincII dataset, aligned against predicted sites with at least one read coverage in the original HincII experiment. Sample order is given, left to right, in Additional file 5 : Table S1.
    Figure Legend Snippet: Fraction of predicted sites covered in samples from a F 2 admixture population. Reads from each F 2 sample were aligned to predicted sites, then predicted sites were placed in 2 bp bins, with the fraction covered in each bin indicated by the heatmap. A) The RsaI dataset, aligned against total predicted sites. B) RsaI dataset, aligned against the subset of predicted sites with sequencing coverage in the original RsaI B73 GBS experiment. C) HincII dataset, aligned against total predicted sites. D) HincII dataset, aligned against predicted sites with at least one read coverage in the original HincII experiment. Sample order is given, left to right, in Additional file 5 : Table S1.

    Techniques Used: Sequencing

    2) Product Images from "Flexible and scalable genotyping-by-sequencing strategies for population studies"

    Article Title: Flexible and scalable genotyping-by-sequencing strategies for population studies

    Journal: BMC Genomics

    doi: 10.1186/1471-2164-15-979

    Fraction of predicted sites covered in samples from a F 2 admixture population. Reads from each F 2 sample were aligned to predicted sites, then predicted sites were placed in 2 bp bins, with the fraction covered in each bin indicated by the heatmap. A) The RsaI dataset, aligned against total predicted sites. B) RsaI dataset, aligned against the subset of predicted sites with sequencing coverage in the original RsaI B73 GBS experiment. C) HincII dataset, aligned against total predicted sites. D) HincII dataset, aligned against predicted sites with at least one read coverage in the original HincII experiment. Sample order is given, left to right, in Additional file 5 : Table S1.
    Figure Legend Snippet: Fraction of predicted sites covered in samples from a F 2 admixture population. Reads from each F 2 sample were aligned to predicted sites, then predicted sites were placed in 2 bp bins, with the fraction covered in each bin indicated by the heatmap. A) The RsaI dataset, aligned against total predicted sites. B) RsaI dataset, aligned against the subset of predicted sites with sequencing coverage in the original RsaI B73 GBS experiment. C) HincII dataset, aligned against total predicted sites. D) HincII dataset, aligned against predicted sites with at least one read coverage in the original HincII experiment. Sample order is given, left to right, in Additional file 5 : Table S1.

    Techniques Used: Sequencing

    Related Articles

    Conjugation Assay:

    Article Title: Updated molecular epidemiology of carbapenem-non-susceptible Escherichia coli in Taiwan: first identification of KPC-2 or NDM-1-producing E. coli in Taiwan
    Article Snippet: Transfer of bla NDM-1 and plasmid DNA analysis Plasmid conjugation was performed using E. coli J53 AzR as the recipient strain. .. The plasmids were extracted from these transconjugants using the standard alkaline lysis method, and fingerprints of the plasmids were generated by digestion with Hinc II or Pvu II (New England Biolabs, Beverly, MA).

    Sequencing:

    Article Title: Flexible and scalable genotyping-by-sequencing strategies for population studies
    Article Snippet: Paragraph title: GBS library preparation and sequencing ... Genomic DNA from B73 and the Nipponbarre was digested with MlyI (R0610), AluI (R0137), RsaI (R0167), EcoRV (R0195), StuI (R0187), HaeIII (R0108), and HincII (R0103, New England Biolabs).

    Article Title: Global remodeling of nucleosome positions in C. elegans
    Article Snippet: .. We identified well-positioned nucleosomes in each sequence read profile using the following cutoffs: Rsa I, nucleosomes marked by reads with height 4 and above (1.3% of all reads); Hinc II, nucleosomes marked by reads with height 3 and above (1.1% of all reads); Gu & Fire [ ], nucleosomes marked by reads with height 3 and above (0.9% of all reads); Valouev et al. [ ], nucleosomes marked by reads with height 9 and above (1.5% of all reads). ..

    Agarose Gel Electrophoresis:

    Article Title: Nucleoprotein complex intermediates in HIV-1 integration
    Article Snippet: Digest 500 μg of the plasmid DNA with 500 U each of ScaI and HincII (New England Biolabs) at a DNA concentration of 0.3 mg/ml. .. Pour a preparative 1% agarose gel (SeaKem GTG) in TBE (89 mM Tris, 89 mM boric acid, 2 mM EDTA, pH 8.0) buffer.

