deoxynucleotide triphosphates  (New England Biolabs)


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    Structured Review

    New England Biolabs deoxynucleotide triphosphates
    Deoxynucleotide Triphosphates, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 93/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/deoxynucleotide triphosphates/product/New England Biolabs
    Average 93 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    deoxynucleotide triphosphates - by Bioz Stars, 2020-01
    93/100 stars

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    Related Articles

    Clone Assay:

    Article Title: DNA-Based Diet Analysis for Any Predator
    Article Snippet: For the Sarasota samples, 17–20 clones were SSCP screened and representative sequences generated all as described below. .. PCR reaction conditions for all 16SPLSUFwd/16SPLSURv PCR's were: 0.4 µM 16SPLSUFwd and 0.4 µM 16SPLSURv primer mixes, 1× AmpliTaq® Gold Buffer (Applied Biosystems), 2 mM MgCl2+ , 1× BSA (New England Biolabs), 100 µM dNTP's (New England Biolabs), 0.75 units AmpliTaq® Gold DNA polymerase (Applied Biosystems), 0.05× SYBR® Green I (Molecular Probes) and the described amount of template for each 16SPLSUFwd/16SPLSURv PCR in a 25 µl total volume.

    Centrifugation:

    Article Title: Intestinal enteroendocrine lineage cells possess homeostatic and injury-inducible stem cell activity
    Article Snippet: The fragments were precipitated with 70 mM sodium acetate (Life Technologies, Foster City, CA), 40 µg glycogen (Life Technologies, Foster City, CA) and 70% ethanol at −80°C for 1 hour followed by centrifugation and washing with 70% ethanol. .. The first strand reaction was performed with 200 units of SuperScript II (Life Technologies, Foster City, CA) with 0.625 mM dNTP’s (NEB, Ipswitch, MA) and 8 units SUPERase RNase Inhibitor (Life Technologies, Foster City, CA) at 25°C for 10 minutes, then 42°C for 50 minutes, then 75°C for 15 minutes and cooled to 4°C.

    Amplification:

    Article Title: Phylogenetic analysis of Shiga toxin 1 and Shiga toxin 2 genes associated with disease outbreaks
    Article Snippet: Paragraph title: Amplification of Stx genes ... PCR master mix was made to final concentration of 1 × ThermoPol Reaction Buffer (New England BioLabs, Beverly, MA), 500 μM dNTP's (New England BioLabs), 0.02 units/μl Vent exo(-) polymerase (New England BioLabs), and 1 μM of each of the stx1 primers or stx2 primers.

    Article Title: DNA-Based Diet Analysis for Any Predator
    Article Snippet: The Pac I digested PCR product was then directly cloned, 35–52 clones directly amplified, SSCP screened and representative variant sequences generated all as described below. .. PCR reaction conditions for all 16SPLSUFwd/16SPLSURv PCR's were: 0.4 µM 16SPLSUFwd and 0.4 µM 16SPLSURv primer mixes, 1× AmpliTaq® Gold Buffer (Applied Biosystems), 2 mM MgCl2+ , 1× BSA (New England Biolabs), 100 µM dNTP's (New England Biolabs), 0.75 units AmpliTaq® Gold DNA polymerase (Applied Biosystems), 0.05× SYBR® Green I (Molecular Probes) and the described amount of template for each 16SPLSUFwd/16SPLSURv PCR in a 25 µl total volume.

    Article Title: Diversity of Mycobacterium tuberculosis Complex from Cattle Lymph Nodes in Eastern Cape Province
    Article Snippet: .. The PCR amplification mixture for each reaction contained 1x master mix (0.05 U/μ l) Taq polymerase, 0.2 mM each of the deoxynucleotide triphosphates (New England Biolabs, Inc., Hitchin, UK), 2 mM MgCl2 , 2 μ M of each primer pair, and 2 μ l of DNA, and nuclease-free water was added to make a total volume of 25 μ l. Amplification was achieved using a MyCycler™ Thermal Cycler (Bio-Rad, Cape Town, South Africa) with 1 cycle of denaturing at 95°C for 15 minutes, followed by 38 cycles of 1 minute at 95°C and 1 minute at 72°C, followed by 1 cycle of final extension at 72°C for 10 minutes. .. The positive (H37Rv strain) and negative (sterile nuclease-free water) controls were added to the amplification.

    Article Title: Intestinal enteroendocrine lineage cells possess homeostatic and injury-inducible stem cell activity
    Article Snippet: Each entire sample was input into the Ambion WT Expression Kit (Life Technologies, Foster City, CA) to perform double stranded cDNA synthesis followed by in vitro transcription to generate amplified cRNA. .. The first strand reaction was performed with 200 units of SuperScript II (Life Technologies, Foster City, CA) with 0.625 mM dNTP’s (NEB, Ipswitch, MA) and 8 units SUPERase RNase Inhibitor (Life Technologies, Foster City, CA) at 25°C for 10 minutes, then 42°C for 50 minutes, then 75°C for 15 minutes and cooled to 4°C.

