standard taq reaction buffer  (New England Biolabs)


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    Name:
    Standard Taq Reaction Buffer Pack
    Description:
    Standard Taq Reaction Buffer Pack 6 0 ml
    Catalog Number:
    B9014S
    Price:
    22
    Size:
    6 0 ml
    Category:
    Buffers
    Score:
    85
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    Structured Review

    New England Biolabs standard taq reaction buffer
    Standard Taq Reaction Buffer Pack
    Standard Taq Reaction Buffer Pack 6 0 ml
    https://www.bioz.com/result/standard taq reaction buffer/product/New England Biolabs
    Average 99 stars, based on 4 article reviews
    Price from $9.99 to $1999.99
    standard taq reaction buffer - by Bioz Stars, 2019-10
    99/100 stars

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    Related Articles

    Amplification:

    Article Title: A Simple Isothermal DNA Amplification Method to Screen Black Flies for Onchocerca volvulus Infection
    Article Snippet: LAMP primers B3 and F3 were used to PCR amplify OvGST1a in 25 µL reactions containing 3 µL DNA template, 0.2 µM of each primer, and 1.25 U of Taq DNA polymerase in 1× standard buffer (New England Biolabs) containing 3.5 mM MgCl2 , 0.2 mM and 0.2 mM dNTP each. .. PCR products were visualized by UV transillumination in a 1.5% agarose gel after electrophoresis and staining with ethidium bromide.

    Article Title: Impact of swapping soils on the endophytic bacterial communities of pre-domesticated, ancient and modern maize
    Article Snippet: A PCR mastermix was made with the following components per 25 μl volume: 2.5 μl Standard Taq Buffer (New England Biolabs), 0.5 μl of 25 mM dNTP mix, 0.5 μl of 10 mM 27 F-Degen primer with sequence AGRRTTYGATYMTGGYTYAG [ ] (where R = A + G, Y = C + T, M = A + C), 0.5 μl of 10 mM 1492r primer with sequence GGTTACCTTGTTACGACTT [ ], 0.25 μl of 50 mM MgCl2 , 0.25 μl of Standard Taq (New England Biolabs), 50 ng of total DNA, and double distilled water up to 25 μl total. .. A PCR mastermix was made with the following components per 25 μl volume: 2.5 μl Standard Taq Buffer (New England Biolabs), 0.5 μl of 25 mM dNTP mix, 0.5 μl of 10 mM 27 F-Degen primer with sequence AGRRTTYGATYMTGGYTYAG [ ] (where R = A + G, Y = C + T, M = A + C), 0.5 μl of 10 mM 1492r primer with sequence GGTTACCTTGTTACGACTT [ ], 0.25 μl of 50 mM MgCl2 , 0.25 μl of Standard Taq (New England Biolabs), 50 ng of total DNA, and double distilled water up to 25 μl total.

    Article Title: De Novo Assembly and Characterization of Four Anthozoan (Phylum Cnidaria) Transcriptomes
    Article Snippet: The product was purified and A-tailed in a reaction with nuclease-free water, 1× NEB Standard Taq buffer (New England Biolabs, MA), 1 mM dATP, and 2 units of NEB Standard Taq (New England Biolabs, MA) at 68° for 2 hr. .. The product was purified and A-tailed in a reaction with nuclease-free water, 1× NEB Standard Taq buffer (New England Biolabs, MA), 1 mM dATP, and 2 units of NEB Standard Taq (New England Biolabs, MA) at 68° for 2 hr.

    Article Title: CRISPR-MVLST subtyping of Salmonella enterica subsp. enterica serovars Typhimurium and Heidelberg and application in identifying outbreak isolates
    Article Snippet: Paragraph title: PCR amplification ... PCR reactions were performed in a total volume of 25 μl: 1.5 μl template, 0.3 μl Taq (1.5 units; New England Bio Labs, Ipswich, MA), 0.2 μl 10 mM dNTPs, 1 μl of each 10 μM primer, 2.5 μl of 10× Taq buffer and 18.5 μl water.

    Article Title: 16S rRNA Terminal Restriction Fragment Length Polymorphism for the Characterization of the Nasopharyngeal Microbiota
    Article Snippet: Purified PCR products were checked for correct amplification size and purity using the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA) with the DNA 7500 LabChip kit. .. The enzymatic digestions were performed in a total volume of 20 µl using 40 ng of the amplified and purified PCR product, 1 µl NEB Reaction Buffer (New England Biolabs, Ipswich, MA) 1 (for digestion with Tsp509I ) or 4 (Hpy166II ) and 0.5 µl of the restriction enzymes Tsp509I or Hpy166II . .. Digestion conditions were 3 h at 65°C for TSP509I and 3 h at 37°C with 20 min enzyme inactivation at 65°C for Hpy166II , respectively.

    Article Title: Ocean currents influence the genetic structure of an intertidal mollusc in southeastern Australia - implications for predicting the movement of passive dispersers across a marine biogeographic barrier
    Article Snippet: Approximately 650 base pairs (bp) of the mitochondrial cytochrome oxidase I gene (COI ) was amplified for 10 individuals from each sample site by PCR using primers HCO and LCO (Folmer et al. ). .. PCRs were prepared in 25 μL volumes each containing 10.25 μL ddH2O, 1× reaction buffer, 5.0 μL dNTPs (1 mmol/L), 0.4 μmol/L HCO primer (10 μmol/L), 0.4 μmol/L LCO primer (10 μmol/L), 0.25 units NEB taq (Biosciences, New England), and 5 μL DNA extract.

    Article Title: Identification and mapping in spring wheat of genetic factors controlling stem rust resistance and the study of their epistatic interactions across multiple environments
    Article Snippet: When the plants reached the 1 to 2 leaf stage, 3 cm leaf segments from primary leaves were harvested for genomic DNA isolation. .. A 10 μl PCR reaction consisting of DNA (final concentration of 2.4 ng/μl), Ultrapure double distilled H2 0 (Gibco), 10 % PCR Buffer without MgCl2 [Invitrogen cat.#18067-017: 200 mM Tris–HCl (pH 8.4), 500 mM KCl], 10 mM dNTPs (Roche), 1.5 mM MgCl2 (Invitrogen), 0.07 U μl−1 Taq (5 U of activity μl−1 ) NEB, and 2 ηg μl−1 forward and 2 ηg μl−1 reverse primer was used for the DNA amplification process. .. The PCR conditions were: initial denaturation at 94 °C (3 min), followed by 44 cycles of 94 °C (1 min), 55 or 60 °C annealing (1 min), and 72 °C extension (1 min) with a final extension at 72 °C for 10 min.

    Article Title: RAD marker microarrays enable rapid mapping of zebrafish mutations
    Article Snippet: PCR reactions were carried out in 50 μl under the following conditions: 50 ng template, 1 × Thermopol Buffer (New England Biolabs), 2.5 U Taq (New England Biolabs), 0.2 mmol/l dNTPs (Fermentas, Burlington, Ontario, Canada), 0.4 μmol/l forward primer, and 0.2 μmol/l reverse primer. .. Touchdown amplification was applied, with primer annealing temperature dropping 2°C every other cycle from 65°C to 55°C, after which 25 additional cycles were carried out [ ].

    Positive Control:

    Article Title: A Simple Isothermal DNA Amplification Method to Screen Black Flies for Onchocerca volvulus Infection
    Article Snippet: LAMP primers B3 and F3 were used to PCR amplify OvGST1a in 25 µL reactions containing 3 µL DNA template, 0.2 µM of each primer, and 1.25 U of Taq DNA polymerase in 1× standard buffer (New England Biolabs) containing 3.5 mM MgCl2 , 0.2 mM and 0.2 mM dNTP each. .. PCR products were visualized by UV transillumination in a 1.5% agarose gel after electrophoresis and staining with ethidium bromide.

    Synthesized:

    Article Title: De Novo Assembly and Characterization of Four Anthozoan (Phylum Cnidaria) Transcriptomes
    Article Snippet: First strand cDNA was synthesized using ProtoScript M-MuLV FS-cDNA Synthesis Kit (New England Biolabs, MA) according to the manufacturer’s protocol and modified oligonucleotides in Supporting Information , Table S1 . .. The product was purified and A-tailed in a reaction with nuclease-free water, 1× NEB Standard Taq buffer (New England Biolabs, MA), 1 mM dATP, and 2 units of NEB Standard Taq (New England Biolabs, MA) at 68° for 2 hr.

    Neutralization:

    Article Title: Vitamin E inhibits the UVAI induction of “light” and “dark” cyclobutane pyrimidine dimers, and oxidatively generated DNA damage, in keratinocytes
    Article Snippet: T4endoV (0.1 U/mL), or hOGG1 (3.2 U/mL), or enzyme reaction buffer alone, was added to each gel (both enzymes were purchased from New England Biolabs, Hitchin, UK). .. Slides were subsequently transferred to ice-cold electrophoresis buffer (NaOH 10 M, EDTA 200 mM, pH 13 in ddH2 O) and incubated for 20 min in the dark.

    Terminal Restriction Fragment Length Polymorphism:

    Article Title: Impact of swapping soils on the endophytic bacterial communities of pre-domesticated, ancient and modern maize
    Article Snippet: Paragraph title: DNA extraction and Terminal Restriction Fragment Length Polymorphism (TRFLP) from plant tissues and soil ... A PCR mastermix was made with the following components per 25 μl volume: 2.5 μl Standard Taq Buffer (New England Biolabs), 0.5 μl of 25 mM dNTP mix, 0.5 μl of 10 mM 27 F-Degen primer with sequence AGRRTTYGATYMTGGYTYAG [ ] (where R = A + G, Y = C + T, M = A + C), 0.5 μl of 10 mM 1492r primer with sequence GGTTACCTTGTTACGACTT [ ], 0.25 μl of 50 mM MgCl2 , 0.25 μl of Standard Taq (New England Biolabs), 50 ng of total DNA, and double distilled water up to 25 μl total.

    Article Title: 16S rRNA Terminal Restriction Fragment Length Polymorphism for the Characterization of the Nasopharyngeal Microbiota
    Article Snippet: Paragraph title: T-RFLP Digestion and Detection Limits ... The enzymatic digestions were performed in a total volume of 20 µl using 40 ng of the amplified and purified PCR product, 1 µl NEB Reaction Buffer (New England Biolabs, Ipswich, MA) 1 (for digestion with Tsp509I ) or 4 (Hpy166II ) and 0.5 µl of the restriction enzymes Tsp509I or Hpy166II .

    SYBR Green Assay:

    Article Title: Prp8 retinitis pigmentosa mutants cause defects in the transition between the catalytic steps of splicing
    Article Snippet: Reactions were then diluted between 1:75 and 1:250 with water prior to analysis by qPCR. .. For qPCR, 10 µL of diluted cDNA from reverse transcription was combined with 0.25 mM each gene-specific primer, 1× SYBR green (Roche), 0.625 µL dimethyl sulfoxide (Invitrogen), 0.4 mM dTNPs (Fermentas), 1× Standard Taq Buffer (NEB) and 0.25 µL Standard Taq (NEB) and water to a total volume of 25 µL. qPCR cycle conditions were 95°C 3 min, 39 cycles of 95°C 15 sec, 55°C 30 sec, 72°C 15 sec, followed by one cycle at 72°C for 3 min. Exon primers were designed to be within the 3′ exon of all genes tested and were used to measure total RNA levels. pre-mRNA levels were assessed using intron primers. .. The product of these primes spanned an intron–exon junction to ensure that only pre-mRNA was measured.

    Article Title: Cooperative activity of GABP with PU.1 or C/EBPε regulates lamin B receptor gene expression, implicating their roles in granulocyte nuclear maturation
    Article Snippet: Real-time PCR was performed by using 2 μl of purified DNA as template, SsoAdvanced SYBR Green Supermix (Bio-Rad) and the following primers at a final concentration of 0.2 pmol/μl: Proximal Ets site: (F) 5′-AACAGCACGGCGAAGTAG-3′ and (R) 5′-CCCCTTACACTTGCCACC-3′, Distal Ets site: (F) 5′-GATCTGTTTGTCCCCAGCTAC-3′ and (R) 5′-ACTTTGTGAGCACTTGAGACC-3′, and Proximal Cebp site: (F) 5′-CTCGGAGTAGGATTCGTCTTTAAG-3′ and (R) 5′-GATTTGTCATTGCCGTTGGG-3′. .. A 25 μl PCR reaction was also performed using 2 μl of purified DNA from EML cells using 1X standard Taq reaction buffer (New England BioLabs), 1 U of Taq DNA polymerase, plus 0.2 pmol/μl of same forward and reverse primers for proximal and distal Ets sites as mentioned above.

