r0146  (New England Biolabs)


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    Name:
    XhoI
    Description:
    XhoI 25 000 units
    Catalog Number:
    r0146l
    Price:
    290
    Size:
    25 000 units
    Category:
    Restriction Enzymes
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    Structured Review

    New England Biolabs r0146
    XhoI
    XhoI 25 000 units
    https://www.bioz.com/result/r0146/product/New England Biolabs
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    r0146 - by Bioz Stars, 2021-02
    99/100 stars

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    Related Articles

    Polymerase Chain Reaction:

    Article Title:
    Article Snippet: .. Restriction enzyme analysis of PCR products containing the CYP2B6 exon-9 region was performed by incubating 2 μ g DNA with 100 U XhoI (NEB) overnight. .. Total RNA was isolated using Trizol (Invitrogen).

    Article Title: A partial form of recessive STAT1 deficiency in humans
    Article Snippet: .. PCR products and empty pSPL3 plasmids (provided by Ralph Burkhardt, The Rockefeller University) were digested with Xho I and BamH 1 (New England BioLabs). .. Plasmids were then dephosphorylated, and 50 ng of purified plasmids and 250 ng of purified PCR products were ligated with T4 ligase (New England BioLabs).

    Article Title: A rationally designed nanoparticle for RNA interference therapy in B-lineage lymphoid malignancies
    Article Snippet: .. The correct PCR products (FL: 2541-bp and ΔE12–14: 2208-bp) were ligated into the 8497-bp lentiviral vector pCL6-2AEGwo through the NheI and XhoI restriction sites (underlined) using the Quick Ligase kit (New England Biolabs catalog no. M2200L) following the manufacturer's instructions. .. The pCL6-2AEGwo lentiviral backbone vector, a kind gift from Dr. Zanxian Xia, School of Biological Science and Technology, Central South University, Changsha, Hunan 410078, China, contains both a “ribosome-skip” fragment encoding the 2A-like peptide APVKQTLNFDLLKLAGDVESNPGP and an in-frame eGFP fluorescent coding sequence downstream of a multiple cloning site.

    Article Title: Generation of a New Frizzled 2 Flox Mouse Model to Clarify Its Role in Development
    Article Snippet: .. Digestion reactions consisted of 500ng of PCR product, 20 units of either XhoI (R1046S, NEB) or AgeI (R3552S, NEB) in their specified buffers. ..

    Incubation:

    Article Title: CTCF-mediated Genomic Effects of BART Region on Epstein-Barr Virus Chromatin 3D Structure in Gastric Carcinoma Cells
    Article Snippet: .. Nuclei were permeabilized by incubation with 0.5% SDS at 62 °C for 10 min. A half of DNA was digested with 100 units of XhoI (New England Biolabs (NEB), Ipswic, MA, USA) and ligated in the nucleus followed by in situ 3C protocol [ ]. .. Other half of DNA was digested with 100 units of MboI (NEB) and ligated in the nucleus followed by in situ Hi-C protocol [ ].

    Agarose Gel Electrophoresis:

    Article Title: A Germination-Specific Endo-?-Mannanase Gene Is Expressed in the Micropylar Endosperm Cap of Tomato Seeds 1
    Article Snippet: .. Genomic DNA (10 μg) was digested with the restriction enzymes Bam HI, Xba I, and Xho I (New England Biolabs), separated on a 1.0% (w/v) agarose gel, and transferred to positively charged membranes (Hybond-N+ , Amersham Pharmacia Biotech). .. Prehybridization, hybridization, washing, and detection were performed as described for cDNA library screening.

    In Situ:

    Article Title: CTCF-mediated Genomic Effects of BART Region on Epstein-Barr Virus Chromatin 3D Structure in Gastric Carcinoma Cells
    Article Snippet: .. Nuclei were permeabilized by incubation with 0.5% SDS at 62 °C for 10 min. A half of DNA was digested with 100 units of XhoI (New England Biolabs (NEB), Ipswic, MA, USA) and ligated in the nucleus followed by in situ 3C protocol [ ]. .. Other half of DNA was digested with 100 units of MboI (NEB) and ligated in the nucleus followed by in situ Hi-C protocol [ ].