    In Vitro:

    Article Title: Global remodeling of nucleosome positions in C. elegans
    Article Snippet: Paragraph title: Reconstitution of in vitro nucleosomes (invitrosomes) ... To produce DNA templates for both the Rsa I and Hinc II experiments, 40 μg of high-molecular weight genomic DNA was digested with 200 units of either restriction enzyme Rsa I or Hinc II (New England BioLabs) with the supplied buffers and 1X BSA (New England BioLabs).

    Nucleic Acid Electrophoresis:

    Article Title: Nucleoprotein complex intermediates in HIV-1 integration
    Article Snippet: Because the linear ~1 kb viral DNA substrate must be excised from plasmid pSca355 and purified by gel electrophoresis, it is advisable to start with a 500 μg or larger scale of plasmid preparation. .. Digest 500 μg of the plasmid DNA with 500 U each of ScaI and HincII (New England Biolabs) at a DNA concentration of 0.3 mg/ml.

    Isolation:

    Article Title: Global remodeling of nucleosome positions in C. elegans
    Article Snippet: RNA was removed by digesting the isolated nucleic acid with RNAse A (Roche) followed by phenol/chloroform, chloroform extraction and ethanol precipitation. .. To produce DNA templates for both the Rsa I and Hinc II experiments, 40 μg of high-molecular weight genomic DNA was digested with 200 units of either restriction enzyme Rsa I or Hinc II (New England BioLabs) with the supplied buffers and 1X BSA (New England BioLabs).

    Generated:

    Article Title: Updated molecular epidemiology of carbapenem-non-susceptible Escherichia coli in Taiwan: first identification of KPC-2 or NDM-1-producing E. coli in Taiwan
    Article Snippet: .. The plasmids were extracted from these transconjugants using the standard alkaline lysis method, and fingerprints of the plasmids were generated by digestion with Hinc II or Pvu II (New England Biolabs, Beverly, MA). .. Pulsed-field gel electrophoresis (PFGE) Total DNA was prepared, and PFGE was performed as described [ ].

    Purification:

    Article Title: Nucleoprotein complex intermediates in HIV-1 integration
    Article Snippet: Because the linear ~1 kb viral DNA substrate must be excised from plasmid pSca355 and purified by gel electrophoresis, it is advisable to start with a 500 μg or larger scale of plasmid preparation. .. Digest 500 μg of the plasmid DNA with 500 U each of ScaI and HincII (New England Biolabs) at a DNA concentration of 0.3 mg/ml.

    Concentration Assay:

    Article Title: Nucleoprotein complex intermediates in HIV-1 integration
    Article Snippet: .. Digest 500 μg of the plasmid DNA with 500 U each of ScaI and HincII (New England Biolabs) at a DNA concentration of 0.3 mg/ml. .. Incubate the reaction mixture at 37 °C for 2 h. Purification of the 1513 bp DNA fragment.

    Article Title: Global remodeling of nucleosome positions in C. elegans
    Article Snippet: Reconstitution of in vitro nucleosomes (invitrosomes) Naked genomic DNA from wild-type C . elegans (N2 strain) was isolated by digesting flash-frozen worms with proteinase K (Roche, 2mg/ml final concentration) in worm lysis buffer (0.1M Tris–HCl at pH 8.5, 0.1 M NaCl, 50 mM EDTA, 1% SDS) at 65°C for 45 min followed by phenol, phenol/chloroform, chloroform extraction and ethanol precipitation. .. To produce DNA templates for both the Rsa I and Hinc II experiments, 40 μg of high-molecular weight genomic DNA was digested with 200 units of either restriction enzyme Rsa I or Hinc II (New England BioLabs) with the supplied buffers and 1X BSA (New England BioLabs).

    Incubation:

    Article Title: Updated molecular epidemiology of carbapenem-non-susceptible Escherichia coli in Taiwan: first identification of KPC-2 or NDM-1-producing E. coli in Taiwan
    Article Snippet: The recipients and bla NDM-1 -carrrying donor samples were separately inoculated into brain-heart infusion broth and incubated at 37°C for 4 h. The samples were then mixed at a ratio of 10:1 (Donor:Recipient, by volume) for overnight incubation at 37°C. .. The plasmids were extracted from these transconjugants using the standard alkaline lysis method, and fingerprints of the plasmids were generated by digestion with Hinc II or Pvu II (New England Biolabs, Beverly, MA).

    other:

    Article Title: Global remodeling of nucleosome positions in C. elegans
    Article Snippet: The filter was applied to all cut sites, which on average occur once per 490 bp for Rsa I (GTAC) and once per 2109 bp for Hinc II (GTYRAC).