    Article Title: Diversity of Mycobacterium tuberculosis Complex from Cattle Lymph Nodes in Eastern Cape Province
    Article Snippet: .. The PCR amplification mixture for each reaction contained 1x master mix (0.05 U/ μ l) Taq polymerase, 0.2 mM each of the deoxynucleotide triphosphates (New England Biolabs, Inc., Hitchin, UK), 2 mM MgCl2 , 2 μ M of each primer pair, and 2 μ l of DNA, and nuclease-free water was added to make a total volume of 25 μ l. Amplification was achieved using a MyCycler™ Thermal Cycler (Bio-Rad, Cape Town, South Africa) with 1 cycle of denaturing at 95°C for 15 minutes, followed by 38 cycles of 1 minute at 95°C and 1 minute at 72°C, followed by 1 cycle of final extension at 72°C for 10 minutes. .. The positive (H37Rv strain) and negative (sterile nuclease-free water) controls were added to the amplification.

    Synthesized:

    Article Title: RNA sequencing reveals retinal transcriptome changes in STZ-induced diabetic rats
    Article Snippet: The first strand of cDNA was then synthesized using random hexamer-primed reverse transcription (Super Script® II Reverse Transcriptase; Invitrogen; Thermo Fisher Scientific, Inc.) according to the manufacturer's protocol. .. Second strand buffer (Invitrogen; Thermo Fisher Scientific, Inc.), deoxynucleotide triphosphates (New England Biolabs, Inc.), RNase H (Second Strand Master Mix; Invitrogen; Thermo Fisher Scientific, Inc.) and DNA polymerase I (Second Strand Master Mix; Invitrogen; Thermo Fisher Scientific, Inc.) were added to synthesize the second strand.

    SYBR Green Assay:

    Article Title: DNA-Based Diet Analysis for Any Predator
    Article Snippet: .. PCR reaction conditions for all 16SPLSUFwd/16SPLSURv PCR's were: 0.4 µM 16SPLSUFwd and 0.4 µM 16SPLSURv primer mixes, 1× AmpliTaq® Gold Buffer (Applied Biosystems), 2 mM MgCl2+ , 1× BSA (New England Biolabs), 100 µM dNTP's (New England Biolabs), 0.75 units AmpliTaq® Gold DNA polymerase (Applied Biosystems), 0.05× SYBR® Green I (Molecular Probes) and the described amount of template for each 16SPLSUFwd/16SPLSURv PCR in a 25 µl total volume. .. PCR thermocycling conditions were an initial denaturation at 95°C for 7.5 minutes followed by repeated cycles (details below) of 95°C for 15 seconds, 52°C for 45 seconds and 72°C for 45 seconds.

    Random Hexamer Labeling:

    Article Title: Intestinal enteroendocrine lineage cells possess homeostatic and injury-inducible stem cell activity
    Article Snippet: 3 µg of random hexamer (Life Technologies, Foster City, CA) was added to the fragmented, purified cRNA and incubated at 70°C for 10 minutes to anneal the primer. .. The first strand reaction was performed with 200 units of SuperScript II (Life Technologies, Foster City, CA) with 0.625 mM dNTP’s (NEB, Ipswitch, MA) and 8 units SUPERase RNase Inhibitor (Life Technologies, Foster City, CA) at 25°C for 10 minutes, then 42°C for 50 minutes, then 75°C for 15 minutes and cooled to 4°C.

    Activity Assay:

    Article Title: Major Shift of Toxigenic V. cholerae O1 from Ogawa to Inaba Serotype Isolated from Clinical and Environmental Samples in Haiti
    Article Snippet: Cultures grown on L-agar was tested for oxidase activity and oxidase-positive colonies were tested for toxigenic V . cholerae O1 or O139 using O1-specific polyvalent and O139-specific antisera (DENKA SEIKEN USA Inc., Campbell, CA), respectively. .. Briefly, PCR was performed using a100 μl mixture containing 10 μl of 10X Buffer, 6 μl of 50 mM MgCl2 (Invitrogen, Carlsbad, CA), 1 μl of 10 mM deoxynucleotide triphosphates (New England BioLabs, Ipswich, MA), 1 μl of 5 U Taq DNA polymerase (Invitrogen, Carlsbad, CA) and 20 μm of each primer.

    Expressing:

    Article Title: Intestinal enteroendocrine lineage cells possess homeostatic and injury-inducible stem cell activity
    Article Snippet: Each entire sample was input into the Ambion WT Expression Kit (Life Technologies, Foster City, CA) to perform double stranded cDNA synthesis followed by in vitro transcription to generate amplified cRNA. .. The first strand reaction was performed with 200 units of SuperScript II (Life Technologies, Foster City, CA) with 0.625 mM dNTP’s (NEB, Ipswitch, MA) and 8 units SUPERase RNase Inhibitor (Life Technologies, Foster City, CA) at 25°C for 10 minutes, then 42°C for 50 minutes, then 75°C for 15 minutes and cooled to 4°C.

