turbo dnase i  (Thermo Fisher)


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    Structured Review

    Thermo Fisher turbo dnase i
    CarH Bm footprints at the PcarH and PcrtI promoter regions. A , representative <t>DNase</t> I and hydroxyl radical footprinting in the dark on the sense and antisense strands of a 170-bp P carH or P crtI probe without or with CarH Bm (400 n m with 5-fold molar excess
    Turbo Dnase I, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 96/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/turbo dnase i/product/Thermo Fisher
    Average 96 stars, based on 7 article reviews
    Price from $9.99 to $1999.99
    turbo dnase i - by Bioz Stars, 2020-04
    96/100 stars

    Images

    1) Product Images from "Plasticity in oligomerization, operator architecture, and DNA binding in the mode of action of a bacterial B12-based photoreceptor"

    Article Title: Plasticity in oligomerization, operator architecture, and DNA binding in the mode of action of a bacterial B12-based photoreceptor

    Journal: The Journal of Biological Chemistry

    doi: 10.1074/jbc.RA118.004838

    CarH Bm footprints at the PcarH and PcrtI promoter regions. A , representative DNase I and hydroxyl radical footprinting in the dark on the sense and antisense strands of a 170-bp P carH or P crtI probe without or with CarH Bm (400 n m with 5-fold molar excess
    Figure Legend Snippet: CarH Bm footprints at the PcarH and PcrtI promoter regions. A , representative DNase I and hydroxyl radical footprinting in the dark on the sense and antisense strands of a 170-bp P carH or P crtI probe without or with CarH Bm (400 n m with 5-fold molar excess

    Techniques Used: Footprinting

    Related Articles

    Centrifugation:

    Article Title: mRNA regions where 80S ribosomes pause during translation elongation in vivo interact with protein uS19, a component of the decoding site
    Article Snippet: Finally, the cells were harvested with ice-cold PBS and centrifuged at 1000 g. The cell pellet was lysed in three volumes of lysis buffer (20 mM Tris–HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl2 , 1mM DTT, 1% Triton-X100, 100 μg/ml of cycloheximide and 0.02 U/μl of Turbo DNase I (Ambion)) for 10 min on ice and then triturated through 29 G needle 10 times. .. The cell lysate was clarified by centrifugation at 20 000 g for 15 min at 4°C and the supernatant was transferred into a new Eppendorf tube.

    Article Title: Spliceosome profiling visualizes operations of a dynamic RNP at nucleotide resolution
    Article Snippet: RNA was initially checked by RT-qPCR and later by Bioanalyzer for enrichment of U2, U5 and U6 snRNAs after DNase treatment with 6 units TURBO DNase I (Invitrogen) and purification using the Zymo RNA Clean and Concentrate kit. .. RNA was initially checked by RT-qPCR and later by Bioanalyzer for enrichment of U2, U5 and U6 snRNAs after DNase treatment with 6 units TURBO DNase I (Invitrogen) and purification using the Zymo RNA Clean and Concentrate kit.

    Article Title: Epstein-Barr Virus BBRF2 Is Required for Maximum Infectivity
    Article Snippet: To assay the cell-free virus level, the culture supernatants were treated with Turbo DNase I (Thermo Fisher Scientific) to eliminate naked EBV DNA and subjected to DNA extraction using a DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany). .. For Akata cells, supernatants were collected at two days after addition of an anti-IgG antibody, followed by centrifugation and filtration.

    Amplification:

    Article Title: Evolution of the HIV-1 Rev Response Element during Natural Infection Reveals Nucleotide Changes That Correlate with Altered Structure and Increased Activity over Time
    Article Snippet: Templates for in vitro transcription were generated by PCR amplification of RREs from plasmids containing synthetic sequences (Integrated DNA Technologies) using oligonucleotides designed to introduce both a T7 promoter sequence at the 5′ end of the 234-nt and 351-nt RREs and a structure cassette at the 3′ end of the 351-nt RREs (Table S1). .. In vitro transcription reactions were treated with Turbo DNase I (Life Technologies) for 1 h at 37°C to digest the DNA template and heated to 85°C for 2 min, and RNA was fractionated on a denaturing gel (5% polyacrylamide [19:1], 1× Tris-borate-EDTA [TBE], 7 M urea) at a constant temperature (45°C, 30 W maximum).

    Filtration:

    Article Title: Epstein-Barr Virus BBRF2 Is Required for Maximum Infectivity
    Article Snippet: To assay the cell-free virus level, the culture supernatants were treated with Turbo DNase I (Thermo Fisher Scientific) to eliminate naked EBV DNA and subjected to DNA extraction using a DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany). .. For Akata cells, supernatants were collected at two days after addition of an anti-IgG antibody, followed by centrifugation and filtration.

    Stable Transfection:

    Article Title: mRNA regions where 80S ribosomes pause during translation elongation in vivo interact with protein uS19, a component of the decoding site
    Article Snippet: Paragraph title: PAR-CLIP analysis of a stable cell line producing FLAG uS19 ... Finally, the cells were harvested with ice-cold PBS and centrifuged at 1000 g. The cell pellet was lysed in three volumes of lysis buffer (20 mM Tris–HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl2 , 1mM DTT, 1% Triton-X100, 100 μg/ml of cycloheximide and 0.02 U/μl of Turbo DNase I (Ambion)) for 10 min on ice and then triturated through 29 G needle 10 times.

