apo i  (New England Biolabs)


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    Name:
    ApoI
    Description:
    ApoI 5 000 units
    Catalog Number:
    r0566l
    Price:
    290
    Size:
    5 000 units
    Category:
    Restriction Enzymes
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    Structured Review

    New England Biolabs apo i
    ApoI
    ApoI 5 000 units
    https://www.bioz.com/result/apo i/product/New England Biolabs
    Average 95 stars, based on 16 article reviews
    Price from $9.99 to $1999.99
    apo i - by Bioz Stars, 2020-08
    95/100 stars

    Images

    1) Product Images from "Exploiting native forces to capture chromosome conformation in mammalian cell nuclei"

    Article Title: Exploiting native forces to capture chromosome conformation in mammalian cell nuclei

    Journal: Molecular Systems Biology

    doi: 10.15252/msb.20167311

    Features of i3C performed in HUVEC s Overview of the i3C protocol. Living cells are harvested in a close‐to‐physiological buffer (PB; step 1); intact nuclei isolated by mild NP‐40 treatment (step 2); chromatin digested using Apo I or Nla III, nuclei spun to release unattached chromatin (step 3); and leave cut chromatin bound to the nuclear substructure (step 4). Then, ligation takes places in situ , and DNA is isolated (step 5). Percentage of total cell chromatin present at the different steps of the procedure (± SD; n = 2). Relative contribution of the different HUVEC ChromHMM features in each i3C fraction. i4C‐seq (blue shades) and conventional 4C (gray shades) were performed side by side in HUVECs, using Apo I and the SAMD4A TSS as a viewpoint (triangle); profiles from two replicates are overlaid. The browser view shows interactions in the ˜1 Mbp around SAMD4A . The zoom‐in shows interactions in the SAMD4A TAD (gray rectangle). Strong (red) and intermediate (brown) interactions called by fourSig , RefSeq gene models, and ENCODE ChIP‐seq data are shown below.
    Figure Legend Snippet: Features of i3C performed in HUVEC s Overview of the i3C protocol. Living cells are harvested in a close‐to‐physiological buffer (PB; step 1); intact nuclei isolated by mild NP‐40 treatment (step 2); chromatin digested using Apo I or Nla III, nuclei spun to release unattached chromatin (step 3); and leave cut chromatin bound to the nuclear substructure (step 4). Then, ligation takes places in situ , and DNA is isolated (step 5). Percentage of total cell chromatin present at the different steps of the procedure (± SD; n = 2). Relative contribution of the different HUVEC ChromHMM features in each i3C fraction. i4C‐seq (blue shades) and conventional 4C (gray shades) were performed side by side in HUVECs, using Apo I and the SAMD4A TSS as a viewpoint (triangle); profiles from two replicates are overlaid. The browser view shows interactions in the ˜1 Mbp around SAMD4A . The zoom‐in shows interactions in the SAMD4A TAD (gray rectangle). Strong (red) and intermediate (brown) interactions called by fourSig , RefSeq gene models, and ENCODE ChIP‐seq data are shown below.

    Techniques Used: Isolation, Ligation, In Situ, Chromatin Immunoprecipitation

    TALE ‐ iD verifies native looping at the human ZFPM 2 locus An overview of TALE‐iD. A construct encoding a TALE DNA‐binding domain that targets an active enhancer in the ZFPM2 first intron is fused to a bacterial Dam methylase and introduced into K562 cells. Cells are harvested 48 h after transfection; genomic DNA is isolated and digested with Dpn I to reveal sites specifically methylated by the Dam activity. Finally, qPCR using primers flanking different Dpn I sites is used as readout. i4C performed in K562 cells using Apo I and the ZFPM2 TSS as a viewpoint (triangle). i4C interaction in the 458‐kbp ZFPM2 locus is shown, and the enhancer targeted by the TALE‐iD construct is indicated (red triangle). K562 ENCODE ChIP‐seq data are also shown below. qPCR readout at different Dpn I sites. Dpn I sites at the ZFPM2 promoter (p1–p4) and enhancer (e1–e3; positions in panel B) were targeted in qPCRs after restriction digest. Bar plots show log 2 ‐fold enrichment of cut sites (1/ΔΔ C t ) over background Dpn I cutting levels in untransfected K562 cells. Regions c1–c4 serve as controls; region m1 (an enhancer shown to interact with the TSS by i4C) is also methylated as part of a multi‐loop structure. The same Dpn I sites were also tested in transfections involving a construct encoding either a non‐targeting (“scrambled”) TALE domain or the targeting domain fused to an inactive Dam protein (“ΔDam”). * P
    Figure Legend Snippet: TALE ‐ iD verifies native looping at the human ZFPM 2 locus An overview of TALE‐iD. A construct encoding a TALE DNA‐binding domain that targets an active enhancer in the ZFPM2 first intron is fused to a bacterial Dam methylase and introduced into K562 cells. Cells are harvested 48 h after transfection; genomic DNA is isolated and digested with Dpn I to reveal sites specifically methylated by the Dam activity. Finally, qPCR using primers flanking different Dpn I sites is used as readout. i4C performed in K562 cells using Apo I and the ZFPM2 TSS as a viewpoint (triangle). i4C interaction in the 458‐kbp ZFPM2 locus is shown, and the enhancer targeted by the TALE‐iD construct is indicated (red triangle). K562 ENCODE ChIP‐seq data are also shown below. qPCR readout at different Dpn I sites. Dpn I sites at the ZFPM2 promoter (p1–p4) and enhancer (e1–e3; positions in panel B) were targeted in qPCRs after restriction digest. Bar plots show log 2 ‐fold enrichment of cut sites (1/ΔΔ C t ) over background Dpn I cutting levels in untransfected K562 cells. Regions c1–c4 serve as controls; region m1 (an enhancer shown to interact with the TSS by i4C) is also methylated as part of a multi‐loop structure. The same Dpn I sites were also tested in transfections involving a construct encoding either a non‐targeting (“scrambled”) TALE domain or the targeting domain fused to an inactive Dam protein (“ΔDam”). * P

