antartic phosphatase  (New England Biolabs)


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    Name:
    Antarctic Phosphatase
    Description:
    Antarctic Phosphatase 5 000 units
    Catalog Number:
    m0289l
    Price:
    276
    Size:
    5 000 units
    Category:
    Alkaline Phosphatases
    Buy from Supplier


    Structured Review

    New England Biolabs antartic phosphatase
    Antarctic Phosphatase
    Antarctic Phosphatase 5 000 units
    https://www.bioz.com/result/antartic phosphatase/product/New England Biolabs
    Average 90 stars, based on 90 article reviews
    Price from $9.99 to $1999.99
    antartic phosphatase - by Bioz Stars, 2020-01
    90/100 stars

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    Related Articles

    Diagnostic Assay:

    Article Title: Diagnostic and Biological Significance of KIR Expression Profile Determined by RNA-Seq in Natural Killer/T-Cell Lymphoma
    Article Snippet: KIR2DL4 first and second shRNAs were sequentially cloned into the LMP vector to generate the KIR2DL4–1st-2nd–double-shRNA using the following strategy: KIR2DL4–1st shRNA–LMP was digested with EcoRI and then treated with Antarctic Phosphatase (New England BioLabs Inc.) to prevent recircularization. .. Diagnostic restriction mapping and Sanger sequencing with forward and reverse primers were performed to validate each retroviral shRNA construct.

    Clone Assay:

    Article Title: The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin
    Article Snippet: The BsmBI-digested HA was ligated into a dephosphorylated (Antarctic Phosphatase, M0289L; New England Biolabs) and BsmBI-digested preparation of the bidirectional reverse-genetics plasmid pHW2000 ( ) using T4 DNA ligase (M0202S; New England Biolabs). .. For each replicate of the codon-mutant library, we performed three transformations to generate approximately six-million independent clones per replicate library.

    Article Title: Diagnostic and Biological Significance of KIR Expression Profile Determined by RNA-Seq in Natural Killer/T-Cell Lymphoma
    Article Snippet: .. KIR2DL4 first and second shRNAs were sequentially cloned into the LMP vector to generate the KIR2DL4–1st-2nd–double-shRNA using the following strategy: KIR2DL4–1st shRNA–LMP was digested with EcoRI and then treated with Antarctic Phosphatase (New England BioLabs Inc.) to prevent recircularization. .. After that, EcoRI-digested KIR2DL4–2nd shRNA insert, which was generated through amplification with PfuUltra II Fusion HS DNA polymerase (Agilent Technologies), was cloned into KIR2DL4–1st shRNA–LMP ( C).

    Article Title: Protein Engineering of the Transcriptional Activator FhlA To Enhance Hydrogen Production in Escherichia coli
    Article Snippet: .. The epPCR product was cloned into pASKA2701 using the MfeI and HindIII restriction enzymes with Antarctic phosphatase (New England Biolabs, Beverly, MA) treatment of the vector; the ligation mixture was electroporated ( ) into strain JW2701-1 (Δ fhlA ) ( ) (complementation of the fhlA deletion by pASKA2701 was reported by us previously [ ]). .. For epPCR of the fhlA region encoding the N domain of FhlA, the conditions were the same as described above, but primers FhlAfront and FhlAN (see Table S2 in the supplemental material) were used with a 2-min extension time.

    Article Title: Tyrosine Phosphorylation and Dephosphorylation in Burkholderia cenocepacia Affect Biofilm Formation, Growth under Nutritional Deprivation, and Pathogenicity
    Article Snippet: DNA manipulations and cloning were performed as described previously ( ). .. Antarctic phosphatase (New England BioLabs), restriction enzymes (New England BioLabs), and T4 DNA ligase (Roche Applied Science) were used as recommended by the manufacturers.

    Amplification:

    Article Title: Tuberaztecorum sp. nov., a truffle species from Mexico belonging to the Maculatum clade ( Tuberaceae, Pezizales)
    Article Snippet: The ITS region was amplified with the primer pair ITS1f-ITS4 ( , ). .. PCR products were cleaned enzymatically with antarctic phosphatase and endonuclease digestion (New England Biolabs, Ipswich MA).

    Article Title: Engineering Stochasticity in Gene Expression
    Article Snippet: .. In-line RNA structure assays were performed on rcRNA transcripts as described in reference unless otherwise noted. rcRNAs were amplified using primers flanking the T7 promoter and terminator from pACYCDuet-1, transcribed in vitro by a T7 RNA polymerase transcription kit (Epicentre, Madison WI), purified on a 12% denaturing polyacrylamide gel, phosphatased with Antarctic Phosphatase (NEB), radiolabeled on the 5′-most nucleotide, and gel purified as before. ..

    Article Title: Diagnostic and Biological Significance of KIR Expression Profile Determined by RNA-Seq in Natural Killer/T-Cell Lymphoma
    Article Snippet: KIR2DL4 first and second shRNAs were sequentially cloned into the LMP vector to generate the KIR2DL4–1st-2nd–double-shRNA using the following strategy: KIR2DL4–1st shRNA–LMP was digested with EcoRI and then treated with Antarctic Phosphatase (New England BioLabs Inc.) to prevent recircularization. .. After that, EcoRI-digested KIR2DL4–2nd shRNA insert, which was generated through amplification with PfuUltra II Fusion HS DNA polymerase (Agilent Technologies), was cloned into KIR2DL4–1st shRNA–LMP ( C).

    Article Title: Transposase mediated construction of RNA-seq libraries
    Article Snippet: The purified and fragmented RNA was treated with 1 μL of Antarctic Phosphatase (5U/μL; NEB) for 30 min at 37°C, and then heat killed for 5 min at 65°C. .. The end-repaired RNA was then ligated and amplified using the Illumina TruSeq small RNA kit.

    Article Title: Tyrosine Phosphorylation and Dephosphorylation in Burkholderia cenocepacia Affect Biofilm Formation, Growth under Nutritional Deprivation, and Pathogenicity
    Article Snippet: PCR amplification was performed using Taq (5Prime) or HotStar HiFidelity (Qiagen) DNA polymerase. .. Antarctic phosphatase (New England BioLabs), restriction enzymes (New England BioLabs), and T4 DNA ligase (Roche Applied Science) were used as recommended by the manufacturers.