    Synthesized:

    Article Title: Cigarette Smoke Toxins-Induced Mitochondrial Dysfunction and Pancreatitis Involves Aryl Hydrocarbon Receptor Mediated Cyp1 Gene Expression: Protective Effects of Resveratrol
    Article Snippet: .. For real-time PCR analysis, RNA was digested with turbo DNase I (Ambion, Inc), and cDNA was synthesized using 1 μg total RNA as template by using the High Capacity cDNA Archives kit (Applied Biosystems, Inc). .. Relative Cyp1a1 , Cyp1a2 , Cyp1b1 mRNAs and, cytokines and chemokines mRNA levels were measured by standard SYBR Green real-time PCR on an Quant Studio 6 real-time PCR machine (Applied Biosystems, Thermos Fisher) as described before ( ).

    Article Title: Candidate genes expression profiling during wilting in chickpea caused by Fusarium oxysporum f. sp. ciceris race 5
    Article Snippet: To avoid any genomic DNA (gDNA) contamination, ~10μg of RNA extracts were treated with TURBO DNase I (Life Technologies) before to cDNA synthesis. .. Complementary DNAs was synthesized by priming with oligodT12–18 (Life Technologies), using SuperScript III Reverse Transcriptase (Invitrogen) following the instructions of the provider.

    Quantitative RT-PCR:

    Article Title: Plasticity in oligomerization, operator architecture, and DNA binding in the mode of action of a bacterial B12-based photoreceptor
    Article Snippet: Paragraph title: qRT-PCR ... This RNA was treated with Turbo DNase I (Ambion), checked in native 1% agarose gels, and quantified in NanoDrop ND-1000 (Thermo Fisher Scientific).

    Article Title: Spliceosome profiling visualizes operations of a dynamic RNP at nucleotide resolution
    Article Snippet: .. RNA was initially checked by RT-qPCR and later by Bioanalyzer for enrichment of U2, U5 and U6 snRNAs after DNase treatment with 6 units TURBO DNase I (Invitrogen) and purification using the Zymo RNA Clean and Concentrate kit. .. “A” sample RNA was ligated to a pre-adenylated adaptor with a 5′ random hexamer (see ) using T4 RNA ligase 2, truncated, K227Q (NEB) for 2.5 hours at 37°C (25% PEG-8000, 12.5% DMSO, 1X buffer).

    Real-time Polymerase Chain Reaction:

    Article Title: Cigarette Smoke Toxins-Induced Mitochondrial Dysfunction and Pancreatitis Involves Aryl Hydrocarbon Receptor Mediated Cyp1 Gene Expression: Protective Effects of Resveratrol
    Article Snippet: .. For real-time PCR analysis, RNA was digested with turbo DNase I (Ambion, Inc), and cDNA was synthesized using 1 μg total RNA as template by using the High Capacity cDNA Archives kit (Applied Biosystems, Inc). .. Relative Cyp1a1 , Cyp1a2 , Cyp1b1 mRNAs and, cytokines and chemokines mRNA levels were measured by standard SYBR Green real-time PCR on an Quant Studio 6 real-time PCR machine (Applied Biosystems, Thermos Fisher) as described before ( ).

    Article Title: Aspergillus fumigatus calcium-responsive transcription factors regulate cell wall architecture promoting stress tolerance, virulence and caspofungin resistance
    Article Snippet: DNA was digested with Turbo DNase I (Ambion Thermo Scientific) according to manufacturer’s instructions. .. Two μg of total RNA per sample was reverse-transcribed with the High Capacity cDNA Reverse Transcription kit (Thermo Scientifc) using oligo dTV and random primers blend, according to manufacturer’s instructions. qRT-PCRs were run in a StepOne Plus Real Time PCR System (Thermo Scientific) and Power Sybr Green PCR Master Mix (Thermo Scientific) was used.

    Article Title: Epstein-Barr Virus BBRF2 Is Required for Maximum Infectivity
    Article Snippet: Briefly, cells were washed with PBS, lysed by sonication in lysis buffer, treated with proteinase K and, after heat-inactivation of proteinase K, subjected to qPCR analysis. .. To assay the cell-free virus level, the culture supernatants were treated with Turbo DNase I (Thermo Fisher Scientific) to eliminate naked EBV DNA and subjected to DNA extraction using a DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany).

    Incubation:

    Article Title: mRNA regions where 80S ribosomes pause during translation elongation in vivo interact with protein uS19, a component of the decoding site
    Article Snippet: Finally, the cells were harvested with ice-cold PBS and centrifuged at 1000 g. The cell pellet was lysed in three volumes of lysis buffer (20 mM Tris–HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl2 , 1mM DTT, 1% Triton-X100, 100 μg/ml of cycloheximide and 0.02 U/μl of Turbo DNase I (Ambion)) for 10 min on ice and then triturated through 29 G needle 10 times. .. RNase I (Ambion) was added to 1.3 U/μl, and the reaction mixture was incubated at ambient temperature for 45 min, followed by the addition of SUPERase In RNase inhibitor (Thermo Fisher Scientific) to 0.35 U/μl.