    Ligation:

    Article Title: RNA sequencing reveals retinal transcriptome changes in STZ-induced diabetic rats
    Article Snippet: Second strand buffer (Invitrogen; Thermo Fisher Scientific, Inc.), deoxynucleotide triphosphates (New England Biolabs, Inc.), RNase H (Second Strand Master Mix; Invitrogen; Thermo Fisher Scientific, Inc.) and DNA polymerase I (Second Strand Master Mix; Invitrogen; Thermo Fisher Scientific, Inc.) were added to synthesize the second strand. .. The ligation products were selected by size and purified on a Tris-acetate-EDTA-agarose gel (Sigma-Aldrich).

    Generated:

    Article Title: DNA-Based Diet Analysis for Any Predator
    Article Snippet: For the Sarasota samples, 17–20 clones were SSCP screened and representative sequences generated all as described below. .. PCR reaction conditions for all 16SPLSUFwd/16SPLSURv PCR's were: 0.4 µM 16SPLSUFwd and 0.4 µM 16SPLSURv primer mixes, 1× AmpliTaq® Gold Buffer (Applied Biosystems), 2 mM MgCl2+ , 1× BSA (New England Biolabs), 100 µM dNTP's (New England Biolabs), 0.75 units AmpliTaq® Gold DNA polymerase (Applied Biosystems), 0.05× SYBR® Green I (Molecular Probes) and the described amount of template for each 16SPLSUFwd/16SPLSURv PCR in a 25 µl total volume.

    Polymerase Chain Reaction:

    Article Title: Phylogenetic analysis of Shiga toxin 1 and Shiga toxin 2 genes associated with disease outbreaks
    Article Snippet: .. PCR master mix was made to final concentration of 1 × ThermoPol Reaction Buffer (New England BioLabs, Beverly, MA), 500 μM dNTP's (New England BioLabs), 0.02 units/μl Vent exo(-) polymerase (New England BioLabs), and 1 μM of each of the stx1 primers or stx2 primers. .. Five microliters of each amplification reaction was analyzed by 1% agarose gel electrophoresis.

    Article Title: DNA-Based Diet Analysis for Any Predator
    Article Snippet: .. PCR reaction conditions for all 16SPLSUFwd/16SPLSURv PCR's were: 0.4 µM 16SPLSUFwd and 0.4 µM 16SPLSURv primer mixes, 1× AmpliTaq® Gold Buffer (Applied Biosystems), 2 mM MgCl2+ , 1× BSA (New England Biolabs), 100 µM dNTP's (New England Biolabs), 0.75 units AmpliTaq® Gold DNA polymerase (Applied Biosystems), 0.05× SYBR® Green I (Molecular Probes) and the described amount of template for each 16SPLSUFwd/16SPLSURv PCR in a 25 µl total volume. .. PCR thermocycling conditions were an initial denaturation at 95°C for 7.5 minutes followed by repeated cycles (details below) of 95°C for 15 seconds, 52°C for 45 seconds and 72°C for 45 seconds.

    Article Title: Diversity of Mycobacterium tuberculosis Complex from Cattle Lymph Nodes in Eastern Cape Province
    Article Snippet: .. The PCR amplification mixture for each reaction contained 1x master mix (0.05 U/μ l) Taq polymerase, 0.2 mM each of the deoxynucleotide triphosphates (New England Biolabs, Inc., Hitchin, UK), 2 mM MgCl2 , 2 μ M of each primer pair, and 2 μ l of DNA, and nuclease-free water was added to make a total volume of 25 μ l. Amplification was achieved using a MyCycler™ Thermal Cycler (Bio-Rad, Cape Town, South Africa) with 1 cycle of denaturing at 95°C for 15 minutes, followed by 38 cycles of 1 minute at 95°C and 1 minute at 72°C, followed by 1 cycle of final extension at 72°C for 10 minutes. .. The positive (H37Rv strain) and negative (sterile nuclease-free water) controls were added to the amplification.

    Article Title: Association of cytotoxic T lymphocyte-associated antigen 4 gene single nucleotide polymorphism with type 1 diabetes mellitus in Madurai population of Southern India
    Article Snippet: .. A 25μl polymerase chain reactions (PCR) recipe was prepared using 2μl of 5μM Forward primer (5’-GCTCTACTTCCTGAAGACCT-3’) and Reverse primer (5’-AGTCTCACTCACCTTTGCAG- 3’)[ ] (Fermentas Life Sciences, Germany),~200 ng Genomic DNA, 1 U of Taq polymerase (Bangalore Genei, India) dNTP's 200μM (New England Biolabs, Beverly, MA), 10ΧPCR buffer with MgCl2 and the volume was made up with nuclease free water. ..