    Techniques Used: Construct, Binding Assay, Transfection, Isolation, Methylation, Activity Assay, Real-time Polymerase Chain Reaction, Chromatin Immunoprecipitation

    2) Product Images from "Culex pipiens crossing type diversity is governed by an amplified and polymorphic operon of Wolbachia"

    Article Title: Culex pipiens crossing type diversity is governed by an amplified and polymorphic operon of Wolbachia

    Journal: Nature Communications

    doi: 10.1038/s41467-017-02749-w

    c idA _IV gene polymorphic regions and PCR-RFLP tests for specific variants. a Schematic representation of the architecture of cidA _IV polymorphism. The black line represents the cidA_IV sequence with a focus on the two polymorphic regions. Non-polymorphic regions were shortened and represented as a dashed line. Numbers in red under the line represent nucleotide positions, and the numbers in blue indicate amino-acid positions. The overlapping oligonucleotides used for PCR amplification are represented by arrows numbered as in Supplementary Table 2 . Both polymorphic regions were studied, but only the upstream matched the compatibility profile; its four different sequences (α, β γ, and δ) were followed by one of the two possible sequences (1 or 2) in the downstream polymorphic region. A different color code was used for α (purple), β (light blue), γ (light green), and δ (yellow) sequences in the upstream part of the cidA gene. b The repertoire of cidA _IV variants is different in “compatible” and “incompatible” lines. cidA _IV(δ) is present only in lines with “incompatible” crossing type. The names of the C . pipiens lines used to set-up the PCR-RFLP ( c ) test are highlighted in red. c PCR-RFLP tests for distinguishing between cidA _IV variants on the basis of the upstream polymorphic region. A 778 bp fragment was amplified with primers 1/13. Double digestion with Apo I and Hpy 188I distinguished between cidA _IV(α) (six fragments: 471; 122; 57; 53; 51; and 24 bp), cidA _IV(β) and cidA _IV(γ) (six fragments: 441; 122; 83; 57; 51; and 24 bp), and cidA _IV(δ) (five fragments: 524; 122; 57; 51; and 24 bp). Panel to the left of the electrophoresis gel: PCR-RFLP on DNA from clones; right panel: PCR-RFLP on DNA from the Istanbul, Harash, Ichkeul 13, and Ichkeul 09 lines. On the right of the gel, a schematic representation of the PCR-RFLP profiles of these lines. Digestion bands that are specific of the variants are represented with the color code established in a . Bands that are not used to discriminate between the variants are represented in black on the bottom of the schematic gel
    Figure Legend Snippet: c idA _IV gene polymorphic regions and PCR-RFLP tests for specific variants. a Schematic representation of the architecture of cidA _IV polymorphism. The black line represents the cidA_IV sequence with a focus on the two polymorphic regions. Non-polymorphic regions were shortened and represented as a dashed line. Numbers in red under the line represent nucleotide positions, and the numbers in blue indicate amino-acid positions. The overlapping oligonucleotides used for PCR amplification are represented by arrows numbered as in Supplementary Table 2 . Both polymorphic regions were studied, but only the upstream matched the compatibility profile; its four different sequences (α, β γ, and δ) were followed by one of the two possible sequences (1 or 2) in the downstream polymorphic region. A different color code was used for α (purple), β (light blue), γ (light green), and δ (yellow) sequences in the upstream part of the cidA gene. b The repertoire of cidA _IV variants is different in “compatible” and “incompatible” lines. cidA _IV(δ) is present only in lines with “incompatible” crossing type. The names of the C . pipiens lines used to set-up the PCR-RFLP ( c ) test are highlighted in red. c PCR-RFLP tests for distinguishing between cidA _IV variants on the basis of the upstream polymorphic region. A 778 bp fragment was amplified with primers 1/13. Double digestion with Apo I and Hpy 188I distinguished between cidA _IV(α) (six fragments: 471; 122; 57; 53; 51; and 24 bp), cidA _IV(β) and cidA _IV(γ) (six fragments: 441; 122; 83; 57; 51; and 24 bp), and cidA _IV(δ) (five fragments: 524; 122; 57; 51; and 24 bp). Panel to the left of the electrophoresis gel: PCR-RFLP on DNA from clones; right panel: PCR-RFLP on DNA from the Istanbul, Harash, Ichkeul 13, and Ichkeul 09 lines. On the right of the gel, a schematic representation of the PCR-RFLP profiles of these lines. Digestion bands that are specific of the variants are represented with the color code established in a . Bands that are not used to discriminate between the variants are represented in black on the bottom of the schematic gel

    Techniques Used: Polymerase Chain Reaction, Sequencing, Amplification, Electrophoresis, Clone Assay

    3) Product Images from "Culex pipiens crossing type diversity is governed by an amplified and polymorphic operon of Wolbachia"

    Article Title: Culex pipiens crossing type diversity is governed by an amplified and polymorphic operon of Wolbachia