    Article Title: A Variable Region in GP4 of European-Type Porcine Reproductive and Respiratory Syndrome Virus Induces Neutralizing Antibodies Against Homologous But Not Heterologous Virus Strains
    Article Snippet: A region containing the complete ORF4 sequence was amplified using Taq Polymerase (Invitrogen Corp., Carlsbad, CA), and the following primers: forward primer 5′-cggcccaittccatccigag-3′, recognizing the complement sequence of nucleotides 12756–12775 upstream of ORF4 in LV (5′-cggcccaattccatccggag-3′), and reverse primer 5′-cattcagctcgcataicgtcaag-3′, recognizing nucleotides 13631–13653 downstream of ORF4 in LV (5′-cttgacgatatgcgagctgaatg-3′). .. PCR products were treated with Exonuclease I and Antarctic Phosphatase (New England BioLabs, Ipswich, MA), and used directly for cycle sequencing with a Big Dye Terminator Cycle sequencing kit V1.1 (Applied Biosystems), and the aforementioned primers.

    Synthesized:

    Article Title: Intronless β-Globin Reporter: A Tool for Studying Nuclear RNA Stability Elements
    Article Snippet: When the appropriate genomic material is not available, the ENE insert is created by annealing chemically synthesized oligonucleotides. .. Antarctic phosphatase (New England BioLabs).

    Construct:

    Article Title: Diagnostic and Biological Significance of KIR Expression Profile Determined by RNA-Seq in Natural Killer/T-Cell Lymphoma
    Article Snippet: KIR2DL4 first and second shRNAs were sequentially cloned into the LMP vector to generate the KIR2DL4–1st-2nd–double-shRNA using the following strategy: KIR2DL4–1st shRNA–LMP was digested with EcoRI and then treated with Antarctic Phosphatase (New England BioLabs Inc.) to prevent recircularization. .. Diagnostic restriction mapping and Sanger sequencing with forward and reverse primers were performed to validate each retroviral shRNA construct.

    Article Title: Mutations in TBX18 Cause Dominant Urinary Tract Malformations via Transcriptional Dysregulation of Ureter Development
    Article Snippet: Proteins used for electrophoretic mobility shift assay (EMSA) were generated from prK5.Myc.TBX18 expression constructs for TBX18 wild-type and mutant proteins using the SP6-coupled TNT Wheat Germ Extract System (Promega) for SP6-directed in vitro translation according to the supplier’s instructions. .. The fragment was dephosphorylated with Antarctic Phosphatase (New England Biolabs) for 1 hr at 37°C.

    Incubation:

    Article Title: TAK1 determines susceptibility to endoplasmic reticulum stress and leptin resistance in the hypothalamus
    Article Snippet: .. To dephosphorylate proteins, protein extracts were incubated with antarctic phosphatase (New England Biolabs) at 30°C for 30 min. To determine PERK phosphorylation, protein extracts that had been treated with or without phosphatase were separated in a 7% polyacrylamide gel and analyzed by immunoblotting. .. Fibroblasts were seeded on glass coverslips in 6-well plates 24 h prior to fixation.

    Article Title: nextPARS: parallel probing of RNA structures in Illumina
    Article Snippet: .. For the phosphatase treatment, we incubated at 37°C for 30 min a reaction mixture with 16 µL of the nondigested, V1- and S1-digested samples, 2.5 µL of 10× phosphatase buffer, 2.5 µL of nuclease-free water, 1 µL of RNase inhibitor, and 3 µL of Antarctic phosphatase (New England BioLabs). .. After 5 min at 65°C, we put samples on ice and added 4 µL of T4 Polynucleotide Kinase (PNK, New England BioLabs), 5 µL of 10× PNK buffer, 10 µL of ATP 10 mM, 1 µL of RNase inhibitor and nuclease-free water up to a total volume of 50 µL.

    Article Title: Transposase mediated construction of RNA-seq libraries
    Article Snippet: The purified and fragmented RNA was treated with 1 μL of Antarctic Phosphatase (5U/μL; NEB) for 30 min at 37°C, and then heat killed for 5 min at 65°C. .. The samples were then incubated with 2 μL of T4 Polynucleotide Kinase (2U/μL; Epicentre) and 0.7 mM ATP for 30 min at 37°C, followed by purification using an RNeasy MinElute kit (Qiagen).

    Formalin-fixed Paraffin-Embedded:

    Article Title: A Non-invasive Radiomic Method Using 18F-FDG PET Predicts Isocitrate Dehydrogenase Genotype and Prognosis in Patients With Glioma
    Article Snippet: DNA was isolated from formalin-fixed, paraffin-embedded tumor tissue using the Simplex OUP®FFPE DNA extraction kit (TIB, China), and the quantity was assessed by spectrophotometry using a NanoDrop 2000 (Thermo Fisher, US). .. PCR products were treated with Exonuclease I and Antarctic Phosphatase (New England Biolabs, UK) and sequenced using a Genetic Analyzers 3500 (Thermo Fisher, US).

    Activity Assay:

    Article Title: Potentiating tumor immunity using aptamer-targeted RNAi to render CD8+ T cells resistant to TGFβ inhibition
    Article Snippet: Synthetic DNA sequences (Integrated DNA Technologies), with XhoI 5′ and NotI 3′ overhangs, corresponding to the tested siRNA sequences were ligated into the 3′ end of the gene for Renilla luciferase in the ψCHECK-2 vector (Promega), digested with XhoI and NotI restriction enzymes and dephosphorylated with Antarctic phosphatase (New England Biolabs). .. 24 hours post-transfection, Renilla and Firefly (transfection control) luciferase activity were measured using the Dual-Glo Luciferase Kit (Promega).

    Expressing:

    Article Title: Diagnostic and Biological Significance of KIR Expression Profile Determined by RNA-Seq in Natural Killer/T-Cell Lymphoma
    Article Snippet: Paragraph title: Design and Expression of Single or Double shRNAs for KIR2DL4 Knockdown in NK-Cell Lines ... KIR2DL4 first and second shRNAs were sequentially cloned into the LMP vector to generate the KIR2DL4–1st-2nd–double-shRNA using the following strategy: KIR2DL4–1st shRNA–LMP was digested with EcoRI and then treated with Antarctic Phosphatase (New England BioLabs Inc.) to prevent recircularization.