    Article Title: Major Shift of Toxigenic V. cholerae O1 from Ogawa to Inaba Serotype Isolated from Clinical and Environmental Samples in Haiti
    Article Snippet: .. Briefly, PCR was performed using a100 μl mixture containing 10 μl of 10X Buffer, 6 μl of 50 mM MgCl2 (Invitrogen, Carlsbad, CA), 1 μl of 10 mM deoxynucleotide triphosphates (New England BioLabs, Ipswich, MA), 1 μl of 5 U Taq DNA polymerase (Invitrogen, Carlsbad, CA) and 20 μm of each primer. ..

    Article Title: Diversity of Mycobacterium tuberculosis Complex from Cattle Lymph Nodes in Eastern Cape Province
    Article Snippet: .. The PCR amplification mixture for each reaction contained 1x master mix (0.05 U/ μ l) Taq polymerase, 0.2 mM each of the deoxynucleotide triphosphates (New England Biolabs, Inc., Hitchin, UK), 2 mM MgCl2 , 2 μ M of each primer pair, and 2 μ l of DNA, and nuclease-free water was added to make a total volume of 25 μ l. Amplification was achieved using a MyCycler™ Thermal Cycler (Bio-Rad, Cape Town, South Africa) with 1 cycle of denaturing at 95°C for 15 minutes, followed by 38 cycles of 1 minute at 95°C and 1 minute at 72°C, followed by 1 cycle of final extension at 72°C for 10 minutes. .. The positive (H37Rv strain) and negative (sterile nuclease-free water) controls were added to the amplification.

    Binding Assay:

    Article Title: Human cells contain a factor that facilitates the DNA glycosylase-mediated excision of oxidized bases from occluded sites in nucleosomes
    Article Snippet: Tg excision reactions were conducted at 37°C, and initiated by the addition of DNA or nucleosome substrates to varying amounts of nuclear extract in 25 mM HEPES-pH 8, 100 mM KOAc, 5% glycerol, 250 uM each deoxynucleotide triphosphates (NEB), and 0.5 ug/ul bovine serum albumin (NEB). .. Buffers also contained either 2.5 mM adenosine triphosphate (ATP) and 2.5 mM Mg2+ (remodeler permissive conditions) or 5 mM EDTA (remodeler non-permissive conditions), and 155 nM mono- and di-nucleosome length, dsDNA (prepared from chicken chromatin, as above), which helped suppress nonspecific DNA binding to Tg-containing substrates.

    Magnetic Beads:

    Article Title: RNA sequencing reveals retinal transcriptome changes in STZ-induced diabetic rats
    Article Snippet: Subsequently, the mRNA was enriched using oligo (dT) magnetic beads (for eukaryotes; Dynabeads® mRNA Purification kit). .. Second strand buffer (Invitrogen; Thermo Fisher Scientific, Inc.), deoxynucleotide triphosphates (New England Biolabs, Inc.), RNase H (Second Strand Master Mix; Invitrogen; Thermo Fisher Scientific, Inc.) and DNA polymerase I (Second Strand Master Mix; Invitrogen; Thermo Fisher Scientific, Inc.) were added to synthesize the second strand.

    Isolation:

    Article Title: Association of cytotoxic T lymphocyte-associated antigen 4 gene single nucleotide polymorphism with type 1 diabetes mellitus in Madurai population of Southern India
    Article Snippet: [ ] Isolated DNA was confirmed electrophoretically (0.8%) and quantified by spectrophotometric absorption at 260 nm. .. A 25μl polymerase chain reactions (PCR) recipe was prepared using 2μl of 5μM Forward primer (5’-GCTCTACTTCCTGAAGACCT-3’) and Reverse primer (5’-AGTCTCACTCACCTTTGCAG- 3’)[ ] (Fermentas Life Sciences, Germany),~200 ng Genomic DNA, 1 U of Taq polymerase (Bangalore Genei, India) dNTP's 200μM (New England Biolabs, Beverly, MA), 10ΧPCR buffer with MgCl2 and the volume was made up with nuclease free water.

    Article Title: Major Shift of Toxigenic V. cholerae O1 from Ogawa to Inaba Serotype Isolated from Clinical and Environmental Samples in Haiti
    Article Snippet: To amplify and sequence wbeT gene of V . cholerae isolated from clinical and environmental samples in Haiti, chromosomal DNA of each isolate of interest was extracted using GenElute Bacterial Genomic DNA kits (Sigma-Aldrich, St. Louise, MO) following manufacturer’s recommendation. .. Briefly, PCR was performed using a100 μl mixture containing 10 μl of 10X Buffer, 6 μl of 50 mM MgCl2 (Invitrogen, Carlsbad, CA), 1 μl of 10 mM deoxynucleotide triphosphates (New England BioLabs, Ipswich, MA), 1 μl of 5 U Taq DNA polymerase (Invitrogen, Carlsbad, CA) and 20 μm of each primer.