    Journal: Nature Communications

    doi: 10.1038/s41467-017-02749-w

    c idA _IV gene polymorphic regions and PCR-RFLP tests for specific variants. a Schematic representation of the architecture of cidA _IV polymorphism. The black line represents the cidA_IV . Both polymorphic regions were studied, but only the upstream matched the compatibility profile; its four different sequences (α, β γ, and δ) were followed by one of the two possible sequences (1 or 2) in the downstream polymorphic region. A different color code was used for α (purple), β (light blue), γ (light green), and δ (yellow) sequences in the upstream part of the cidA gene. b The repertoire of cidA _IV variants is different in “compatible” and “incompatible” lines. cidA _IV(δ) is present only in lines with “incompatible” crossing type. The names of the C . pipiens lines used to set-up the PCR-RFLP ( c ) test are highlighted in red. c PCR-RFLP tests for distinguishing between cidA _IV variants on the basis of the upstream polymorphic region. A 778 bp fragment was amplified with primers 1/13. Double digestion with Apo I and Hpy 188I distinguished between cidA _IV(α) (six fragments: 471; 122; 57; 53; 51; and 24 bp), cidA _IV(β) and cidA _IV(γ) (six fragments: 441; 122; 83; 57; 51; and 24 bp), and cidA _IV(δ) (five fragments: 524; 122; 57; 51; and 24 bp). Panel to the left of the electrophoresis gel: PCR-RFLP on DNA from clones; right panel: PCR-RFLP on DNA from the Istanbul, Harash, Ichkeul 13, and Ichkeul 09 lines. On the right of the gel, a schematic representation of the PCR-RFLP profiles of these lines. Digestion bands that are specific of the variants are represented with the color code established in a . Bands that are not used to discriminate between the variants are represented in black on the bottom of the schematic gel
    Figure Legend Snippet: c idA _IV gene polymorphic regions and PCR-RFLP tests for specific variants. a Schematic representation of the architecture of cidA _IV polymorphism. The black line represents the cidA_IV . Both polymorphic regions were studied, but only the upstream matched the compatibility profile; its four different sequences (α, β γ, and δ) were followed by one of the two possible sequences (1 or 2) in the downstream polymorphic region. A different color code was used for α (purple), β (light blue), γ (light green), and δ (yellow) sequences in the upstream part of the cidA gene. b The repertoire of cidA _IV variants is different in “compatible” and “incompatible” lines. cidA _IV(δ) is present only in lines with “incompatible” crossing type. The names of the C . pipiens lines used to set-up the PCR-RFLP ( c ) test are highlighted in red. c PCR-RFLP tests for distinguishing between cidA _IV variants on the basis of the upstream polymorphic region. A 778 bp fragment was amplified with primers 1/13. Double digestion with Apo I and Hpy 188I distinguished between cidA _IV(α) (six fragments: 471; 122; 57; 53; 51; and 24 bp), cidA _IV(β) and cidA _IV(γ) (six fragments: 441; 122; 83; 57; 51; and 24 bp), and cidA _IV(δ) (five fragments: 524; 122; 57; 51; and 24 bp). Panel to the left of the electrophoresis gel: PCR-RFLP on DNA from clones; right panel: PCR-RFLP on DNA from the Istanbul, Harash, Ichkeul 13, and Ichkeul 09 lines. On the right of the gel, a schematic representation of the PCR-RFLP profiles of these lines. Digestion bands that are specific of the variants are represented with the color code established in a . Bands that are not used to discriminate between the variants are represented in black on the bottom of the schematic gel

    Techniques Used: Polymerase Chain Reaction, Amplification, Electrophoresis, Clone Assay

    4) Product Images from "Chloroquine-Resistant Haplotype Plasmodium falciparum Parasites, Haiti"

    Article Title: Chloroquine-Resistant Haplotype Plasmodium falciparum Parasites, Haiti

    Journal: Emerging Infectious Diseases

    doi: 10.3201/eid1505.081063

    Agarose gel electrophoresis of amplicons for the Plasmodium falciparum chloroquine (CQ) resistance transporter gene digested with Apo I. Lane 1, DNA molecular mass standards (Stds) (Invitrogen, Carlsbad, CA, USA); lanes 2 and 3, amplicons susceptible to cleavage by Apo I, showing 2 fragments of 100 and 34 bp, consistent with infection by only CQ-susceptible haplotype parasites; lanes 4 and 5, amplicons partially resistant to cleavage by Apo I, showing 3 fragments of 134, 100, and 34 bp, consistent with mixed infections by CQ-resistant and CQ-susceptible haplotype parasites; lane 6, positive control (Pos ctrl), amplicon from CQ-susceptible Haiti I/CDC strain ( 26 ), showing 2 fragments of 100 and 34 bp; lane 7, negative control (Neg ctrl), amplicon from CQ-resistant Indochina (Indo) I/CDC strain ( 33 ), showing 1 fragment of 134 bp.
    Figure Legend Snippet: Agarose gel electrophoresis of amplicons for the Plasmodium falciparum chloroquine (CQ) resistance transporter gene digested with Apo I. Lane 1, DNA molecular mass standards (Stds) (Invitrogen, Carlsbad, CA, USA); lanes 2 and 3, amplicons susceptible to cleavage by Apo I, showing 2 fragments of 100 and 34 bp, consistent with infection by only CQ-susceptible haplotype parasites; lanes 4 and 5, amplicons partially resistant to cleavage by Apo I, showing 3 fragments of 134, 100, and 34 bp, consistent with mixed infections by CQ-resistant and CQ-susceptible haplotype parasites; lane 6, positive control (Pos ctrl), amplicon from CQ-susceptible Haiti I/CDC strain ( 26 ), showing 2 fragments of 100 and 34 bp; lane 7, negative control (Neg ctrl), amplicon from CQ-resistant Indochina (Indo) I/CDC strain ( 33 ), showing 1 fragment of 134 bp.

    Techniques Used: Agarose Gel Electrophoresis, Infection, Positive Control, Amplification, Negative Control

    Agarose gel electrophoresis of amplicons for the Plasmodium falciparum chloroquine (CQ) resistance transporter gene digested with Apo I. Lane 1, DNA molecular mass standards (Stds) (Invitrogen, Carlsbad, CA, USA); lanes 2 and 3, amplicons susceptible to cleavage by Apo I, showing 2 fragments of 100 and 34 bp, consistent with infection by only CQ-susceptible haplotype parasites; lanes 4 and 5, amplicons partially resistant to cleavage by Apo I, showing 3 fragments of 134, 100, and 34 bp, consistent with mixed infections by CQ-resistant and CQ-susceptible haplotype parasites; lane 6, positive control (Pos ctrl), amplicon from CQ-susceptible Haiti I/CDC strain ( 26 ), showing 2 fragments of 100 and 34 bp; lane 7, negative control (Neg ctrl), amplicon from CQ-resistant Indochina (Indo) I/CDC strain ( 33 ), showing 1 fragment of 134 bp.
    Figure Legend Snippet: Agarose gel electrophoresis of amplicons for the Plasmodium falciparum chloroquine (CQ) resistance transporter gene digested with Apo I. Lane 1, DNA molecular mass standards (Stds) (Invitrogen, Carlsbad, CA, USA); lanes 2 and 3, amplicons susceptible to cleavage by Apo I, showing 2 fragments of 100 and 34 bp, consistent with infection by only CQ-susceptible haplotype parasites; lanes 4 and 5, amplicons partially resistant to cleavage by Apo I, showing 3 fragments of 134, 100, and 34 bp, consistent with mixed infections by CQ-resistant and CQ-susceptible haplotype parasites; lane 6, positive control (Pos ctrl), amplicon from CQ-susceptible Haiti I/CDC strain ( 26 ), showing 2 fragments of 100 and 34 bp; lane 7, negative control (Neg ctrl), amplicon from CQ-resistant Indochina (Indo) I/CDC strain ( 33 ), showing 1 fragment of 134 bp.

