bseri  (New England Biolabs)


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    Name:
    BseRI
    Description:
    BseRI 1 000 units
    Catalog Number:
    R0581L
    Price:
    302
    Category:
    Restriction Enzymes
    Size:
    1 000 units
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    Structured Review

    New England Biolabs bseri
    BseRI
    BseRI 1 000 units
    https://www.bioz.com/result/bseri/product/New England Biolabs
    Average 93 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    bseri - by Bioz Stars, 2021-04
    93/100 stars

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    1) Product Images from "TransMPRA: A framework for assaying the role of many trans-acting factors at many enhancers"

    Article Title: TransMPRA: A framework for assaying the role of many trans-acting factors at many enhancers

    Journal: bioRxiv

    doi: 10.1101/2020.09.30.321323

    Cloning strategy. First a Pol3-associated U6 promoter and SV40 transcription termination element are cloned into the piggyBac cassette plasmid (“Prepare”). The cloned fragment contains a cloning site with two BseRI cut sites and homology for Gibson assembly. Then a gRNA library along with a scaffold region are cloned into the cloning site (“Step 1”). This fragment also contains a cloning site. A random barcode is added (“Step 2a”). Before continuing, we sequence the amplicon to associate barcodes to guides (“Step 2b”). The minimal promoter is added between the barcode and the gRNA scaffold (“Step 3”). Finally, we clone the library of putative enhancer elements adjacent to the random barcode resulting in the final construct (“Step 4”). Regions labeled with H represent regions of homology used for Gibson assembly.
    Figure Legend Snippet: Cloning strategy. First a Pol3-associated U6 promoter and SV40 transcription termination element are cloned into the piggyBac cassette plasmid (“Prepare”). The cloned fragment contains a cloning site with two BseRI cut sites and homology for Gibson assembly. Then a gRNA library along with a scaffold region are cloned into the cloning site (“Step 1”). This fragment also contains a cloning site. A random barcode is added (“Step 2a”). Before continuing, we sequence the amplicon to associate barcodes to guides (“Step 2b”). The minimal promoter is added between the barcode and the gRNA scaffold (“Step 3”). Finally, we clone the library of putative enhancer elements adjacent to the random barcode resulting in the final construct (“Step 4”). Regions labeled with H represent regions of homology used for Gibson assembly.

    Techniques Used: Clone Assay, Plasmid Preparation, Sequencing, Amplification, Construct, Labeling

    Related Articles

    Sequencing:

    Article Title: Neuronal activity disrupts myelinated axon integrity in the absence of NKCC1b
    Article Snippet: Cell-type–specific targeting of slc12a2b in neurons and myelinating glial cells To disrupt slc12a2b function specifically in neurons or myelinating glial cells, we cloned the highly efficient slc12a2b guide sequence targeting exon 1 into a Tol2 modular vector system that allows coexpression of Cas9 under a tissue-specific promoter ( ). .. Oligonucleotides encoding the 20 bp slc12a2b exon 1 guide sequence (Integrated DNA Technologies) were ligated into the pDestTol2CG2-U6:gRNA destination vector (Addgene) following BseRI (NEB) restriction digest under the zebrafish U6-3 promoter. .. This vector also contains GFP under the heart-specific cmlc2 promoter as a marker of transgenesis.

    Plasmid Preparation:

    Article Title: Neuronal activity disrupts myelinated axon integrity in the absence of NKCC1b
    Article Snippet: Cell-type–specific targeting of slc12a2b in neurons and myelinating glial cells To disrupt slc12a2b function specifically in neurons or myelinating glial cells, we cloned the highly efficient slc12a2b guide sequence targeting exon 1 into a Tol2 modular vector system that allows coexpression of Cas9 under a tissue-specific promoter ( ). .. Oligonucleotides encoding the 20 bp slc12a2b exon 1 guide sequence (Integrated DNA Technologies) were ligated into the pDestTol2CG2-U6:gRNA destination vector (Addgene) following BseRI (NEB) restriction digest under the zebrafish U6-3 promoter. .. This vector also contains GFP under the heart-specific cmlc2 promoter as a marker of transgenesis.

    Article Title: Ultrasensitive deletion detection links mitochondrial DNA replication, disease, and aging
    Article Snippet: A sample of control plasmid DNA (4 μg) was cut with HpaI (New England Biolabs Inc., Catalog # R0105S) to generate a 2392 bp deletion between positions 10,014–12,405. .. A second deletion plasmid was generated using BseRI (New England Biolabs Inc., Catalog # R0581S), which cut at positions 9323 and 12,974 to generate a 3652 bp deletion. .. A third control plasmid generated by using PmeI and NdeI (New England Biolabs Inc., Catalog # R0560S and R0111S), which cut at positions 10,419 and 10,722, respectively (304 bp deletion).