    Article Title: PRMT1-mediated methylation of the microprocessor-associated proteins regulates microRNA biogenesis
    Article Snippet: An aliquot (10%) of DNA-digested lysates was used as input while the remaining protein extract (90%) was split in two fractions and incubated overnight at 4°C with either IgG (Millipore), anti-DGCR8 (Abcam), or anti-ILF3 (Bethyl) rabbit antibodies. .. Afterwards, the dynabeads were washed 4 times with Washing Buffer I (PBS supplemented with 1% NP-40, 0.5% NaDeoxycholate, 300 mM NaCl, 1× Roche protease inhibitor mix and 25 U/ml Superase-RNAse inhibitor), resuspended in RNAse-free water and treated again with Turbo DNAse I (Thermo Fisher Scientific) for 30 min at 37°C.

    Article Title: Aspergillus fumigatus calcium-responsive transcription factors regulate cell wall architecture promoting stress tolerance, virulence and caspofungin resistance
    Article Snippet: RNA extraction and gene expression analysis Strains were grown from 1x107 conidia in MM for 20 h at 37°C before being incubated with 200mM CaCl2 for 10 and 30 min. Mycelia were ground to a fine powder in liquid N2 and total RNA was extracted with Trizol reagent (Thermo Scientific) according to the manufacturer’s protocol. .. DNA was digested with Turbo DNase I (Ambion Thermo Scientific) according to manufacturer’s instructions.

    Infection:

    Article Title: Epstein-Barr Virus BBRF2 Is Required for Maximum Infectivity
    Article Snippet: To assay the cell-free virus level, the culture supernatants were treated with Turbo DNase I (Thermo Fisher Scientific) to eliminate naked EBV DNA and subjected to DNA extraction using a DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany). .. For infectivity assays, culture supernatants of HEK293 cells were collected, centrifuged, and filtered after three days of BZLF1 transfection.

    Cell Culture:

    Article Title: Plasticity in oligomerization, operator architecture, and DNA binding in the mode of action of a bacterial B12-based photoreceptor
    Article Snippet: A 10-ml cell culture in LB grown overnight in the dark at 37 °C was diluted 1:100 with fresh LB and grown in the dark or light for 5 h to an optical density at 600 nm of ∼0.8. .. This RNA was treated with Turbo DNase I (Ambion), checked in native 1% agarose gels, and quantified in NanoDrop ND-1000 (Thermo Fisher Scientific).

    Article Title: mRNA regions where 80S ribosomes pause during translation elongation in vivo interact with protein uS19, a component of the decoding site
    Article Snippet: Typically, adherent pAG-1(FLAG uS19)-derivatized HEK293 cells in four 15-cm Petri dishes were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% FBS and 100 U/ml of Penicillin–Streptomycin (all from Thermo Fisher Scientific) in CO2 -incubator (5% CO2 ) at 37°C. .. Finally, the cells were harvested with ice-cold PBS and centrifuged at 1000 g. The cell pellet was lysed in three volumes of lysis buffer (20 mM Tris–HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl2 , 1mM DTT, 1% Triton-X100, 100 μg/ml of cycloheximide and 0.02 U/μl of Turbo DNase I (Ambion)) for 10 min on ice and then triturated through 29 G needle 10 times.

    Expressing:

    Article Title: Aspergillus fumigatus calcium-responsive transcription factors regulate cell wall architecture promoting stress tolerance, virulence and caspofungin resistance
    Article Snippet: Paragraph title: RNA extraction and gene expression analysis ... DNA was digested with Turbo DNase I (Ambion Thermo Scientific) according to manufacturer’s instructions.

    Modification:

    Article Title: mRNA regions where 80S ribosomes pause during translation elongation in vivo interact with protein uS19, a component of the decoding site
    Article Snippet: Typically, adherent pAG-1(FLAG uS19)-derivatized HEK293 cells in four 15-cm Petri dishes were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% FBS and 100 U/ml of Penicillin–Streptomycin (all from Thermo Fisher Scientific) in CO2 -incubator (5% CO2 ) at 37°C. .. Finally, the cells were harvested with ice-cold PBS and centrifuged at 1000 g. The cell pellet was lysed in three volumes of lysis buffer (20 mM Tris–HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl2 , 1mM DTT, 1% Triton-X100, 100 μg/ml of cycloheximide and 0.02 U/μl of Turbo DNase I (Ambion)) for 10 min on ice and then triturated through 29 G needle 10 times.

    Transfection:

    Article Title: Epstein-Barr Virus BBRF2 Is Required for Maximum Infectivity
    Article Snippet: To assay the cell-free virus level, the culture supernatants were treated with Turbo DNase I (Thermo Fisher Scientific) to eliminate naked EBV DNA and subjected to DNA extraction using a DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany). .. For infectivity assays, culture supernatants of HEK293 cells were collected, centrifuged, and filtered after three days of BZLF1 transfection.