    Article Title: Global remodeling of nucleosome positions in C. elegans
    Article Snippet: Additionally, a no-DNA control sample was processed in parallel to the Rsa I and Hinc II samples.

    Article Title: Replication-coupled DNA Interstrand Crosslink repair in Xenopus egg extracts
    Article Snippet: HincII and SapI restriction enzymes (NEB).

    Article Title: Global remodeling of nucleosome positions in C. elegans
    Article Snippet: The read coverage for each dataset is 0.086 reads per base in Rsa I, 0.048 reads per base in Hinc II, 0.040 reads per base in Gu and Fire, 0.44 reads per base in Valouev et al., 0.58 reads per base in embryos, 0.84 reads per base in adults, 0.67 reads per base in germlineless adults, and 0.58 reads per base in the nucleosome-free control experiment.

    Plasmid Preparation:

    Article Title: Updated molecular epidemiology of carbapenem-non-susceptible Escherichia coli in Taiwan: first identification of KPC-2 or NDM-1-producing E. coli in Taiwan
    Article Snippet: Paragraph title: Transfer of bla NDM-1 and plasmid DNA analysis ... The plasmids were extracted from these transconjugants using the standard alkaline lysis method, and fingerprints of the plasmids were generated by digestion with Hinc II or Pvu II (New England Biolabs, Beverly, MA).

    Article Title: Nucleoprotein complex intermediates in HIV-1 integration
    Article Snippet: .. Digest 500 μg of the plasmid DNA with 500 U each of ScaI and HincII (New England Biolabs) at a DNA concentration of 0.3 mg/ml. .. Incubate the reaction mixture at 37 °C for 2 h. Purification of the 1513 bp DNA fragment.

    Polyacrylamide Gel Electrophoresis:

    Article Title: An Intronic Sequence Element Mediates Both Activation and Repression of Rat Fibroblast Growth Factor Receptor 2 Pre-mRNA Splicing
    Article Snippet: .. In order to analyze the splicing products of pI-11-FL and pI-11-FS, we digested the RT-PCR products with Ava I and Hin cII and performed polyacrylamide gel electrophoresis. .. When stable transfections with pI-11-FL and pI-11-FS were analyzed as shown in Fig. C and D, the primary product was 380 or 377 bp, and this product contained almost exclusively exon IIIb in DT3 cells and IIIc in AT3 cells.

    Alkaline Lysis:

    Article Title: Updated molecular epidemiology of carbapenem-non-susceptible Escherichia coli in Taiwan: first identification of KPC-2 or NDM-1-producing E. coli in Taiwan
    Article Snippet: .. The plasmids were extracted from these transconjugants using the standard alkaline lysis method, and fingerprints of the plasmids were generated by digestion with Hinc II or Pvu II (New England Biolabs, Beverly, MA). .. Pulsed-field gel electrophoresis (PFGE) Total DNA was prepared, and PFGE was performed as described [ ].

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: An Intronic Sequence Element Mediates Both Activation and Repression of Rat Fibroblast Growth Factor Receptor 2 Pre-mRNA Splicing
    Article Snippet: .. In order to analyze the splicing products of pI-11-FL and pI-11-FS, we digested the RT-PCR products with Ava I and Hin cII and performed polyacrylamide gel electrophoresis. .. When stable transfections with pI-11-FL and pI-11-FS were analyzed as shown in Fig. C and D, the primary product was 380 or 377 bp, and this product contained almost exclusively exon IIIb in DT3 cells and IIIc in AT3 cells.

    Lysis:

    Article Title: Global remodeling of nucleosome positions in C. elegans
    Article Snippet: Reconstitution of in vitro nucleosomes (invitrosomes) Naked genomic DNA from wild-type C . elegans (N2 strain) was isolated by digesting flash-frozen worms with proteinase K (Roche, 2mg/ml final concentration) in worm lysis buffer (0.1M Tris–HCl at pH 8.5, 0.1 M NaCl, 50 mM EDTA, 1% SDS) at 65°C for 45 min followed by phenol, phenol/chloroform, chloroform extraction and ethanol precipitation. .. To produce DNA templates for both the Rsa I and Hinc II experiments, 40 μg of high-molecular weight genomic DNA was digested with 200 units of either restriction enzyme Rsa I or Hinc II (New England BioLabs) with the supplied buffers and 1X BSA (New England BioLabs).