    Labeling:

    Article Title: Evolution of coordinated mutagenesis and somatic hypermutation in VH5
    Article Snippet: Following the protocol of , polymerase buffer and dNTP’s (NEB) were added to the hybridized templates at 37°C along with T7 DNA polymerase. .. The reaction was stopped by adding loading dye at various time points and immediately cooling to create labeled primer extension fragments.

    Purification:

    Article Title: RNA sequencing reveals retinal transcriptome changes in STZ-induced diabetic rats
    Article Snippet: Subsequently, the mRNA was enriched using oligo (dT) magnetic beads (for eukaryotes; Dynabeads® mRNA Purification kit). .. Second strand buffer (Invitrogen; Thermo Fisher Scientific, Inc.), deoxynucleotide triphosphates (New England Biolabs, Inc.), RNase H (Second Strand Master Mix; Invitrogen; Thermo Fisher Scientific, Inc.) and DNA polymerase I (Second Strand Master Mix; Invitrogen; Thermo Fisher Scientific, Inc.) were added to synthesize the second strand.

    Article Title: Intestinal enteroendocrine lineage cells possess homeostatic and injury-inducible stem cell activity
    Article Snippet: 3 µg of random hexamer (Life Technologies, Foster City, CA) was added to the fragmented, purified cRNA and incubated at 70°C for 10 minutes to anneal the primer. .. The first strand reaction was performed with 200 units of SuperScript II (Life Technologies, Foster City, CA) with 0.625 mM dNTP’s (NEB, Ipswitch, MA) and 8 units SUPERase RNase Inhibitor (Life Technologies, Foster City, CA) at 25°C for 10 minutes, then 42°C for 50 minutes, then 75°C for 15 minutes and cooled to 4°C.

    Article Title: Major Shift of Toxigenic V. cholerae O1 from Ogawa to Inaba Serotype Isolated from Clinical and Environmental Samples in Haiti
    Article Snippet: Briefly, PCR was performed using a100 μl mixture containing 10 μl of 10X Buffer, 6 μl of 50 mM MgCl2 (Invitrogen, Carlsbad, CA), 1 μl of 10 mM deoxynucleotide triphosphates (New England BioLabs, Ipswich, MA), 1 μl of 5 U Taq DNA polymerase (Invitrogen, Carlsbad, CA) and 20 μm of each primer. .. The remaining PCR product (90 μl) was purified using QIAquick PCR purification kit (Qiagen, Valencia, CA) and the purified product was sequenced at Interdisciplinary Center for Biotechnology Research (ICBR) in the University of Florida.

    Sequencing:

    Article Title: Phylogenetic analysis of Shiga toxin 1 and Shiga toxin 2 genes associated with disease outbreaks
    Article Snippet: The stx2 primers amplified the entire 1241 bp sequence. .. PCR master mix was made to final concentration of 1 × ThermoPol Reaction Buffer (New England BioLabs, Beverly, MA), 500 μM dNTP's (New England BioLabs), 0.02 units/μl Vent exo(-) polymerase (New England BioLabs), and 1 μM of each of the stx1 primers or stx2 primers.

    Article Title: Human cells contain a factor that facilitates the DNA glycosylase-mediated excision of oxidized bases from occluded sites in nucleosomes
    Article Snippet: Tg excision reactions were conducted at 37°C, and initiated by the addition of DNA or nucleosome substrates to varying amounts of nuclear extract in 25 mM HEPES-pH 8, 100 mM KOAc, 5% glycerol, 250 uM each deoxynucleotide triphosphates (NEB), and 0.5 ug/ul bovine serum albumin (NEB). .. Samples were then mixed with 2 volumes of formamide/20mM EDTA, heated again to 95° C for 2 minutes, and fractionated using 8% sequencing gels.

    Article Title: Intestinal enteroendocrine lineage cells possess homeostatic and injury-inducible stem cell activity
    Article Snippet: Paragraph title: Bulk cell RNA library prep and sequencing ... The first strand reaction was performed with 200 units of SuperScript II (Life Technologies, Foster City, CA) with 0.625 mM dNTP’s (NEB, Ipswitch, MA) and 8 units SUPERase RNase Inhibitor (Life Technologies, Foster City, CA) at 25°C for 10 minutes, then 42°C for 50 minutes, then 75°C for 15 minutes and cooled to 4°C.

    Article Title: Major Shift of Toxigenic V. cholerae O1 from Ogawa to Inaba Serotype Isolated from Clinical and Environmental Samples in Haiti
    Article Snippet: To amplify and sequence wbeT gene of V . cholerae isolated from clinical and environmental samples in Haiti, chromosomal DNA of each isolate of interest was extracted using GenElute Bacterial Genomic DNA kits (Sigma-Aldrich, St. Louise, MO) following manufacturer’s recommendation. .. Briefly, PCR was performed using a100 μl mixture containing 10 μl of 10X Buffer, 6 μl of 50 mM MgCl2 (Invitrogen, Carlsbad, CA), 1 μl of 10 mM deoxynucleotide triphosphates (New England BioLabs, Ipswich, MA), 1 μl of 5 U Taq DNA polymerase (Invitrogen, Carlsbad, CA) and 20 μm of each primer.