    Article Title: Mutations in TBX18 Cause Dominant Urinary Tract Malformations via Transcriptional Dysregulation of Ureter Development
    Article Snippet: Proteins used for electrophoretic mobility shift assay (EMSA) were generated from prK5.Myc.TBX18 expression constructs for TBX18 wild-type and mutant proteins using the SP6-coupled TNT Wheat Germ Extract System (Promega) for SP6-directed in vitro translation according to the supplier’s instructions. .. The fragment was dephosphorylated with Antarctic Phosphatase (New England Biolabs) for 1 hr at 37°C.

    Genome Wide:

    Article Title: nextPARS: parallel probing of RNA structures in Illumina
    Article Snippet: With the aim to have higher sequencing throughput and multiplexing capacity, we implemented an adapted PARS protocol to the Illumina sequencing platform to study genome-wide the secondary structure of RNA molecules, which we named “nextPARS” ( ). .. For the phosphatase treatment, we incubated at 37°C for 30 min a reaction mixture with 16 µL of the nondigested, V1- and S1-digested samples, 2.5 µL of 10× phosphatase buffer, 2.5 µL of nuclease-free water, 1 µL of RNase inhibitor, and 3 µL of Antarctic phosphatase (New England BioLabs).

    Transformation Assay:

    Article Title: The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin
    Article Snippet: The BsmBI-digested HA was ligated into a dephosphorylated (Antarctic Phosphatase, M0289L; New England Biolabs) and BsmBI-digested preparation of the bidirectional reverse-genetics plasmid pHW2000 ( ) using T4 DNA ligase (M0202S; New England Biolabs). .. A 1:4000 dilution of each transformation was plated in parallel to enable estimation of the number of unique transformants—we obtained at least two-million unique colonies per transformation.

    Derivative Assay:

    Article Title: The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin
    Article Snippet: The libraries were created in full biological triplicate, meaning that each experimental replicate was derived from an independent plasmid mutant library. .. The BsmBI-digested HA was ligated into a dephosphorylated (Antarctic Phosphatase, M0289L; New England Biolabs) and BsmBI-digested preparation of the bidirectional reverse-genetics plasmid pHW2000 ( ) using T4 DNA ligase (M0202S; New England Biolabs).

    Transfection:

    Article Title: Potentiating tumor immunity using aptamer-targeted RNAi to render CD8+ T cells resistant to TGFβ inhibition
    Article Snippet: Synthetic DNA sequences (Integrated DNA Technologies), with XhoI 5′ and NotI 3′ overhangs, corresponding to the tested siRNA sequences were ligated into the 3′ end of the gene for Renilla luciferase in the ψCHECK-2 vector (Promega), digested with XhoI and NotI restriction enzymes and dephosphorylated with Antarctic phosphatase (New England Biolabs). .. 24 hours post-transfection, Renilla and Firefly (transfection control) luciferase activity were measured using the Dual-Glo Luciferase Kit (Promega).

    Ligation:

    Article Title: nextPARS: parallel probing of RNA structures in Illumina
    Article Snippet: In PARS, the first ligation is the 5′adapter and the second one the 3′ adaptor after a phosphatase treatment. .. For the phosphatase treatment, we incubated at 37°C for 30 min a reaction mixture with 16 µL of the nondigested, V1- and S1-digested samples, 2.5 µL of 10× phosphatase buffer, 2.5 µL of nuclease-free water, 1 µL of RNase inhibitor, and 3 µL of Antarctic phosphatase (New England BioLabs).

    Article Title: Protein Engineering of the Transcriptional Activator FhlA To Enhance Hydrogen Production in Escherichia coli
    Article Snippet: .. The epPCR product was cloned into pASKA2701 using the MfeI and HindIII restriction enzymes with Antarctic phosphatase (New England Biolabs, Beverly, MA) treatment of the vector; the ligation mixture was electroporated ( ) into strain JW2701-1 (Δ fhlA ) ( ) (complementation of the fhlA deletion by pASKA2701 was reported by us previously [ ]). .. For epPCR of the fhlA region encoding the N domain of FhlA, the conditions were the same as described above, but primers FhlAfront and FhlAN (see Table S2 in the supplemental material) were used with a 2-min extension time.

    Article Title: Transposase mediated construction of RNA-seq libraries
    Article Snippet: The purified and fragmented RNA was treated with 1 μL of Antarctic Phosphatase (5U/μL; NEB) for 30 min at 37°C, and then heat killed for 5 min at 65°C. .. This involves sequential ligation of 3′ and 5′ adapters, followed by reverse transcription and PCR to amplify the completed libraries.

    Protease Inhibitor:

    Article Title: Mutations in TBX18 Cause Dominant Urinary Tract Malformations via Transcriptional Dysregulation of Ureter Development
    Article Snippet: The fragment was dephosphorylated with Antarctic Phosphatase (New England Biolabs) for 1 hr at 37°C. .. Binding reactions for gel shift assays contained 2–5 μl of in vitro translated myc-tagged protein in a total volume of 20 μl of HEPES buffer (25 mM HEPES [pH 7.4], 10% glycerol, 75 mM NaCl, 0.25 mM EDTA, 1 mM MgCl2 , 0.1% Nonidet P-40, 10 μg/ml BSA, 1 mM DTT) with 1 tablet/10 ml Complete Mini EDTA-free protease inhibitor Cocktail (Roche Applied Science) and 1.5 μg of double-stranded poly(dI-dC) (Roche).

    Generated:

    Article Title: Diagnostic and Biological Significance of KIR Expression Profile Determined by RNA-Seq in Natural Killer/T-Cell Lymphoma
    Article Snippet: First, forkhead box-P3 shRNA was removed by gel extraction using QIAquick Gel Extraction Kit (Qiagen Inc.) after double-digestion with the XhoI and EcoRI restriction enzymes, which generated sticky overhangs. .. KIR2DL4 first and second shRNAs were sequentially cloned into the LMP vector to generate the KIR2DL4–1st-2nd–double-shRNA using the following strategy: KIR2DL4–1st shRNA–LMP was digested with EcoRI and then treated with Antarctic Phosphatase (New England BioLabs Inc.) to prevent recircularization.