    Techniques Used: Agarose Gel Electrophoresis, Infection, Positive Control, Amplification, Negative Control

    5) Product Images from "Chloroquine-Resistant Haplotype Plasmodium falciparum Parasites, Haiti"

    Article Title: Chloroquine-Resistant Haplotype Plasmodium falciparum Parasites, Haiti

    Journal: Emerging Infectious Diseases

    doi: 10.3201/eid1505.081063

    Agarose gel electrophoresis of amplicons for the Plasmodium falciparum chloroquine (CQ) resistance transporter gene digested with Apo I. Lane 1, DNA molecular mass standards (Stds) (Invitrogen, Carlsbad, CA, USA); lanes 2 and 3, amplicons susceptible to cleavage by Apo I, showing 2 fragments of 100 and 34 bp, consistent with infection by only CQ-susceptible haplotype parasites; lanes 4 and 5, amplicons partially resistant to cleavage by Apo I, showing 3 fragments of 134, 100, and 34 bp, consistent with mixed infections by CQ-resistant and CQ-susceptible haplotype parasites; lane 6, positive control (Pos ctrl), amplicon from CQ-susceptible Haiti I/CDC strain ( 26 ), showing 2 fragments of 100 and 34 bp; lane 7, negative control (Neg ctrl), amplicon from CQ-resistant Indochina (Indo) I/CDC strain ( 33 ), showing 1 fragment of 134 bp.
    Figure Legend Snippet: Agarose gel electrophoresis of amplicons for the Plasmodium falciparum chloroquine (CQ) resistance transporter gene digested with Apo I. Lane 1, DNA molecular mass standards (Stds) (Invitrogen, Carlsbad, CA, USA); lanes 2 and 3, amplicons susceptible to cleavage by Apo I, showing 2 fragments of 100 and 34 bp, consistent with infection by only CQ-susceptible haplotype parasites; lanes 4 and 5, amplicons partially resistant to cleavage by Apo I, showing 3 fragments of 134, 100, and 34 bp, consistent with mixed infections by CQ-resistant and CQ-susceptible haplotype parasites; lane 6, positive control (Pos ctrl), amplicon from CQ-susceptible Haiti I/CDC strain ( 26 ), showing 2 fragments of 100 and 34 bp; lane 7, negative control (Neg ctrl), amplicon from CQ-resistant Indochina (Indo) I/CDC strain ( 33 ), showing 1 fragment of 134 bp.

    Techniques Used: Agarose Gel Electrophoresis, Infection, Positive Control, Amplification, Negative Control

    Agarose gel electrophoresis of amplicons for the Plasmodium falciparum chloroquine (CQ) resistance transporter gene digested with Apo I. Lane 1, DNA molecular mass standards (Stds) (Invitrogen, Carlsbad, CA, USA); lanes 2 and 3, amplicons susceptible to cleavage by Apo I, showing 2 fragments of 100 and 34 bp, consistent with infection by only CQ-susceptible haplotype parasites; lanes 4 and 5, amplicons partially resistant to cleavage by Apo I, showing 3 fragments of 134, 100, and 34 bp, consistent with mixed infections by CQ-resistant and CQ-susceptible haplotype parasites; lane 6, positive control (Pos ctrl), amplicon from CQ-susceptible Haiti I/CDC strain ( 26 ), showing 2 fragments of 100 and 34 bp; lane 7, negative control (Neg ctrl), amplicon from CQ-resistant Indochina (Indo) I/CDC strain ( 33 ), showing 1 fragment of 134 bp.
    Figure Legend Snippet: Agarose gel electrophoresis of amplicons for the Plasmodium falciparum chloroquine (CQ) resistance transporter gene digested with Apo I. Lane 1, DNA molecular mass standards (Stds) (Invitrogen, Carlsbad, CA, USA); lanes 2 and 3, amplicons susceptible to cleavage by Apo I, showing 2 fragments of 100 and 34 bp, consistent with infection by only CQ-susceptible haplotype parasites; lanes 4 and 5, amplicons partially resistant to cleavage by Apo I, showing 3 fragments of 134, 100, and 34 bp, consistent with mixed infections by CQ-resistant and CQ-susceptible haplotype parasites; lane 6, positive control (Pos ctrl), amplicon from CQ-susceptible Haiti I/CDC strain ( 26 ), showing 2 fragments of 100 and 34 bp; lane 7, negative control (Neg ctrl), amplicon from CQ-resistant Indochina (Indo) I/CDC strain ( 33 ), showing 1 fragment of 134 bp.

    Techniques Used: Agarose Gel Electrophoresis, Infection, Positive Control, Amplification, Negative Control

    Related Articles

    Polymerase Chain Reaction:

    Article Title: Characterization of Neisseria meningitidis Isolates from Recent Outbreaks in Ethiopia and Comparison with Those Recovered during the Epidemic of 1988 to 1989
    Article Snippet: .. Following purification of the tbpB PCR product with the QIAquick purification kit (QIAGEN), macrorestriction fragments were obtained by digestion of the purified tbpB product using the restriction endonucleases ApoI and SspI (New England Biolabs Inc., Beverly, MA) according to the manufacturer's instructions. .. The fragments were thereafter separated on 2% agarose gels, stained with ethidium bromide, and compared with band patterns of similarly digested tbpB PCR products from a control strain, Z1054 ( tbpB allele 1).