    Article Title: Probiotic Escherichia coli inhibits biofilm formation of pathogenic E. coli via extracellular activity of DegP
    Article Snippet: The degP gene was amplified by PCR with degPfd and degPrv primers (Supplementary Table ) using Pfu polymerase at 98 °C for 30 s, with 35 cycles of 98 °C for 30 s, 54 °C for 30 s, and 72 °C for 1 min, as well as a final extension of 72 °C for 5 min followed by DNA purification using a CyclePure kit (Omega Bio-Tek, Norcross, GA). .. The pCA24N plasmid and degP PCR products were digested with restriction enzymes BseRI and HindIII (New England Biolabs, Ipswich, MA, USA) and purified. .. The insert and vector were ligated by incubating with T4 DNA ligase (New England Biolabs, Ipswich, MA, USA) at 16 °C overnight.

    Article Title: Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal
    Article Snippet: The PCR program was set as 94°C for 5 min, followed by 30 cycles at 94°C for 1 min, 55°C for 1 min, and 72°C for 2 min, with a final extension step of 72°C for 7 min. .. The epPCR product was cloned into pCA24N_ bdcA using restriction enzymes BseRI and HindIII after treating the plasmid with Antarctic phosphatase (New England Biolabs). .. The ligation mixture was electroporated into BW25113 bdcA .

    Article Title: TransMPRA: A framework for assaying the role of many trans-acting factors at many enhancers
    Article Snippet: Further below, we describe our sequencing strategy for associating random barcodes with guides. .. Following the inclusion of the random barcodes, we digested the plasmid library with BseRI (NEB R0581L) and agarose gel size-selected the linearized fragment. .. The ORI minimal promoter and flanking region was PCR amplified from the hSTARR-seq plasmid (Addgene #99296) with a custom primer that included homology for Gibson cloning and KAPA HiFi HotStart ReadyMix (Kapa KK2602) and then was agarose gel size-selected.

    Article Title: Bio-Inspired Synthesis of Hybrid Silica Nanoparticles Templated from Elastin-like Polypeptide Micelles
    Article Snippet: .. Restriction enzymes BglI, NdeI, BseRI, AcuI, BamHI and XbaI, T4 DNA Ligase and calf intestinal phosphatase (CIP) were purchased from New England Biolabs (Ipswich, MA). pET-24a(+) vector was purchased from Novagen Inc. (Madison, WI). .. BL21 E. coli competent cells were purchased from EdgeBio (Gaithersburg, MD).

    Generated:

    Article Title: Ultrasensitive deletion detection links mitochondrial DNA replication, disease, and aging
    Article Snippet: A sample of control plasmid DNA (4 μg) was cut with HpaI (New England Biolabs Inc., Catalog # R0105S) to generate a 2392 bp deletion between positions 10,014–12,405. .. A second deletion plasmid was generated using BseRI (New England Biolabs Inc., Catalog # R0581S), which cut at positions 9323 and 12,974 to generate a 3652 bp deletion. .. A third control plasmid generated by using PmeI and NdeI (New England Biolabs Inc., Catalog # R0560S and R0111S), which cut at positions 10,419 and 10,722, respectively (304 bp deletion).

    Polymerase Chain Reaction:

    Article Title: Probiotic Escherichia coli inhibits biofilm formation of pathogenic E. coli via extracellular activity of DegP
    Article Snippet: The degP gene was amplified by PCR with degPfd and degPrv primers (Supplementary Table ) using Pfu polymerase at 98 °C for 30 s, with 35 cycles of 98 °C for 30 s, 54 °C for 30 s, and 72 °C for 1 min, as well as a final extension of 72 °C for 5 min followed by DNA purification using a CyclePure kit (Omega Bio-Tek, Norcross, GA). .. The pCA24N plasmid and degP PCR products were digested with restriction enzymes BseRI and HindIII (New England Biolabs, Ipswich, MA, USA) and purified. .. The insert and vector were ligated by incubating with T4 DNA ligase (New England Biolabs, Ipswich, MA, USA) at 16 °C overnight.

    Purification:

    Article Title: Probiotic Escherichia coli inhibits biofilm formation of pathogenic E. coli via extracellular activity of DegP
    Article Snippet: The degP gene was amplified by PCR with degPfd and degPrv primers (Supplementary Table ) using Pfu polymerase at 98 °C for 30 s, with 35 cycles of 98 °C for 30 s, 54 °C for 30 s, and 72 °C for 1 min, as well as a final extension of 72 °C for 5 min followed by DNA purification using a CyclePure kit (Omega Bio-Tek, Norcross, GA). .. The pCA24N plasmid and degP PCR products were digested with restriction enzymes BseRI and HindIII (New England Biolabs, Ipswich, MA, USA) and purified. .. The insert and vector were ligated by incubating with T4 DNA ligase (New England Biolabs, Ipswich, MA, USA) at 16 °C overnight.