    Concentration Assay:

    Article Title: mRNA regions where 80S ribosomes pause during translation elongation in vivo interact with protein uS19, a component of the decoding site
    Article Snippet: After 6 h, cycloheximide was added to a concentration of 100 μg/ml and the cells were kept on ice for 10 min, followed by washing with ice-cold PBS. .. Finally, the cells were harvested with ice-cold PBS and centrifuged at 1000 g. The cell pellet was lysed in three volumes of lysis buffer (20 mM Tris–HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl2 , 1mM DTT, 1% Triton-X100, 100 μg/ml of cycloheximide and 0.02 U/μl of Turbo DNase I (Ambion)) for 10 min on ice and then triturated through 29 G needle 10 times.

    Article Title: Candidate genes expression profiling during wilting in chickpea caused by Fusarium oxysporum f. sp. ciceris race 5
    Article Snippet: RNA concentration was determined by measuring the optical density using a NanoDrop spectrophotometer. .. To avoid any genomic DNA (gDNA) contamination, ~10μg of RNA extracts were treated with TURBO DNase I (Life Technologies) before to cDNA synthesis.

    Protease Inhibitor:

    Article Title: PRMT1-mediated methylation of the microprocessor-associated proteins regulates microRNA biogenesis
    Article Snippet: .. Afterwards, the dynabeads were washed 4 times with Washing Buffer I (PBS supplemented with 1% NP-40, 0.5% NaDeoxycholate, 300 mM NaCl, 1× Roche protease inhibitor mix and 25 U/ml Superase-RNAse inhibitor), resuspended in RNAse-free water and treated again with Turbo DNAse I (Thermo Fisher Scientific) for 30 min at 37°C. ..

    Introduce:

    Article Title: Evolution of the HIV-1 Rev Response Element during Natural Infection Reveals Nucleotide Changes That Correlate with Altered Structure and Increased Activity over Time
    Article Snippet: Templates for in vitro transcription were generated by PCR amplification of RREs from plasmids containing synthetic sequences (Integrated DNA Technologies) using oligonucleotides designed to introduce both a T7 promoter sequence at the 5′ end of the 234-nt and 351-nt RREs and a structure cassette at the 3′ end of the 351-nt RREs (Table S1). .. In vitro transcription reactions were treated with Turbo DNase I (Life Technologies) for 1 h at 37°C to digest the DNA template and heated to 85°C for 2 min, and RNA was fractionated on a denaturing gel (5% polyacrylamide [19:1], 1× Tris-borate-EDTA [TBE], 7 M urea) at a constant temperature (45°C, 30 W maximum).

    Generated:

    Article Title: Plasticity in oligomerization, operator architecture, and DNA binding in the mode of action of a bacterial B12-based photoreceptor
    Article Snippet: This RNA was treated with Turbo DNase I (Ambion), checked in native 1% agarose gels, and quantified in NanoDrop ND-1000 (Thermo Fisher Scientific). .. Melting and dissociation curves were determined at 60–95 °C, 30 s, and 95 °C, 15 s. Each primer pair was tested for RT-PCR analysis on a standard curve generated from five 10-fold serial dilutions of cDNA.

    Article Title: Evolution of the HIV-1 Rev Response Element during Natural Infection Reveals Nucleotide Changes That Correlate with Altered Structure and Increased Activity over Time
    Article Snippet: Templates for in vitro transcription were generated by PCR amplification of RREs from plasmids containing synthetic sequences (Integrated DNA Technologies) using oligonucleotides designed to introduce both a T7 promoter sequence at the 5′ end of the 234-nt and 351-nt RREs and a structure cassette at the 3′ end of the 351-nt RREs (Table S1). .. In vitro transcription reactions were treated with Turbo DNase I (Life Technologies) for 1 h at 37°C to digest the DNA template and heated to 85°C for 2 min, and RNA was fractionated on a denaturing gel (5% polyacrylamide [19:1], 1× Tris-borate-EDTA [TBE], 7 M urea) at a constant temperature (45°C, 30 W maximum).

    Polymerase Chain Reaction:

    Article Title: Plasticity in oligomerization, operator architecture, and DNA binding in the mode of action of a bacterial B12-based photoreceptor
    Article Snippet: This RNA was treated with Turbo DNase I (Ambion), checked in native 1% agarose gels, and quantified in NanoDrop ND-1000 (Thermo Fisher Scientific). .. RNA (5 μg/20 μl) was reverse transcribed to cDNA with SuperScript IV Reverse Transcriptase (Thermo Fisher Scientific). qRT-PCR was performed in a StepOne instrument (Applied Biosystems) using the 1-Step RT-PCR program cycle for samples containing 1 μl of cDNA, 10 μl of SYBR Green PCR Master Mix (Bio-Rad), and the required primers (400 n m ), which were designed using the Primer Express 3.0 software to amplify an ∼50–150 bp region within each transcript ( sigA served as the reference gene).