    Article Title: Chloroquine-Resistant Haplotype Plasmodium falciparum Parasites, Haiti
    Article Snippet: .. Digestion of Amplicons from pfcrt with Apo I For each sample positive for SSU DNA, an aliquot (10 μL) of the pfcrt gene PCR product was digested with 10 U of Apo I (New England Biolabs, Beverly, MA, USA) according to the manufacturer’s instructions. .. Briefly, 10 U of Apo I in 1× NE buffer 3 (100 mol/L NaCl, 50 mmol/L Tris-HCl, 10 mmol/L MgCl2 , 1 mmol/L dithiothreitol) and bovine serum albumin (100 μg/μL) were incubated overnight with 10 μL of the PCR product at 50°C ( – ).

    Article Title: Culex pipiens crossing type diversity is governed by an amplified and polymorphic operon of Wolbachia
    Article Snippet: .. Double digestion of the PCR products with Apo I and Hpy 188I (New England Biolabs) identified three groups of sequencing: cid A_IV(α) (six fragments: 471; 122; 57; 53; 51; and 24 bp); cidA _IV(β) and cidA _IV(γ) (six fragments: 441; 123; 83; 57; 51; and 24 bp); and cidA _IV(δ) (five fragments: 524; 122; 57; 51; and 24 bp). .. For cidB _IV variants, only the second polymorphic region was found to be correlated with crossing types, so the PCR-RFLP test was designed to discriminate between the cidB _IV(1), cidB _IV(2), and cidB _IV(3) sequences (Fig. ).

    Article Title: Culex pipiens crossing type diversity is governed by an amplified and polymorphic operon of Wolbachia
    Article Snippet: .. Double digestion of the PCR products with Apo I and Hpy 188I (New England Biolabs) identified three groups of sequencing: cid A_IV(α) (six fragments: 471; 122; 57; 53; 51; and 24 bp); cidA _IV(β) and cidA _IV(γ) (six fragments: 441; 123; 83; 57; 51; and 24 bp); and cidA _IV(δ) (five fragments: 524; 122; 57; 51; and 24 bp). .. For cidB _IV variants, only the second polymorphic region was found to be correlated with crossing types, so the PCR-RFLP test was designed to discriminate between the cidB _IV(1), cidB _IV(2), and cidB _IV(3) sequences (Fig. ).

    Sequencing:

    Article Title: Culex pipiens crossing type diversity is governed by an amplified and polymorphic operon of Wolbachia
    Article Snippet: .. Double digestion of the PCR products with Apo I and Hpy 188I (New England Biolabs) identified three groups of sequencing: cid A_IV(α) (six fragments: 471; 122; 57; 53; 51; and 24 bp); cidA _IV(β) and cidA _IV(γ) (six fragments: 441; 123; 83; 57; 51; and 24 bp); and cidA _IV(δ) (five fragments: 524; 122; 57; 51; and 24 bp). .. For cidB _IV variants, only the second polymorphic region was found to be correlated with crossing types, so the PCR-RFLP test was designed to discriminate between the cidB _IV(1), cidB _IV(2), and cidB _IV(3) sequences (Fig. ).

    Article Title: Culex pipiens crossing type diversity is governed by an amplified and polymorphic operon of Wolbachia
    Article Snippet: .. Double digestion of the PCR products with Apo I and Hpy 188I (New England Biolabs) identified three groups of sequencing: cid A_IV(α) (six fragments: 471; 122; 57; 53; 51; and 24 bp); cidA _IV(β) and cidA _IV(γ) (six fragments: 441; 123; 83; 57; 51; and 24 bp); and cidA _IV(δ) (five fragments: 524; 122; 57; 51; and 24 bp). .. For cidB _IV variants, only the second polymorphic region was found to be correlated with crossing types, so the PCR-RFLP test was designed to discriminate between the cidB _IV(1), cidB _IV(2), and cidB _IV(3) sequences (Fig. ).

    Ligation:

    Article Title: Ligation of high-melting-temperature 'clamp' sequence extends the scanning range of rare point-mutational analysis by constant denaturant capillary electrophoresis (CDCE) to most of the human genome
    Article Snippet: .. To generate the HPRT target with the ligated clamp suitable for CDCE analysis (Fig. ), restriction digestion by ApoI (New England Biolabs) was followed by clamp ligation. ..

    Purification:

    Article Title: Characterization of Neisseria meningitidis Isolates from Recent Outbreaks in Ethiopia and Comparison with Those Recovered during the Epidemic of 1988 to 1989
    Article Snippet: .. Following purification of the tbpB PCR product with the QIAquick purification kit (QIAGEN), macrorestriction fragments were obtained by digestion of the purified tbpB product using the restriction endonucleases ApoI and SspI (New England Biolabs Inc., Beverly, MA) according to the manufacturer's instructions. .. The fragments were thereafter separated on 2% agarose gels, stained with ethidium bromide, and compared with band patterns of similarly digested tbpB PCR products from a control strain, Z1054 ( tbpB allele 1).