    Article Title: Mutations in TBX18 Cause Dominant Urinary Tract Malformations via Transcriptional Dysregulation of Ureter Development
    Article Snippet: Proteins used for electrophoretic mobility shift assay (EMSA) were generated from prK5.Myc.TBX18 expression constructs for TBX18 wild-type and mutant proteins using the SP6-coupled TNT Wheat Germ Extract System (Promega) for SP6-directed in vitro translation according to the supplier’s instructions. .. The fragment was dephosphorylated with Antarctic Phosphatase (New England Biolabs) for 1 hr at 37°C.

    DNA Sequencing:

    Article Title: Tuberaztecorum sp. nov., a truffle species from Mexico belonging to the Maculatum clade ( Tuberaceae, Pezizales)
    Article Snippet: Paragraph title: DNA sequencing and phylogenetic analyses ... PCR products were cleaned enzymatically with antarctic phosphatase and endonuclease digestion (New England Biolabs, Ipswich MA).

    Article Title: Tyrosine Phosphorylation and Dephosphorylation in Burkholderia cenocepacia Affect Biofilm Formation, Growth under Nutritional Deprivation, and Pathogenicity
    Article Snippet: Antarctic phosphatase (New England BioLabs), restriction enzymes (New England BioLabs), and T4 DNA ligase (Roche Applied Science) were used as recommended by the manufacturers. .. Antarctic phosphatase (New England BioLabs), restriction enzymes (New England BioLabs), and T4 DNA ligase (Roche Applied Science) were used as recommended by the manufacturers.

    Sequencing:

    Article Title: Tuberaztecorum sp. nov., a truffle species from Mexico belonging to the Maculatum clade ( Tuberaceae, Pezizales)
    Article Snippet: PCR products were cleaned enzymatically with antarctic phosphatase and endonuclease digestion (New England Biolabs, Ipswich MA). .. Sanger sequencing was performed by Big Dye chemistry v3.1 (Applied Biosystems, Foster City, CA) with the forward primer ITS1f and reverse primers ITS4.

    Article Title: A Non-invasive Radiomic Method Using 18F-FDG PET Predicts Isocitrate Dehydrogenase Genotype and Prognosis in Patients With Glioma
    Article Snippet: IDH Mutant Detection IDH1 and IDH2 mutations were detected postoperatively in patient tumor tissue using direct sequencing, as described by Horbinski et al. ( ). .. PCR products were treated with Exonuclease I and Antarctic Phosphatase (New England Biolabs, UK) and sequenced using a Genetic Analyzers 3500 (Thermo Fisher, US).

    Article Title: nextPARS: parallel probing of RNA structures in Illumina
    Article Snippet: With the aim to have higher sequencing throughput and multiplexing capacity, we implemented an adapted PARS protocol to the Illumina sequencing platform to study genome-wide the secondary structure of RNA molecules, which we named “nextPARS” ( ). .. For the phosphatase treatment, we incubated at 37°C for 30 min a reaction mixture with 16 µL of the nondigested, V1- and S1-digested samples, 2.5 µL of 10× phosphatase buffer, 2.5 µL of nuclease-free water, 1 µL of RNase inhibitor, and 3 µL of Antarctic phosphatase (New England BioLabs).

    Article Title: Diagnostic and Biological Significance of KIR Expression Profile Determined by RNA-Seq in Natural Killer/T-Cell Lymphoma
    Article Snippet: KIR2DL4 first and second shRNAs were sequentially cloned into the LMP vector to generate the KIR2DL4–1st-2nd–double-shRNA using the following strategy: KIR2DL4–1st shRNA–LMP was digested with EcoRI and then treated with Antarctic Phosphatase (New England BioLabs Inc.) to prevent recircularization. .. Diagnostic restriction mapping and Sanger sequencing with forward and reverse primers were performed to validate each retroviral shRNA construct.

    Article Title: A Variable Region in GP4 of European-Type Porcine Reproductive and Respiratory Syndrome Virus Induces Neutralizing Antibodies Against Homologous But Not Heterologous Virus Strains
    Article Snippet: .. PCR products were treated with Exonuclease I and Antarctic Phosphatase (New England BioLabs, Ipswich, MA), and used directly for cycle sequencing with a Big Dye Terminator Cycle sequencing kit V1.1 (Applied Biosystems), and the aforementioned primers. .. Cycle sequencing reaction products were purified by ethanol precipitation and separated on an ABI Genetic 310 (Applied Biosystems).

    Recombinant:

    Article Title: Deciphering the Unusual Acylation Pattern of Helicobacter pylori Lipid A ▿ Lipid A ▿ †
    Article Snippet: Paragraph title: Recombinant DNA techniques. ... Restriction endonucleases, T4 DNA ligase, and Antarctic phosphatase were purchased from New England Biolabs.

    Multiplexing:

    Article Title: nextPARS: parallel probing of RNA structures in Illumina
    Article Snippet: With the aim to have higher sequencing throughput and multiplexing capacity, we implemented an adapted PARS protocol to the Illumina sequencing platform to study genome-wide the secondary structure of RNA molecules, which we named “nextPARS” ( ). .. For the phosphatase treatment, we incubated at 37°C for 30 min a reaction mixture with 16 µL of the nondigested, V1- and S1-digested samples, 2.5 µL of 10× phosphatase buffer, 2.5 µL of nuclease-free water, 1 µL of RNase inhibitor, and 3 µL of Antarctic phosphatase (New England BioLabs).

    DNA Extraction:

    Article Title: Tuberaztecorum sp. nov., a truffle species from Mexico belonging to the Maculatum clade ( Tuberaceae, Pezizales)
    Article Snippet: DNA was extracted from truffle fruiting bodies with the chloroform extraction technique using CTAB 2X DNA extraction buffer. .. PCR products were cleaned enzymatically with antarctic phosphatase and endonuclease digestion (New England Biolabs, Ipswich MA).