    Article Title: Evolution of the HIV-1 Rev Response Element during Natural Infection Reveals Nucleotide Changes That Correlate with Altered Structure and Increased Activity over Time
    Article Snippet: Templates for in vitro transcription were generated by PCR amplification of RREs from plasmids containing synthetic sequences (Integrated DNA Technologies) using oligonucleotides designed to introduce both a T7 promoter sequence at the 5′ end of the 234-nt and 351-nt RREs and a structure cassette at the 3′ end of the 351-nt RREs (Table S1). .. In vitro transcription reactions were treated with Turbo DNase I (Life Technologies) for 1 h at 37°C to digest the DNA template and heated to 85°C for 2 min, and RNA was fractionated on a denaturing gel (5% polyacrylamide [19:1], 1× Tris-borate-EDTA [TBE], 7 M urea) at a constant temperature (45°C, 30 W maximum).

    Article Title: Aspergillus fumigatus calcium-responsive transcription factors regulate cell wall architecture promoting stress tolerance, virulence and caspofungin resistance
    Article Snippet: DNA was digested with Turbo DNase I (Ambion Thermo Scientific) according to manufacturer’s instructions. .. Two μg of total RNA per sample was reverse-transcribed with the High Capacity cDNA Reverse Transcription kit (Thermo Scientifc) using oligo dTV and random primers blend, according to manufacturer’s instructions. qRT-PCRs were run in a StepOne Plus Real Time PCR System (Thermo Scientific) and Power Sybr Green PCR Master Mix (Thermo Scientific) was used.

    Sequencing:

    Article Title: Evolution of the HIV-1 Rev Response Element during Natural Infection Reveals Nucleotide Changes That Correlate with Altered Structure and Increased Activity over Time
    Article Snippet: Templates for in vitro transcription were generated by PCR amplification of RREs from plasmids containing synthetic sequences (Integrated DNA Technologies) using oligonucleotides designed to introduce both a T7 promoter sequence at the 5′ end of the 234-nt and 351-nt RREs and a structure cassette at the 3′ end of the 351-nt RREs (Table S1). .. In vitro transcription reactions were treated with Turbo DNase I (Life Technologies) for 1 h at 37°C to digest the DNA template and heated to 85°C for 2 min, and RNA was fractionated on a denaturing gel (5% polyacrylamide [19:1], 1× Tris-borate-EDTA [TBE], 7 M urea) at a constant temperature (45°C, 30 W maximum).

    Article Title: Candidate genes expression profiling during wilting in chickpea caused by Fusarium oxysporum f. sp. ciceris race 5
    Article Snippet: To avoid any genomic DNA (gDNA) contamination, ~10μg of RNA extracts were treated with TURBO DNase I (Life Technologies) before to cDNA synthesis. .. Next, we tested the presence of genomic DNA (gDNA) contamination in the cDNA samples using a primer pair designed in two different exons of the NAD-dependent malic chickpea sequence XM_004510782 (gDNAF, 5’-GTTGATACCAGCAGCAGCAAC-3’ ; gDNAR, 5’-TTAGTGCCAAAGACAAAGGGGA-’3’ ).

    Article Title: Early cold stress responses in post-meiotic anthers from tolerant and sensitive rice cultivars
    Article Snippet: .. Illumina sequencing Upon treatment with TURBO DNAse I (AMBION), 4 μg of RNA from each sample were used to produce sequencing libraries with the TruSeq mRNA sample preparation kit (Illumina). .. Sequencing of poly(A) RNA samples was carried out in multiplex (6 samples per lane, single 50 bp reads) with Illumina Hi-seq 2000 platform at IGA Technology Services (Udine, Italy).

    Sonication:

    Article Title: Epstein-Barr Virus BBRF2 Is Required for Maximum Infectivity
    Article Snippet: Briefly, cells were washed with PBS, lysed by sonication in lysis buffer, treated with proteinase K and, after heat-inactivation of proteinase K, subjected to qPCR analysis. .. To assay the cell-free virus level, the culture supernatants were treated with Turbo DNase I (Thermo Fisher Scientific) to eliminate naked EBV DNA and subjected to DNA extraction using a DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany).

    Affinity Purification:

    Article Title: Spliceosome profiling visualizes operations of a dynamic RNP at nucleotide resolution
    Article Snippet: RNA was precipitated with 2 μl GlycoBlue in 0.3 M sodium acetate and 50% isopropanol, then recovered by centrifugation for 30 min at 18400xg at 4°C and washed with 70% ethanol. .. RNA was initially checked by RT-qPCR and later by Bioanalyzer for enrichment of U2, U5 and U6 snRNAs after DNase treatment with 6 units TURBO DNase I (Invitrogen) and purification using the Zymo RNA Clean and Concentrate kit.

    DNA Extraction:

    Article Title: Epstein-Barr Virus BBRF2 Is Required for Maximum Infectivity
    Article Snippet: .. To assay the cell-free virus level, the culture supernatants were treated with Turbo DNase I (Thermo Fisher Scientific) to eliminate naked EBV DNA and subjected to DNA extraction using a DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany). .. Extracellular EBV DNA was quantified by qPCR, as described previously [ ].