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  • 95
    New England Biolabs apo i
    Features of i3C performed in HUVEC s Overview of the i3C protocol. Living cells are harvested in a close‐to‐physiological buffer (PB; step 1); intact nuclei isolated by mild NP‐40 treatment (step 2); chromatin digested using <t>Apo</t> I or Nla III, nuclei spun to release unattached chromatin (step 3); and leave cut chromatin bound to the nuclear substructure (step 4). Then, ligation takes places in situ , and DNA is isolated (step 5). Percentage of total cell chromatin present at the different steps of the procedure (± SD; n = 2). Relative contribution of the different HUVEC ChromHMM features in each i3C fraction. i4C‐seq (blue shades) and conventional 4C (gray shades) were performed side by side in HUVECs, using Apo I and the SAMD4A TSS as a viewpoint (triangle); profiles from two replicates are overlaid. The browser view shows interactions in the ˜1 Mbp around SAMD4A . The zoom‐in shows interactions in the SAMD4A TAD (gray rectangle). Strong (red) and intermediate (brown) interactions called by fourSig , RefSeq gene models, and ENCODE ChIP‐seq data are shown below.
    Apo I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/apo i/product/New England Biolabs
    Average 95 stars, based on 16 article reviews
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    New England Biolabs restriction enzyme apo i
    Identification of two missense mutations in TMEM67 . ( a ) Sequence analysis of TMEM67 showing sequence variants in exon 20 (indicated by asterisks above the sequence tracks) in a carrier, and in an affected lamb, compared to an unaffected lamb. Below the unaffected sequence, the <t>Apo</t> I restriction site is indicated (black bar) ( b ) Apo I restriction fragment length polymorphism generated by the sequence variants caused different restriction digestion patterns for the affected and carrier lambs, compared to unaffected lambs; M, marker; U, unaffected pattern; C, carrier pattern; A, affected pattern. ( c ) Alignment of mutant with wild type partial sequences of meckelin from multiple species. The diagram shows the isoleucine to asparagine amino acid substitution at position 681 (I681N), and isoleucine to serine substitution at position 687 (I687S) in an affected lamb (MKS sheep), compared to the unaffected ( Ovis aries ) meckelin sequence (boxed). The partial meckelin sequence is aligned with ten orthologous sequences from other species. The boxes show the affected amino acids, and conservation of an isoleucine amino acid at these positions in several vertebrate species, including humans and zebrafish. The amino acids in the grey portion mark the beginning of a transmembrane domain in meckelin.
    Restriction Enzyme Apo I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 85/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/restriction enzyme apo i/product/New England Biolabs
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    New England Biolabs apo i taq i
    Visualized differentially expressed TDFs between Sea Island cotton fibers and Upland cotton fibers in cDNA-AFLP analyses. Lane 1 to 3 show Upland cotton ( G. hirsutum cv. CRI 8) fibers and Lane 4 to 6 show Sea Island cotton ( G . barbadense cv. Pima90-53) fibers. Eco RI/ Mse I and Apo I/ <t>Taq</t> I are the restriction enzyme combinations used in cDNA-AFLP analyses. Arrowheads show the differentially expressed FLA TDFs.
    Apo I Taq I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Features of i3C performed in HUVEC s Overview of the i3C protocol. Living cells are harvested in a close‐to‐physiological buffer (PB; step 1); intact nuclei isolated by mild NP‐40 treatment (step 2); chromatin digested using Apo I or Nla III, nuclei spun to release unattached chromatin (step 3); and leave cut chromatin bound to the nuclear substructure (step 4). Then, ligation takes places in situ , and DNA is isolated (step 5). Percentage of total cell chromatin present at the different steps of the procedure (± SD; n = 2). Relative contribution of the different HUVEC ChromHMM features in each i3C fraction. i4C‐seq (blue shades) and conventional 4C (gray shades) were performed side by side in HUVECs, using Apo I and the SAMD4A TSS as a viewpoint (triangle); profiles from two replicates are overlaid. The browser view shows interactions in the ˜1 Mbp around SAMD4A . The zoom‐in shows interactions in the SAMD4A TAD (gray rectangle). Strong (red) and intermediate (brown) interactions called by fourSig , RefSeq gene models, and ENCODE ChIP‐seq data are shown below.

    Journal: Molecular Systems Biology

    Article Title: Exploiting native forces to capture chromosome conformation in mammalian cell nuclei

    doi: 10.15252/msb.20167311

    Figure Lengend Snippet: Features of i3C performed in HUVEC s Overview of the i3C protocol. Living cells are harvested in a close‐to‐physiological buffer (PB; step 1); intact nuclei isolated by mild NP‐40 treatment (step 2); chromatin digested using Apo I or Nla III, nuclei spun to release unattached chromatin (step 3); and leave cut chromatin bound to the nuclear substructure (step 4). Then, ligation takes places in situ , and DNA is isolated (step 5). Percentage of total cell chromatin present at the different steps of the procedure (± SD; n = 2). Relative contribution of the different HUVEC ChromHMM features in each i3C fraction. i4C‐seq (blue shades) and conventional 4C (gray shades) were performed side by side in HUVECs, using Apo I and the SAMD4A TSS as a viewpoint (triangle); profiles from two replicates are overlaid. The browser view shows interactions in the ˜1 Mbp around SAMD4A . The zoom‐in shows interactions in the SAMD4A TAD (gray rectangle). Strong (red) and intermediate (brown) interactions called by fourSig , RefSeq gene models, and ENCODE ChIP‐seq data are shown below.

    Article Snippet: Next, chromatin is digested with 500 units of Apo I or Nla III (New England Biolabs; 33°C, 30–45 min) without shaking.

    Techniques: Isolation, Ligation, In Situ, Chromatin Immunoprecipitation

    TALE ‐ iD verifies native looping at the human ZFPM 2 locus An overview of TALE‐iD. A construct encoding a TALE DNA‐binding domain that targets an active enhancer in the ZFPM2 first intron is fused to a bacterial Dam methylase and introduced into K562 cells. Cells are harvested 48 h after transfection; genomic DNA is isolated and digested with Dpn I to reveal sites specifically methylated by the Dam activity. Finally, qPCR using primers flanking different Dpn I sites is used as readout. i4C performed in K562 cells using Apo I and the ZFPM2 TSS as a viewpoint (triangle). i4C interaction in the 458‐kbp ZFPM2 locus is shown, and the enhancer targeted by the TALE‐iD construct is indicated (red triangle). K562 ENCODE ChIP‐seq data are also shown below. qPCR readout at different Dpn I sites. Dpn I sites at the ZFPM2 promoter (p1–p4) and enhancer (e1–e3; positions in panel B) were targeted in qPCRs after restriction digest. Bar plots show log 2 ‐fold enrichment of cut sites (1/ΔΔ C t ) over background Dpn I cutting levels in untransfected K562 cells. Regions c1–c4 serve as controls; region m1 (an enhancer shown to interact with the TSS by i4C) is also methylated as part of a multi‐loop structure. The same Dpn I sites were also tested in transfections involving a construct encoding either a non‐targeting (“scrambled”) TALE domain or the targeting domain fused to an inactive Dam protein (“ΔDam”). * P