    Incubation:

    Article Title: Protein-Tyrosine Kinase Activity Profiling in Knock Down Zebrafish Embryos
    Article Snippet: The zebrafish embryo lysates were analysed by applying an aliquot of the lysate in kinase reaction buffer (Abl reaction buffer [New England Biolabs], consisting of 100 mM MgCl2 , 10 mM EGTA, 20 mM DTT and 0.1% Brij 35 in 500 mM Tris/HCl, pH 7.5) containing 12.5 µg/ml fluoresceine labelled PY20 antibody against phosphotyrosine (Exalpha, USA), and 400 µM ATP (Sigma) to the PamChip peptide array. .. The zebrafish embryo lysates were analysed by applying an aliquot of the lysate in kinase reaction buffer (Abl reaction buffer [New England Biolabs], consisting of 100 mM MgCl2 , 10 mM EGTA, 20 mM DTT and 0.1% Brij 35 in 500 mM Tris/HCl, pH 7.5) containing 12.5 µg/ml fluoresceine labelled PY20 antibody against phosphotyrosine (Exalpha, USA), and 400 µM ATP (Sigma) to the PamChip peptide array.

    Article Title: De Novo Assembly and Characterization of Four Anthozoan (Phylum Cnidaria) Transcriptomes
    Article Snippet: The product was purified and A-tailed in a reaction with nuclease-free water, 1× NEB Standard Taq buffer (New England Biolabs, MA), 1 mM dATP, and 2 units of NEB Standard Taq (New England Biolabs, MA) at 68° for 2 hr. .. Tailed templates were ligated to double stranded adaptors prepared with oligonucleotides from the Illumina Customer Sequence Letter (version August 12, 2014, ; Table S1 ).

    Article Title: Vitamin E inhibits the UVAI induction of “light” and “dark” cyclobutane pyrimidine dimers, and oxidatively generated DNA damage, in keratinocytes
    Article Snippet: T4endoV (0.1 U/mL), or hOGG1 (3.2 U/mL), or enzyme reaction buffer alone, was added to each gel (both enzymes were purchased from New England Biolabs, Hitchin, UK). .. T4endoV (0.1 U/mL), or hOGG1 (3.2 U/mL), or enzyme reaction buffer alone, was added to each gel (both enzymes were purchased from New England Biolabs, Hitchin, UK).

    Article Title: Prp8 retinitis pigmentosa mutants cause defects in the transition between the catalytic steps of splicing
    Article Snippet: Briefly, for reverse transcription 2 µg of DNase-treated total RNA was incubated with 0.5 µL of 1 mg/mL dN9 primers (Life Technologies) in a total volume of 10 µL at 65°C for 5 min and then chilled on ice for 5 min. Four microliters of 5× First Strand Synthesis Buffer (Invitrogen), 1 µL 10 mM dNTPs (Fermentas), 1 µL 0.1 M DTT (Invitrogen), 1 µL Superscript III Reverse Transcriptase (Invitrogen), and 3 µL of water were added to bring the total reaction volume to 20 µL. .. For qPCR, 10 µL of diluted cDNA from reverse transcription was combined with 0.25 mM each gene-specific primer, 1× SYBR green (Roche), 0.625 µL dimethyl sulfoxide (Invitrogen), 0.4 mM dTNPs (Fermentas), 1× Standard Taq Buffer (NEB) and 0.25 µL Standard Taq (NEB) and water to a total volume of 25 µL. qPCR cycle conditions were 95°C 3 min, 39 cycles of 95°C 15 sec, 55°C 30 sec, 72°C 15 sec, followed by one cycle at 72°C for 3 min. Exon primers were designed to be within the 3′ exon of all genes tested and were used to measure total RNA levels. pre-mRNA levels were assessed using intron primers.

    Single Cell Gel Electrophoresis:

    Article Title: Vitamin E inhibits the UVAI induction of “light” and “dark” cyclobutane pyrimidine dimers, and oxidatively generated DNA damage, in keratinocytes
    Article Snippet: Paragraph title: Measurement of DNA damage by the comet assay ... T4endoV (0.1 U/mL), or hOGG1 (3.2 U/mL), or enzyme reaction buffer alone, was added to each gel (both enzymes were purchased from New England Biolabs, Hitchin, UK).

    In Silico:

    Article Title: Impact of swapping soils on the endophytic bacterial communities of pre-domesticated, ancient and modern maize
    Article Snippet: A PCR mastermix was made with the following components per 25 μl volume: 2.5 μl Standard Taq Buffer (New England Biolabs), 0.5 μl of 25 mM dNTP mix, 0.5 μl of 10 mM 27 F-Degen primer with sequence AGRRTTYGATYMTGGYTYAG [ ] (where R = A + G, Y = C + T, M = A + C), 0.5 μl of 10 mM 1492r primer with sequence GGTTACCTTGTTACGACTT [ ], 0.25 μl of 50 mM MgCl2 , 0.25 μl of Standard Taq (New England Biolabs), 50 ng of total DNA, and double distilled water up to 25 μl total. .. For the nested PCR, primer 799f with sequence AACMGGATTAGATACCCKG [ ] (where M = A + C, K = G + T), was labelled with 6FAM, and 1492rh with sequence HGGHTACCTTGTTACGACTT (where H = A + T + C) was labelled with Max550, both by Integrated DNA Technologies (USA).

    Modification:

    Article Title: De Novo Assembly and Characterization of Four Anthozoan (Phylum Cnidaria) Transcriptomes
    Article Snippet: First strand cDNA was synthesized using ProtoScript M-MuLV FS-cDNA Synthesis Kit (New England Biolabs, MA) according to the manufacturer’s protocol and modified oligonucleotides in Supporting Information , Table S1 . .. The product was purified and A-tailed in a reaction with nuclease-free water, 1× NEB Standard Taq buffer (New England Biolabs, MA), 1 mM dATP, and 2 units of NEB Standard Taq (New England Biolabs, MA) at 68° for 2 hr.

    Article Title: Real-Time PCR Assays To Address Genetic Diversity among Strains of Mycoplasma hyopneumoniae
    Article Snippet: These assays were then used to test DNA from each of the isolates in Table . .. Some assays were performed as previously published ( , , ), while others ( , , , , ) were modified by substituting MasterAmp E buffer (Epicentre Biotechnologies, Madison, WI) for the published buffer with their published cycling parameters in reaction mixtures consisting of 1× Master Amp E, 0.4 mM each forward and reverse primer, 2.5 U of Taq (New England Biolabs, Inc., Ipswich, ME), template containing 1 to 10 ng of DNA, and a sufficient quantity of PCR-grade water to a final volume of 25 μl. .. The primer pairs from nested-set PCRs were run as individual assays (not as nested sets) to independently evaluate the ability of each primer pair to form products.

    Real-time Polymerase Chain Reaction:

    Article Title: Prp8 retinitis pigmentosa mutants cause defects in the transition between the catalytic steps of splicing
    Article Snippet: Reactions were then diluted between 1:75 and 1:250 with water prior to analysis by qPCR. .. For qPCR, 10 µL of diluted cDNA from reverse transcription was combined with 0.25 mM each gene-specific primer, 1× SYBR green (Roche), 0.625 µL dimethyl sulfoxide (Invitrogen), 0.4 mM dTNPs (Fermentas), 1× Standard Taq Buffer (NEB) and 0.25 µL Standard Taq (NEB) and water to a total volume of 25 µL. qPCR cycle conditions were 95°C 3 min, 39 cycles of 95°C 15 sec, 55°C 30 sec, 72°C 15 sec, followed by one cycle at 72°C for 3 min. Exon primers were designed to be within the 3′ exon of all genes tested and were used to measure total RNA levels. pre-mRNA levels were assessed using intron primers. .. The product of these primes spanned an intron–exon junction to ensure that only pre-mRNA was measured.

    Article Title: Cooperative activity of GABP with PU.1 or C/EBPε regulates lamin B receptor gene expression, implicating their roles in granulocyte nuclear maturation
    Article Snippet: Paragraph title: Chromatin Immunoprecipitation (ChIP) and real-time PCR assay ... A 25 μl PCR reaction was also performed using 2 μl of purified DNA from EML cells using 1X standard Taq reaction buffer (New England BioLabs), 1 U of Taq DNA polymerase, plus 0.2 pmol/μl of same forward and reverse primers for proximal and distal Ets sites as mentioned above.

    Derivative Assay:

    Article Title: Protein-Tyrosine Kinase Activity Profiling in Knock Down Zebrafish Embryos
    Article Snippet: Each peptide represents a 15 amino acid sequence, of which 13 residues are derived from a known phosphorylation site from Swissprot and Phosphobase databases ( ). .. The zebrafish embryo lysates were analysed by applying an aliquot of the lysate in kinase reaction buffer (Abl reaction buffer [New England Biolabs], consisting of 100 mM MgCl2 , 10 mM EGTA, 20 mM DTT and 0.1% Brij 35 in 500 mM Tris/HCl, pH 7.5) containing 12.5 µg/ml fluoresceine labelled PY20 antibody against phosphotyrosine (Exalpha, USA), and 400 µM ATP (Sigma) to the PamChip peptide array.

    Ligation:

    Article Title: De Novo Assembly and Characterization of Four Anthozoan (Phylum Cnidaria) Transcriptomes
    Article Snippet: The product was purified and A-tailed in a reaction with nuclease-free water, 1× NEB Standard Taq buffer (New England Biolabs, MA), 1 mM dATP, and 2 units of NEB Standard Taq (New England Biolabs, MA) at 68° for 2 hr. .. Purified, tailed cDNA was combined with T4 DNA ligase buffer (New England Biolabs, MA), T4 DNA ligase (New England Biolabs, MA), and the double stranded adaptors, and the solution was incubated at 12° for at least 6 hr.

    Infection:

    Article Title: A new insect cell glycoengineering approach provides baculovirus-inducible glycogene expression and increases human-type glycosylation efficiency
    Article Snippet: At various times after infection with AchEPO-His, total RNA was extracted from 5×106 Sf9, Sfie1SWT, or Sf39KSWT cells using the RNA- Solv ® (Omega Biotech) reagent according to the manufacturer’s protocol. .. The resulting cDNA preparations were treated with RNAse H and used for PCR reactions with Taq Polymerase and Crimson Taq Buffer (New England Biolabs).

    Generated:

    Article Title: Allopatric Speciation within a Cryptic Species Complex of Australasian Octopuses
    Article Snippet: 25 µL reactions comprised 0.1 µL Taq (Onetaq, New England Biolabs ), 2.5 µL 10 x buffer (Paq5000™), 2 µL dNTP mix (10 µM, Bioline ), 0.5 µL forward primer (10 µM), 0.5 µL reverse primer (10 µM), 17.4 µL ddH2 O and 2 µL DNA (diluted to between 1–5 ng/µL). .. 25 µL reactions comprised 0.1 µL Taq (Onetaq, New England Biolabs ), 2.5 µL 10 x buffer (Paq5000™), 2 µL dNTP mix (10 µM, Bioline ), 0.5 µL forward primer (10 µM), 0.5 µL reverse primer (10 µM), 17.4 µL ddH2 O and 2 µL DNA (diluted to between 1–5 ng/µL).

    Polymerase Chain Reaction:

    Article Title: A Recurrent Stop-Codon Mutation in Succinate Dehydrogenase Subunit B Gene in Normal Peripheral Blood and Childhood T-Cell Acute Leukemia
    Article Snippet: The 30th (last) cycle of the PCR was completed to produce fluorescently-labeled homo-duplex extension products. .. Fifteen µL of the fluorescently-labeled PCR products, which contained ∼200–300 ng of DNA, were directly digested by 10 U of Taq I RE, 1× Taq I RE buffer and 1× Bovine Serum Albumin (all from New England Biolabs) overnight in a 25 µL reaction volume. .. To ensure complete digestion, the reaction was re-dosed with another 10 U of Taq I RE in a 5 µL volume and continued for at least another four hours in the following day.

