ncii  (New England Biolabs)


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    Structured Review

    New England Biolabs ncii
    Ncii, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ncii/product/New England Biolabs
    Average 94 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    ncii - by Bioz Stars, 2022-07
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    New England Biolabs nci i
    Gene targeting of zebrafish rh1-1 . A : Schematic representation of the zebrafish rh1-1 locus characterized by a single exon encoding 354 amino acid proteins and 5′ and 3′ UTRs. B : Alignment of Rho N- and C-terminal amino acid sequences across species. Numbering is based on the predicted zebrafish rh1–1 . The conserved N-linked glycosylation sequence and VXPX targeting sequence are underlined. C : DNA sequence and amino acid overlay of zebrafish rh1–1 5′- (left) and 3′- (right) coding sequences. Blue text represents the CRISPR PAM sequence. Underlined DNA represents the target for guide RNA hybridization. The purple overscore represent restriction sites for <t>Nci</t> I or Bbs I. Arrows indicate predicted Cas9 cleavage sites. D : Diagrammatic representation of the 253-bp 5′- rh1–1 gene amplicon and the predicted products following digestion with Nci I. E : RFLP analysis of a 253-bp PCR product spanning the 5′ rh1–1 gene (C, undigested control) and digested with Nci I (N) shows retention of the original amplicon (arrow) from pooled DNA from injected embryos versus complete digestion of the PCR product of uninjected control DNA (arrowhead). F : Diagrammatic representation of the 325-bp 3′-amplicon and the predicted products following digestion with Bbs I. G : RFLP analysis of a 325-bp PCR product (C, undigested control) spanning the 3′ rh1–1 sequence digested with Bbs I (B). The PCR product (arrow) from uninjected-controls was digested to near completion, yielding two visible bands of 102 and 182 bp. The 284-bp band (arrowhead) following loss of the 5′- Bbs I site is clearly visible in the injected embryos relative to the controls. The following sequences were used for the RHO alignment: Danio rerio ( NP571159.1 ), X. laevis ( NP001080517.1 ), Mus musculus ( NP663358.1 ), Bos taurus ( NP001014890.1 ), and Homo sapiens ( NP000530.1 ).
    Nci I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nci i/product/New England Biolabs
    Average 94 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    nci i - by Bioz Stars, 2022-07
    94/100 stars
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    Gene targeting of zebrafish rh1-1 . A : Schematic representation of the zebrafish rh1-1 locus characterized by a single exon encoding 354 amino acid proteins and 5′ and 3′ UTRs. B : Alignment of Rho N- and C-terminal amino acid sequences across species. Numbering is based on the predicted zebrafish rh1–1 . The conserved N-linked glycosylation sequence and VXPX targeting sequence are underlined. C : DNA sequence and amino acid overlay of zebrafish rh1–1 5′- (left) and 3′- (right) coding sequences. Blue text represents the CRISPR PAM sequence. Underlined DNA represents the target for guide RNA hybridization. The purple overscore represent restriction sites for Nci I or Bbs I. Arrows indicate predicted Cas9 cleavage sites. D : Diagrammatic representation of the 253-bp 5′- rh1–1 gene amplicon and the predicted products following digestion with Nci I. E : RFLP analysis of a 253-bp PCR product spanning the 5′ rh1–1 gene (C, undigested control) and digested with Nci I (N) shows retention of the original amplicon (arrow) from pooled DNA from injected embryos versus complete digestion of the PCR product of uninjected control DNA (arrowhead). F : Diagrammatic representation of the 325-bp 3′-amplicon and the predicted products following digestion with Bbs I. G : RFLP analysis of a 325-bp PCR product (C, undigested control) spanning the 3′ rh1–1 sequence digested with Bbs I (B). The PCR product (arrow) from uninjected-controls was digested to near completion, yielding two visible bands of 102 and 182 bp. The 284-bp band (arrowhead) following loss of the 5′- Bbs I site is clearly visible in the injected embryos relative to the controls. The following sequences were used for the RHO alignment: Danio rerio ( NP571159.1 ), X. laevis ( NP001080517.1 ), Mus musculus ( NP663358.1 ), Bos taurus ( NP001014890.1 ), and Homo sapiens ( NP000530.1 ).