    Antiviral Assay:

    Article Title: An Intronic Sequence Element Mediates Both Activation and Repression of Rat Fibroblast Growth Factor Receptor 2 Pre-mRNA Splicing
    Article Snippet: .. Because exon IIIb contains an Ava I site not present in IIIc, and exon IIIc contains two Hin cII sites not present in IIIb, we expected the inclusion of IIIb to result in a 367-bp product which is cut with Ava I but not Hin cII, and we expected the inclusion of IIIc to result in a 364-bp product which is cut only by Hin cII. ..

    Article Title: An Intronic Sequence Element Mediates Both Activation and Repression of Rat Fibroblast Growth Factor Receptor 2 Pre-mRNA Splicing
    Article Snippet: .. In order to analyze the splicing products of pI-11-FL and pI-11-FS, we digested the RT-PCR products with Ava I and Hin cII and performed polyacrylamide gel electrophoresis. .. When stable transfections with pI-11-FL and pI-11-FS were analyzed as shown in Fig. C and D, the primary product was 380 or 377 bp, and this product contained almost exclusively exon IIIb in DT3 cells and IIIc in AT3 cells.

    Recombinant:

    Article Title: Global remodeling of nucleosome positions in C. elegans
    Article Snippet: To produce DNA templates for both the Rsa I and Hinc II experiments, 40 μg of high-molecular weight genomic DNA was digested with 200 units of either restriction enzyme Rsa I or Hinc II (New England BioLabs) with the supplied buffers and 1X BSA (New England BioLabs). .. The Rsa I and Hinc II DNA digestions were assembled with recombinant Xenopus histones (a gift from Geeta Narlikar) into nucleosomes as described previously [ ] at a 1.1:1 molar ratio of DNA to histone octamer, such that on average one nucleosome would form per 850 bp or 3500 bp of DNA for the Rsa I and Hinc II reconstitutions, respectively.

    Ethanol Precipitation:

    Article Title: Global remodeling of nucleosome positions in C. elegans
    Article Snippet: RNA was removed by digesting the isolated nucleic acid with RNAse A (Roche) followed by phenol/chloroform, chloroform extraction and ethanol precipitation. .. To produce DNA templates for both the Rsa I and Hinc II experiments, 40 μg of high-molecular weight genomic DNA was digested with 200 units of either restriction enzyme Rsa I or Hinc II (New England BioLabs) with the supplied buffers and 1X BSA (New England BioLabs).

    Staining:

    Article Title: Nucleoprotein complex intermediates in HIV-1 integration
    Article Snippet: Digest 500 μg of the plasmid DNA with 500 U each of ScaI and HincII (New England Biolabs) at a DNA concentration of 0.3 mg/ml. .. Add DNA loading buffer (containing Na dodecyl sulfate [SDS]) to the restriction digestion mixture, and electrophorese at 5 V/cm for 1 h. Stain the gel with ethidium bromide, visualize under UV light, and excise the 1513 bp band.

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    New England Biolabs hincii
    Effect of read count on marker dataset size and imputation. Fraction of shared post-filter, pre-imputation genetic markers and fraction of post-imputation shared genome with original sample for subsamplings of A) <t>RsaI</t> F 2 -44 and B) <t>HincII</t> F 2 -23. C) Imputed genomes for each subsample in RsaI F 2 -44 displayed in concentric rings. Sample read count declines from the outermost ring to the innermost. D) Imputed genomes for each subsample in HincII F 2 -23 displayed in concentric circles. Sample read count declines from the outermost ring to the innermost.
    Hincii, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hincii/product/New England Biolabs
    Average 99 stars, based on 10 article reviews
    Price from $9.99 to $1999.99
    hincii - by Bioz Stars, 2020-04
    99/100 stars
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    Effect of read count on marker dataset size and imputation. Fraction of shared post-filter, pre-imputation genetic markers and fraction of post-imputation shared genome with original sample for subsamplings of A) RsaI F 2 -44 and B) HincII F 2 -23. C) Imputed genomes for each subsample in RsaI F 2 -44 displayed in concentric rings. Sample read count declines from the outermost ring to the innermost. D) Imputed genomes for each subsample in HincII F 2 -23 displayed in concentric circles. Sample read count declines from the outermost ring to the innermost.