    Article Title: A Simple Isothermal DNA Amplification Method to Screen Black Flies for Onchocerca volvulus Infection
    Article Snippet: For determination of amplification measured by color change (purple to sky blue), 0.15 µL of 120 µM hydroxy naphthol blue (HNB, Sigma-Aldrich Inc, St. Louis, MO, USA) was added to the reaction mixture. .. LAMP primers B3 and F3 were used to PCR amplify OvGST1a in 25 µL reactions containing 3 µL DNA template, 0.2 µM of each primer, and 1.25 U of Taq DNA polymerase in 1× standard buffer (New England Biolabs) containing 3.5 mM MgCl2 , 0.2 mM and 0.2 mM dNTP each. .. All reactions were denatured once at 94°C for 5 min followed by 35 cycles of the following cycling conditions: 30 s at 94°C, 1 min at 53°C, 1 min at 72°C, and a final extension for 5 min at 72°C using a Gene Amp PCR system 9700 (Applied Biosystems).

    Article Title: Impact of swapping soils on the endophytic bacterial communities of pre-domesticated, ancient and modern maize
    Article Snippet: Total DNA from 250 mg of soil or sand was extracted using Powersoil DNA isolation kits (MoBio, USA), and DNA was quantified using a Nanodrop (Thermo Scientific, USA). .. A PCR mastermix was made with the following components per 25 μl volume: 2.5 μl Standard Taq Buffer (New England Biolabs), 0.5 μl of 25 mM dNTP mix, 0.5 μl of 10 mM 27 F-Degen primer with sequence AGRRTTYGATYMTGGYTYAG [ ] (where R = A + G, Y = C + T, M = A + C), 0.5 μl of 10 mM 1492r primer with sequence GGTTACCTTGTTACGACTT [ ], 0.25 μl of 50 mM MgCl2 , 0.25 μl of Standard Taq (New England Biolabs), 50 ng of total DNA, and double distilled water up to 25 μl total. .. Amplification was for 35 cycles in a PTC200 DNA Thermal Cycler (MJ Scientific, USA) using the following program: 96°C for 3 min, 35X (94°C for 30 sec, 48°C for 30 sec, 72°C for 1:30 min), 72°C for 7 min.

    Article Title: De Novo Assembly and Characterization of Four Anthozoan (Phylum Cnidaria) Transcriptomes
    Article Snippet: Second strand synthesis was performed by incubating first-strand cDNA with 1× NEBNext Second Strand Synthesis Buffer (New England Biolabs, MA), 0.2 mM dNTPs, 15 units of Escherichia coli DNA ligase (New England Biolabs, MA), 75 units of E. coli DNA polymerase I (New England Biolabs, MA), and 3 units of RNase H (New England Biolabs, MA) for 2 hr at 16°. cDNA was purified using the GeneJet PCR Purification Kit (Fermentas, MA) and then fragmented using NEBNext dsDNA Fragmentase (New England Biolabs, MA) according to the manufacturer’s protocol, with the addition of 5 mM MgCl2 and 1 mg ml−1 BSA (New England Biolabs, MA). .. The product was purified and A-tailed in a reaction with nuclease-free water, 1× NEB Standard Taq buffer (New England Biolabs, MA), 1 mM dATP, and 2 units of NEB Standard Taq (New England Biolabs, MA) at 68° for 2 hr.

    Article Title: Fine Mapping of the Barley Chromosome 6H Net Form Net Blotch Susceptibility Locus
    Article Snippet: The parameters for the PCR reactions were as follows: 94° for 5 min, followed by 35 cycles of 94° for 30 sec, 62° for 30 sec, and 72° for 60 sec, followed by a final extension at 72° for 7 min. .. The PCR reactions consisted of 1.25 units NEB Standard Taq polymerase, forward and reverse primers (1.2 µM), NEB Standard Taq buffer (1 ×), and dNTPs (200 µM), in 25 µl reactions. .. PCR products were visualized on a 1% agarose gel containing GelRed (Biotium, CA) and subsequently purified using E.Z.N.A.

    Article Title: Fine Mapping of the Barley Chromosome 6H Net Form Net Blotch Susceptibility Locus
    Article Snippet: Additionally, 2 µL of each reaction was separated on a 1% agarose gel containing GelRed to ensure successful reactions. .. The barcoding PCR reaction consisted of 0.235 µl of H2 O, 0.625 µl NEB Standard Taq Buffer (1.25 ×), 0.1 µl dNTPs (500 µM), 1 µl universal reverse primer (1 µM), 1 µl unique barcode adaptor primer (0.4 µM), 0.04 µl of NEB Taq polymerase (0.2 units), and 2 µl template (diluted primary PCR reaction). .. PCR parameters are the same as the primary reaction.

    Article Title: A new insect cell glycoengineering approach provides baculovirus-inducible glycogene expression and increases human-type glycosylation efficiency
    Article Snippet: The RNA preparations were treated with RNAse-free DNAse I (New England Biolabs), and then 400 ng of each were reverse transcribed at 50°C for 30 min with Thermoscript Reverse Transcriptase (Life Technologies) and oligo(dT)31 -VN (5′-TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN-3′) as the primer. .. The resulting cDNA preparations were treated with RNAse H and used for PCR reactions with Taq Polymerase and Crimson Taq Buffer (New England Biolabs). .. The PCR conditions included an initial denaturation step of 95°C for 30 seconds, followed by 30 (MGAT1, MGAT2, B4GALT1, SAS, ST3GAL4b, SfRPL3) or 33 (GNPE, CMAS, CSAT, ST6GAL1) cycles of denaturation at 95°C for 15 seconds, annealing at 50°C for 20 seconds, and extension at 68°C for 30 seconds.

    Article Title: Cooperative activity of GABP with PU.1 or C/EBPε regulates lamin B receptor gene expression, implicating their roles in granulocyte nuclear maturation
    Article Snippet: Data analysis was performed using the ΔΔCT method. .. A 25 μl PCR reaction was also performed using 2 μl of purified DNA from EML cells using 1X standard Taq reaction buffer (New England BioLabs), 1 U of Taq DNA polymerase, plus 0.2 pmol/μl of same forward and reverse primers for proximal and distal Ets sites as mentioned above. .. PCR was carried out for 28 cycles by using 1 cycle of 95°C for 1 min; 30 cycles of 95°C, 63°C and 72°C each at 30 s and finally 1 cycle of 72°C for 5 min. Five microliters of PCR product was electrophoresed on 0.9 % agarose gel and bands were visualized by staining the gel in ethidium bromide.

    Article Title: Real-Time PCR Assays To Address Genetic Diversity among Strains of Mycoplasma hyopneumoniae
    Article Snippet: These assays were then used to test DNA from each of the isolates in Table . .. Some assays were performed as previously published ( , , ), while others ( , , , , ) were modified by substituting MasterAmp E buffer (Epicentre Biotechnologies, Madison, WI) for the published buffer with their published cycling parameters in reaction mixtures consisting of 1× Master Amp E, 0.4 mM each forward and reverse primer, 2.5 U of Taq (New England Biolabs, Inc., Ipswich, ME), template containing 1 to 10 ng of DNA, and a sufficient quantity of PCR-grade water to a final volume of 25 μl. .. The primer pairs from nested-set PCRs were run as individual assays (not as nested sets) to independently evaluate the ability of each primer pair to form products.

    Article Title: CRISPR-MVLST subtyping of Salmonella enterica subsp. enterica serovars Typhimurium and Heidelberg and application in identifying outbreak isolates
    Article Snippet: Primers for amplification of all four genomic loci are listed in Table . .. PCR reactions were performed in a total volume of 25 μl: 1.5 μl template, 0.3 μl Taq (1.5 units; New England Bio Labs, Ipswich, MA), 0.2 μl 10 mM dNTPs, 1 μl of each 10 μM primer, 2.5 μl of 10× Taq buffer and 18.5 μl water. .. PCR conditions were as follows and the annealing temperatures (AT) are listed in Table : initial denaturation step of 10 minutes at 94°C followed by 35 cycles of 1 minute at 94°C, 1 minute at AT and extension for 1 minute (fimH and sseL ) or 1.5 minutes (CRISPR1 and CRISPR2) at 72°C; a final extension step was done at 72°C for 8 minutes.

    Article Title: 16S rRNA Terminal Restriction Fragment Length Polymorphism for the Characterization of the Nasopharyngeal Microbiota
    Article Snippet: Purified PCR products were checked for correct amplification size and purity using the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA) with the DNA 7500 LabChip kit. .. The enzymatic digestions were performed in a total volume of 20 µl using 40 ng of the amplified and purified PCR product, 1 µl NEB Reaction Buffer (New England Biolabs, Ipswich, MA) 1 (for digestion with Tsp509I ) or 4 (Hpy166II ) and 0.5 µl of the restriction enzymes Tsp509I or Hpy166II . .. Digestion conditions were 3 h at 65°C for TSP509I and 3 h at 37°C with 20 min enzyme inactivation at 65°C for Hpy166II , respectively.

    Article Title: Ocean currents influence the genetic structure of an intertidal mollusc in southeastern Australia - implications for predicting the movement of passive dispersers across a marine biogeographic barrier
    Article Snippet: Approximately 650 base pairs (bp) of the mitochondrial cytochrome oxidase I gene (COI ) was amplified for 10 individuals from each sample site by PCR using primers HCO and LCO (Folmer et al. ). .. PCRs were prepared in 25 μL volumes each containing 10.25 μL ddH2O, 1× reaction buffer, 5.0 μL dNTPs (1 mmol/L), 0.4 μmol/L HCO primer (10 μmol/L), 0.4 μmol/L LCO primer (10 μmol/L), 0.25 units NEB taq (Biosciences, New England), and 5 μL DNA extract.

    Article Title: Identification and mapping in spring wheat of genetic factors controlling stem rust resistance and the study of their epistatic interactions across multiple environments
    Article Snippet: When the plants reached the 1 to 2 leaf stage, 3 cm leaf segments from primary leaves were harvested for genomic DNA isolation. .. A 10 μl PCR reaction consisting of DNA (final concentration of 2.4 ng/μl), Ultrapure double distilled H2 0 (Gibco), 10 % PCR Buffer without MgCl2 [Invitrogen cat.#18067-017: 200 mM Tris–HCl (pH 8.4), 500 mM KCl], 10 mM dNTPs (Roche), 1.5 mM MgCl2 (Invitrogen), 0.07 U μl−1 Taq (5 U of activity μl−1 ) NEB, and 2 ηg μl−1 forward and 2 ηg μl−1 reverse primer was used for the DNA amplification process. .. The PCR conditions were: initial denaturation at 94 °C (3 min), followed by 44 cycles of 94 °C (1 min), 55 or 60 °C annealing (1 min), and 72 °C extension (1 min) with a final extension at 72 °C for 10 min.

    Article Title: RAD marker microarrays enable rapid mapping of zebrafish mutations
    Article Snippet: Genomic DNA samples were digested with Eco RI (New England Biolabs, Ipswich, MA, USA) and short linkers (5'-GACTCCTCGACTCTCACATCTGGACATA-3', 5'-Phos-AATTTATGTCCAGATGTGAGAGTC-3') were ligated to the fragment ends using previously described conditions [ ]. .. PCR reactions were carried out in 50 μl under the following conditions: 50 ng template, 1 × Thermopol Buffer (New England Biolabs), 2.5 U Taq (New England Biolabs), 0.2 mmol/l dNTPs (Fermentas, Burlington, Ontario, Canada), 0.4 μmol/l forward primer, and 0.2 μmol/l reverse primer. .. Touchdown amplification was applied, with primer annealing temperature dropping 2°C every other cycle from 65°C to 55°C, after which 25 additional cycles were carried out [ ].

    Peptide Microarray:

    Article Title: Protein-Tyrosine Kinase Activity Profiling in Knock Down Zebrafish Embryos
    Article Snippet: Two N-terminal residues link the phosphosite sequence to the solid support of the 3-dimensional chip. .. The zebrafish embryo lysates were analysed by applying an aliquot of the lysate in kinase reaction buffer (Abl reaction buffer [New England Biolabs], consisting of 100 mM MgCl2 , 10 mM EGTA, 20 mM DTT and 0.1% Brij 35 in 500 mM Tris/HCl, pH 7.5) containing 12.5 µg/ml fluoresceine labelled PY20 antibody against phosphotyrosine (Exalpha, USA), and 400 µM ATP (Sigma) to the PamChip peptide array. .. Prior to application of the sample, the chips were blocked using a solution of 2% BSA (Bovine Serum Albumin, Fraction V, Calbiochem, Germany), and washed 2 times using kinase reaction buffer.