    Article Title: A Non-invasive Radiomic Method Using 18F-FDG PET Predicts Isocitrate Dehydrogenase Genotype and Prognosis in Patients With Glioma
    Article Snippet: DNA was isolated from formalin-fixed, paraffin-embedded tumor tissue using the Simplex OUP®FFPE DNA extraction kit (TIB, China), and the quantity was assessed by spectrophotometry using a NanoDrop 2000 (Thermo Fisher, US). .. PCR products were treated with Exonuclease I and Antarctic Phosphatase (New England Biolabs, UK) and sequenced using a Genetic Analyzers 3500 (Thermo Fisher, US).

    RNA Sequencing Assay:

    Article Title: Transposase mediated construction of RNA-seq libraries
    Article Snippet: Paragraph title: Standard directional RNA-seq library construction ... The purified and fragmented RNA was treated with 1 μL of Antarctic Phosphatase (5U/μL; NEB) for 30 min at 37°C, and then heat killed for 5 min at 65°C.

    Mutagenesis:

    Article Title: A Non-invasive Radiomic Method Using 18F-FDG PET Predicts Isocitrate Dehydrogenase Genotype and Prognosis in Patients With Glioma
    Article Snippet: Paragraph title: IDH Mutant Detection ... PCR products were treated with Exonuclease I and Antarctic Phosphatase (New England Biolabs, UK) and sequenced using a Genetic Analyzers 3500 (Thermo Fisher, US).

    Article Title: The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin
    Article Snippet: Paragraph title: Generation of HA codon mutation library ... The BsmBI-digested HA was ligated into a dephosphorylated (Antarctic Phosphatase, M0289L; New England Biolabs) and BsmBI-digested preparation of the bidirectional reverse-genetics plasmid pHW2000 ( ) using T4 DNA ligase (M0202S; New England Biolabs).

    Article Title: Protein Engineering of the Transcriptional Activator FhlA To Enhance Hydrogen Production in Escherichia coli
    Article Snippet: Paragraph title: Random mutagenesis of fhlA . ... The epPCR product was cloned into pASKA2701 using the MfeI and HindIII restriction enzymes with Antarctic phosphatase (New England Biolabs, Beverly, MA) treatment of the vector; the ligation mixture was electroporated ( ) into strain JW2701-1 (Δ fhlA ) ( ) (complementation of the fhlA deletion by pASKA2701 was reported by us previously [ ]).

    Article Title: Mutations in TBX18 Cause Dominant Urinary Tract Malformations via Transcriptional Dysregulation of Ureter Development
    Article Snippet: Proteins used for electrophoretic mobility shift assay (EMSA) were generated from prK5.Myc.TBX18 expression constructs for TBX18 wild-type and mutant proteins using the SP6-coupled TNT Wheat Germ Extract System (Promega) for SP6-directed in vitro translation according to the supplier’s instructions. .. The fragment was dephosphorylated with Antarctic Phosphatase (New England Biolabs) for 1 hr at 37°C.

    Isolation:

    Article Title: Deciphering the Unusual Acylation Pattern of Helicobacter pylori Lipid A ▿ Lipid A ▿ †
    Article Snippet: DNA fragments were isolated from agarose gels using a Qiaquick Gel Extraction Kit (Qiagen). .. Restriction endonucleases, T4 DNA ligase, and Antarctic phosphatase were purchased from New England Biolabs.

    Article Title: A Non-invasive Radiomic Method Using 18F-FDG PET Predicts Isocitrate Dehydrogenase Genotype and Prognosis in Patients With Glioma
    Article Snippet: DNA was isolated from formalin-fixed, paraffin-embedded tumor tissue using the Simplex OUP®FFPE DNA extraction kit (TIB, China), and the quantity was assessed by spectrophotometry using a NanoDrop 2000 (Thermo Fisher, US). .. PCR products were treated with Exonuclease I and Antarctic Phosphatase (New England Biolabs, UK) and sequenced using a Genetic Analyzers 3500 (Thermo Fisher, US).

    Luciferase:

    Article Title: Potentiating tumor immunity using aptamer-targeted RNAi to render CD8+ T cells resistant to TGFβ inhibition
    Article Snippet: .. Synthetic DNA sequences (Integrated DNA Technologies), with XhoI 5′ and NotI 3′ overhangs, corresponding to the tested siRNA sequences were ligated into the 3′ end of the gene for Renilla luciferase in the ψCHECK-2 vector (Promega), digested with XhoI and NotI restriction enzymes and dephosphorylated with Antarctic phosphatase (New England Biolabs). .. For assay, HEK293T cells were co-transfected with 100 ng of the ψCHECK vector and various concentration (0.1–10 nM) of siRNA or aptamer-siRNA conjugates in a 24 well plate using Lipofectamine 2000 (Thermo Fisher Scientific).

    Electrophoretic Mobility Shift Assay:

    Article Title: Mutations in TBX18 Cause Dominant Urinary Tract Malformations via Transcriptional Dysregulation of Ureter Development
    Article Snippet: Paragraph title: Electrophoretic Mobility Shift Assay ... The fragment was dephosphorylated with Antarctic Phosphatase (New England Biolabs) for 1 hr at 37°C.

    Purification:

    Article Title: Deciphering the Unusual Acylation Pattern of Helicobacter pylori Lipid A ▿ Lipid A ▿ †
    Article Snippet: PCR clean up was performed using a Qiaquick PCR Purification Kit (Qiagen). .. Restriction endonucleases, T4 DNA ligase, and Antarctic phosphatase were purchased from New England Biolabs.

    Article Title: Engineering Stochasticity in Gene Expression
    Article Snippet: .. In-line RNA structure assays were performed on rcRNA transcripts as described in reference unless otherwise noted. rcRNAs were amplified using primers flanking the T7 promoter and terminator from pACYCDuet-1, transcribed in vitro by a T7 RNA polymerase transcription kit (Epicentre, Madison WI), purified on a 12% denaturing polyacrylamide gel, phosphatased with Antarctic Phosphatase (NEB), radiolabeled on the 5′-most nucleotide, and gel purified as before. ..