    Nucleic Acid Electrophoresis:

    Article Title: Epstein-Barr Virus BBRF2 Is Required for Maximum Infectivity
    Article Snippet: The samples were subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis, followed by immunoblotting. .. To assay the cell-free virus level, the culture supernatants were treated with Turbo DNase I (Thermo Fisher Scientific) to eliminate naked EBV DNA and subjected to DNA extraction using a DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany).

    In Vivo:

    Article Title: Genome-wide CRISPR screen identifies host dependency factors for influenza A virus infection
    Article Snippet: Paragraph title: In vivo cross-linking coupled immunoprecipitation with anti-eIF4E antibody ... Extracts from the two fractions were combined and treated with Turbo DNase I (Ambion) and RNase inhibitor (NEB) prior to pre-clearing using protein-G agarose to remove non-specific contaminants that bind agarose.

    Irradiation:

    Article Title: mRNA regions where 80S ribosomes pause during translation elongation in vivo interact with protein uS19, a component of the decoding site
    Article Snippet: Cross-linking was performed by irradiation of the cells with UV light at 365 nm (0.5 J/cm2 ) in Bio-Link (Vilber Lourmat) on ice. .. Finally, the cells were harvested with ice-cold PBS and centrifuged at 1000 g. The cell pellet was lysed in three volumes of lysis buffer (20 mM Tris–HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl2 , 1mM DTT, 1% Triton-X100, 100 μg/ml of cycloheximide and 0.02 U/μl of Turbo DNase I (Ambion)) for 10 min on ice and then triturated through 29 G needle 10 times.

    Isolation:

    Article Title: SCA8 RAN polySer protein preferentially accumulates in white matter regions and is regulated by eIF3F
    Article Snippet: Paragraph title: RNA isolation ... Any contaminant genomic DNA was removed using Turbo DNase I (Thermo Fisher, Waltham, MA).

    Article Title: Spliceosome profiling visualizes operations of a dynamic RNP at nucleotide resolution
    Article Snippet: RNA was initially checked by RT-qPCR and later by Bioanalyzer for enrichment of U2, U5 and U6 snRNAs after DNase treatment with 6 units TURBO DNase I (Invitrogen) and purification using the Zymo RNA Clean and Concentrate kit. .. RNA was initially checked by RT-qPCR and later by Bioanalyzer for enrichment of U2, U5 and U6 snRNAs after DNase treatment with 6 units TURBO DNase I (Invitrogen) and purification using the Zymo RNA Clean and Concentrate kit.

    Article Title: Cigarette Smoke Toxins-Induced Mitochondrial Dysfunction and Pancreatitis Involves Aryl Hydrocarbon Receptor Mediated Cyp1 Gene Expression: Protective Effects of Resveratrol
    Article Snippet: Total RNA was isolated from fresh pancreatic tissues using TRIzol reagent (Invitrogen), according to the manufacturer’s recommended protocol. .. For real-time PCR analysis, RNA was digested with turbo DNase I (Ambion, Inc), and cDNA was synthesized using 1 μg total RNA as template by using the High Capacity cDNA Archives kit (Applied Biosystems, Inc).

    Article Title: Genome-wide CRISPR screen identifies host dependency factors for influenza A virus infection
    Article Snippet: Extracts from the two fractions were combined and treated with Turbo DNase I (Ambion) and RNase inhibitor (NEB) prior to pre-clearing using protein-G agarose to remove non-specific contaminants that bind agarose. .. The immunoprecipitates were subject to heat inactivation at 56 °C for 15 min before subjecting to RNA isolation with 3 volumes of Trizol (Invitrogen).

    Article Title: Candidate genes expression profiling during wilting in chickpea caused by Fusarium oxysporum f. sp. ciceris race 5
    Article Snippet: Paragraph title: RNA isolation, cDNA synthesis and quality controls ... To avoid any genomic DNA (gDNA) contamination, ~10μg of RNA extracts were treated with TURBO DNase I (Life Technologies) before to cDNA synthesis.

    RNA Extraction:

    Article Title: Aspergillus fumigatus calcium-responsive transcription factors regulate cell wall architecture promoting stress tolerance, virulence and caspofungin resistance
    Article Snippet: Paragraph title: RNA extraction and gene expression analysis ... DNA was digested with Turbo DNase I (Ambion Thermo Scientific) according to manufacturer’s instructions.

    Purification:

    Article Title: Plasticity in oligomerization, operator architecture, and DNA binding in the mode of action of a bacterial B12-based photoreceptor
    Article Snippet: RNA was purified using the PureLink RNA Minikit (ThermoFisher Scientific) and recommended protocols for TRIzol/chloroform extraction, isopropyl alcohol precipitation, and 70% ethanol wash. .. This RNA was treated with Turbo DNase I (Ambion), checked in native 1% agarose gels, and quantified in NanoDrop ND-1000 (Thermo Fisher Scientific).

    Article Title: Spliceosome profiling visualizes operations of a dynamic RNP at nucleotide resolution
    Article Snippet: .. RNA was initially checked by RT-qPCR and later by Bioanalyzer for enrichment of U2, U5 and U6 snRNAs after DNase treatment with 6 units TURBO DNase I (Invitrogen) and purification using the Zymo RNA Clean and Concentrate kit. .. “A” sample RNA was ligated to a pre-adenylated adaptor with a 5′ random hexamer (see ) using T4 RNA ligase 2, truncated, K227Q (NEB) for 2.5 hours at 37°C (25% PEG-8000, 12.5% DMSO, 1X buffer).