    Agarose Gel Electrophoresis:

    Article Title: Phylogenetic analysis of Shiga toxin 1 and Shiga toxin 2 genes associated with disease outbreaks
    Article Snippet: PCR master mix was made to final concentration of 1 × ThermoPol Reaction Buffer (New England BioLabs, Beverly, MA), 500 μM dNTP's (New England BioLabs), 0.02 units/μl Vent exo(-) polymerase (New England BioLabs), and 1 μM of each of the stx1 primers or stx2 primers. .. Five microliters of each amplification reaction was analyzed by 1% agarose gel electrophoresis.

    Article Title: Diversity of Mycobacterium tuberculosis Complex from Cattle Lymph Nodes in Eastern Cape Province
    Article Snippet: The PCR amplification mixture for each reaction contained 1x master mix (0.05 U/μ l) Taq polymerase, 0.2 mM each of the deoxynucleotide triphosphates (New England Biolabs, Inc., Hitchin, UK), 2 mM MgCl2 , 2 μ M of each primer pair, and 2 μ l of DNA, and nuclease-free water was added to make a total volume of 25 μ l. Amplification was achieved using a MyCycler™ Thermal Cycler (Bio-Rad, Cape Town, South Africa) with 1 cycle of denaturing at 95°C for 15 minutes, followed by 38 cycles of 1 minute at 95°C and 1 minute at 72°C, followed by 1 cycle of final extension at 72°C for 10 minutes. .. The amplicons were segregated on 3% agarose gel (Whitehead Scientific (Pty) Ltd., Cape Town, South Africa) using 100 bp ladder (New England Biolabs Inc., Hitchin, UK) as the size marker.

    Article Title: Major Shift of Toxigenic V. cholerae O1 from Ogawa to Inaba Serotype Isolated from Clinical and Environmental Samples in Haiti
    Article Snippet: Briefly, PCR was performed using a100 μl mixture containing 10 μl of 10X Buffer, 6 μl of 50 mM MgCl2 (Invitrogen, Carlsbad, CA), 1 μl of 10 mM deoxynucleotide triphosphates (New England BioLabs, Ipswich, MA), 1 μl of 5 U Taq DNA polymerase (Invitrogen, Carlsbad, CA) and 20 μm of each primer. .. 10 μl of PCR products were then electrophoresed on 1% agarose gel to visualize the band specific for wbeT gene.

    Article Title: Diversity of Mycobacterium tuberculosis Complex from Cattle Lymph Nodes in Eastern Cape Province
    Article Snippet: The PCR amplification mixture for each reaction contained 1x master mix (0.05 U/ μ l) Taq polymerase, 0.2 mM each of the deoxynucleotide triphosphates (New England Biolabs, Inc., Hitchin, UK), 2 mM MgCl2 , 2 μ M of each primer pair, and 2 μ l of DNA, and nuclease-free water was added to make a total volume of 25 μ l. Amplification was achieved using a MyCycler™ Thermal Cycler (Bio-Rad, Cape Town, South Africa) with 1 cycle of denaturing at 95°C for 15 minutes, followed by 38 cycles of 1 minute at 95°C and 1 minute at 72°C, followed by 1 cycle of final extension at 72°C for 10 minutes. .. The amplicons were segregated on 3% agarose gel (Whitehead Scientific (Pty) Ltd., Cape Town, South Africa) using 100 bp ladder (New England Biolabs Inc., Hitchin, UK) as the size marker.

    Software:

    Article Title: DNA-Based Diet Analysis for Any Predator
    Article Snippet: PCR reaction conditions for all 16SPLSUFwd/16SPLSURv PCR's were: 0.4 µM 16SPLSUFwd and 0.4 µM 16SPLSURv primer mixes, 1× AmpliTaq® Gold Buffer (Applied Biosystems), 2 mM MgCl2+ , 1× BSA (New England Biolabs), 100 µM dNTP's (New England Biolabs), 0.75 units AmpliTaq® Gold DNA polymerase (Applied Biosystems), 0.05× SYBR® Green I (Molecular Probes) and the described amount of template for each 16SPLSUFwd/16SPLSURv PCR in a 25 µl total volume. .. Scat PCR amplifications were conducted on a Real Time PCR thermocycler and associated software (Chromo4™ detection system: MJ research) and stopped within the exponential phase (usually between 15 and 25 cycles) in order to minimise PCR drift .