    Article Title: The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin
    Article Snippet: The final products from the codon mutagenesis PCR were gel purified and digested with BsmBI (R0580L; New England Biolabs, Ipswich, Massachusetts). .. The BsmBI-digested HA was ligated into a dephosphorylated (Antarctic Phosphatase, M0289L; New England Biolabs) and BsmBI-digested preparation of the bidirectional reverse-genetics plasmid pHW2000 ( ) using T4 DNA ligase (M0202S; New England Biolabs).

    Article Title: nextPARS: parallel probing of RNA structures in Illumina
    Article Snippet: For the phosphatase treatment, we incubated at 37°C for 30 min a reaction mixture with 16 µL of the nondigested, V1- and S1-digested samples, 2.5 µL of 10× phosphatase buffer, 2.5 µL of nuclease-free water, 1 µL of RNase inhibitor, and 3 µL of Antarctic phosphatase (New England BioLabs). .. After 1 h of incubation at 37°C, samples were purified using the RNeasy MiniElute Cleanup Kit following manufacturer's instructions (Qiagen) with a 10 µL RNase-free water final elution step.

    Article Title: Transposase mediated construction of RNA-seq libraries
    Article Snippet: .. The purified and fragmented RNA was treated with 1 μL of Antarctic Phosphatase (5U/μL; NEB) for 30 min at 37°C, and then heat killed for 5 min at 65°C. .. The samples were then incubated with 2 μL of T4 Polynucleotide Kinase (2U/μL; Epicentre) and 0.7 mM ATP for 30 min at 37°C, followed by purification using an RNeasy MinElute kit (Qiagen).

    Article Title: A Variable Region in GP4 of European-Type Porcine Reproductive and Respiratory Syndrome Virus Induces Neutralizing Antibodies Against Homologous But Not Heterologous Virus Strains
    Article Snippet: PCR products were treated with Exonuclease I and Antarctic Phosphatase (New England BioLabs, Ipswich, MA), and used directly for cycle sequencing with a Big Dye Terminator Cycle sequencing kit V1.1 (Applied Biosystems), and the aforementioned primers. .. Cycle sequencing reaction products were purified by ethanol precipitation and separated on an ABI Genetic 310 (Applied Biosystems).

    Polymerase Chain Reaction:

    Article Title: Deciphering the Unusual Acylation Pattern of Helicobacter pylori Lipid A ▿ Lipid A ▿ †
    Article Snippet: PCR clean up was performed using a Qiaquick PCR Purification Kit (Qiagen). .. Restriction endonucleases, T4 DNA ligase, and Antarctic phosphatase were purchased from New England Biolabs.

    Article Title: Tuberaztecorum sp. nov., a truffle species from Mexico belonging to the Maculatum clade ( Tuberaceae, Pezizales)
    Article Snippet: .. PCR products were cleaned enzymatically with antarctic phosphatase and endonuclease digestion (New England Biolabs, Ipswich MA). .. Sanger sequencing was performed by Big Dye chemistry v3.1 (Applied Biosystems, Foster City, CA) with the forward primer ITS1f and reverse primers ITS4.

    Article Title: Intronless β-Globin Reporter: A Tool for Studying Nuclear RNA Stability Elements
    Article Snippet: Reagents and equipment for performing PCR (e.g. Phusion® high-fidelity DNA polymerase), chemically synthesized PCR primers with an ApaI site, and genomic material. .. Antarctic phosphatase (New England BioLabs).

    Article Title: A Non-invasive Radiomic Method Using 18F-FDG PET Predicts Isocitrate Dehydrogenase Genotype and Prognosis in Patients With Glioma
    Article Snippet: .. PCR products were treated with Exonuclease I and Antarctic Phosphatase (New England Biolabs, UK) and sequenced using a Genetic Analyzers 3500 (Thermo Fisher, US). .. 18 F-FDG PET Data Acquisition and Tumor Segmentation 18 F-FDG was produced in situ using an RDS-111 Cyclotron (CTI, US).

    Article Title: The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin
    Article Snippet: The final products from the codon mutagenesis PCR were gel purified and digested with BsmBI (R0580L; New England Biolabs, Ipswich, Massachusetts). .. The BsmBI-digested HA was ligated into a dephosphorylated (Antarctic Phosphatase, M0289L; New England Biolabs) and BsmBI-digested preparation of the bidirectional reverse-genetics plasmid pHW2000 ( ) using T4 DNA ligase (M0202S; New England Biolabs).

    Article Title: Diagnostic and Biological Significance of KIR Expression Profile Determined by RNA-Seq in Natural Killer/T-Cell Lymphoma
    Article Snippet: The siRNAs were converted to 97-mer shRNA-miRNAs and PCR-amplified with the high-fidelity PfuUltra II Fusion HS DNA Polymerase (Agilent Technologies) to be cloned in the miR-30–adapted retroviral vector, microRNA-adapted retroviral vector MSCV-LTRmiR30-PIG (LMP) (Addgene; ; plasmid number 24071), which was digested at the XhoI and EcoRI restriction sites to remove the forkhead box-P3 shRNA according to the manufacturer's instructions (Thermo Fisher Scientific Inc, Rochester, NY) ( A). .. KIR2DL4 first and second shRNAs were sequentially cloned into the LMP vector to generate the KIR2DL4–1st-2nd–double-shRNA using the following strategy: KIR2DL4–1st shRNA–LMP was digested with EcoRI and then treated with Antarctic Phosphatase (New England BioLabs Inc.) to prevent recircularization.

    Article Title: Transposase mediated construction of RNA-seq libraries
    Article Snippet: The purified and fragmented RNA was treated with 1 μL of Antarctic Phosphatase (5U/μL; NEB) for 30 min at 37°C, and then heat killed for 5 min at 65°C. .. This involves sequential ligation of 3′ and 5′ adapters, followed by reverse transcription and PCR to amplify the completed libraries.

    Article Title: Tyrosine Phosphorylation and Dephosphorylation in Burkholderia cenocepacia Affect Biofilm Formation, Growth under Nutritional Deprivation, and Pathogenicity
    Article Snippet: PCR amplification was performed using Taq (5Prime) or HotStar HiFidelity (Qiagen) DNA polymerase. .. Antarctic phosphatase (New England BioLabs), restriction enzymes (New England BioLabs), and T4 DNA ligase (Roche Applied Science) were used as recommended by the manufacturers.