    Journal: Molecular Vision

    Article Title: Targeted disruption of the endogenous zebrafish rhodopsin locus as models of rapid rod photoreceptor degeneration

    doi:

    Figure Lengend Snippet: Gene targeting of zebrafish rh1-1 . A : Schematic representation of the zebrafish rh1-1 locus characterized by a single exon encoding 354 amino acid proteins and 5′ and 3′ UTRs. B : Alignment of Rho N- and C-terminal amino acid sequences across species. Numbering is based on the predicted zebrafish rh1–1 . The conserved N-linked glycosylation sequence and VXPX targeting sequence are underlined. C : DNA sequence and amino acid overlay of zebrafish rh1–1 5′- (left) and 3′- (right) coding sequences. Blue text represents the CRISPR PAM sequence. Underlined DNA represents the target for guide RNA hybridization. The purple overscore represent restriction sites for Nci I or Bbs I. Arrows indicate predicted Cas9 cleavage sites. D : Diagrammatic representation of the 253-bp 5′- rh1–1 gene amplicon and the predicted products following digestion with Nci I. E : RFLP analysis of a 253-bp PCR product spanning the 5′ rh1–1 gene (C, undigested control) and digested with Nci I (N) shows retention of the original amplicon (arrow) from pooled DNA from injected embryos versus complete digestion of the PCR product of uninjected control DNA (arrowhead). F : Diagrammatic representation of the 325-bp 3′-amplicon and the predicted products following digestion with Bbs I. G : RFLP analysis of a 325-bp PCR product (C, undigested control) spanning the 3′ rh1–1 sequence digested with Bbs I (B). The PCR product (arrow) from uninjected-controls was digested to near completion, yielding two visible bands of 102 and 182 bp. The 284-bp band (arrowhead) following loss of the 5′- Bbs I site is clearly visible in the injected embryos relative to the controls. The following sequences were used for the RHO alignment: Danio rerio ( NP571159.1 ), X. laevis ( NP001080517.1 ), Mus musculus ( NP663358.1 ), Bos taurus ( NP001014890.1 ), and Homo sapiens ( NP000530.1 ).

    Article Snippet: For the restriction fragment length polymorphism (RFLP) analysis of 5′ rh1-1 , a 253-bp product was amplified (forward primer: 5′ ACA GTC CTG CCC AGA CAT CTA 3′; reverse primer: 5′ ATG GTG ACG TAC AGC GTG AG 3′) and digested with Nci I ( New England Biolabs , Ipswich, MA).

    Techniques: Sequencing, CRISPR, Hybridization, Amplification, Polymerase Chain Reaction, Injection

    a PCR amplification of nagt gene (1.4 kb) from Moroccan L. infantum strains. b , c , d PCR-amplified nagt digested with Nci I, Nae I, and Alw I, respectively. The numbers above and below the digested fragments indicate their sizes. Lanes 1–5: DNA samples of Moroccan L. infantum isolates 1 to 5; NC: Negative control; M: Molecular marker HyperLader™ 100 bp plus (Bioline, Taunton, MA, USA). e RFLP maps illustrating the nagt genotype identified in this work and those identified by Waki et al. [ 34 ]*. The vertical numbers indicate the cut position of each enzyme

    Journal: Infectious Diseases of Poverty

    Article Title: Genetic polymorphism in Leishmania infantum isolates from human and animals determined by nagt PCR-RFLP

    doi: 10.1186/s40249-018-0439-y

    Figure Lengend Snippet: a PCR amplification of nagt gene (1.4 kb) from Moroccan L. infantum strains. b , c , d PCR-amplified nagt digested with Nci I, Nae I, and Alw I, respectively. The numbers above and below the digested fragments indicate their sizes. Lanes 1–5: DNA samples of Moroccan L. infantum isolates 1 to 5; NC: Negative control; M: Molecular marker HyperLader™ 100 bp plus (Bioline, Taunton, MA, USA). e RFLP maps illustrating the nagt genotype identified in this work and those identified by Waki et al. [ 34 ]*. The vertical numbers indicate the cut position of each enzyme

    Article Snippet: The thermocycler settings were an initial denaturation at 95 °C for 5 min, 30 cycles at 94 °C for 60 s, 58 °C for 60 s, and 72 °C for 90 s, and a final extension step at 72 °C for 5 min. Further RFLP analysis of the PCR-amplified nagt gene was performed separately using three restriction enzymes: Nae I, Alw I, and Nci I (New England Biolabs, Ipswich, MA, USA).

    Techniques: Polymerase Chain Reaction, Amplification, Negative Control, Marker

    Targeted point mutation (851G→A, R284Q) of Spata16 by CRISPR/Cas9. ( A ) Targeting scheme of the point mutation (851G→A, R284Q) in the fourth exon of mouse Spata16 . Spata16 consists of eleven exons. The point mutation was introduced into mouse ES cells using the HDR donor plasmid with 0.5 kb homology arms. Blue indicates the sgRNA sequence. Red indicates a G→A mutation at the last nucleotide (851st coding exon) of the fourth exon of Spata16 . Capital and small letters indicate nucleotides of exons and introns, respectively; ( B ) The genotyping of point-mutant mice by Nci I digestion. The Nci I recognition site (5′-CCCGG-3′) was disrupted due to the G→A mutation of the fourth exon. In wild-type mice, two bands (1372 bp and 1569 bp) were detected after Nci I digestion; ( C ) Direct sequencing of PCR products in Spata16 pm/pm mice. The G→A mutation at the last nucleotide (851st coding exon) of the fourth exon is indicated by the orange square; ( D ) RT-PCR analysis of a testis in Spata16 pm/pm mice. The 498-bp band was amplified from wild-type and Spata16 pm/pm mice. A point mutation causing an inappropriate splicing was not found in Spata16 pm/pm mouse testes; ( E ) Representative testicular histology sections stained with hematoxylin and eosin. Spermatogenesis in Spata16 pm/pm mice looked normal compared with that in Spata16 pm/wt mice. Scale bars: 100 μm; ( F ) Cauda epididymal spermatozoa from Spata16 pm/wt and Spata16 pm/pm mice. There were no sperm morphology differences between Spata16 pm/wt and Spata16 pm/pm mice. Spata16 pm/pm males were fertile. Scale bars: 50 μm.

    Journal: International Journal of Molecular Sciences

    Article Title: Human Globozoospermia-Related Gene Spata16 Is Required for Sperm Formation Revealed by CRISPR/Cas9-Mediated Mouse Models

    doi: 10.3390/ijms18102208

    Figure Lengend Snippet: Targeted point mutation (851G→A, R284Q) of Spata16 by CRISPR/Cas9. ( A ) Targeting scheme of the point mutation (851G→A, R284Q) in the fourth exon of mouse Spata16 . Spata16 consists of eleven exons. The point mutation was introduced into mouse ES cells using the HDR donor plasmid with 0.5 kb homology arms. Blue indicates the sgRNA sequence. Red indicates a G→A mutation at the last nucleotide (851st coding exon) of the fourth exon of Spata16 . Capital and small letters indicate nucleotides of exons and introns, respectively; ( B ) The genotyping of point-mutant mice by Nci I digestion. The Nci I recognition site (5′-CCCGG-3′) was disrupted due to the G→A mutation of the fourth exon. In wild-type mice, two bands (1372 bp and 1569 bp) were detected after Nci I digestion; ( C ) Direct sequencing of PCR products in Spata16 pm/pm mice. The G→A mutation at the last nucleotide (851st coding exon) of the fourth exon is indicated by the orange square; ( D ) RT-PCR analysis of a testis in Spata16 pm/pm mice. The 498-bp band was amplified from wild-type and Spata16 pm/pm mice. A point mutation causing an inappropriate splicing was not found in Spata16 pm/pm mouse testes; ( E ) Representative testicular histology sections stained with hematoxylin and eosin. Spermatogenesis in Spata16 pm/pm mice looked normal compared with that in Spata16 pm/wt mice. Scale bars: 100 μm; ( F ) Cauda epididymal spermatozoa from Spata16 pm/wt and Spata16 pm/pm mice. There were no sperm morphology differences between Spata16 pm/wt and Spata16 pm/pm mice. Spata16 pm/pm males were fertile. Scale bars: 50 μm.

    Article Snippet: Spata16 point mutant mice were genotyped by Nci I restriction enzyme (New England Biolabs, Ipswich, MA, USA) digestion following PCR.

    Techniques: Mutagenesis, CRISPR, Plasmid Preparation, Sequencing, Mouse Assay, Polymerase Chain Reaction, Reverse Transcription Polymerase Chain Reaction, Amplification, Staining

    Presence of the mutation within the index family. A: Pedigree of the family, with the filled symbols representing the affected members and the proband indicated by an arrow . B: Restriction analysis with Nci I; mutation present in the mother and daughter

    Journal:

    Article Title: A Novel Missense Mutation in the Second Extracellular Domain of GJB2, p.Ser183Phe, Causes a Syndrome of Focal Palmoplantar Keratoderma with Deafness

    doi: 10.2353/ajpath.2008.080049

    Figure Lengend Snippet: Presence of the mutation within the index family. A: Pedigree of the family, with the filled symbols representing the affected members and the proband indicated by an arrow . B: Restriction analysis with Nci I; mutation present in the mother and daughter

    Article Snippet: The mutation eliminates an Nci I (New England Biolabs, Frankfurt am Main, Germany) restriction site (the wild type contains two Nci I sites).

    Techniques: Mutagenesis