    Real-time Polymerase Chain Reaction:

    Article Title: DNA-Based Diet Analysis for Any Predator
    Article Snippet: PCR reaction conditions for all 16SPLSUFwd/16SPLSURv PCR's were: 0.4 µM 16SPLSUFwd and 0.4 µM 16SPLSURv primer mixes, 1× AmpliTaq® Gold Buffer (Applied Biosystems), 2 mM MgCl2+ , 1× BSA (New England Biolabs), 100 µM dNTP's (New England Biolabs), 0.75 units AmpliTaq® Gold DNA polymerase (Applied Biosystems), 0.05× SYBR® Green I (Molecular Probes) and the described amount of template for each 16SPLSUFwd/16SPLSURv PCR in a 25 µl total volume. .. Scat PCR amplifications were conducted on a Real Time PCR thermocycler and associated software (Chromo4™ detection system: MJ research) and stopped within the exponential phase (usually between 15 and 25 cycles) in order to minimise PCR drift .

    Sample Prep:

    Article Title: Intestinal enteroendocrine lineage cells possess homeostatic and injury-inducible stem cell activity
    Article Snippet: 1 µg of cRNA was fragmented in 1× Fragmentation Buffer (mRNA-seq Sample Prep Kit, Illumina, Hayward, CA) at 94°C for 5 minutes, then placed on ice and the reaction was stopped by the addition of 20 mM EDTA. .. The first strand reaction was performed with 200 units of SuperScript II (Life Technologies, Foster City, CA) with 0.625 mM dNTP’s (NEB, Ipswitch, MA) and 8 units SUPERase RNase Inhibitor (Life Technologies, Foster City, CA) at 25°C for 10 minutes, then 42°C for 50 minutes, then 75°C for 15 minutes and cooled to 4°C.

    In Vitro:

    Article Title: Intestinal enteroendocrine lineage cells possess homeostatic and injury-inducible stem cell activity
    Article Snippet: Each entire sample was input into the Ambion WT Expression Kit (Life Technologies, Foster City, CA) to perform double stranded cDNA synthesis followed by in vitro transcription to generate amplified cRNA. .. The first strand reaction was performed with 200 units of SuperScript II (Life Technologies, Foster City, CA) with 0.625 mM dNTP’s (NEB, Ipswitch, MA) and 8 units SUPERase RNase Inhibitor (Life Technologies, Foster City, CA) at 25°C for 10 minutes, then 42°C for 50 minutes, then 75°C for 15 minutes and cooled to 4°C.

    Incubation:

    Article Title: Human cells contain a factor that facilitates the DNA glycosylase-mediated excision of oxidized bases from occluded sites in nucleosomes
    Article Snippet: Tg excision reactions were conducted at 37°C, and initiated by the addition of DNA or nucleosome substrates to varying amounts of nuclear extract in 25 mM HEPES-pH 8, 100 mM KOAc, 5% glycerol, 250 uM each deoxynucleotide triphosphates (NEB), and 0.5 ug/ul bovine serum albumin (NEB). .. To monitor DNA glycosylase activities, aliquots taken at varying times were quenched in 0.5% sodium dodecyl sulfate, 20 mM EDTA, 1.4 mg/ml proteinase K. After 20 min of incubation at 37°C, abasic sites were converted to strand breaks by adding sodium hydroxide to 333 mM, and heating samples at 95°C for 2 minutes.

    Article Title: Intestinal enteroendocrine lineage cells possess homeostatic and injury-inducible stem cell activity
    Article Snippet: 3 µg of random hexamer (Life Technologies, Foster City, CA) was added to the fragmented, purified cRNA and incubated at 70°C for 10 minutes to anneal the primer. .. The first strand reaction was performed with 200 units of SuperScript II (Life Technologies, Foster City, CA) with 0.625 mM dNTP’s (NEB, Ipswitch, MA) and 8 units SUPERase RNase Inhibitor (Life Technologies, Foster City, CA) at 25°C for 10 minutes, then 42°C for 50 minutes, then 75°C for 15 minutes and cooled to 4°C.

    Concentration Assay:

    Article Title: Phylogenetic analysis of Shiga toxin 1 and Shiga toxin 2 genes associated with disease outbreaks
    Article Snippet: .. PCR master mix was made to final concentration of 1 × ThermoPol Reaction Buffer (New England BioLabs, Beverly, MA), 500 μM dNTP's (New England BioLabs), 0.02 units/μl Vent exo(-) polymerase (New England BioLabs), and 1 μM of each of the stx1 primers or stx2 primers. .. Five microliters of each amplification reaction was analyzed by 1% agarose gel electrophoresis.

    Article Title: Intestinal enteroendocrine lineage cells possess homeostatic and injury-inducible stem cell activity
    Article Snippet: The cRNA was purified following the manufacturer’s instructions and the concentration was determined by a NanoDrop instrument (Thermo Fisher Scientific, Waltham, MA). .. The first strand reaction was performed with 200 units of SuperScript II (Life Technologies, Foster City, CA) with 0.625 mM dNTP’s (NEB, Ipswitch, MA) and 8 units SUPERase RNase Inhibitor (Life Technologies, Foster City, CA) at 25°C for 10 minutes, then 42°C for 50 minutes, then 75°C for 15 minutes and cooled to 4°C.