    Imaging:

    Article Title: Protein-Tyrosine Kinase Activity Profiling in Knock Down Zebrafish Embryos
    Article Snippet: Data was captured by real-time imaging of the fluorescence signal by CCD imaging , . .. The zebrafish embryo lysates were analysed by applying an aliquot of the lysate in kinase reaction buffer (Abl reaction buffer [New England Biolabs], consisting of 100 mM MgCl2 , 10 mM EGTA, 20 mM DTT and 0.1% Brij 35 in 500 mM Tris/HCl, pH 7.5) containing 12.5 µg/ml fluoresceine labelled PY20 antibody against phosphotyrosine (Exalpha, USA), and 400 µM ATP (Sigma) to the PamChip peptide array.

    Article Title: Identification and mapping in spring wheat of genetic factors controlling stem rust resistance and the study of their epistatic interactions across multiple environments
    Article Snippet: A 10 μl PCR reaction consisting of DNA (final concentration of 2.4 ng/μl), Ultrapure double distilled H2 0 (Gibco), 10 % PCR Buffer without MgCl2 [Invitrogen cat.#18067-017: 200 mM Tris–HCl (pH 8.4), 500 mM KCl], 10 mM dNTPs (Roche), 1.5 mM MgCl2 (Invitrogen), 0.07 U μl−1 Taq (5 U of activity μl−1 ) NEB, and 2 ηg μl−1 forward and 2 ηg μl−1 reverse primer was used for the DNA amplification process. .. The amplification products were resolved by capillary electrophoresis using an ABI3130XL DNA fragment analyser (Applied Biosystems), or by horizontal high resolution agarose electrophoresis using 2 % Metaphor and 1 % agarose LE gels at 4 V cm−1 in TBE (0.045 M TRIS, 0.045 M Borate, and 0.001 M EDTA) buffer and stained with ethidium bromide (0.5 μg ml−1 ).

    Sequencing:

    Article Title: A Recurrent Stop-Codon Mutation in Succinate Dehydrogenase Subunit B Gene in Normal Peripheral Blood and Childhood T-Cell Acute Leukemia
    Article Snippet: Fifteen µL of the fluorescently-labeled PCR products, which contained ∼200–300 ng of DNA, were directly digested by 10 U of Taq I RE, 1× Taq I RE buffer and 1× Bovine Serum Albumin (all from New England Biolabs) overnight in a 25 µL reaction volume. .. The fluorescently-labeled and Taq I-RE digested PCR products were run in capillary gel electrophoresis (3100 Avant Genetic Analyzer, ABI Prism, Applied Biosystems/HITACHI).

    Article Title: Protein-Tyrosine Kinase Activity Profiling in Knock Down Zebrafish Embryos
    Article Snippet: Two N-terminal residues link the phosphosite sequence to the solid support of the 3-dimensional chip. .. The zebrafish embryo lysates were analysed by applying an aliquot of the lysate in kinase reaction buffer (Abl reaction buffer [New England Biolabs], consisting of 100 mM MgCl2 , 10 mM EGTA, 20 mM DTT and 0.1% Brij 35 in 500 mM Tris/HCl, pH 7.5) containing 12.5 µg/ml fluoresceine labelled PY20 antibody against phosphotyrosine (Exalpha, USA), and 400 µM ATP (Sigma) to the PamChip peptide array.

    Article Title: Impact of swapping soils on the endophytic bacterial communities of pre-domesticated, ancient and modern maize
    Article Snippet: Total DNA from 250 mg of soil or sand was extracted using Powersoil DNA isolation kits (MoBio, USA), and DNA was quantified using a Nanodrop (Thermo Scientific, USA). .. A PCR mastermix was made with the following components per 25 μl volume: 2.5 μl Standard Taq Buffer (New England Biolabs), 0.5 μl of 25 mM dNTP mix, 0.5 μl of 10 mM 27 F-Degen primer with sequence AGRRTTYGATYMTGGYTYAG [ ] (where R = A + G, Y = C + T, M = A + C), 0.5 μl of 10 mM 1492r primer with sequence GGTTACCTTGTTACGACTT [ ], 0.25 μl of 50 mM MgCl2 , 0.25 μl of Standard Taq (New England Biolabs), 50 ng of total DNA, and double distilled water up to 25 μl total. .. Amplification was for 35 cycles in a PTC200 DNA Thermal Cycler (MJ Scientific, USA) using the following program: 96°C for 3 min, 35X (94°C for 30 sec, 48°C for 30 sec, 72°C for 1:30 min), 72°C for 7 min.

    Article Title: De Novo Assembly and Characterization of Four Anthozoan (Phylum Cnidaria) Transcriptomes
    Article Snippet: Paragraph title: Preparation of sequencing libraries ... The product was purified and A-tailed in a reaction with nuclease-free water, 1× NEB Standard Taq buffer (New England Biolabs, MA), 1 mM dATP, and 2 units of NEB Standard Taq (New England Biolabs, MA) at 68° for 2 hr.

    Article Title: Fine Mapping of the Barley Chromosome 6H Net Form Net Blotch Susceptibility Locus
    Article Snippet: The PCR reactions consisted of 1.25 units NEB Standard Taq polymerase, forward and reverse primers (1.2 µM), NEB Standard Taq buffer (1 ×), and dNTPs (200 µM), in 25 µl reactions. .. The PCR reactions consisted of 1.25 units NEB Standard Taq polymerase, forward and reverse primers (1.2 µM), NEB Standard Taq buffer (1 ×), and dNTPs (200 µM), in 25 µl reactions.

    Article Title: Fine Mapping of the Barley Chromosome 6H Net Form Net Blotch Susceptibility Locus
    Article Snippet: Paragraph title: PCR-GBS library preparation and ion torrent sequencing ... The barcoding PCR reaction consisted of 0.235 µl of H2 O, 0.625 µl NEB Standard Taq Buffer (1.25 ×), 0.1 µl dNTPs (500 µM), 1 µl universal reverse primer (1 µM), 1 µl unique barcode adaptor primer (0.4 µM), 0.04 µl of NEB Taq polymerase (0.2 units), and 2 µl template (diluted primary PCR reaction).

    Article Title: Allopatric Speciation within a Cryptic Species Complex of Australasian Octopuses
    Article Snippet: Paragraph title: Sequencing ... 25 µL reactions comprised 0.1 µL Taq (Onetaq, New England Biolabs ), 2.5 µL 10 x buffer (Paq5000™), 2 µL dNTP mix (10 µM, Bioline ), 0.5 µL forward primer (10 µM), 0.5 µL reverse primer (10 µM), 17.4 µL ddH2 O and 2 µL DNA (diluted to between 1–5 ng/µL).

    Article Title: RAD marker microarrays enable rapid mapping of zebrafish mutations
    Article Snippet: PCR reactions were carried out in 50 μl under the following conditions: 50 ng template, 1 × Thermopol Buffer (New England Biolabs), 2.5 U Taq (New England Biolabs), 0.2 mmol/l dNTPs (Fermentas, Burlington, Ontario, Canada), 0.4 μmol/l forward primer, and 0.2 μmol/l reverse primer. .. PCR reactions were carried out in 50 μl under the following conditions: 50 ng template, 1 × Thermopol Buffer (New England Biolabs), 2.5 U Taq (New England Biolabs), 0.2 mmol/l dNTPs (Fermentas, Burlington, Ontario, Canada), 0.4 μmol/l forward primer, and 0.2 μmol/l reverse primer.

    DNA Extraction:

    Article Title: Impact of swapping soils on the endophytic bacterial communities of pre-domesticated, ancient and modern maize
    Article Snippet: Paragraph title: DNA extraction and Terminal Restriction Fragment Length Polymorphism (TRFLP) from plant tissues and soil ... A PCR mastermix was made with the following components per 25 μl volume: 2.5 μl Standard Taq Buffer (New England Biolabs), 0.5 μl of 25 mM dNTP mix, 0.5 μl of 10 mM 27 F-Degen primer with sequence AGRRTTYGATYMTGGYTYAG [ ] (where R = A + G, Y = C + T, M = A + C), 0.5 μl of 10 mM 1492r primer with sequence GGTTACCTTGTTACGACTT [ ], 0.25 μl of 50 mM MgCl2 , 0.25 μl of Standard Taq (New England Biolabs), 50 ng of total DNA, and double distilled water up to 25 μl total.

    Article Title: Identification and mapping in spring wheat of genetic factors controlling stem rust resistance and the study of their epistatic interactions across multiple environments
    Article Snippet: When the plants reached the 1 to 2 leaf stage, 3 cm leaf segments from primary leaves were harvested for genomic DNA isolation. .. A 10 μl PCR reaction consisting of DNA (final concentration of 2.4 ng/μl), Ultrapure double distilled H2 0 (Gibco), 10 % PCR Buffer without MgCl2 [Invitrogen cat.#18067-017: 200 mM Tris–HCl (pH 8.4), 500 mM KCl], 10 mM dNTPs (Roche), 1.5 mM MgCl2 (Invitrogen), 0.07 U μl−1 Taq (5 U of activity μl−1 ) NEB, and 2 ηg μl−1 forward and 2 ηg μl−1 reverse primer was used for the DNA amplification process.

    Nucleic Acid Electrophoresis:

    Article Title: A Recurrent Stop-Codon Mutation in Succinate Dehydrogenase Subunit B Gene in Normal Peripheral Blood and Childhood T-Cell Acute Leukemia
    Article Snippet: Paragraph title: Quantification of the R46X mutation by TaqI RE digestion and capillary gel electrophoresis ... Fifteen µL of the fluorescently-labeled PCR products, which contained ∼200–300 ng of DNA, were directly digested by 10 U of Taq I RE, 1× Taq I RE buffer and 1× Bovine Serum Albumin (all from New England Biolabs) overnight in a 25 µL reaction volume.

    Fluorescence:

    Article Title: Protein-Tyrosine Kinase Activity Profiling in Knock Down Zebrafish Embryos
    Article Snippet: Data was captured by real-time imaging of the fluorescence signal by CCD imaging , . .. The zebrafish embryo lysates were analysed by applying an aliquot of the lysate in kinase reaction buffer (Abl reaction buffer [New England Biolabs], consisting of 100 mM MgCl2 , 10 mM EGTA, 20 mM DTT and 0.1% Brij 35 in 500 mM Tris/HCl, pH 7.5) containing 12.5 µg/ml fluoresceine labelled PY20 antibody against phosphotyrosine (Exalpha, USA), and 400 µM ATP (Sigma) to the PamChip peptide array.

    Mutagenesis:

    Article Title: A Recurrent Stop-Codon Mutation in Succinate Dehydrogenase Subunit B Gene in Normal Peripheral Blood and Childhood T-Cell Acute Leukemia
    Article Snippet: Paragraph title: Quantification of the R46X mutation by TaqI RE digestion and capillary gel electrophoresis ... Fifteen µL of the fluorescently-labeled PCR products, which contained ∼200–300 ng of DNA, were directly digested by 10 U of Taq I RE, 1× Taq I RE buffer and 1× Bovine Serum Albumin (all from New England Biolabs) overnight in a 25 µL reaction volume.

    Article Title: Prp8 retinitis pigmentosa mutants cause defects in the transition between the catalytic steps of splicing
    Article Snippet: For qPCR, 10 µL of diluted cDNA from reverse transcription was combined with 0.25 mM each gene-specific primer, 1× SYBR green (Roche), 0.625 µL dimethyl sulfoxide (Invitrogen), 0.4 mM dTNPs (Fermentas), 1× Standard Taq Buffer (NEB) and 0.25 µL Standard Taq (NEB) and water to a total volume of 25 µL. qPCR cycle conditions were 95°C 3 min, 39 cycles of 95°C 15 sec, 55°C 30 sec, 72°C 15 sec, followed by one cycle at 72°C for 3 min. Exon primers were designed to be within the 3′ exon of all genes tested and were used to measure total RNA levels. pre-mRNA levels were assessed using intron primers. .. For qPCR, 10 µL of diluted cDNA from reverse transcription was combined with 0.25 mM each gene-specific primer, 1× SYBR green (Roche), 0.625 µL dimethyl sulfoxide (Invitrogen), 0.4 mM dTNPs (Fermentas), 1× Standard Taq Buffer (NEB) and 0.25 µL Standard Taq (NEB) and water to a total volume of 25 µL. qPCR cycle conditions were 95°C 3 min, 39 cycles of 95°C 15 sec, 55°C 30 sec, 72°C 15 sec, followed by one cycle at 72°C for 3 min. Exon primers were designed to be within the 3′ exon of all genes tested and were used to measure total RNA levels. pre-mRNA levels were assessed using intron primers.