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: Plasticity in oligomerization, operator architecture, and DNA binding in the mode of action of a bacterial B12-based photoreceptor
    Article Snippet: This RNA was treated with Turbo DNase I (Ambion), checked in native 1% agarose gels, and quantified in NanoDrop ND-1000 (Thermo Fisher Scientific). .. RNA (5 μg/20 μl) was reverse transcribed to cDNA with SuperScript IV Reverse Transcriptase (Thermo Fisher Scientific). qRT-PCR was performed in a StepOne instrument (Applied Biosystems) using the 1-Step RT-PCR program cycle for samples containing 1 μl of cDNA, 10 μl of SYBR Green PCR Master Mix (Bio-Rad), and the required primers (400 n m ), which were designed using the Primer Express 3.0 software to amplify an ∼50–150 bp region within each transcript ( sigA served as the reference gene).

    Software:

    Article Title: Plasticity in oligomerization, operator architecture, and DNA binding in the mode of action of a bacterial B12-based photoreceptor
    Article Snippet: This RNA was treated with Turbo DNase I (Ambion), checked in native 1% agarose gels, and quantified in NanoDrop ND-1000 (Thermo Fisher Scientific). .. RNA (5 μg/20 μl) was reverse transcribed to cDNA with SuperScript IV Reverse Transcriptase (Thermo Fisher Scientific). qRT-PCR was performed in a StepOne instrument (Applied Biosystems) using the 1-Step RT-PCR program cycle for samples containing 1 μl of cDNA, 10 μl of SYBR Green PCR Master Mix (Bio-Rad), and the required primers (400 n m ), which were designed using the Primer Express 3.0 software to amplify an ∼50–150 bp region within each transcript ( sigA served as the reference gene).

    SYBR Green Assay:

    Article Title: Plasticity in oligomerization, operator architecture, and DNA binding in the mode of action of a bacterial B12-based photoreceptor
    Article Snippet: This RNA was treated with Turbo DNase I (Ambion), checked in native 1% agarose gels, and quantified in NanoDrop ND-1000 (Thermo Fisher Scientific). .. RNA (5 μg/20 μl) was reverse transcribed to cDNA with SuperScript IV Reverse Transcriptase (Thermo Fisher Scientific). qRT-PCR was performed in a StepOne instrument (Applied Biosystems) using the 1-Step RT-PCR program cycle for samples containing 1 μl of cDNA, 10 μl of SYBR Green PCR Master Mix (Bio-Rad), and the required primers (400 n m ), which were designed using the Primer Express 3.0 software to amplify an ∼50–150 bp region within each transcript ( sigA served as the reference gene).

    Article Title: Cigarette Smoke Toxins-Induced Mitochondrial Dysfunction and Pancreatitis Involves Aryl Hydrocarbon Receptor Mediated Cyp1 Gene Expression: Protective Effects of Resveratrol
    Article Snippet: For real-time PCR analysis, RNA was digested with turbo DNase I (Ambion, Inc), and cDNA was synthesized using 1 μg total RNA as template by using the High Capacity cDNA Archives kit (Applied Biosystems, Inc). .. Relative Cyp1a1 , Cyp1a2 , Cyp1b1 mRNAs and, cytokines and chemokines mRNA levels were measured by standard SYBR Green real-time PCR on an Quant Studio 6 real-time PCR machine (Applied Biosystems, Thermos Fisher) as described before ( ).

    Article Title: Aspergillus fumigatus calcium-responsive transcription factors regulate cell wall architecture promoting stress tolerance, virulence and caspofungin resistance
    Article Snippet: DNA was digested with Turbo DNase I (Ambion Thermo Scientific) according to manufacturer’s instructions. .. Two μg of total RNA per sample was reverse-transcribed with the High Capacity cDNA Reverse Transcription kit (Thermo Scientifc) using oligo dTV and random primers blend, according to manufacturer’s instructions. qRT-PCRs were run in a StepOne Plus Real Time PCR System (Thermo Scientific) and Power Sybr Green PCR Master Mix (Thermo Scientific) was used.

    Multiplex Assay:

    Article Title: Early cold stress responses in post-meiotic anthers from tolerant and sensitive rice cultivars
    Article Snippet: Illumina sequencing Upon treatment with TURBO DNAse I (AMBION), 4 μg of RNA from each sample were used to produce sequencing libraries with the TruSeq mRNA sample preparation kit (Illumina). .. Sequencing of poly(A) RNA samples was carried out in multiplex (6 samples per lane, single 50 bp reads) with Illumina Hi-seq 2000 platform at IGA Technology Services (Udine, Italy).

    Sample Prep:

    Article Title: Early cold stress responses in post-meiotic anthers from tolerant and sensitive rice cultivars
    Article Snippet: .. Illumina sequencing Upon treatment with TURBO DNAse I (AMBION), 4 μg of RNA from each sample were used to produce sequencing libraries with the TruSeq mRNA sample preparation kit (Illumina). .. Sequencing of poly(A) RNA samples was carried out in multiplex (6 samples per lane, single 50 bp reads) with Illumina Hi-seq 2000 platform at IGA Technology Services (Udine, Italy).