    Journal: Molecular Systems Biology

    Article Title: Exploiting native forces to capture chromosome conformation in mammalian cell nuclei

    doi: 10.15252/msb.20167311

    Figure Lengend Snippet: TALE ‐ iD verifies native looping at the human ZFPM 2 locus An overview of TALE‐iD. A construct encoding a TALE DNA‐binding domain that targets an active enhancer in the ZFPM2 first intron is fused to a bacterial Dam methylase and introduced into K562 cells. Cells are harvested 48 h after transfection; genomic DNA is isolated and digested with Dpn I to reveal sites specifically methylated by the Dam activity. Finally, qPCR using primers flanking different Dpn I sites is used as readout. i4C performed in K562 cells using Apo I and the ZFPM2 TSS as a viewpoint (triangle). i4C interaction in the 458‐kbp ZFPM2 locus is shown, and the enhancer targeted by the TALE‐iD construct is indicated (red triangle). K562 ENCODE ChIP‐seq data are also shown below. qPCR readout at different Dpn I sites. Dpn I sites at the ZFPM2 promoter (p1–p4) and enhancer (e1–e3; positions in panel B) were targeted in qPCRs after restriction digest. Bar plots show log 2 ‐fold enrichment of cut sites (1/ΔΔ C t ) over background Dpn I cutting levels in untransfected K562 cells. Regions c1–c4 serve as controls; region m1 (an enhancer shown to interact with the TSS by i4C) is also methylated as part of a multi‐loop structure. The same Dpn I sites were also tested in transfections involving a construct encoding either a non‐targeting (“scrambled”) TALE domain or the targeting domain fused to an inactive Dam protein (“ΔDam”). * P

    Article Snippet: Next, chromatin is digested with 500 units of Apo I or Nla III (New England Biolabs; 33°C, 30–45 min) without shaking.

    Techniques: Construct, Binding Assay, Transfection, Isolation, Methylation, Activity Assay, Real-time Polymerase Chain Reaction, Chromatin Immunoprecipitation

    c idA _IV gene polymorphic regions and PCR-RFLP tests for specific variants. a Schematic representation of the architecture of cidA _IV polymorphism. The black line represents the cidA_IV sequence with a focus on the two polymorphic regions. Non-polymorphic regions were shortened and represented as a dashed line. Numbers in red under the line represent nucleotide positions, and the numbers in blue indicate amino-acid positions. The overlapping oligonucleotides used for PCR amplification are represented by arrows numbered as in Supplementary Table 2 . Both polymorphic regions were studied, but only the upstream matched the compatibility profile; its four different sequences (α, β γ, and δ) were followed by one of the two possible sequences (1 or 2) in the downstream polymorphic region. A different color code was used for α (purple), β (light blue), γ (light green), and δ (yellow) sequences in the upstream part of the cidA gene. b The repertoire of cidA _IV variants is different in “compatible” and “incompatible” lines. cidA _IV(δ) is present only in lines with “incompatible” crossing type. The names of the C . pipiens lines used to set-up the PCR-RFLP ( c ) test are highlighted in red. c PCR-RFLP tests for distinguishing between cidA _IV variants on the basis of the upstream polymorphic region. A 778 bp fragment was amplified with primers 1/13. Double digestion with Apo I and Hpy 188I distinguished between cidA _IV(α) (six fragments: 471; 122; 57; 53; 51; and 24 bp), cidA _IV(β) and cidA _IV(γ) (six fragments: 441; 122; 83; 57; 51; and 24 bp), and cidA _IV(δ) (five fragments: 524; 122; 57; 51; and 24 bp). Panel to the left of the electrophoresis gel: PCR-RFLP on DNA from clones; right panel: PCR-RFLP on DNA from the Istanbul, Harash, Ichkeul 13, and Ichkeul 09 lines. On the right of the gel, a schematic representation of the PCR-RFLP profiles of these lines. Digestion bands that are specific of the variants are represented with the color code established in a . Bands that are not used to discriminate between the variants are represented in black on the bottom of the schematic gel

    Journal: Nature Communications

    Article Title: Culex pipiens crossing type diversity is governed by an amplified and polymorphic operon of Wolbachia

    doi: 10.1038/s41467-017-02749-w

    Figure Lengend Snippet: c idA _IV gene polymorphic regions and PCR-RFLP tests for specific variants. a Schematic representation of the architecture of cidA _IV polymorphism. The black line represents the cidA_IV sequence with a focus on the two polymorphic regions. Non-polymorphic regions were shortened and represented as a dashed line. Numbers in red under the line represent nucleotide positions, and the numbers in blue indicate amino-acid positions. The overlapping oligonucleotides used for PCR amplification are represented by arrows numbered as in Supplementary Table 2 . Both polymorphic regions were studied, but only the upstream matched the compatibility profile; its four different sequences (α, β γ, and δ) were followed by one of the two possible sequences (1 or 2) in the downstream polymorphic region. A different color code was used for α (purple), β (light blue), γ (light green), and δ (yellow) sequences in the upstream part of the cidA gene. b The repertoire of cidA _IV variants is different in “compatible” and “incompatible” lines. cidA _IV(δ) is present only in lines with “incompatible” crossing type. The names of the C . pipiens lines used to set-up the PCR-RFLP ( c ) test are highlighted in red. c PCR-RFLP tests for distinguishing between cidA _IV variants on the basis of the upstream polymorphic region. A 778 bp fragment was amplified with primers 1/13. Double digestion with Apo I and Hpy 188I distinguished between cidA _IV(α) (six fragments: 471; 122; 57; 53; 51; and 24 bp), cidA _IV(β) and cidA _IV(γ) (six fragments: 441; 122; 83; 57; 51; and 24 bp), and cidA _IV(δ) (five fragments: 524; 122; 57; 51; and 24 bp). Panel to the left of the electrophoresis gel: PCR-RFLP on DNA from clones; right panel: PCR-RFLP on DNA from the Istanbul, Harash, Ichkeul 13, and Ichkeul 09 lines. On the right of the gel, a schematic representation of the PCR-RFLP profiles of these lines. Digestion bands that are specific of the variants are represented with the color code established in a . Bands that are not used to discriminate between the variants are represented in black on the bottom of the schematic gel