    Isolation:

    Article Title: De Novo Assembly and Characterization of Four Anthozoan (Phylum Cnidaria) Transcriptomes
    Article Snippet: Polyadenylated RNA was purified from 10 µg of total RNA using the Magnetic mRNA Isolation Kit (New England Biolabs, MA). .. The product was purified and A-tailed in a reaction with nuclease-free water, 1× NEB Standard Taq buffer (New England Biolabs, MA), 1 mM dATP, and 2 units of NEB Standard Taq (New England Biolabs, MA) at 68° for 2 hr.

    Article Title: Prp8 retinitis pigmentosa mutants cause defects in the transition between the catalytic steps of splicing
    Article Snippet: Paragraph title: RNA isolation and RT-qPCR ... For qPCR, 10 µL of diluted cDNA from reverse transcription was combined with 0.25 mM each gene-specific primer, 1× SYBR green (Roche), 0.625 µL dimethyl sulfoxide (Invitrogen), 0.4 mM dTNPs (Fermentas), 1× Standard Taq Buffer (NEB) and 0.25 µL Standard Taq (NEB) and water to a total volume of 25 µL. qPCR cycle conditions were 95°C 3 min, 39 cycles of 95°C 15 sec, 55°C 30 sec, 72°C 15 sec, followed by one cycle at 72°C for 3 min. Exon primers were designed to be within the 3′ exon of all genes tested and were used to measure total RNA levels. pre-mRNA levels were assessed using intron primers.

    Size-exclusion Chromatography:

    Article Title: Fine Mapping of the Barley Chromosome 6H Net Form Net Blotch Susceptibility Locus
    Article Snippet: The parameters for the PCR reactions were as follows: 94° for 5 min, followed by 35 cycles of 94° for 30 sec, 62° for 30 sec, and 72° for 60 sec, followed by a final extension at 72° for 7 min. .. The PCR reactions consisted of 1.25 units NEB Standard Taq polymerase, forward and reverse primers (1.2 µM), NEB Standard Taq buffer (1 ×), and dNTPs (200 µM), in 25 µl reactions.

    Article Title: Fine Mapping of the Barley Chromosome 6H Net Form Net Blotch Susceptibility Locus
    Article Snippet: The primary PCR reaction was conducted as follows: Initial denaturation at 94° for 10 min, 10 cycles of 94° for 20 sec and 64° decreasing each cycle by 0.8° for 60 sec, followed by 20 cycles of 94° for 20 sec, 57° for 60 sec, and 68° for 30 sec, ending with a final extension of 72° for 3 min. .. The barcoding PCR reaction consisted of 0.235 µl of H2 O, 0.625 µl NEB Standard Taq Buffer (1.25 ×), 0.1 µl dNTPs (500 µM), 1 µl universal reverse primer (1 µM), 1 µl unique barcode adaptor primer (0.4 µM), 0.04 µl of NEB Taq polymerase (0.2 units), and 2 µl template (diluted primary PCR reaction).

    Article Title: Prp8 retinitis pigmentosa mutants cause defects in the transition between the catalytic steps of splicing
    Article Snippet: Reactions were then diluted between 1:75 and 1:250 with water prior to analysis by qPCR. .. For qPCR, 10 µL of diluted cDNA from reverse transcription was combined with 0.25 mM each gene-specific primer, 1× SYBR green (Roche), 0.625 µL dimethyl sulfoxide (Invitrogen), 0.4 mM dTNPs (Fermentas), 1× Standard Taq Buffer (NEB) and 0.25 µL Standard Taq (NEB) and water to a total volume of 25 µL. qPCR cycle conditions were 95°C 3 min, 39 cycles of 95°C 15 sec, 55°C 30 sec, 72°C 15 sec, followed by one cycle at 72°C for 3 min. Exon primers were designed to be within the 3′ exon of all genes tested and were used to measure total RNA levels. pre-mRNA levels were assessed using intron primers. .. The product of these primes spanned an intron–exon junction to ensure that only pre-mRNA was measured.

    Purification:

    Article Title: De Novo Assembly and Characterization of Four Anthozoan (Phylum Cnidaria) Transcriptomes
    Article Snippet: Fragmented cDNA was purified and the ends were repaired using NEB Quick Blunting Kit (New England Biolabs, MA) according to manufacturer’s protocol. .. The product was purified and A-tailed in a reaction with nuclease-free water, 1× NEB Standard Taq buffer (New England Biolabs, MA), 1 mM dATP, and 2 units of NEB Standard Taq (New England Biolabs, MA) at 68° for 2 hr. .. Tailed templates were ligated to double stranded adaptors prepared with oligonucleotides from the Illumina Customer Sequence Letter (version August 12, 2014, ; Table S1 ).

    Article Title: Fine Mapping of the Barley Chromosome 6H Net Form Net Blotch Susceptibility Locus
    Article Snippet: The barcoding PCR reaction consisted of 0.235 µl of H2 O, 0.625 µl NEB Standard Taq Buffer (1.25 ×), 0.1 µl dNTPs (500 µM), 1 µl universal reverse primer (1 µM), 1 µl unique barcode adaptor primer (0.4 µM), 0.04 µl of NEB Taq polymerase (0.2 units), and 2 µl template (diluted primary PCR reaction). .. Following PCR, the plate was briefly centrifuged and each sample was diluted by adding 15 µl of H2 O.

    Article Title: Cooperative activity of GABP with PU.1 or C/EBPε regulates lamin B receptor gene expression, implicating their roles in granulocyte nuclear maturation
    Article Snippet: Data analysis was performed using the ΔΔCT method. .. A 25 μl PCR reaction was also performed using 2 μl of purified DNA from EML cells using 1X standard Taq reaction buffer (New England BioLabs), 1 U of Taq DNA polymerase, plus 0.2 pmol/μl of same forward and reverse primers for proximal and distal Ets sites as mentioned above. .. PCR was carried out for 28 cycles by using 1 cycle of 95°C for 1 min; 30 cycles of 95°C, 63°C and 72°C each at 30 s and finally 1 cycle of 72°C for 5 min. Five microliters of PCR product was electrophoresed on 0.9 % agarose gel and bands were visualized by staining the gel in ethidium bromide.

    Article Title: 16S rRNA Terminal Restriction Fragment Length Polymorphism for the Characterization of the Nasopharyngeal Microbiota
    Article Snippet: Purified PCR products were checked for correct amplification size and purity using the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA) with the DNA 7500 LabChip kit. .. The enzymatic digestions were performed in a total volume of 20 µl using 40 ng of the amplified and purified PCR product, 1 µl NEB Reaction Buffer (New England Biolabs, Ipswich, MA) 1 (for digestion with Tsp509I ) or 4 (Hpy166II ) and 0.5 µl of the restriction enzymes Tsp509I or Hpy166II . .. Digestion conditions were 3 h at 65°C for TSP509I and 3 h at 37°C with 20 min enzyme inactivation at 65°C for Hpy166II , respectively.

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: A new insect cell glycoengineering approach provides baculovirus-inducible glycogene expression and increases human-type glycosylation efficiency
    Article Snippet: Paragraph title: 2.5. RT-PCR assays ... The resulting cDNA preparations were treated with RNAse H and used for PCR reactions with Taq Polymerase and Crimson Taq Buffer (New England Biolabs).

    Quantitative RT-PCR:

    Article Title: Prp8 retinitis pigmentosa mutants cause defects in the transition between the catalytic steps of splicing
    Article Snippet: Paragraph title: RNA isolation and RT-qPCR ... For qPCR, 10 µL of diluted cDNA from reverse transcription was combined with 0.25 mM each gene-specific primer, 1× SYBR green (Roche), 0.625 µL dimethyl sulfoxide (Invitrogen), 0.4 mM dTNPs (Fermentas), 1× Standard Taq Buffer (NEB) and 0.25 µL Standard Taq (NEB) and water to a total volume of 25 µL. qPCR cycle conditions were 95°C 3 min, 39 cycles of 95°C 15 sec, 55°C 30 sec, 72°C 15 sec, followed by one cycle at 72°C for 3 min. Exon primers were designed to be within the 3′ exon of all genes tested and were used to measure total RNA levels. pre-mRNA levels were assessed using intron primers.

    Staining:

    Article Title: A Simple Isothermal DNA Amplification Method to Screen Black Flies for Onchocerca volvulus Infection
    Article Snippet: LAMP primers B3 and F3 were used to PCR amplify OvGST1a in 25 µL reactions containing 3 µL DNA template, 0.2 µM of each primer, and 1.25 U of Taq DNA polymerase in 1× standard buffer (New England Biolabs) containing 3.5 mM MgCl2 , 0.2 mM and 0.2 mM dNTP each. .. All reactions were denatured once at 94°C for 5 min followed by 35 cycles of the following cycling conditions: 30 s at 94°C, 1 min at 53°C, 1 min at 72°C, and a final extension for 5 min at 72°C using a Gene Amp PCR system 9700 (Applied Biosystems).

    Article Title: Vitamin E inhibits the UVAI induction of “light” and “dark” cyclobutane pyrimidine dimers, and oxidatively generated DNA damage, in keratinocytes
    Article Snippet: T4endoV (0.1 U/mL), or hOGG1 (3.2 U/mL), or enzyme reaction buffer alone, was added to each gel (both enzymes were purchased from New England Biolabs, Hitchin, UK). .. Finally, slides were rinsed with neutralization solution (0.4 M Trizma Base, pH 7.5; Sigma) for 20 min and then washed with ddH2 O for 10 min.

    Article Title: Identification and mapping in spring wheat of genetic factors controlling stem rust resistance and the study of their epistatic interactions across multiple environments
    Article Snippet: A 10 μl PCR reaction consisting of DNA (final concentration of 2.4 ng/μl), Ultrapure double distilled H2 0 (Gibco), 10 % PCR Buffer without MgCl2 [Invitrogen cat.#18067-017: 200 mM Tris–HCl (pH 8.4), 500 mM KCl], 10 mM dNTPs (Roche), 1.5 mM MgCl2 (Invitrogen), 0.07 U μl−1 Taq (5 U of activity μl−1 ) NEB, and 2 ηg μl−1 forward and 2 ηg μl−1 reverse primer was used for the DNA amplification process. .. A 10 μl PCR reaction consisting of DNA (final concentration of 2.4 ng/μl), Ultrapure double distilled H2 0 (Gibco), 10 % PCR Buffer without MgCl2 [Invitrogen cat.#18067-017: 200 mM Tris–HCl (pH 8.4), 500 mM KCl], 10 mM dNTPs (Roche), 1.5 mM MgCl2 (Invitrogen), 0.07 U μl−1 Taq (5 U of activity μl−1 ) NEB, and 2 ηg μl−1 forward and 2 ηg μl−1 reverse primer was used for the DNA amplification process.

    Nested PCR:

    Article Title: Impact of swapping soils on the endophytic bacterial communities of pre-domesticated, ancient and modern maize
    Article Snippet: A PCR mastermix was made with the following components per 25 μl volume: 2.5 μl Standard Taq Buffer (New England Biolabs), 0.5 μl of 25 mM dNTP mix, 0.5 μl of 10 mM 27 F-Degen primer with sequence AGRRTTYGATYMTGGYTYAG [ ] (where R = A + G, Y = C + T, M = A + C), 0.5 μl of 10 mM 1492r primer with sequence GGTTACCTTGTTACGACTT [ ], 0.25 μl of 50 mM MgCl2 , 0.25 μl of Standard Taq (New England Biolabs), 50 ng of total DNA, and double distilled water up to 25 μl total. .. A PCR mastermix was made with the following components per 25 μl volume: 2.5 μl Standard Taq Buffer (New England Biolabs), 0.5 μl of 25 mM dNTP mix, 0.5 μl of 10 mM 27 F-Degen primer with sequence AGRRTTYGATYMTGGYTYAG [ ] (where R = A + G, Y = C + T, M = A + C), 0.5 μl of 10 mM 1492r primer with sequence GGTTACCTTGTTACGACTT [ ], 0.25 μl of 50 mM MgCl2 , 0.25 μl of Standard Taq (New England Biolabs), 50 ng of total DNA, and double distilled water up to 25 μl total.