    Article Title: A Variable Region in GP4 of European-Type Porcine Reproductive and Respiratory Syndrome Virus Induces Neutralizing Antibodies Against Homologous But Not Heterologous Virus Strains
    Article Snippet: .. PCR products were treated with Exonuclease I and Antarctic Phosphatase (New England BioLabs, Ipswich, MA), and used directly for cycle sequencing with a Big Dye Terminator Cycle sequencing kit V1.1 (Applied Biosystems), and the aforementioned primers. .. Cycle sequencing reaction products were purified by ethanol precipitation and separated on an ABI Genetic 310 (Applied Biosystems).

    shRNA:

    Article Title: Diagnostic and Biological Significance of KIR Expression Profile Determined by RNA-Seq in Natural Killer/T-Cell Lymphoma
    Article Snippet: .. KIR2DL4 first and second shRNAs were sequentially cloned into the LMP vector to generate the KIR2DL4–1st-2nd–double-shRNA using the following strategy: KIR2DL4–1st shRNA–LMP was digested with EcoRI and then treated with Antarctic Phosphatase (New England BioLabs Inc.) to prevent recircularization. .. After that, EcoRI-digested KIR2DL4–2nd shRNA insert, which was generated through amplification with PfuUltra II Fusion HS DNA polymerase (Agilent Technologies), was cloned into KIR2DL4–1st shRNA–LMP ( C).

    Plasmid Preparation:

    Article Title: Intronless β-Globin Reporter: A Tool for Studying Nuclear RNA Stability Elements
    Article Snippet: Paragraph title: 2.1 Construction of a βΔ1,2-ENE reporter plasmid ... Antarctic phosphatase (New England BioLabs).

    Article Title: The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin
    Article Snippet: .. The BsmBI-digested HA was ligated into a dephosphorylated (Antarctic Phosphatase, M0289L; New England Biolabs) and BsmBI-digested preparation of the bidirectional reverse-genetics plasmid pHW2000 ( ) using T4 DNA ligase (M0202S; New England Biolabs). .. Column-purified ligations were electroporated into ElectroMAX DH10B T1 phage-resistant competent cells (12033-015; Invitrogen, Carlsbad, California) and plated on LB plates containing 100 μg/ml of ampicilin.

    Article Title: Potentiating tumor immunity using aptamer-targeted RNAi to render CD8+ T cells resistant to TGFβ inhibition
    Article Snippet: .. Synthetic DNA sequences (Integrated DNA Technologies), with XhoI 5′ and NotI 3′ overhangs, corresponding to the tested siRNA sequences were ligated into the 3′ end of the gene for Renilla luciferase in the ψCHECK-2 vector (Promega), digested with XhoI and NotI restriction enzymes and dephosphorylated with Antarctic phosphatase (New England Biolabs). .. For assay, HEK293T cells were co-transfected with 100 ng of the ψCHECK vector and various concentration (0.1–10 nM) of siRNA or aptamer-siRNA conjugates in a 24 well plate using Lipofectamine 2000 (Thermo Fisher Scientific).

    Article Title: Diagnostic and Biological Significance of KIR Expression Profile Determined by RNA-Seq in Natural Killer/T-Cell Lymphoma
    Article Snippet: .. KIR2DL4 first and second shRNAs were sequentially cloned into the LMP vector to generate the KIR2DL4–1st-2nd–double-shRNA using the following strategy: KIR2DL4–1st shRNA–LMP was digested with EcoRI and then treated with Antarctic Phosphatase (New England BioLabs Inc.) to prevent recircularization. .. After that, EcoRI-digested KIR2DL4–2nd shRNA insert, which was generated through amplification with PfuUltra II Fusion HS DNA polymerase (Agilent Technologies), was cloned into KIR2DL4–1st shRNA–LMP ( C).

    Article Title: Protein Engineering of the Transcriptional Activator FhlA To Enhance Hydrogen Production in Escherichia coli
    Article Snippet: .. The epPCR product was cloned into pASKA2701 using the MfeI and HindIII restriction enzymes with Antarctic phosphatase (New England Biolabs, Beverly, MA) treatment of the vector; the ligation mixture was electroporated ( ) into strain JW2701-1 (Δ fhlA ) ( ) (complementation of the fhlA deletion by pASKA2701 was reported by us previously [ ]). .. For epPCR of the fhlA region encoding the N domain of FhlA, the conditions were the same as described above, but primers FhlAfront and FhlAN (see Table S2 in the supplemental material) were used with a 2-min extension time.

    Article Title: Mutations in TBX18 Cause Dominant Urinary Tract Malformations via Transcriptional Dysregulation of Ureter Development
    Article Snippet: The annealed oligonucleotides were subcloned as BamHI/NcoI fragments into pKS vector (Stratagene) and released by BamHI/AseI as a 214 bp fragment. .. The fragment was dephosphorylated with Antarctic Phosphatase (New England Biolabs) for 1 hr at 37°C.

    Binding Assay:

    Article Title: Mutations in TBX18 Cause Dominant Urinary Tract Malformations via Transcriptional Dysregulation of Ureter Development
    Article Snippet: The fragment was dephosphorylated with Antarctic Phosphatase (New England Biolabs) for 1 hr at 37°C. .. Binding reactions for gel shift assays contained 2–5 μl of in vitro translated myc-tagged protein in a total volume of 20 μl of HEPES buffer (25 mM HEPES [pH 7.4], 10% glycerol, 75 mM NaCl, 0.25 mM EDTA, 1 mM MgCl2 , 0.1% Nonidet P-40, 10 μg/ml BSA, 1 mM DTT) with 1 tablet/10 ml Complete Mini EDTA-free protease inhibitor Cocktail (Roche Applied Science) and 1.5 μg of double-stranded poly(dI-dC) (Roche).