    Article Title: Evolution of coordinated mutagenesis and somatic hypermutation in VH5
    Article Snippet: Following the protocol of , polymerase buffer and dNTP’s (NEB) were added to the hybridized templates at 37°C along with T7 DNA polymerase. .. The end-labeled products were visualized as discrete bands when separated on a large-format 7% polyacrylamide gel containing urea (7 M final concentration).

    End Labeling:

    Article Title: Evolution of coordinated mutagenesis and somatic hypermutation in VH5
    Article Snippet: Radioactive end-labeling of primers was conducted by using T4 polynucleotide kinase (NEB) and [32 Pγ]-ATP (MP Biomedicals, Solon, OH) as per standard protocols. .. Following the protocol of , polymerase buffer and dNTP’s (NEB) were added to the hybridized templates at 37°C along with T7 DNA polymerase.

    Marker:

    Article Title: Diversity of Mycobacterium tuberculosis Complex from Cattle Lymph Nodes in Eastern Cape Province
    Article Snippet: The PCR amplification mixture for each reaction contained 1x master mix (0.05 U/μ l) Taq polymerase, 0.2 mM each of the deoxynucleotide triphosphates (New England Biolabs, Inc., Hitchin, UK), 2 mM MgCl2 , 2 μ M of each primer pair, and 2 μ l of DNA, and nuclease-free water was added to make a total volume of 25 μ l. Amplification was achieved using a MyCycler™ Thermal Cycler (Bio-Rad, Cape Town, South Africa) with 1 cycle of denaturing at 95°C for 15 minutes, followed by 38 cycles of 1 minute at 95°C and 1 minute at 72°C, followed by 1 cycle of final extension at 72°C for 10 minutes. .. The amplicons were segregated on 3% agarose gel (Whitehead Scientific (Pty) Ltd., Cape Town, South Africa) using 100 bp ladder (New England Biolabs Inc., Hitchin, UK) as the size marker.

    Article Title: Diversity of Mycobacterium tuberculosis Complex from Cattle Lymph Nodes in Eastern Cape Province
    Article Snippet: The PCR amplification mixture for each reaction contained 1x master mix (0.05 U/ μ l) Taq polymerase, 0.2 mM each of the deoxynucleotide triphosphates (New England Biolabs, Inc., Hitchin, UK), 2 mM MgCl2 , 2 μ M of each primer pair, and 2 μ l of DNA, and nuclease-free water was added to make a total volume of 25 μ l. Amplification was achieved using a MyCycler™ Thermal Cycler (Bio-Rad, Cape Town, South Africa) with 1 cycle of denaturing at 95°C for 15 minutes, followed by 38 cycles of 1 minute at 95°C and 1 minute at 72°C, followed by 1 cycle of final extension at 72°C for 10 minutes. .. The amplicons were segregated on 3% agarose gel (Whitehead Scientific (Pty) Ltd., Cape Town, South Africa) using 100 bp ladder (New England Biolabs Inc., Hitchin, UK) as the size marker.

    Variant Assay:

    Article Title: DNA-Based Diet Analysis for Any Predator
    Article Snippet: The Pac I digested PCR product was then directly cloned, 35–52 clones directly amplified, SSCP screened and representative variant sequences generated all as described below. .. PCR reaction conditions for all 16SPLSUFwd/16SPLSURv PCR's were: 0.4 µM 16SPLSUFwd and 0.4 µM 16SPLSURv primer mixes, 1× AmpliTaq® Gold Buffer (Applied Biosystems), 2 mM MgCl2+ , 1× BSA (New England Biolabs), 100 µM dNTP's (New England Biolabs), 0.75 units AmpliTaq® Gold DNA polymerase (Applied Biosystems), 0.05× SYBR® Green I (Molecular Probes) and the described amount of template for each 16SPLSUFwd/16SPLSURv PCR in a 25 µl total volume.

    Environmental Sampling:

    Article Title: Major Shift of Toxigenic V. cholerae O1 from Ogawa to Inaba Serotype Isolated from Clinical and Environmental Samples in Haiti
    Article Snippet: To amplify and sequence wbeT gene of V . cholerae isolated from clinical and environmental samples in Haiti, chromosomal DNA of each isolate of interest was extracted using GenElute Bacterial Genomic DNA kits (Sigma-Aldrich, St. Louise, MO) following manufacturer’s recommendation. .. Briefly, PCR was performed using a100 μl mixture containing 10 μl of 10X Buffer, 6 μl of 50 mM MgCl2 (Invitrogen, Carlsbad, CA), 1 μl of 10 mM deoxynucleotide triphosphates (New England BioLabs, Ipswich, MA), 1 μl of 5 U Taq DNA polymerase (Invitrogen, Carlsbad, CA) and 20 μm of each primer.

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