    Article Title: Polymorphisms in K13 and Falcipain-2 Associated with Artemisinin Resistance Are Not Prevalent in Plasmodium falciparum Isolated from Ugandan Children
    Article Snippet: For the FP2 gene, 2 nested PCR reactions were utilized to amplify the entire gene, spanning nucleotides 1–873 and 271–1455. .. For both loci, first and second round amplifications were performed in 25 µl reactions containing 160 nM primers (Integrated DNA Technologies), 160 µM dNTPs (Invitrogen), 1 unit Taq DNA Polymerase (New England BioLabs), and 2 µl DNA/primary reaction template in 1x Standard Taq Buffer (New England BioLabs).

    Chloramphenicol Acetyltransferase Assay:

    Article Title: Identification and mapping in spring wheat of genetic factors controlling stem rust resistance and the study of their epistatic interactions across multiple environments
    Article Snippet: When the plants reached the 1 to 2 leaf stage, 3 cm leaf segments from primary leaves were harvested for genomic DNA isolation. .. A 10 μl PCR reaction consisting of DNA (final concentration of 2.4 ng/μl), Ultrapure double distilled H2 0 (Gibco), 10 % PCR Buffer without MgCl2 [Invitrogen cat.#18067-017: 200 mM Tris–HCl (pH 8.4), 500 mM KCl], 10 mM dNTPs (Roche), 1.5 mM MgCl2 (Invitrogen), 0.07 U μl−1 Taq (5 U of activity μl−1 ) NEB, and 2 ηg μl−1 forward and 2 ηg μl−1 reverse primer was used for the DNA amplification process. .. The PCR conditions were: initial denaturation at 94 °C (3 min), followed by 44 cycles of 94 °C (1 min), 55 or 60 °C annealing (1 min), and 72 °C extension (1 min) with a final extension at 72 °C for 10 min.

    Chromatin Immunoprecipitation:

    Article Title: Protein-Tyrosine Kinase Activity Profiling in Knock Down Zebrafish Embryos
    Article Snippet: Two N-terminal residues link the phosphosite sequence to the solid support of the 3-dimensional chip. .. The zebrafish embryo lysates were analysed by applying an aliquot of the lysate in kinase reaction buffer (Abl reaction buffer [New England Biolabs], consisting of 100 mM MgCl2 , 10 mM EGTA, 20 mM DTT and 0.1% Brij 35 in 500 mM Tris/HCl, pH 7.5) containing 12.5 µg/ml fluoresceine labelled PY20 antibody against phosphotyrosine (Exalpha, USA), and 400 µM ATP (Sigma) to the PamChip peptide array.

    Article Title: Cooperative activity of GABP with PU.1 or C/EBPε regulates lamin B receptor gene expression, implicating their roles in granulocyte nuclear maturation
    Article Snippet: Paragraph title: Chromatin Immunoprecipitation (ChIP) and real-time PCR assay ... A 25 μl PCR reaction was also performed using 2 μl of purified DNA from EML cells using 1X standard Taq reaction buffer (New England BioLabs), 1 U of Taq DNA polymerase, plus 0.2 pmol/μl of same forward and reverse primers for proximal and distal Ets sites as mentioned above.

    Plasmid Preparation:

    Article Title: Fine Mapping of the Barley Chromosome 6H Net Form Net Blotch Susceptibility Locus
    Article Snippet: The PCR reactions consisted of 1.25 units NEB Standard Taq polymerase, forward and reverse primers (1.2 µM), NEB Standard Taq buffer (1 ×), and dNTPs (200 µM), in 25 µl reactions. .. The PCR reactions consisted of 1.25 units NEB Standard Taq polymerase, forward and reverse primers (1.2 µM), NEB Standard Taq buffer (1 ×), and dNTPs (200 µM), in 25 µl reactions.

    Software:

    Article Title: Protein-Tyrosine Kinase Activity Profiling in Knock Down Zebrafish Embryos
    Article Snippet: The zebrafish embryo lysates were analysed by applying an aliquot of the lysate in kinase reaction buffer (Abl reaction buffer [New England Biolabs], consisting of 100 mM MgCl2 , 10 mM EGTA, 20 mM DTT and 0.1% Brij 35 in 500 mM Tris/HCl, pH 7.5) containing 12.5 µg/ml fluoresceine labelled PY20 antibody against phosphotyrosine (Exalpha, USA), and 400 µM ATP (Sigma) to the PamChip peptide array. .. The zebrafish embryo lysates were analysed by applying an aliquot of the lysate in kinase reaction buffer (Abl reaction buffer [New England Biolabs], consisting of 100 mM MgCl2 , 10 mM EGTA, 20 mM DTT and 0.1% Brij 35 in 500 mM Tris/HCl, pH 7.5) containing 12.5 µg/ml fluoresceine labelled PY20 antibody against phosphotyrosine (Exalpha, USA), and 400 µM ATP (Sigma) to the PamChip peptide array.

    Article Title: Fine Mapping of the Barley Chromosome 6H Net Form Net Blotch Susceptibility Locus
    Article Snippet: The PCR reactions consisted of 1.25 units NEB Standard Taq polymerase, forward and reverse primers (1.2 µM), NEB Standard Taq buffer (1 ×), and dNTPs (200 µM), in 25 µl reactions. .. The PCR reactions consisted of 1.25 units NEB Standard Taq polymerase, forward and reverse primers (1.2 µM), NEB Standard Taq buffer (1 ×), and dNTPs (200 µM), in 25 µl reactions.

    Electrophoresis:

    Article Title: A Simple Isothermal DNA Amplification Method to Screen Black Flies for Onchocerca volvulus Infection
    Article Snippet: LAMP primers B3 and F3 were used to PCR amplify OvGST1a in 25 µL reactions containing 3 µL DNA template, 0.2 µM of each primer, and 1.25 U of Taq DNA polymerase in 1× standard buffer (New England Biolabs) containing 3.5 mM MgCl2 , 0.2 mM and 0.2 mM dNTP each. .. All reactions were denatured once at 94°C for 5 min followed by 35 cycles of the following cycling conditions: 30 s at 94°C, 1 min at 53°C, 1 min at 72°C, and a final extension for 5 min at 72°C using a Gene Amp PCR system 9700 (Applied Biosystems).

    Article Title: Vitamin E inhibits the UVAI induction of “light” and “dark” cyclobutane pyrimidine dimers, and oxidatively generated DNA damage, in keratinocytes
    Article Snippet: T4endoV (0.1 U/mL), or hOGG1 (3.2 U/mL), or enzyme reaction buffer alone, was added to each gel (both enzymes were purchased from New England Biolabs, Hitchin, UK). .. T4endoV (0.1 U/mL), or hOGG1 (3.2 U/mL), or enzyme reaction buffer alone, was added to each gel (both enzymes were purchased from New England Biolabs, Hitchin, UK).

    Article Title: 16S rRNA Terminal Restriction Fragment Length Polymorphism for the Characterization of the Nasopharyngeal Microbiota
    Article Snippet: The enzymatic digestions were performed in a total volume of 20 µl using 40 ng of the amplified and purified PCR product, 1 µl NEB Reaction Buffer (New England Biolabs, Ipswich, MA) 1 (for digestion with Tsp509I ) or 4 (Hpy166II ) and 0.5 µl of the restriction enzymes Tsp509I or Hpy166II . .. The enzymatic digestions were performed in a total volume of 20 µl using 40 ng of the amplified and purified PCR product, 1 µl NEB Reaction Buffer (New England Biolabs, Ipswich, MA) 1 (for digestion with Tsp509I ) or 4 (Hpy166II ) and 0.5 µl of the restriction enzymes Tsp509I or Hpy166II .

    Article Title: Identification and mapping in spring wheat of genetic factors controlling stem rust resistance and the study of their epistatic interactions across multiple environments
    Article Snippet: A 10 μl PCR reaction consisting of DNA (final concentration of 2.4 ng/μl), Ultrapure double distilled H2 0 (Gibco), 10 % PCR Buffer without MgCl2 [Invitrogen cat.#18067-017: 200 mM Tris–HCl (pH 8.4), 500 mM KCl], 10 mM dNTPs (Roche), 1.5 mM MgCl2 (Invitrogen), 0.07 U μl−1 Taq (5 U of activity μl−1 ) NEB, and 2 ηg μl−1 forward and 2 ηg μl−1 reverse primer was used for the DNA amplification process. .. A 10 μl PCR reaction consisting of DNA (final concentration of 2.4 ng/μl), Ultrapure double distilled H2 0 (Gibco), 10 % PCR Buffer without MgCl2 [Invitrogen cat.#18067-017: 200 mM Tris–HCl (pH 8.4), 500 mM KCl], 10 mM dNTPs (Roche), 1.5 mM MgCl2 (Invitrogen), 0.07 U μl−1 Taq (5 U of activity μl−1 ) NEB, and 2 ηg μl−1 forward and 2 ηg μl−1 reverse primer was used for the DNA amplification process.

    Multiplex Assay:

    Article Title: De Novo Assembly and Characterization of Four Anthozoan (Phylum Cnidaria) Transcriptomes
    Article Snippet: The product was purified and A-tailed in a reaction with nuclease-free water, 1× NEB Standard Taq buffer (New England Biolabs, MA), 1 mM dATP, and 2 units of NEB Standard Taq (New England Biolabs, MA) at 68° for 2 hr. .. Ligation products were purified and then amplified using custom sample-specific barcodes (“indices”) designed with a 3-bp minimum Hamming distance based on Illumina barcodes ( ) ( Table S1 ).

    Selection:

    Article Title: Fine Mapping of the Barley Chromosome 6H Net Form Net Blotch Susceptibility Locus
    Article Snippet: A set of these ESTs were selected at ∼60 kb intervals using predicted function as the criteria for selection, as certain genes have a higher probability of containing polymorphisms compared to others. .. The PCR reactions consisted of 1.25 units NEB Standard Taq polymerase, forward and reverse primers (1.2 µM), NEB Standard Taq buffer (1 ×), and dNTPs (200 µM), in 25 µl reactions.

    Agarose Gel Electrophoresis:

    Article Title: A Simple Isothermal DNA Amplification Method to Screen Black Flies for Onchocerca volvulus Infection
    Article Snippet: LAMP primers B3 and F3 were used to PCR amplify OvGST1a in 25 µL reactions containing 3 µL DNA template, 0.2 µM of each primer, and 1.25 U of Taq DNA polymerase in 1× standard buffer (New England Biolabs) containing 3.5 mM MgCl2 , 0.2 mM and 0.2 mM dNTP each. .. All reactions were denatured once at 94°C for 5 min followed by 35 cycles of the following cycling conditions: 30 s at 94°C, 1 min at 53°C, 1 min at 72°C, and a final extension for 5 min at 72°C using a Gene Amp PCR system 9700 (Applied Biosystems).

    Article Title: Fine Mapping of the Barley Chromosome 6H Net Form Net Blotch Susceptibility Locus
    Article Snippet: Additionally, 2 µL of each reaction was separated on a 1% agarose gel containing GelRed to ensure successful reactions. .. The barcoding PCR reaction consisted of 0.235 µl of H2 O, 0.625 µl NEB Standard Taq Buffer (1.25 ×), 0.1 µl dNTPs (500 µM), 1 µl universal reverse primer (1 µM), 1 µl unique barcode adaptor primer (0.4 µM), 0.04 µl of NEB Taq polymerase (0.2 units), and 2 µl template (diluted primary PCR reaction).