    Article Snippet: Double digestion of the PCR products with Apo I and Hpy 188I (New England Biolabs) identified three groups of sequencing: cid A_IV(α) (six fragments: 471; 122; 57; 53; 51; and 24 bp); cidA _IV(β) and cidA _IV(γ) (six fragments: 441; 123; 83; 57; 51; and 24 bp); and cidA _IV(δ) (five fragments: 524; 122; 57; 51; and 24 bp).

    Techniques: Polymerase Chain Reaction, Sequencing, Amplification, Electrophoresis, Clone Assay

    Identification of two missense mutations in TMEM67 . ( a ) Sequence analysis of TMEM67 showing sequence variants in exon 20 (indicated by asterisks above the sequence tracks) in a carrier, and in an affected lamb, compared to an unaffected lamb. Below the unaffected sequence, the Apo I restriction site is indicated (black bar) ( b ) Apo I restriction fragment length polymorphism generated by the sequence variants caused different restriction digestion patterns for the affected and carrier lambs, compared to unaffected lambs; M, marker; U, unaffected pattern; C, carrier pattern; A, affected pattern. ( c ) Alignment of mutant with wild type partial sequences of meckelin from multiple species. The diagram shows the isoleucine to asparagine amino acid substitution at position 681 (I681N), and isoleucine to serine substitution at position 687 (I687S) in an affected lamb (MKS sheep), compared to the unaffected ( Ovis aries ) meckelin sequence (boxed). The partial meckelin sequence is aligned with ten orthologous sequences from other species. The boxes show the affected amino acids, and conservation of an isoleucine amino acid at these positions in several vertebrate species, including humans and zebrafish. The amino acids in the grey portion mark the beginning of a transmembrane domain in meckelin.

    Journal: Scientific Reports

    Article Title: An ovine hepatorenal fibrocystic model of a Meckel-like syndrome associated with dysmorphic primary cilia and TMEM67 mutations

    doi: 10.1038/s41598-017-01519-4

    Figure Lengend Snippet: Identification of two missense mutations in TMEM67 . ( a ) Sequence analysis of TMEM67 showing sequence variants in exon 20 (indicated by asterisks above the sequence tracks) in a carrier, and in an affected lamb, compared to an unaffected lamb. Below the unaffected sequence, the Apo I restriction site is indicated (black bar) ( b ) Apo I restriction fragment length polymorphism generated by the sequence variants caused different restriction digestion patterns for the affected and carrier lambs, compared to unaffected lambs; M, marker; U, unaffected pattern; C, carrier pattern; A, affected pattern. ( c ) Alignment of mutant with wild type partial sequences of meckelin from multiple species. The diagram shows the isoleucine to asparagine amino acid substitution at position 681 (I681N), and isoleucine to serine substitution at position 687 (I687S) in an affected lamb (MKS sheep), compared to the unaffected ( Ovis aries ) meckelin sequence (boxed). The partial meckelin sequence is aligned with ten orthologous sequences from other species. The boxes show the affected amino acids, and conservation of an isoleucine amino acid at these positions in several vertebrate species, including humans and zebrafish. The amino acids in the grey portion mark the beginning of a transmembrane domain in meckelin.

    Article Snippet: Restriction enzyme digestion (PCR-restriction fragment length polymorphism (RFLP) genotyping) Genotyping was carried out following amplification of exon 20 of TMEM67 using PCR primers (refer to Supplementary Table ) for 30 cycles at 95 °C for 30 sec, 55 °C for 30 sec, 72 °C for 1 min, followed by digestion of the PCR product (612 bp) using the restriction enzyme Apo I (New England Biolabs Inc., Ipswich, MA, USA) at 50 °C.

    Techniques: Sequencing, Generated, Marker, Mutagenesis

    Visualized differentially expressed TDFs between Sea Island cotton fibers and Upland cotton fibers in cDNA-AFLP analyses. Lane 1 to 3 show Upland cotton ( G. hirsutum cv. CRI 8) fibers and Lane 4 to 6 show Sea Island cotton ( G . barbadense cv. Pima90-53) fibers. Eco RI/ Mse I and Apo I/ Taq I are the restriction enzyme combinations used in cDNA-AFLP analyses. Arrowheads show the differentially expressed FLA TDFs.

    Journal: PLoS ONE

    Article Title: Characterization and Expression Analysis of a Fiber Differentially Expressed Fasciclin-like Arabinogalactan Protein Gene in Sea Island Cotton Fibers

    doi: 10.1371/journal.pone.0070185

    Figure Lengend Snippet: Visualized differentially expressed TDFs between Sea Island cotton fibers and Upland cotton fibers in cDNA-AFLP analyses. Lane 1 to 3 show Upland cotton ( G. hirsutum cv. CRI 8) fibers and Lane 4 to 6 show Sea Island cotton ( G . barbadense cv. Pima90-53) fibers. Eco RI/ Mse I and Apo I/ Taq I are the restriction enzyme combinations used in cDNA-AFLP analyses. Arrowheads show the differentially expressed FLA TDFs.

    Article Snippet: Two combinations of restriction enzyme of Mse I/Eco RI and Apo I/Taq I (New England Biolabs, USA) were used in cDNA-AFLP analysis.

    Techniques: cDNA-AFLP Assay