    Sample Prep:

    Article Title: nextPARS: parallel probing of RNA structures in Illumina
    Article Snippet: Paragraph title: nextPARS: library preparation using TruSeq Small RNA Sample Preparation Kit (Illumina) ... For the phosphatase treatment, we incubated at 37°C for 30 min a reaction mixture with 16 µL of the nondigested, V1- and S1-digested samples, 2.5 µL of 10× phosphatase buffer, 2.5 µL of nuclease-free water, 1 µL of RNase inhibitor, and 3 µL of Antarctic phosphatase (New England BioLabs).

    In Vitro:

    Article Title: Engineering Stochasticity in Gene Expression
    Article Snippet: .. In-line RNA structure assays were performed on rcRNA transcripts as described in reference unless otherwise noted. rcRNAs were amplified using primers flanking the T7 promoter and terminator from pACYCDuet-1, transcribed in vitro by a T7 RNA polymerase transcription kit (Epicentre, Madison WI), purified on a 12% denaturing polyacrylamide gel, phosphatased with Antarctic Phosphatase (NEB), radiolabeled on the 5′-most nucleotide, and gel purified as before. ..

    Article Title: nextPARS: parallel probing of RNA structures in Illumina
    Article Snippet: In PARS, after the in vitro folding and RNase digestion step, the authors include a random fragmentation step and a size selection of RNA fragments by a column cleanup that we skip in the nextPARS protocol. .. For the phosphatase treatment, we incubated at 37°C for 30 min a reaction mixture with 16 µL of the nondigested, V1- and S1-digested samples, 2.5 µL of 10× phosphatase buffer, 2.5 µL of nuclease-free water, 1 µL of RNase inhibitor, and 3 µL of Antarctic phosphatase (New England BioLabs).

    Article Title: Mutations in TBX18 Cause Dominant Urinary Tract Malformations via Transcriptional Dysregulation of Ureter Development
    Article Snippet: Proteins used for electrophoretic mobility shift assay (EMSA) were generated from prK5.Myc.TBX18 expression constructs for TBX18 wild-type and mutant proteins using the SP6-coupled TNT Wheat Germ Extract System (Promega) for SP6-directed in vitro translation according to the supplier’s instructions. .. The fragment was dephosphorylated with Antarctic Phosphatase (New England Biolabs) for 1 hr at 37°C.

    Selection:

    Article Title: nextPARS: parallel probing of RNA structures in Illumina
    Article Snippet: In PARS, after the in vitro folding and RNase digestion step, the authors include a random fragmentation step and a size selection of RNA fragments by a column cleanup that we skip in the nextPARS protocol. .. For the phosphatase treatment, we incubated at 37°C for 30 min a reaction mixture with 16 µL of the nondigested, V1- and S1-digested samples, 2.5 µL of 10× phosphatase buffer, 2.5 µL of nuclease-free water, 1 µL of RNase inhibitor, and 3 µL of Antarctic phosphatase (New England BioLabs).

    Ethanol Precipitation:

    Article Title: A Variable Region in GP4 of European-Type Porcine Reproductive and Respiratory Syndrome Virus Induces Neutralizing Antibodies Against Homologous But Not Heterologous Virus Strains
    Article Snippet: PCR products were treated with Exonuclease I and Antarctic Phosphatase (New England BioLabs, Ipswich, MA), and used directly for cycle sequencing with a Big Dye Terminator Cycle sequencing kit V1.1 (Applied Biosystems), and the aforementioned primers. .. Cycle sequencing reaction products were purified by ethanol precipitation and separated on an ABI Genetic 310 (Applied Biosystems).

    Spectrophotometry:

    Article Title: A Non-invasive Radiomic Method Using 18F-FDG PET Predicts Isocitrate Dehydrogenase Genotype and Prognosis in Patients With Glioma
    Article Snippet: DNA was isolated from formalin-fixed, paraffin-embedded tumor tissue using the Simplex OUP®FFPE DNA extraction kit (TIB, China), and the quantity was assessed by spectrophotometry using a NanoDrop 2000 (Thermo Fisher, US). .. PCR products were treated with Exonuclease I and Antarctic Phosphatase (New England Biolabs, UK) and sequenced using a Genetic Analyzers 3500 (Thermo Fisher, US).

    Concentration Assay:

    Article Title: Potentiating tumor immunity using aptamer-targeted RNAi to render CD8+ T cells resistant to TGFβ inhibition
    Article Snippet: Synthetic DNA sequences (Integrated DNA Technologies), with XhoI 5′ and NotI 3′ overhangs, corresponding to the tested siRNA sequences were ligated into the 3′ end of the gene for Renilla luciferase in the ψCHECK-2 vector (Promega), digested with XhoI and NotI restriction enzymes and dephosphorylated with Antarctic phosphatase (New England Biolabs). .. For assay, HEK293T cells were co-transfected with 100 ng of the ψCHECK vector and various concentration (0.1–10 nM) of siRNA or aptamer-siRNA conjugates in a 24 well plate using Lipofectamine 2000 (Thermo Fisher Scientific).

    Gel Extraction:

    Article Title: Deciphering the Unusual Acylation Pattern of Helicobacter pylori Lipid A ▿ Lipid A ▿ †
    Article Snippet: DNA fragments were isolated from agarose gels using a Qiaquick Gel Extraction Kit (Qiagen). .. Restriction endonucleases, T4 DNA ligase, and Antarctic phosphatase were purchased from New England Biolabs.

    Article Title: Diagnostic and Biological Significance of KIR Expression Profile Determined by RNA-Seq in Natural Killer/T-Cell Lymphoma
    Article Snippet: First, forkhead box-P3 shRNA was removed by gel extraction using QIAquick Gel Extraction Kit (Qiagen Inc.) after double-digestion with the XhoI and EcoRI restriction enzymes, which generated sticky overhangs. .. KIR2DL4 first and second shRNAs were sequentially cloned into the LMP vector to generate the KIR2DL4–1st-2nd–double-shRNA using the following strategy: KIR2DL4–1st shRNA–LMP was digested with EcoRI and then treated with Antarctic Phosphatase (New England BioLabs Inc.) to prevent recircularization.

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    New England Biolabs antarctic phosphatase
    Antarctic Phosphatase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 90/100, based on 87 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/antarctic phosphatase/product/New England Biolabs
    Average 90 stars, based on 87 article reviews
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