    Clone Assay:

    Article Title: Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal
    Article Snippet: The PCR program was set as 94°C for 5 min, followed by 30 cycles at 94°C for 1 min, 55°C for 1 min, and 72°C for 2 min, with a final extension step of 72°C for 7 min. .. The epPCR product was cloned into pCA24N_ bdcA using restriction enzymes BseRI and HindIII after treating the plasmid with Antarctic phosphatase (New England Biolabs). .. The ligation mixture was electroporated into BW25113 bdcA .

    Agarose Gel Electrophoresis:

    Article Title: TransMPRA: A framework for assaying the role of many trans-acting factors at many enhancers
    Article Snippet: Further below, we describe our sequencing strategy for associating random barcodes with guides. .. Following the inclusion of the random barcodes, we digested the plasmid library with BseRI (NEB R0581L) and agarose gel size-selected the linearized fragment. .. The ORI minimal promoter and flanking region was PCR amplified from the hSTARR-seq plasmid (Addgene #99296) with a custom primer that included homology for Gibson cloning and KAPA HiFi HotStart ReadyMix (Kapa KK2602) and then was agarose gel size-selected.

    Positron Emission Tomography:

    Article Title: Bio-Inspired Synthesis of Hybrid Silica Nanoparticles Templated from Elastin-like Polypeptide Micelles
    Article Snippet: .. Restriction enzymes BglI, NdeI, BseRI, AcuI, BamHI and XbaI, T4 DNA Ligase and calf intestinal phosphatase (CIP) were purchased from New England Biolabs (Ipswich, MA). pET-24a(+) vector was purchased from Novagen Inc. (Madison, WI). .. BL21 E. coli competent cells were purchased from EdgeBio (Gaithersburg, MD).

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  • 93
    New England Biolabs bseri
    Cloning strategy. First a Pol3-associated U6 promoter and SV40 transcription termination element are cloned into the piggyBac cassette plasmid (“Prepare”). The cloned fragment contains a cloning site with two <t>BseRI</t> cut sites and homology for Gibson assembly. Then a gRNA library along with a scaffold region are cloned into the cloning site (“Step 1”). This fragment also contains a cloning site. A random barcode is added (“Step 2a”). Before continuing, we sequence the amplicon to associate <t>barcodes</t> to guides (“Step 2b”). The minimal promoter is added between the barcode and the gRNA scaffold (“Step 3”). Finally, we clone the library of putative enhancer elements adjacent to the random barcode resulting in the final construct (“Step 4”). Regions labeled with H represent regions of homology used for Gibson assembly.
    Bseri, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bseri/product/New England Biolabs
    Average 93 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    bseri - by Bioz Stars, 2021-04
    93/100 stars
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    Cloning strategy. First a Pol3-associated U6 promoter and SV40 transcription termination element are cloned into the piggyBac cassette plasmid (“Prepare”). The cloned fragment contains a cloning site with two BseRI cut sites and homology for Gibson assembly. Then a gRNA library along with a scaffold region are cloned into the cloning site (“Step 1”). This fragment also contains a cloning site. A random barcode is added (“Step 2a”). Before continuing, we sequence the amplicon to associate barcodes to guides (“Step 2b”). The minimal promoter is added between the barcode and the gRNA scaffold (“Step 3”). Finally, we clone the library of putative enhancer elements adjacent to the random barcode resulting in the final construct (“Step 4”). Regions labeled with H represent regions of homology used for Gibson assembly.

    Journal: bioRxiv

    Article Title: TransMPRA: A framework for assaying the role of many trans-acting factors at many enhancers

    doi: 10.1101/2020.09.30.321323

    Figure Lengend Snippet: Cloning strategy. First a Pol3-associated U6 promoter and SV40 transcription termination element are cloned into the piggyBac cassette plasmid (“Prepare”). The cloned fragment contains a cloning site with two BseRI cut sites and homology for Gibson assembly. Then a gRNA library along with a scaffold region are cloned into the cloning site (“Step 1”). This fragment also contains a cloning site. A random barcode is added (“Step 2a”). Before continuing, we sequence the amplicon to associate barcodes to guides (“Step 2b”). The minimal promoter is added between the barcode and the gRNA scaffold (“Step 3”). Finally, we clone the library of putative enhancer elements adjacent to the random barcode resulting in the final construct (“Step 4”). Regions labeled with H represent regions of homology used for Gibson assembly.

    Article Snippet: Following the inclusion of the random barcodes, we digested the plasmid library with BseRI (NEB R0581L) and agarose gel size-selected the linearized fragment.

    Techniques: Clone Assay, Plasmid Preparation, Sequencing, Amplification, Construct, Labeling