    Plasmid Preparation:

    Article Title: A rationally designed nanoparticle for RNA interference therapy in B-lineage lymphoid malignancies
    Article Snippet: .. The correct PCR products (FL: 2541-bp and ΔE12–14: 2208-bp) were ligated into the 8497-bp lentiviral vector pCL6-2AEGwo through the NheI and XhoI restriction sites (underlined) using the Quick Ligase kit (New England Biolabs catalog no. M2200L) following the manufacturer's instructions. .. The pCL6-2AEGwo lentiviral backbone vector, a kind gift from Dr. Zanxian Xia, School of Biological Science and Technology, Central South University, Changsha, Hunan 410078, China, contains both a “ribosome-skip” fragment encoding the 2A-like peptide APVKQTLNFDLLKLAGDVESNPGP and an in-frame eGFP fluorescent coding sequence downstream of a multiple cloning site.

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    New England Biolabs xhoi restriction sites underlined
    Effect of CD22ΔE12 vs. CD22 WT on clonogenicity and self-renewal rate of ALL cells. [A1] Depicted is a representative 1% agarose gel showing the PCR products of FL CD22 and CD22ΔE12–14. [A.2] Subcloning of the CD22 FL or CD22ΔE12–14 genes into the <t>lentiviral</t> pCL6-2AEGwo vector through NheI and <t>XhoI</t> restriction sites was confirmed through restriction enzyme digestion and DNA sequencing. Depicted is a representative 1% agarose gel showing that the generated lentiviral constructs have the correct size FL CD22 (2.5-kb) or CD22ΔE12–14 (2.2-kb) inserts. [B.1] In order to confirm that the lentiviral vectors can be used to achieve expression of FL and truncated CD22 in human cells, 293T cells were transfected with lentiviral constructs for FL CD22, CD22ΔE12–14, as well as pCL6-2AEGwo lentiviral vector without any subcloned CD22. 48 h post transfection cells were examined for FL CD22 and CD22ΔE12–14 mRNA by RT-PCR using the P7, P9, and P10 primer pairs. The P7 primer set was used to amplify a 182-bp region (c.2180–c.2361) of the CD22 cDNA extending from Exon 11 to Exon 13 and spanning the entire Exon 12. The P9 primer set was used amplify a 160-bp region (c.2304–c.2463) of the CD22 cDNA extending from Exon 12 to Exon 14 and spanning the entire Exon 13. The P10 primer set was used to amplify a 213-bp region (c.433–c.645) of Exon 4 of the CD22 cDNA present in both wildtype CD22 and CD22ΔE12–14 mRNA species. As expected all primer sets yielded PCR products in cells transfected with the FL CD22 vector and only the P10 primer set yielded a PCR product in cells transfected with the CD22ΔE12–14 vector. [B.2 and B3] The increased expression levels of the full-length and truncated proteins in transduced 293-T cells (depicted in B.2) and ALL-1 cells (depicted in B.3) were confirmed to be similar by Western blot analysis done at 96 h post-transduction. [C D] ALL cell lines DAUDI (Burkitt's leukemia/B-ALL) (panels C1 C.2) and ALL1 (BCR-ABL + B-precursor ALL) (panel C3) were transduced (trans) with wildtype and mutant human CD22 genes using the pCL6-2AEGwo lentiviral vector and then assayed for colony formation in semi-solid methylcellulose cultures without additional stroma support or cytokines. Colony formation was examined using an inverted Nikon Eclipse TS100 microscope with an Epifluorescence attachment. Images were taken using a Digital Sight DS-2MBW Nikon camera (System magnification: 100× or 200 × as indicated). Green fluorescence of colonies resulting from GFP expression confirms successful transduction of the cell lines. [D] Depicted are bar graphs comparing the mean colony numbers in cultures of untransduced and transduced cells.
    Xhoi Restriction Sites Underlined, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 709 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Effect of CD22ΔE12 vs. CD22 WT on clonogenicity and self-renewal rate of ALL cells. [A1] Depicted is a representative 1% agarose gel showing the PCR products of FL CD22 and CD22ΔE12–14. [A.2] Subcloning of the CD22 FL or CD22ΔE12–14 genes into the lentiviral pCL6-2AEGwo vector through NheI and XhoI restriction sites was confirmed through restriction enzyme digestion and DNA sequencing. Depicted is a representative 1% agarose gel showing that the generated lentiviral constructs have the correct size FL CD22 (2.5-kb) or CD22ΔE12–14 (2.2-kb) inserts. [B.1] In order to confirm that the lentiviral vectors can be used to achieve expression of FL and truncated CD22 in human cells, 293T cells were transfected with lentiviral constructs for FL CD22, CD22ΔE12–14, as well as pCL6-2AEGwo lentiviral vector without any subcloned CD22. 48 h post transfection cells were examined for FL CD22 and CD22ΔE12–14 mRNA by RT-PCR using the P7, P9, and P10 primer pairs. The P7 primer set was used to amplify a 182-bp region (c.2180–c.2361) of the CD22 cDNA extending from Exon 11 to Exon 13 and spanning the entire Exon 12. The P9 primer set was used amplify a 160-bp region (c.2304–c.2463) of the CD22 cDNA extending from Exon 12 to Exon 14 and spanning the entire Exon 13. The P10 primer set was used to amplify a 213-bp region (c.433–c.645) of Exon 4 of the CD22 cDNA present in both wildtype CD22 and CD22ΔE12–14 mRNA species. As expected all primer sets yielded PCR products in cells transfected with the FL CD22 vector and only the P10 primer set yielded a PCR product in cells transfected with the CD22ΔE12–14 vector. [B.2 and B3] The increased expression levels of the full-length and truncated proteins in transduced 293-T cells (depicted in B.2) and ALL-1 cells (depicted in B.3) were confirmed to be similar by Western blot analysis done at 96 h post-transduction. [C D] ALL cell lines DAUDI (Burkitt's leukemia/B-ALL) (panels C1 C.2) and ALL1 (BCR-ABL + B-precursor ALL) (panel C3) were transduced (trans) with wildtype and mutant human CD22 genes using the pCL6-2AEGwo lentiviral vector and then assayed for colony formation in semi-solid methylcellulose cultures without additional stroma support or cytokines. Colony formation was examined using an inverted Nikon Eclipse TS100 microscope with an Epifluorescence attachment. Images were taken using a Digital Sight DS-2MBW Nikon camera (System magnification: 100× or 200 × as indicated). Green fluorescence of colonies resulting from GFP expression confirms successful transduction of the cell lines. [D] Depicted are bar graphs comparing the mean colony numbers in cultures of untransduced and transduced cells.