    In Vitro:

    Article Title: Evolution of the HIV-1 Rev Response Element during Natural Infection Reveals Nucleotide Changes That Correlate with Altered Structure and Increased Activity over Time
    Article Snippet: .. In vitro transcription reactions were treated with Turbo DNase I (Life Technologies) for 1 h at 37°C to digest the DNA template and heated to 85°C for 2 min, and RNA was fractionated on a denaturing gel (5% polyacrylamide [19:1], 1× Tris-borate-EDTA [TBE], 7 M urea) at a constant temperature (45°C, 30 W maximum). ..

    Spectrophotometry:

    Article Title: Candidate genes expression profiling during wilting in chickpea caused by Fusarium oxysporum f. sp. ciceris race 5
    Article Snippet: RNA concentration was determined by measuring the optical density using a NanoDrop spectrophotometer. .. To avoid any genomic DNA (gDNA) contamination, ~10μg of RNA extracts were treated with TURBO DNase I (Life Technologies) before to cDNA synthesis.

    Immunoprecipitation:

    Article Title: PRMT1-mediated methylation of the microprocessor-associated proteins regulates microRNA biogenesis
    Article Snippet: Paragraph title: UV-crosslinked RNA immunoprecipitation (UV-RIP) ... Afterwards, the dynabeads were washed 4 times with Washing Buffer I (PBS supplemented with 1% NP-40, 0.5% NaDeoxycholate, 300 mM NaCl, 1× Roche protease inhibitor mix and 25 U/ml Superase-RNAse inhibitor), resuspended in RNAse-free water and treated again with Turbo DNAse I (Thermo Fisher Scientific) for 30 min at 37°C.

    Article Title: Genome-wide CRISPR screen identifies host dependency factors for influenza A virus infection
    Article Snippet: Paragraph title: In vivo cross-linking coupled immunoprecipitation with anti-eIF4E antibody ... Extracts from the two fractions were combined and treated with Turbo DNase I (Ambion) and RNase inhibitor (NEB) prior to pre-clearing using protein-G agarose to remove non-specific contaminants that bind agarose.

    Lysis:

    Article Title: Plasticity in oligomerization, operator architecture, and DNA binding in the mode of action of a bacterial B12-based photoreceptor
    Article Snippet: These were resuspended in 200 μl of RNase-free lysis buffer (10 m m Tris, pH 8.0, 1 m m EDTA, 10 m m NaCl, 1% SDS) and lysed in a Mini-beadbeater (BioSpec). .. This RNA was treated with Turbo DNase I (Ambion), checked in native 1% agarose gels, and quantified in NanoDrop ND-1000 (Thermo Fisher Scientific).

    Article Title: mRNA regions where 80S ribosomes pause during translation elongation in vivo interact with protein uS19, a component of the decoding site
    Article Snippet: .. Finally, the cells were harvested with ice-cold PBS and centrifuged at 1000 g. The cell pellet was lysed in three volumes of lysis buffer (20 mM Tris–HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl2 , 1mM DTT, 1% Triton-X100, 100 μg/ml of cycloheximide and 0.02 U/μl of Turbo DNase I (Ambion)) for 10 min on ice and then triturated through 29 G needle 10 times. .. The cell lysate was clarified by centrifugation at 20 000 g for 15 min at 4°C and the supernatant was transferred into a new Eppendorf tube.

    Article Title: PRMT1-mediated methylation of the microprocessor-associated proteins regulates microRNA biogenesis
    Article Snippet: Cells were lysed with Lysis Buffer (0.5% NP-40, 0.5% NaDeoxycholate, 1× Roche protease inhibitors mixture (04693116001 MERCK), 25 U/ml Superase-RNAse inhibitor (Thermo Fisher Scientific) in PBS for 30 min at 4°C and then treated with 30 U of Turbo DNAseI (Thermo Fisher Scientific) for 30 min at 37°C. .. Afterwards, the dynabeads were washed 4 times with Washing Buffer I (PBS supplemented with 1% NP-40, 0.5% NaDeoxycholate, 300 mM NaCl, 1× Roche protease inhibitor mix and 25 U/ml Superase-RNAse inhibitor), resuspended in RNAse-free water and treated again with Turbo DNAse I (Thermo Fisher Scientific) for 30 min at 37°C.

    Article Title: Epstein-Barr Virus BBRF2 Is Required for Maximum Infectivity
    Article Snippet: Briefly, cells were washed with PBS, lysed by sonication in lysis buffer, treated with proteinase K and, after heat-inactivation of proteinase K, subjected to qPCR analysis. .. To assay the cell-free virus level, the culture supernatants were treated with Turbo DNase I (Thermo Fisher Scientific) to eliminate naked EBV DNA and subjected to DNA extraction using a DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany).

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    Thermo Fisher turbo dnase i
    Turbo Dnase I, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    turbo dnase i - by Bioz Stars, 2020-04
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