    Article Title: CRISPR-MVLST subtyping of Salmonella enterica subsp. enterica serovars Typhimurium and Heidelberg and application in identifying outbreak isolates
    Article Snippet: PCR reactions were performed in a total volume of 25 μl: 1.5 μl template, 0.3 μl Taq (1.5 units; New England Bio Labs, Ipswich, MA), 0.2 μl 10 mM dNTPs, 1 μl of each 10 μM primer, 2.5 μl of 10× Taq buffer and 18.5 μl water. .. PCR conditions were as follows and the annealing temperatures (AT) are listed in Table : initial denaturation step of 10 minutes at 94°C followed by 35 cycles of 1 minute at 94°C, 1 minute at AT and extension for 1 minute (fimH and sseL ) or 1.5 minutes (CRISPR1 and CRISPR2) at 72°C; a final extension step was done at 72°C for 8 minutes.

    Article Title: RAD marker microarrays enable rapid mapping of zebrafish mutations
    Article Snippet: PCR reactions were carried out in 50 μl under the following conditions: 50 ng template, 1 × Thermopol Buffer (New England Biolabs), 2.5 U Taq (New England Biolabs), 0.2 mmol/l dNTPs (Fermentas, Burlington, Ontario, Canada), 0.4 μmol/l forward primer, and 0.2 μmol/l reverse primer. .. Touchdown amplification was applied, with primer annealing temperature dropping 2°C every other cycle from 65°C to 55°C, after which 25 additional cycles were carried out [ ].

    Concentration Assay:

    Article Title: Cooperative activity of GABP with PU.1 or C/EBPε regulates lamin B receptor gene expression, implicating their roles in granulocyte nuclear maturation
    Article Snippet: Real-time PCR was performed by using 2 μl of purified DNA as template, SsoAdvanced SYBR Green Supermix (Bio-Rad) and the following primers at a final concentration of 0.2 pmol/μl: Proximal Ets site: (F) 5′-AACAGCACGGCGAAGTAG-3′ and (R) 5′-CCCCTTACACTTGCCACC-3′, Distal Ets site: (F) 5′-GATCTGTTTGTCCCCAGCTAC-3′ and (R) 5′-ACTTTGTGAGCACTTGAGACC-3′, and Proximal Cebp site: (F) 5′-CTCGGAGTAGGATTCGTCTTTAAG-3′ and (R) 5′-GATTTGTCATTGCCGTTGGG-3′. .. A 25 μl PCR reaction was also performed using 2 μl of purified DNA from EML cells using 1X standard Taq reaction buffer (New England BioLabs), 1 U of Taq DNA polymerase, plus 0.2 pmol/μl of same forward and reverse primers for proximal and distal Ets sites as mentioned above.

    Article Title: Identification and mapping in spring wheat of genetic factors controlling stem rust resistance and the study of their epistatic interactions across multiple environments
    Article Snippet: When the plants reached the 1 to 2 leaf stage, 3 cm leaf segments from primary leaves were harvested for genomic DNA isolation. .. A 10 μl PCR reaction consisting of DNA (final concentration of 2.4 ng/μl), Ultrapure double distilled H2 0 (Gibco), 10 % PCR Buffer without MgCl2 [Invitrogen cat.#18067-017: 200 mM Tris–HCl (pH 8.4), 500 mM KCl], 10 mM dNTPs (Roche), 1.5 mM MgCl2 (Invitrogen), 0.07 U μl−1 Taq (5 U of activity μl−1 ) NEB, and 2 ηg μl−1 forward and 2 ηg μl−1 reverse primer was used for the DNA amplification process. .. The PCR conditions were: initial denaturation at 94 °C (3 min), followed by 44 cycles of 94 °C (1 min), 55 or 60 °C annealing (1 min), and 72 °C extension (1 min) with a final extension at 72 °C for 10 min.

    Marker:

    Article Title: Fine Mapping of the Barley Chromosome 6H Net Form Net Blotch Susceptibility Locus
    Article Snippet: Paragraph title: STS/SNP marker development ... The PCR reactions consisted of 1.25 units NEB Standard Taq polymerase, forward and reverse primers (1.2 µM), NEB Standard Taq buffer (1 ×), and dNTPs (200 µM), in 25 µl reactions.

    Lysis:

    Article Title: Vitamin E inhibits the UVAI induction of “light” and “dark” cyclobutane pyrimidine dimers, and oxidatively generated DNA damage, in keratinocytes
    Article Snippet: After removing the lysis buffer, slides were washed with ice-cold ddH2 O for 10 min (in the dark, to prevent adventitious DNA damage). .. T4endoV (0.1 U/mL), or hOGG1 (3.2 U/mL), or enzyme reaction buffer alone, was added to each gel (both enzymes were purchased from New England Biolabs, Hitchin, UK).

    Activity Assay:

    Article Title: Identification and mapping in spring wheat of genetic factors controlling stem rust resistance and the study of their epistatic interactions across multiple environments
    Article Snippet: When the plants reached the 1 to 2 leaf stage, 3 cm leaf segments from primary leaves were harvested for genomic DNA isolation. .. A 10 μl PCR reaction consisting of DNA (final concentration of 2.4 ng/μl), Ultrapure double distilled H2 0 (Gibco), 10 % PCR Buffer without MgCl2 [Invitrogen cat.#18067-017: 200 mM Tris–HCl (pH 8.4), 500 mM KCl], 10 mM dNTPs (Roche), 1.5 mM MgCl2 (Invitrogen), 0.07 U μl−1 Taq (5 U of activity μl−1 ) NEB, and 2 ηg μl−1 forward and 2 ηg μl−1 reverse primer was used for the DNA amplification process. .. The PCR conditions were: initial denaturation at 94 °C (3 min), followed by 44 cycles of 94 °C (1 min), 55 or 60 °C annealing (1 min), and 72 °C extension (1 min) with a final extension at 72 °C for 10 min.

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  • 99
    New England Biolabs taq dna polymerase supertaq
    <t>DNA</t> modification and bypass during bisulfite treatment. ( A ) Scheme of the chemical reaction of cytidine: Treatment with bisulfite generates the non-aromatic, non-planar 5,6-dihydrouridine-6-sulfonate (dhU6S), which decomposes to uracil upon treatment with base (and heat). ( B ) Primer extension activity of different polymerases <t>(Taq,</t> 5D4, 3A10, E10, TgoT) on template T1 either unmodified (C), bisulfite-treated and desulfonated (Reagent 1, 80°C, 20 min) (converting dC to dU) (D) or bisulfite-treated (Reagent 1) but not desulphonated (converting dC to dhU6S) (S). Polymerases 5D4 and 3A10 are able to generate full-length (+20) products even from the non-desulphonated template (S). ( C ) Time-course comparison of primer extension activity of Taq and 5D4 on T1 either unmodified (C) or bisulfite-treated with (D) or without desulphonation (S). (P: primer).
    Taq Dna Polymerase Supertaq, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 931 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/taq dna polymerase supertaq/product/New England Biolabs
    Average 99 stars, based on 931 article reviews
    Price from $9.99 to $1999.99
    taq dna polymerase supertaq - by Bioz Stars, 2019-10
    99/100 stars
      Buy from Supplier

    99
    New England Biolabs restriction enzyme taq i
    Restriction enzyme digestion patterns obtained with Ear I. For B clarridgeiae , B. elizabethae , and B. vinsonii subsp. berkhoffii , positive identification is facilitated by obtaining the digestion pattern with Ear I in addition to <t>Taq</t> I.
    Restriction Enzyme Taq I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/restriction enzyme taq i/product/New England Biolabs
    Average 99 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
    restriction enzyme taq i - by Bioz Stars, 2019-10
    99/100 stars
      Buy from Supplier

    Image Search Results


    DNA modification and bypass during bisulfite treatment. ( A ) Scheme of the chemical reaction of cytidine: Treatment with bisulfite generates the non-aromatic, non-planar 5,6-dihydrouridine-6-sulfonate (dhU6S), which decomposes to uracil upon treatment with base (and heat). ( B ) Primer extension activity of different polymerases (Taq, 5D4, 3A10, E10, TgoT) on template T1 either unmodified (C), bisulfite-treated and desulfonated (Reagent 1, 80°C, 20 min) (converting dC to dU) (D) or bisulfite-treated (Reagent 1) but not desulphonated (converting dC to dhU6S) (S). Polymerases 5D4 and 3A10 are able to generate full-length (+20) products even from the non-desulphonated template (S). ( C ) Time-course comparison of primer extension activity of Taq and 5D4 on T1 either unmodified (C) or bisulfite-treated with (D) or without desulphonation (S). (P: primer).

    Journal: Nucleic Acids Research

    Article Title: A polymerase engineered for bisulfite sequencing

    doi: 10.1093/nar/gkv798

    Figure Lengend Snippet: DNA modification and bypass during bisulfite treatment. ( A ) Scheme of the chemical reaction of cytidine: Treatment with bisulfite generates the non-aromatic, non-planar 5,6-dihydrouridine-6-sulfonate (dhU6S), which decomposes to uracil upon treatment with base (and heat). ( B ) Primer extension activity of different polymerases (Taq, 5D4, 3A10, E10, TgoT) on template T1 either unmodified (C), bisulfite-treated and desulfonated (Reagent 1, 80°C, 20 min) (converting dC to dU) (D) or bisulfite-treated (Reagent 1) but not desulphonated (converting dC to dhU6S) (S). Polymerases 5D4 and 3A10 are able to generate full-length (+20) products even from the non-desulphonated template (S). ( C ) Time-course comparison of primer extension activity of Taq and 5D4 on T1 either unmodified (C) or bisulfite-treated with (D) or without desulphonation (S). (P: primer).

    Article Snippet: Taq DNA polymerase (SuperTaq) was obtained from HT Biotechnology (Cambridge) and Q5 polymerase from New England Biolabs.

    Techniques: Modification, Activity Assay

    Amplification of 24 individual human genomic loci. Comparison of PCR performance of Taq (top) panel, with two different Taq/5D4 blends (5/1 (middle panel); 10/1 (bottom panel)) on the amplification of 24 different promotor regions in bisulfite-treated and fully desulphonated human genomic DNA. Both blends are able to amplify a significantly larger number of loci than Taq alone and together enable amplification of 18 out of 24 loci (75%).

    Journal: Nucleic Acids Research

    Article Title: A polymerase engineered for bisulfite sequencing

    doi: 10.1093/nar/gkv798

    Figure Lengend Snippet: Amplification of 24 individual human genomic loci. Comparison of PCR performance of Taq (top) panel, with two different Taq/5D4 blends (5/1 (middle panel); 10/1 (bottom panel)) on the amplification of 24 different promotor regions in bisulfite-treated and fully desulphonated human genomic DNA. Both blends are able to amplify a significantly larger number of loci than Taq alone and together enable amplification of 18 out of 24 loci (75%).

    Article Snippet: Taq DNA polymerase (SuperTaq) was obtained from HT Biotechnology (Cambridge) and Q5 polymerase from New England Biolabs.

    Techniques: Amplification, Polymerase Chain Reaction

    PCR amplification of bisulfite-treated plasmid templates. PCR amplification of bisulfite-treated high GC and low GC content templates ranging from 200–600 bp in size using fully desulphonated templates and three different 5D4/Taq blends (1/10, 1/5, 1/1) with progressively lower Taq content and Taq alone on low dC content plasmid regions (top panel) and high dC content plasmid regions (bottom panel). On templates with low dC content (and hence lower levels of dU and residual dhU6S adducts post bisulfite treatment and desulphonation) either Taq or Taq/5D4 polymerase blends with a high amount of Taq perform best. In contrast on the higher dC content templates only blends containing 5D4 yield amplicons with Taq/5D4 blends (10/1; 5/1) superior to 5D4/Taq 1/1 blend, while Taq alone does not yield any amplification products. Thus only 5D4/Taq blends are able to copy the high GC content templates indicating that the blended enzymes are more efficient at copying templates containing sporadic dUs (and dhU6S adducts) and dU homopolymer stretches. Low molecular weight bands result from primer-dimer formation. (M: E-Gel ® Low Range Quantitative DNA Ladder).