    Journal: EBioMedicine

    Article Title: A rationally designed nanoparticle for RNA interference therapy in B-lineage lymphoid malignancies

    doi: 10.1016/j.ebiom.2014.10.013

    Figure Lengend Snippet: Effect of CD22ΔE12 vs. CD22 WT on clonogenicity and self-renewal rate of ALL cells. [A1] Depicted is a representative 1% agarose gel showing the PCR products of FL CD22 and CD22ΔE12–14. [A.2] Subcloning of the CD22 FL or CD22ΔE12–14 genes into the lentiviral pCL6-2AEGwo vector through NheI and XhoI restriction sites was confirmed through restriction enzyme digestion and DNA sequencing. Depicted is a representative 1% agarose gel showing that the generated lentiviral constructs have the correct size FL CD22 (2.5-kb) or CD22ΔE12–14 (2.2-kb) inserts. [B.1] In order to confirm that the lentiviral vectors can be used to achieve expression of FL and truncated CD22 in human cells, 293T cells were transfected with lentiviral constructs for FL CD22, CD22ΔE12–14, as well as pCL6-2AEGwo lentiviral vector without any subcloned CD22. 48 h post transfection cells were examined for FL CD22 and CD22ΔE12–14 mRNA by RT-PCR using the P7, P9, and P10 primer pairs. The P7 primer set was used to amplify a 182-bp region (c.2180–c.2361) of the CD22 cDNA extending from Exon 11 to Exon 13 and spanning the entire Exon 12. The P9 primer set was used amplify a 160-bp region (c.2304–c.2463) of the CD22 cDNA extending from Exon 12 to Exon 14 and spanning the entire Exon 13. The P10 primer set was used to amplify a 213-bp region (c.433–c.645) of Exon 4 of the CD22 cDNA present in both wildtype CD22 and CD22ΔE12–14 mRNA species. As expected all primer sets yielded PCR products in cells transfected with the FL CD22 vector and only the P10 primer set yielded a PCR product in cells transfected with the CD22ΔE12–14 vector. [B.2 and B3] The increased expression levels of the full-length and truncated proteins in transduced 293-T cells (depicted in B.2) and ALL-1 cells (depicted in B.3) were confirmed to be similar by Western blot analysis done at 96 h post-transduction. [C D] ALL cell lines DAUDI (Burkitt's leukemia/B-ALL) (panels C1 C.2) and ALL1 (BCR-ABL + B-precursor ALL) (panel C3) were transduced (trans) with wildtype and mutant human CD22 genes using the pCL6-2AEGwo lentiviral vector and then assayed for colony formation in semi-solid methylcellulose cultures without additional stroma support or cytokines. Colony formation was examined using an inverted Nikon Eclipse TS100 microscope with an Epifluorescence attachment. Images were taken using a Digital Sight DS-2MBW Nikon camera (System magnification: 100× or 200 × as indicated). Green fluorescence of colonies resulting from GFP expression confirms successful transduction of the cell lines. [D] Depicted are bar graphs comparing the mean colony numbers in cultures of untransduced and transduced cells.

    Article Snippet: The correct PCR products (FL: 2541-bp and ΔE12–14: 2208-bp) were ligated into the 8497-bp lentiviral vector pCL6-2AEGwo through the NheI and XhoI restriction sites (underlined) using the Quick Ligase kit (New England Biolabs catalog no. M2200L) following the manufacturer's instructions.

    Techniques: Agarose Gel Electrophoresis, Polymerase Chain Reaction, Subcloning, Plasmid Preparation, DNA Sequencing, Generated, Construct, Expressing, Transfection, Reverse Transcription Polymerase Chain Reaction, Western Blot, Transduction, Mutagenesis, Microscopy, Fluorescence

    dmc1-E157D bypasses mei5 but not rad51 with respect to CO formation. (a) Southern blot analysis at the HIS4 :: LEU2 hotspot following digestion of genomic DNA from meiotic time course experiments with XhoI. Time points shown from left to right are: 0h, 6h, 8h, 10h, 24h. (b) Quantitation of 1D gels shown in (a) and meiotic progression data; black–wild-type, light blue –mei5 , purple –rad51 , red –dmc1-E157D , gray –dmc1-E157D mei5 , green –dmc1-E157D rad51 , yellow –dmc1-E157D mei5 rad51 . To score meiotic progression, ≥50 cells were scored per time point. Strains used in experiments in the order in which they appear in figure, left to right: DKB3698, DKB6320, DKB3710, DKB6342, DKB6300, DKB6393, DKB6412.

    Journal: PLoS Genetics

    Article Title: A mutant form of Dmc1 that bypasses the requirement for accessory protein Mei5-Sae3 reveals independent activities of Mei5-Sae3 and Rad51 in Dmc1 filament stability

    doi: 10.1371/journal.pgen.1008217

    Figure Lengend Snippet: dmc1-E157D bypasses mei5 but not rad51 with respect to CO formation. (a) Southern blot analysis at the HIS4 :: LEU2 hotspot following digestion of genomic DNA from meiotic time course experiments with XhoI. Time points shown from left to right are: 0h, 6h, 8h, 10h, 24h. (b) Quantitation of 1D gels shown in (a) and meiotic progression data; black–wild-type, light blue –mei5 , purple –rad51 , red –dmc1-E157D , gray –dmc1-E157D mei5 , green –dmc1-E157D rad51 , yellow –dmc1-E157D mei5 rad51 . To score meiotic progression, ≥50 cells were scored per time point. Strains used in experiments in the order in which they appear in figure, left to right: DKB3698, DKB6320, DKB3710, DKB6342, DKB6300, DKB6393, DKB6412.

    Article Snippet: Approximately 2 micrograms DNA per sample was then digested with XhoI or PstI (as indicated in figure legend) restriction enzyme (New England BioLabs) and processed as described previously [ ].

    Techniques: Southern Blot, Quantitation Assay

    Agarose gel electrophoresis analysis of 3 combinant expression plasmid. The plasmid was confirmed by PCR and double digestion using NcoI and XhoI. Lane 1 was the fragment of recombinant plasmid DNA pTriEx-1.1 Hygro-β 2 -AR. Lane 2 was the electrophoresis results of digested products containing 2 fragments (6951 bp and 1257 bp). A 3300 bp fragment (lane 3 and lane 4) was amplified by PCR from the recombinant plasmid, which was identical with the sum of the size of target gene and vector sequences between NcoI and XhoI.

    Journal: PLoS ONE

    Article Title: Multiresidue Method for Analysis of β Agonists in Swine Urine by Enzyme Linked Receptor Assay Based on β2 Adrenergic Receptor Expressed in HEK293 Cells

    doi: 10.1371/journal.pone.0139176

    Figure Lengend Snippet: Agarose gel electrophoresis analysis of 3 combinant expression plasmid. The plasmid was confirmed by PCR and double digestion using NcoI and XhoI. Lane 1 was the fragment of recombinant plasmid DNA pTriEx-1.1 Hygro-β 2 -AR. Lane 2 was the electrophoresis results of digested products containing 2 fragments (6951 bp and 1257 bp). A 3300 bp fragment (lane 3 and lane 4) was amplified by PCR from the recombinant plasmid, which was identical with the sum of the size of target gene and vector sequences between NcoI and XhoI.

    Article Snippet: The restriction enzymes of NcoI and XhoI were purchased from NEB (Ipswich, MA, USA).

    Techniques: Agarose Gel Electrophoresis, Expressing, Plasmid Preparation, Polymerase Chain Reaction, Recombinant, Electrophoresis, Amplification

    Confirmation of chromatin interaction by 3C-semi-quantitative (sq)PCR assay. A) Sites of XhoI restriction sites and 3C-sqPCR primers on EBV genome. B) 3C-sqPCR assay using 147K (S14) region as a view primer. EBV genome in SNU719 cells were cut by XhoI restriction enzyme, ligated by T4 DNA ligase, and then purified as described previously. Resultant EBV genome DNA was subjected to 3C-sqPCR assay. C) 3C-sqPCR assay using 135K (S13) region as a view primer. D) Summary of 3C-sqPCR assay data in table. O and o stand for strong and weak chromatin interactions, respectively. x stands for no detection. E) A simple diagram to indicate a DNA loop cluster mediated by BARTp CTCF BS associated chromatin interactions in SNU719 cells.

    Journal: bioRxiv

    Article Title: CTCF-mediated Genomic Effects of BART Region on Epstein-Barr Virus Chromatin 3D Structure in Gastric Carcinoma Cells

    doi: 10.1101/2020.12.03.409722

    Figure Lengend Snippet: Confirmation of chromatin interaction by 3C-semi-quantitative (sq)PCR assay. A) Sites of XhoI restriction sites and 3C-sqPCR primers on EBV genome. B) 3C-sqPCR assay using 147K (S14) region as a view primer. EBV genome in SNU719 cells were cut by XhoI restriction enzyme, ligated by T4 DNA ligase, and then purified as described previously. Resultant EBV genome DNA was subjected to 3C-sqPCR assay. C) 3C-sqPCR assay using 135K (S13) region as a view primer. D) Summary of 3C-sqPCR assay data in table. O and o stand for strong and weak chromatin interactions, respectively. x stands for no detection. E) A simple diagram to indicate a DNA loop cluster mediated by BARTp CTCF BS associated chromatin interactions in SNU719 cells.

    Article Snippet: Nuclei were permeabilized by incubation with 0.5% SDS at 62 °C for 10 min. A half of DNA was digested with 100 units of XhoI (New England Biolabs (NEB), Ipswic, MA, USA) and ligated in the nucleus followed by in situ 3C protocol [ ].

    Techniques: Purification

    Confirmation of chromatin interaction affected by BARTp CTCF BS mutation. A) and B) Sites of XhoI restriction sites and 3C primers on EBV genome. EBV genome in HEK293-B(-) S13 +/− (Wt/Mt) EBV cells. were cut by XhoI restriction enzyme, ligated by T4 DNA ligase, and then purified as described previously. Resultant EBV genome DNA was subjected to 3C semi-quantitative PCR assay with view-point primers designed around 147K and 135K, respectively. C) Summary of 3C assays. O and o stand for strong and weak chromatin interactions, respectively. X stands for no detection. D) Simple diagrams to indicate a DNA loop cluster mediated by BARTp CTCF BS associated chromatin interactions in HEK293-EBV B(+/−) S13 +/− (Wt/Mt) cells.

    Journal: bioRxiv

    Article Title: CTCF-mediated Genomic Effects of BART Region on Epstein-Barr Virus Chromatin 3D Structure in Gastric Carcinoma Cells

    doi: 10.1101/2020.12.03.409722

    Figure Lengend Snippet: Confirmation of chromatin interaction affected by BARTp CTCF BS mutation. A) and B) Sites of XhoI restriction sites and 3C primers on EBV genome. EBV genome in HEK293-B(-) S13 +/− (Wt/Mt) EBV cells. were cut by XhoI restriction enzyme, ligated by T4 DNA ligase, and then purified as described previously. Resultant EBV genome DNA was subjected to 3C semi-quantitative PCR assay with view-point primers designed around 147K and 135K, respectively. C) Summary of 3C assays. O and o stand for strong and weak chromatin interactions, respectively. X stands for no detection. D) Simple diagrams to indicate a DNA loop cluster mediated by BARTp CTCF BS associated chromatin interactions in HEK293-EBV B(+/−) S13 +/− (Wt/Mt) cells.

    Article Snippet: Nuclei were permeabilized by incubation with 0.5% SDS at 62 °C for 10 min. A half of DNA was digested with 100 units of XhoI (New England Biolabs (NEB), Ipswic, MA, USA) and ligated in the nucleus followed by in situ 3C protocol [ ].

    Techniques: Mutagenesis, Purification, Real-time Polymerase Chain Reaction