    Journal: BMC Genomics

    Article Title: Flexible and scalable genotyping-by-sequencing strategies for population studies

    doi: 10.1186/1471-2164-15-979

    Figure Lengend Snippet: Effect of read count on marker dataset size and imputation. Fraction of shared post-filter, pre-imputation genetic markers and fraction of post-imputation shared genome with original sample for subsamplings of A) RsaI F 2 -44 and B) HincII F 2 -23. C) Imputed genomes for each subsample in RsaI F 2 -44 displayed in concentric rings. Sample read count declines from the outermost ring to the innermost. D) Imputed genomes for each subsample in HincII F 2 -23 displayed in concentric circles. Sample read count declines from the outermost ring to the innermost.

    Article Snippet: Genomic DNA from B73 and the Nipponbarre was digested with MlyI (R0610), AluI (R0137), RsaI (R0167), EcoRV (R0195), StuI (R0187), HaeIII (R0108), and HincII (R0103, New England Biolabs).

    Techniques: Marker

    Trait mapping for yellowy ( y1 ) and sugary ( su1 ) in an F 2 admixture population. A green line in the plots annotates the locations of both genes. Pre-imputation markers are shown in black and grey. Markers, post-imputation and error correction are shown in color. A) RsaI GBS dataset, su1 map. B) RsaI GBS dataset, y1 map. C) HincII GBS dataset, su1 map. D) RsaI GBS dataset, y1 map.

    Journal: BMC Genomics

    Article Title: Flexible and scalable genotyping-by-sequencing strategies for population studies

    doi: 10.1186/1471-2164-15-979

    Figure Lengend Snippet: Trait mapping for yellowy ( y1 ) and sugary ( su1 ) in an F 2 admixture population. A green line in the plots annotates the locations of both genes. Pre-imputation markers are shown in black and grey. Markers, post-imputation and error correction are shown in color. A) RsaI GBS dataset, su1 map. B) RsaI GBS dataset, y1 map. C) HincII GBS dataset, su1 map. D) RsaI GBS dataset, y1 map.

    Article Snippet: Genomic DNA from B73 and the Nipponbarre was digested with MlyI (R0610), AluI (R0137), RsaI (R0167), EcoRV (R0195), StuI (R0187), HaeIII (R0108), and HincII (R0103, New England Biolabs).

    Techniques:

    Fraction of predicted sites covered in samples from a F 2 admixture population. Reads from each F 2 sample were aligned to predicted sites, then predicted sites were placed in 2 bp bins, with the fraction covered in each bin indicated by the heatmap. A) The RsaI dataset, aligned against total predicted sites. B) RsaI dataset, aligned against the subset of predicted sites with sequencing coverage in the original RsaI B73 GBS experiment. C) HincII dataset, aligned against total predicted sites. D) HincII dataset, aligned against predicted sites with at least one read coverage in the original HincII experiment. Sample order is given, left to right, in Additional file 5 : Table S1.

    Journal: BMC Genomics

    Article Title: Flexible and scalable genotyping-by-sequencing strategies for population studies

    doi: 10.1186/1471-2164-15-979

    Figure Lengend Snippet: Fraction of predicted sites covered in samples from a F 2 admixture population. Reads from each F 2 sample were aligned to predicted sites, then predicted sites were placed in 2 bp bins, with the fraction covered in each bin indicated by the heatmap. A) The RsaI dataset, aligned against total predicted sites. B) RsaI dataset, aligned against the subset of predicted sites with sequencing coverage in the original RsaI B73 GBS experiment. C) HincII dataset, aligned against total predicted sites. D) HincII dataset, aligned against predicted sites with at least one read coverage in the original HincII experiment. Sample order is given, left to right, in Additional file 5 : Table S1.

    Article Snippet: Genomic DNA from B73 and the Nipponbarre was digested with MlyI (R0610), AluI (R0137), RsaI (R0167), EcoRV (R0195), StuI (R0187), HaeIII (R0108), and HincII (R0103, New England Biolabs).

    Techniques: Sequencing