    Journal: Nucleic Acids Research

    Article Title: A polymerase engineered for bisulfite sequencing

    doi: 10.1093/nar/gkv798

    Figure Lengend Snippet: PCR amplification of bisulfite-treated plasmid templates. PCR amplification of bisulfite-treated high GC and low GC content templates ranging from 200–600 bp in size using fully desulphonated templates and three different 5D4/Taq blends (1/10, 1/5, 1/1) with progressively lower Taq content and Taq alone on low dC content plasmid regions (top panel) and high dC content plasmid regions (bottom panel). On templates with low dC content (and hence lower levels of dU and residual dhU6S adducts post bisulfite treatment and desulphonation) either Taq or Taq/5D4 polymerase blends with a high amount of Taq perform best. In contrast on the higher dC content templates only blends containing 5D4 yield amplicons with Taq/5D4 blends (10/1; 5/1) superior to 5D4/Taq 1/1 blend, while Taq alone does not yield any amplification products. Thus only 5D4/Taq blends are able to copy the high GC content templates indicating that the blended enzymes are more efficient at copying templates containing sporadic dUs (and dhU6S adducts) and dU homopolymer stretches. Low molecular weight bands result from primer-dimer formation. (M: E-Gel ® Low Range Quantitative DNA Ladder).

    Article Snippet: Taq DNA polymerase (SuperTaq) was obtained from HT Biotechnology (Cambridge) and Q5 polymerase from New England Biolabs.

    Techniques: Polymerase Chain Reaction, Amplification, Plasmid Preparation, Gas Chromatography, Molecular Weight

    Degree of methylation of individual CpG sites. Promoter regions of four genes ( A — prkcdbp , B — dab2ip , C — ptgs2 , D — ezh2) were amplified with either Taq ot 5D4/Taq blends, using bisulfide-treated genomic DNA from normal cells or LNCapP cells as a template and subjected to deep sequencing. Cyan—methylated CpGs, orange—unmethylated CpGs. Individual CpGs are numbered starting from the 5′ end of the amplicon.

    Journal: Nucleic Acids Research

    Article Title: A polymerase engineered for bisulfite sequencing

    doi: 10.1093/nar/gkv798

    Figure Lengend Snippet: Degree of methylation of individual CpG sites. Promoter regions of four genes ( A — prkcdbp , B — dab2ip , C — ptgs2 , D — ezh2) were amplified with either Taq ot 5D4/Taq blends, using bisulfide-treated genomic DNA from normal cells or LNCapP cells as a template and subjected to deep sequencing. Cyan—methylated CpGs, orange—unmethylated CpGs. Individual CpGs are numbered starting from the 5′ end of the amplicon.

    Article Snippet: Taq DNA polymerase (SuperTaq) was obtained from HT Biotechnology (Cambridge) and Q5 polymerase from New England Biolabs.

    Techniques: Methylation, Amplification, Sequencing

    Single strand binding protein, ET SSB, only has a minor effect on the reduction of artifacts. Taq (NE Biolabs) and AccuPrime Pfx (Life Technologies) DNA polymerases were used in amplification of TALE DNA repeats. The arrows indicate the expected size of the amplification products. PCR conditions are given in the supplementary material .

    Journal: Scientific Reports

    Article Title: PCR amplification of repetitive DNA: a limitation to genome editing technologies and many other applications

    doi: 10.1038/srep05052

    Figure Lengend Snippet: Single strand binding protein, ET SSB, only has a minor effect on the reduction of artifacts. Taq (NE Biolabs) and AccuPrime Pfx (Life Technologies) DNA polymerases were used in amplification of TALE DNA repeats. The arrows indicate the expected size of the amplification products. PCR conditions are given in the supplementary material .

    Article Snippet: The specifications of the DNA polymerases indicate that the Phusion , Q5 , and Taq polymerases from NE Biolabs do not have this ability ( https://www.neb.com/tools-and-resources/selection-charts/dna-polymerase-selection-chart ) but this feature of the PrimeSTAR family TAKARA enzymes and the AccuPrime Pfx (Life Technologies) are not known.

    Techniques: Binding Assay, Amplification, Polymerase Chain Reaction

    Primers that anneal far away from the repetitive DNA perform much better in amplifying the desired product. Taq DNA polymerase (NE Biolabs) was used in the PCR amplification of the indicated region of the pdTALE12 plasmid. PCR conditions are given in the supplementary material .

    Journal: Scientific Reports

    Article Title: PCR amplification of repetitive DNA: a limitation to genome editing technologies and many other applications

    doi: 10.1038/srep05052

    Figure Lengend Snippet: Primers that anneal far away from the repetitive DNA perform much better in amplifying the desired product. Taq DNA polymerase (NE Biolabs) was used in the PCR amplification of the indicated region of the pdTALE12 plasmid. PCR conditions are given in the supplementary material .

    Article Snippet: The specifications of the DNA polymerases indicate that the Phusion , Q5 , and Taq polymerases from NE Biolabs do not have this ability ( https://www.neb.com/tools-and-resources/selection-charts/dna-polymerase-selection-chart ) but this feature of the PrimeSTAR family TAKARA enzymes and the AccuPrime Pfx (Life Technologies) are not known.

    Techniques: Polymerase Chain Reaction, Amplification, Plasmid Preparation

    PCR fragments generated upon a typical PCR amplification from the pTAL2 vector with 12.5 TALE DNA-binding repeats. Plasmid map is shown in Supplementary Fig. 3 . Proofreading Pfu polymerase (Bioline) and normal Taq polymerase (NE Biolabs) were used in PCR amplification. PCR conditions are described in the supplementary material .

    Journal: Scientific Reports

    Article Title: PCR amplification of repetitive DNA: a limitation to genome editing technologies and many other applications

    doi: 10.1038/srep05052

    Figure Lengend Snippet: PCR fragments generated upon a typical PCR amplification from the pTAL2 vector with 12.5 TALE DNA-binding repeats. Plasmid map is shown in Supplementary Fig. 3 . Proofreading Pfu polymerase (Bioline) and normal Taq polymerase (NE Biolabs) were used in PCR amplification. PCR conditions are described in the supplementary material .

    Article Snippet: The specifications of the DNA polymerases indicate that the Phusion , Q5 , and Taq polymerases from NE Biolabs do not have this ability ( https://www.neb.com/tools-and-resources/selection-charts/dna-polymerase-selection-chart ) but this feature of the PrimeSTAR family TAKARA enzymes and the AccuPrime Pfx (Life Technologies) are not known.

    Techniques: Polymerase Chain Reaction, Generated, Amplification, Plasmid Preparation, Binding Assay

    Testing the generality of the model to other template DNAs with repetitive sequences. (A). GFP-coding sequences were cloned into the pBasicS1 vector and their integrity were checked by sequencing and restriction enzyme digestions. (B). PCR results obtained with primers 390 and 570. Taq DNA polymerase (NE Biolabs) was used in PCR amplification. The arrow indicates the sequenced artifact product which contained only one copy of the GFP lacking the filler sequence. See the supplementary material for PCR conditions.

    Journal: Scientific Reports

    Article Title: PCR amplification of repetitive DNA: a limitation to genome editing technologies and many other applications

    doi: 10.1038/srep05052

    Figure Lengend Snippet: Testing the generality of the model to other template DNAs with repetitive sequences. (A). GFP-coding sequences were cloned into the pBasicS1 vector and their integrity were checked by sequencing and restriction enzyme digestions. (B). PCR results obtained with primers 390 and 570. Taq DNA polymerase (NE Biolabs) was used in PCR amplification. The arrow indicates the sequenced artifact product which contained only one copy of the GFP lacking the filler sequence. See the supplementary material for PCR conditions.

    Article Snippet: The specifications of the DNA polymerases indicate that the Phusion , Q5 , and Taq polymerases from NE Biolabs do not have this ability ( https://www.neb.com/tools-and-resources/selection-charts/dna-polymerase-selection-chart ) but this feature of the PrimeSTAR family TAKARA enzymes and the AccuPrime Pfx (Life Technologies) are not known.

    Techniques: Clone Assay, Plasmid Preparation, Sequencing, Polymerase Chain Reaction, Amplification

    DNA polymerization by PCR using a caged primer (17 nt) containing the first caged thymidine (blue square) 10 nt from the 5′ end. PCR generates a caged template which results in a stop of Taq and Pfu polymerase due to the presence of a single-caged thymidine.

    Journal: Nucleic Acids Research

    Article Title: Restriction enzyme-free mutagenesis via the light regulation of DNA polymerization

    doi: 10.1093/nar/gkp150

    Figure Lengend Snippet: DNA polymerization by PCR using a caged primer (17 nt) containing the first caged thymidine (blue square) 10 nt from the 5′ end. PCR generates a caged template which results in a stop of Taq and Pfu polymerase due to the presence of a single-caged thymidine.

    Article Snippet: Each PCR was conducted with one of the forward primers ( WT , P1 , P2 or P3 ), a radioactively labelled reverse primer (Integrated DNA Technologies; 50 pmol), DNA template (1 ng), dNTPs and either Taq DNA polymerase (New England Biolabs, five units) or Phusion DNA Polymerase (New England Biolabs, two units) for 30 cycles.

    Techniques: Polymerase Chain Reaction

    Effects of a caged thymidine nucleobase on the PCR. ( A ) PCR product using Phusion DNA Polymerase. Polymerization is halted in the presence of a caging group, which is confirmed using the truncated primer P3 that affords the same length product. ( B ) PCR product using Taq DNA polymerase. Polymerization is halted in the presence of a caging group, which is confirmed using the truncated primer P3 that affords the same length product.

    Journal: Nucleic Acids Research

    Article Title: Restriction enzyme-free mutagenesis via the light regulation of DNA polymerization

    doi: 10.1093/nar/gkp150

    Figure Lengend Snippet: Effects of a caged thymidine nucleobase on the PCR. ( A ) PCR product using Phusion DNA Polymerase. Polymerization is halted in the presence of a caging group, which is confirmed using the truncated primer P3 that affords the same length product. ( B ) PCR product using Taq DNA polymerase. Polymerization is halted in the presence of a caging group, which is confirmed using the truncated primer P3 that affords the same length product.

    Article Snippet: Each PCR was conducted with one of the forward primers ( WT , P1 , P2 or P3 ), a radioactively labelled reverse primer (Integrated DNA Technologies; 50 pmol), DNA template (1 ng), dNTPs and either Taq DNA polymerase (New England Biolabs, five units) or Phusion DNA Polymerase (New England Biolabs, two units) for 30 cycles.

    Techniques: Polymerase Chain Reaction

    Restriction enzyme digestion patterns obtained with Ear I. For B clarridgeiae , B. elizabethae , and B. vinsonii subsp. berkhoffii , positive identification is facilitated by obtaining the digestion pattern with Ear I in addition to Taq I.

    Journal:

    Article Title: Detection and Identification of Bartonella Species Pathogenic for Humans by PCR Amplification Targeting the Riboflavin Synthase Gene (ribC)

    doi: 10.1128/JCM.41.3.1069-1072.2003

    Figure Lengend Snippet: Restriction enzyme digestion patterns obtained with Ear I. For B clarridgeiae , B. elizabethae , and B. vinsonii subsp. berkhoffii , positive identification is facilitated by obtaining the digestion pattern with Ear I in addition to Taq I.

    Article Snippet: Each reaction mixture in which amplicons were detected was subjected to digestion with the restriction enzyme Taq I (New England Biolabs).

    Techniques:

    Restriction enzyme digestion patterns obtained with Taq I. Digestion mixtures were electrophoresed on 1.5% agarose gels. On each panel, the gel is flanked by a 100-bp ladder (Invitrogen Life Technologies) (lane MW). (A) The three species illustrated are unambiguously identified by the Taq I pattern. However, for the species illustrated in panel B, the Taq I patterns are similar to one another, although clearly distinct from that of the species in panel A.

    Journal:

    Article Title: Detection and Identification of Bartonella Species Pathogenic for Humans by PCR Amplification Targeting the Riboflavin Synthase Gene (ribC)

    doi: 10.1128/JCM.41.3.1069-1072.2003

    Figure Lengend Snippet: Restriction enzyme digestion patterns obtained with Taq I. Digestion mixtures were electrophoresed on 1.5% agarose gels. On each panel, the gel is flanked by a 100-bp ladder (Invitrogen Life Technologies) (lane MW). (A) The three species illustrated are unambiguously identified by the Taq I pattern. However, for the species illustrated in panel B, the Taq I patterns are similar to one another, although clearly distinct from that of the species in panel A.

    Article Snippet: Each reaction mixture in which amplicons were detected was subjected to digestion with the restriction enzyme Taq I (New England Biolabs).

    Techniques: