dna free kit  (Thermo Fisher)


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    Name:
    DNase I
    Description:
    DNase I Deoxyribonuclease I digests single and double stranded DNA to oligodeoxyribonucleotides containing a 5 phosphate Ribonuclease has been reduced to non detectable levels ApplicationsDNase I is suitable for removing DNA from protein preparations nick translating DNA and generating random fragments for dideoxy sequencing NOTE for removing DNA from RNA preparations use Amplification Grade DNase I Cat No 18068 015 SourceDNase I is purified from bovine pancreas Specific activityThe specific activity of DNase I is typically in the range of 10 000 25 000 units mg
    Catalog Number:
    18047019
    Price:
    None
    Category:
    Proteins Enzymes Peptides
    Applications:
    PCR & Real-Time PCR|Reverse Transcription
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    Structured Review

    Thermo Fisher dna free kit
    5′ RACE confirms the location of transcription intiation in HeT-A. The two panels show ethidium bromide stained agarose gels of 5′ RACE reactions using the HeT-A outer and inner primers HR1 and HR2. The sources of <t>RNA</t> were Oregon-R adults or third instar larvae, as indicated. Lanes 1 and 2 correspond to the experimental and control lanes, respectively. The migration of <t>DNA</t> standards (in bp) is indicated to the left of each panel. Below the panels is a sequence corresponding to the largest cloned RACE product obtained from adult RNA. Positions 1–92 and 111–137 are 91/92 and 27/27 matches, respectively, to positions 6999–7090 and 7136–7162 in HeT-A 23Zn (accession no. U06920). Filled circles below two bases indicate the previously identified transcription initiation sites ( 18 ). Lines ending in squares indicate the sites corresponding to three RACE products obtained from adult RNA and a line ending in a circle indicates the site corresponding to the major RACE product from L3 RNA.
    DNase I Deoxyribonuclease I digests single and double stranded DNA to oligodeoxyribonucleotides containing a 5 phosphate Ribonuclease has been reduced to non detectable levels ApplicationsDNase I is suitable for removing DNA from protein preparations nick translating DNA and generating random fragments for dideoxy sequencing NOTE for removing DNA from RNA preparations use Amplification Grade DNase I Cat No 18068 015 SourceDNase I is purified from bovine pancreas Specific activityThe specific activity of DNase I is typically in the range of 10 000 25 000 units mg
    https://www.bioz.com/result/dna free kit/product/Thermo Fisher
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    dna free kit - by Bioz Stars, 2021-03
    86/100 stars

    Images

    1) Product Images from "Identification of multiple transcription initiation, polyadenylation, and splice sites in the Drosophila melanogaster TART family of telomeric retrotransposons"

    Article Title: Identification of multiple transcription initiation, polyadenylation, and splice sites in the Drosophila melanogaster TART family of telomeric retrotransposons

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkl709

    5′ RACE confirms the location of transcription intiation in HeT-A. The two panels show ethidium bromide stained agarose gels of 5′ RACE reactions using the HeT-A outer and inner primers HR1 and HR2. The sources of RNA were Oregon-R adults or third instar larvae, as indicated. Lanes 1 and 2 correspond to the experimental and control lanes, respectively. The migration of DNA standards (in bp) is indicated to the left of each panel. Below the panels is a sequence corresponding to the largest cloned RACE product obtained from adult RNA. Positions 1–92 and 111–137 are 91/92 and 27/27 matches, respectively, to positions 6999–7090 and 7136–7162 in HeT-A 23Zn (accession no. U06920). Filled circles below two bases indicate the previously identified transcription initiation sites ( 18 ). Lines ending in squares indicate the sites corresponding to three RACE products obtained from adult RNA and a line ending in a circle indicates the site corresponding to the major RACE product from L3 RNA.
    Figure Legend Snippet: 5′ RACE confirms the location of transcription intiation in HeT-A. The two panels show ethidium bromide stained agarose gels of 5′ RACE reactions using the HeT-A outer and inner primers HR1 and HR2. The sources of RNA were Oregon-R adults or third instar larvae, as indicated. Lanes 1 and 2 correspond to the experimental and control lanes, respectively. The migration of DNA standards (in bp) is indicated to the left of each panel. Below the panels is a sequence corresponding to the largest cloned RACE product obtained from adult RNA. Positions 1–92 and 111–137 are 91/92 and 27/27 matches, respectively, to positions 6999–7090 and 7136–7162 in HeT-A 23Zn (accession no. U06920). Filled circles below two bases indicate the previously identified transcription initiation sites ( 18 ). Lines ending in squares indicate the sites corresponding to three RACE products obtained from adult RNA and a line ending in a circle indicates the site corresponding to the major RACE product from L3 RNA.

    Techniques Used: Staining, Migration, Sequencing, Clone Assay

    Representative 5′ and 3′ RACE reactions. Each panel is an ethidium bromide stained agarose gel of RACE reactions. Above each panel is a 5′ end or 3′ end designation (5a–5e or 3a–3e, respectively) used for discussion purposes. Lanes 1 and 2 are the experimental and control lanes, respectively. The sources of RNA for the reactions shown were Oregon-R adults (5a, 5c, 5d, 3c, 3d and 3e), S2 cells (5b and 3b), Mk-G(II)12 adults (5e) or Mk-G(II)12 third instar larvae (3a). The TART primers used for the reactions shown were as follows (both outer and inner primers are listed for reactions in which two rounds of PCR with nested primers were used): 5a: TR1 + TR2; 5b: TR6 + TR7; 5c: TCR1 + TCR2; 5d: TAB1; 5e: ADR1 + ADR2; 3a: TA53 + TA54; 3b: TA51 + TA52; 3c: TA3; 3d: TR8 + TR9; and 3e: TA31. White boxes indicate products (which in some cases are very faint) that either corresponded to the major 5′ end used for sequence comparisons (5a) or that met our criteria for representing polyadenylation sites (3a, 3c, 3d and 3e), as determined by sequencing of cloned products (see Materials and Methods). The migration of DNA standards (in bp) is indicated to the left of each panel.
    Figure Legend Snippet: Representative 5′ and 3′ RACE reactions. Each panel is an ethidium bromide stained agarose gel of RACE reactions. Above each panel is a 5′ end or 3′ end designation (5a–5e or 3a–3e, respectively) used for discussion purposes. Lanes 1 and 2 are the experimental and control lanes, respectively. The sources of RNA for the reactions shown were Oregon-R adults (5a, 5c, 5d, 3c, 3d and 3e), S2 cells (5b and 3b), Mk-G(II)12 adults (5e) or Mk-G(II)12 third instar larvae (3a). The TART primers used for the reactions shown were as follows (both outer and inner primers are listed for reactions in which two rounds of PCR with nested primers were used): 5a: TR1 + TR2; 5b: TR6 + TR7; 5c: TCR1 + TCR2; 5d: TAB1; 5e: ADR1 + ADR2; 3a: TA53 + TA54; 3b: TA51 + TA52; 3c: TA3; 3d: TR8 + TR9; and 3e: TA31. White boxes indicate products (which in some cases are very faint) that either corresponded to the major 5′ end used for sequence comparisons (5a) or that met our criteria for representing polyadenylation sites (3a, 3c, 3d and 3e), as determined by sequencing of cloned products (see Materials and Methods). The migration of DNA standards (in bp) is indicated to the left of each panel.

    Techniques Used: Staining, Agarose Gel Electrophoresis, Polymerase Chain Reaction, Sequencing, Clone Assay, Migration

    2) Product Images from "Human proteins that interact with RNA/DNA hybrids"

    Article Title: Human proteins that interact with RNA/DNA hybrids

    Journal: Genome Research

    doi: 10.1101/gr.237362.118

    R-loops at GC-rich regions in the BAMBI promoter and DPP9 3′ UTR. ( A ) Location and GC content of sequences underlying R-loops in BAMBI and DPP9 . ( Top ) R-loop location is marked on gene models of BAMBI and DPP9 . Boxes represent exons, and lines represent introns. Arrows show transcription start site and direction of transcription. ( Bottom ) GC content of the 600-mer and 90-mer sequences corresponding to RNA sequence in the R-loops (blue line). GC content is calculated as (G + C)/(G + C + A + U) in the 50-nt sliding window for 600-mer or 10-nt sliding window for 90-mer. Genome background of GC content is calculated from corresponding regions of 14,587 RefSeq genes that are at least 2 kb long and 1 kb away from neighboring genes. The gray line represents median GC content, and the shade represents ±10%. ( B ) The S9.6 antibody specifically pulled down R-loops at the 3′ UTR of DPP9 . DRIP was carried out using an S9.6 antibody or nonspecific IgG. Precipitated DNA was amplified using primers specific for DPP9 3′ UTR. Primers specific for a previously reported R-loop region at the 3′ UTR of ACTB were used as positive control. (Error bars) SEM of triplicates. ( C ) Integrity of the RNA/DNA hybrid was confirmed using RNase H1 and RNase T1. As expected, RNase H1 specifically digested RNA in the hybrids, leaving ssDNA as a product. RNase T1, which is specific for ssRNA, did not cleave the hybrids.
    Figure Legend Snippet: R-loops at GC-rich regions in the BAMBI promoter and DPP9 3′ UTR. ( A ) Location and GC content of sequences underlying R-loops in BAMBI and DPP9 . ( Top ) R-loop location is marked on gene models of BAMBI and DPP9 . Boxes represent exons, and lines represent introns. Arrows show transcription start site and direction of transcription. ( Bottom ) GC content of the 600-mer and 90-mer sequences corresponding to RNA sequence in the R-loops (blue line). GC content is calculated as (G + C)/(G + C + A + U) in the 50-nt sliding window for 600-mer or 10-nt sliding window for 90-mer. Genome background of GC content is calculated from corresponding regions of 14,587 RefSeq genes that are at least 2 kb long and 1 kb away from neighboring genes. The gray line represents median GC content, and the shade represents ±10%. ( B ) The S9.6 antibody specifically pulled down R-loops at the 3′ UTR of DPP9 . DRIP was carried out using an S9.6 antibody or nonspecific IgG. Precipitated DNA was amplified using primers specific for DPP9 3′ UTR. Primers specific for a previously reported R-loop region at the 3′ UTR of ACTB were used as positive control. (Error bars) SEM of triplicates. ( C ) Integrity of the RNA/DNA hybrid was confirmed using RNase H1 and RNase T1. As expected, RNase H1 specifically digested RNA in the hybrids, leaving ssDNA as a product. RNase T1, which is specific for ssRNA, did not cleave the hybrids.

    Techniques Used: Sequencing, Amplification, Positive Control

    Validation of protein and hybrid interaction. ( A ) The protein and hybrid interaction is shown by biolayer interferometry. Binding of DPP9 RNA/DNA hybrid (red lines) or dsDNA (blue lines) to high concentration (solid lines) or low concentration (dotted lines) of each protein was measured. These proteins showed more avid binding to RNA/DNA hybrid than to dsDNA. Baseline was recorded from 0 to 1000 sec, association of protein with dsDNA or RNA/DNA hybrid from 1000 to 1600 sec, followed by dissociation. ( B ) Immunofluorescence staining in primary human fibroblasts showing colocalization of nucleolin and DDX18 (red) with the R-loops stained by S9.6 RNA/DNA hybrid antibody (green). DAPI staining is in blue. (Scale bar) 1 µm.
    Figure Legend Snippet: Validation of protein and hybrid interaction. ( A ) The protein and hybrid interaction is shown by biolayer interferometry. Binding of DPP9 RNA/DNA hybrid (red lines) or dsDNA (blue lines) to high concentration (solid lines) or low concentration (dotted lines) of each protein was measured. These proteins showed more avid binding to RNA/DNA hybrid than to dsDNA. Baseline was recorded from 0 to 1000 sec, association of protein with dsDNA or RNA/DNA hybrid from 1000 to 1600 sec, followed by dissociation. ( B ) Immunofluorescence staining in primary human fibroblasts showing colocalization of nucleolin and DDX18 (red) with the R-loops stained by S9.6 RNA/DNA hybrid antibody (green). DAPI staining is in blue. (Scale bar) 1 µm.

    Techniques Used: Binding Assay, Concentration Assay, Size-exclusion Chromatography, Immunofluorescence, Staining

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    Article Snippet: Subsection “Fluorescent stains”, last paragraph: Looks like the authors forgot to include the relevant details for qualifying TUNEL positive cells. .. This section was revised and now includes the following details: “Positive controls were generated by pretreating cells with 15 U ml -1 DNase I (Thermo Fischer Scientific). ..

    Concentration Assay:

    Article Title: High-Discrimination Factor Nanosensor Based on Tetrahedral DNA Nanostructures and Gold Nanoparticles for Detection of MiRNA-21 in Live Cells
    Article Snippet: Enzymatic resistance of Au-TDNNs Digestion of the two groups of phosphorothioate-protected Au-TDNNs was probed using the Agilent Cary Eclipse to detect generation of nonspecific FAM fluorescence signals. .. For both human DNase I (Thermo Scientific) and exonuclease III (New England Biolabs) digestion, a common concentration of 3 U/mL was used to digest 2 nM Au-TDNNs samples in PBS. .. FAM fluorescence signals were monitored and recorded over a period of 3 h at 30 min intervals and at 37 °C.

    Isolation:

    Article Title: Extracellular RNAs in periodontopathogenic outer membrane vesicles promote TNF-α production in human macrophages and cross the blood–brain barrier in mice
    Article Snippet: The OMV was obtained from the filtered and concentrated supernatant using ExoBacteria OMV Isolation Kits (SBI, Palo Alto, CA, USA) according to the manufacturer’s protocol. .. Isolated OMVs (50 μl) were treated with 1 μl of RNase A (1 U/μl; Thermo Fisher Scientific, Waltham, MA, USA) and DNase I (2 U/μl; Thermo Fisher Scientific) to 1 ml of the OMVs and incubated at 37°C for 25 min. .. The OMV was purified again using ExoBacteria OMV Isolation Kits.

    Incubation:

    Article Title: Extracellular RNAs in periodontopathogenic outer membrane vesicles promote TNF-α production in human macrophages and cross the blood–brain barrier in mice
    Article Snippet: The OMV was obtained from the filtered and concentrated supernatant using ExoBacteria OMV Isolation Kits (SBI, Palo Alto, CA, USA) according to the manufacturer’s protocol. .. Isolated OMVs (50 μl) were treated with 1 μl of RNase A (1 U/μl; Thermo Fisher Scientific, Waltham, MA, USA) and DNase I (2 U/μl; Thermo Fisher Scientific) to 1 ml of the OMVs and incubated at 37°C for 25 min. .. The OMV was purified again using ExoBacteria OMV Isolation Kits.

    Article Title: A novel G-quadruplex-forming GGA repeat region in the c-myb promoter is a critical regulator of promoter activity
    Article Snippet: Approximately 18 000 cpm of the probe was incubated in a binding buffer (25 mM Tris-HCl (pH 8.0), 50 mM KCl, 6.25 mM MgCl2 , 0.5 mM EDTA (pH 8.0), 10% glycerol, 0.5 mM DTT) for 10 min on ice in the presence of FLAG peptides, or FLAG-MAZ. .. After adding CaCl2 and MgCl2 to 2.5 mM and 5 mM as final concentrations, respectively, 0.01u of DNase I (Invitrogen, Carlsbad, CA, USA) was added to each sample and incubated 2 min at room temperature. ..

    Article Title: Cas9-mediated excision of proximal DNaseI/H3K4me3 signatures confers robust silencing of microRNA and long non-coding RNA genes
    Article Snippet: RNA was extracted using the Trizol (Thermo Fisher) method. .. To remove contaminating DNA the nucleic acid pellet was incubated with DNaseI (Thermo Fisher) and RNase Inhibitor (Promega) for 30 min at 37°C, followed by extraction with PCI (Sigma Aldrich) and precipitation with 30:1 ethanol / 5M sodium acetate. .. Real-time PCR primer pairs are listed in .

    Amplification:

    Article Title: Tropism of Varicella-Zoster Virus for Human Tonsillar CD4+ T Lymphocytes That Express Activation, Memory, and Skin Homing Markers
    Article Snippet: VZV gE transcripts were analyzed by reverse transcription-PCR (RT-PCR) with the SUPERSCRIPT One-Step RT-PCR with PLATINUM Taq system (Invitrogen, Inc.) according to the manufacturer's instruction. .. Prior to cycling amplification, DNA contaminating the RNA sample was removed by incubating 10 ng of template RNA with 5 × 104 cell equivalents with 0.1 U of DNase I (amplification grade; Invitrogen, Inc.) at room temperature for 15 min. ..

    Article Title: DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells
    Article Snippet: .. 35 Amplify the DNase-seq product by following PCR reactions: 10 μL of Dynal bead suspension 10 μL 5X Phusion HF reaction buffer 0.5 μL of PCR primer 1 (25 μM) 0.5 μL of PCR primer 2 (25 μM) 1.25 μL of 10 mM dNTP 0.5 μL of Phusion DNA polymerase 28 μL of water Total volume: 50 μL Denature at 98°C for 30 sec, followed by 12 amplification cycles (98°C, 10 sec; 60°C, 30 sec; 72°C, 15 sec.), extend at 72 °C for 7 min. 36 Load 1 μL of 25 bp DNA marker into one well and 50 μL of PCR products into 2 adjoining wells of 4–20% TBE PAGE gel. .. Perform electrophoresis for 2 hours at 120 V. Pry apart cassette and stain the gel in 1X TE/ethidium bromide in a clean container for 2–3 min. A Representative example of amplification is shown in .

    Polymerase Chain Reaction:

    Article Title: DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells
    Article Snippet: .. 35 Amplify the DNase-seq product by following PCR reactions: 10 μL of Dynal bead suspension 10 μL 5X Phusion HF reaction buffer 0.5 μL of PCR primer 1 (25 μM) 0.5 μL of PCR primer 2 (25 μM) 1.25 μL of 10 mM dNTP 0.5 μL of Phusion DNA polymerase 28 μL of water Total volume: 50 μL Denature at 98°C for 30 sec, followed by 12 amplification cycles (98°C, 10 sec; 60°C, 30 sec; 72°C, 15 sec.), extend at 72 °C for 7 min. 36 Load 1 μL of 25 bp DNA marker into one well and 50 μL of PCR products into 2 adjoining wells of 4–20% TBE PAGE gel. .. Perform electrophoresis for 2 hours at 120 V. Pry apart cassette and stain the gel in 1X TE/ethidium bromide in a clean container for 2–3 min. A Representative example of amplification is shown in .

    Size-exclusion Chromatography:

    Article Title: DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells
    Article Snippet: .. 35 Amplify the DNase-seq product by following PCR reactions: 10 μL of Dynal bead suspension 10 μL 5X Phusion HF reaction buffer 0.5 μL of PCR primer 1 (25 μM) 0.5 μL of PCR primer 2 (25 μM) 1.25 μL of 10 mM dNTP 0.5 μL of Phusion DNA polymerase 28 μL of water Total volume: 50 μL Denature at 98°C for 30 sec, followed by 12 amplification cycles (98°C, 10 sec; 60°C, 30 sec; 72°C, 15 sec.), extend at 72 °C for 7 min. 36 Load 1 μL of 25 bp DNA marker into one well and 50 μL of PCR products into 2 adjoining wells of 4–20% TBE PAGE gel. .. Perform electrophoresis for 2 hours at 120 V. Pry apart cassette and stain the gel in 1X TE/ethidium bromide in a clean container for 2–3 min. A Representative example of amplification is shown in .

    Marker:

    Article Title: DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells
    Article Snippet: .. 35 Amplify the DNase-seq product by following PCR reactions: 10 μL of Dynal bead suspension 10 μL 5X Phusion HF reaction buffer 0.5 μL of PCR primer 1 (25 μM) 0.5 μL of PCR primer 2 (25 μM) 1.25 μL of 10 mM dNTP 0.5 μL of Phusion DNA polymerase 28 μL of water Total volume: 50 μL Denature at 98°C for 30 sec, followed by 12 amplification cycles (98°C, 10 sec; 60°C, 30 sec; 72°C, 15 sec.), extend at 72 °C for 7 min. 36 Load 1 μL of 25 bp DNA marker into one well and 50 μL of PCR products into 2 adjoining wells of 4–20% TBE PAGE gel. .. Perform electrophoresis for 2 hours at 120 V. Pry apart cassette and stain the gel in 1X TE/ethidium bromide in a clean container for 2–3 min. A Representative example of amplification is shown in .

    Polyacrylamide Gel Electrophoresis:

    Article Title: DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells
    Article Snippet: .. 35 Amplify the DNase-seq product by following PCR reactions: 10 μL of Dynal bead suspension 10 μL 5X Phusion HF reaction buffer 0.5 μL of PCR primer 1 (25 μM) 0.5 μL of PCR primer 2 (25 μM) 1.25 μL of 10 mM dNTP 0.5 μL of Phusion DNA polymerase 28 μL of water Total volume: 50 μL Denature at 98°C for 30 sec, followed by 12 amplification cycles (98°C, 10 sec; 60°C, 30 sec; 72°C, 15 sec.), extend at 72 °C for 7 min. 36 Load 1 μL of 25 bp DNA marker into one well and 50 μL of PCR products into 2 adjoining wells of 4–20% TBE PAGE gel. .. Perform electrophoresis for 2 hours at 120 V. Pry apart cassette and stain the gel in 1X TE/ethidium bromide in a clean container for 2–3 min. A Representative example of amplification is shown in .

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  • 95
    Thermo Fisher cell free dna cfdna isolation
    Fragment–length distribution of cell-free <t>DNA</t> isolated from the media of HT-29 and SW480 cells was detected with BioAnalyzer. Electropherograms represent a data plot of size in base pairs (bp) versus fluorescence (FU). Average DNA concentrations were measured with Qubit 1.0 fluorometer. Av. conc.: average concentration.
    Cell Free Dna Cfdna Isolation, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/cell free dna cfdna isolation/product/Thermo Fisher
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    cell free dna cfdna isolation - by Bioz Stars, 2021-03
    95/100 stars
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    99
    Thermo Fisher dna free agent
    RT-PCR analysis for ephrin-B1 and EphB2 in human PBMC. Three kinds of templates were used to validate the results: lane 1, cDNA; lane 2, <t>DNA-cleared</t> <t>RNA;</t> lane 3; genomic DNA.
    Dna Free Agent, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 1 article reviews
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    97
    Thermo Fisher turbo dna free kit
    Overview of EV-BEAMing. <t>EVs</t> from serum or CSF samples were pelleted at 100,000 g for 80 minutes and processed as follows: (1) RNA was extracted and (2) analyzed for total yield and quality using the Bioanalyzer (Agilent). (3) RNA was then reverse transcribed into cDNA and 1/2 of the sample was used to determine the IDH1 cDNA copy number inside EVs by (4) qPCR analysis. (5) The remaining sample was preamplified (14 cycles) and used as input for BEAMing PCR. The resulting <t>DNA-coated</t> beads were interrogated with sequence-specific fluorescent probes to produce beads with wild-type (green) and mutant (red) profiles. (6) The percentage of beads with mutant DNA was determined by FACS and used in conjunction with the qPCR data to determine the minimum number of copies present to allow reliable detection of the mutant message.
    Turbo Dna Free Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 97/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/turbo dna free kit/product/Thermo Fisher
    Average 97 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    turbo dna free kit - by Bioz Stars, 2021-03
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    Image Search Results


    Fragment–length distribution of cell-free DNA isolated from the media of HT-29 and SW480 cells was detected with BioAnalyzer. Electropherograms represent a data plot of size in base pairs (bp) versus fluorescence (FU). Average DNA concentrations were measured with Qubit 1.0 fluorometer. Av. conc.: average concentration.

    Journal: Cells

    Article Title: S-Adenosylmethionine Treatment of Colorectal Cancer Cell Lines Alters DNA Methylation, DNA Repair and Tumor Progression-Related Gene Expression

    doi: 10.3390/cells9081864

    Figure Lengend Snippet: Fragment–length distribution of cell-free DNA isolated from the media of HT-29 and SW480 cells was detected with BioAnalyzer. Electropherograms represent a data plot of size in base pairs (bp) versus fluorescence (FU). Average DNA concentrations were measured with Qubit 1.0 fluorometer. Av. conc.: average concentration.

    Article Snippet: Quantitative and Qualitative Analysis of Cell-Free DNA with DNA IsolationMedium of the treated cells (2.5 mL) was collected and used for cell-free DNA (cfDNA) isolation following centrifugation (10 min at 1000 rpm).

    Techniques: Isolation, Fluorescence, Concentration Assay

    RT-PCR analysis for ephrin-B1 and EphB2 in human PBMC. Three kinds of templates were used to validate the results: lane 1, cDNA; lane 2, DNA-cleared RNA; lane 3; genomic DNA.

    Journal: International Journal of Vascular Medicine

    Article Title: Expression and Function of Ephrin-B1 and Its Cognate Receptor EphB2 in Human Abdominal Aortic Aneurysm

    doi: 10.1155/2012/127149

    Figure Lengend Snippet: RT-PCR analysis for ephrin-B1 and EphB2 in human PBMC. Three kinds of templates were used to validate the results: lane 1, cDNA; lane 2, DNA-cleared RNA; lane 3; genomic DNA.

    Article Snippet: Then, 10 μ g of total RNA was treated with DNA-free agent (Ambion, Austin, TX) and converted to cDNA using random primers and SuperScript II reverse transcriptase (Invitrogen).

    Techniques: Reverse Transcription Polymerase Chain Reaction

    Effects of panicle removal on expression patterns of Diff_SAGs between FL and SL. ( a , b , d , e ) qRT-PCR analyses of independent samples (n = 3) performed for the denoted representative genes of G1-4 with and without panicle removal (“Panicle Removal” and “Control” panels, respectively). Expression levels of representative genes were normalized to those of actin at corresponding time points. Blue and red lines represent temporal expression profiles of genes in FL and SL, respectively. Data are presented as means ± SEM from three biological replicates. ( c ) Relative changes of integrated differences in temporal expression profiles of representative genes between FL and SL with and without panicle removal (top panel); [Diff(FL-SL) PR − Diff(FL-SL) Con ]/Diff(FL-SL) Con . Integrated differences with [Diff(FL-SL) PR ] or without panicle removal [Diff(FL-SL) Con ] were computed by integrating differences in expression levels at each time point using trapezoidal integration. Boxplots of relative changes in integrated differences for genes in each group are shown (bottom panel); *P

    Journal: Scientific Reports

    Article Title: Molecular bases for differential aging programs between flag and second leaves during grain-filling in rice

    doi: 10.1038/s41598-017-07035-9

    Figure Lengend Snippet: Effects of panicle removal on expression patterns of Diff_SAGs between FL and SL. ( a , b , d , e ) qRT-PCR analyses of independent samples (n = 3) performed for the denoted representative genes of G1-4 with and without panicle removal (“Panicle Removal” and “Control” panels, respectively). Expression levels of representative genes were normalized to those of actin at corresponding time points. Blue and red lines represent temporal expression profiles of genes in FL and SL, respectively. Data are presented as means ± SEM from three biological replicates. ( c ) Relative changes of integrated differences in temporal expression profiles of representative genes between FL and SL with and without panicle removal (top panel); [Diff(FL-SL) PR − Diff(FL-SL) Con ]/Diff(FL-SL) Con . Integrated differences with [Diff(FL-SL) PR ] or without panicle removal [Diff(FL-SL) Con ] were computed by integrating differences in expression levels at each time point using trapezoidal integration. Boxplots of relative changes in integrated differences for genes in each group are shown (bottom panel); *P

    Article Snippet: qRT-PCR analyses After DNase (AM1906, ambion) treatment, cDNA was synthesized from approximately 400 ng of total RNA using an ImProm-II Reverse Transcription System (A3800, Promega).

    Techniques: Expressing, Quantitative RT-PCR

    Long-distance AATs and differential N contents between FL and SL. ( a ) Selection procedures for long-distance AAT Diff_SAGs that reflect differential N content profiles between FL and SL (Fig. 1d ). ( b ) Numbers of AAT Diff_SAGs (G1, G3, and G5) of individual AAT subfamilies (see also Supplementary Table 5 ). ( c , d ) qRT-PCR analyses of independent samples (n = 3) performed for denoted AAT genes with and without panicle removal (“Panicle Removal” and “Control” panels, respectively). Expression levels of AAT genes were normalized to those of actin at corresponding time points. Blue and red lines represent temporal expression profiles of genes in FL and SL, respectively. Data are presented as means ± SEM from three biological replicates. ( e ) Relative changes of integrated differences in temporal expression profiles of AAT genes between FL and SL with and without panicle removal (top panel); [Diff(FL-SL) PR − Diff(FL-SL) Con ]/Diff(FL-SL) Con . Integrated differences with [Diff(FL-SL) PR ] or without panicle removal [Diff(FL-SL) Con ] were computed by integrating differences in expression levels at each time point using trapezoidal integration. Boxplots for the absolute relative changes of integrated differences for the two groups of genes (three long-distance AAT genes and negative controls) are shown in the bottom panel. ( f ) Differential total N content profiles (g/dry weight %) during grain filling with and without panicle removal (“Panicle Removal” and “Control” panels, respectively; top panel). Blue and red lines represent temporal N content profiles in FL and SL, respectively. Differences in N contents between FL and SL are shown for each time point (bottom panel). *P

    Journal: Scientific Reports

    Article Title: Molecular bases for differential aging programs between flag and second leaves during grain-filling in rice

    doi: 10.1038/s41598-017-07035-9

    Figure Lengend Snippet: Long-distance AATs and differential N contents between FL and SL. ( a ) Selection procedures for long-distance AAT Diff_SAGs that reflect differential N content profiles between FL and SL (Fig. 1d ). ( b ) Numbers of AAT Diff_SAGs (G1, G3, and G5) of individual AAT subfamilies (see also Supplementary Table 5 ). ( c , d ) qRT-PCR analyses of independent samples (n = 3) performed for denoted AAT genes with and without panicle removal (“Panicle Removal” and “Control” panels, respectively). Expression levels of AAT genes were normalized to those of actin at corresponding time points. Blue and red lines represent temporal expression profiles of genes in FL and SL, respectively. Data are presented as means ± SEM from three biological replicates. ( e ) Relative changes of integrated differences in temporal expression profiles of AAT genes between FL and SL with and without panicle removal (top panel); [Diff(FL-SL) PR − Diff(FL-SL) Con ]/Diff(FL-SL) Con . Integrated differences with [Diff(FL-SL) PR ] or without panicle removal [Diff(FL-SL) Con ] were computed by integrating differences in expression levels at each time point using trapezoidal integration. Boxplots for the absolute relative changes of integrated differences for the two groups of genes (three long-distance AAT genes and negative controls) are shown in the bottom panel. ( f ) Differential total N content profiles (g/dry weight %) during grain filling with and without panicle removal (“Panicle Removal” and “Control” panels, respectively; top panel). Blue and red lines represent temporal N content profiles in FL and SL, respectively. Differences in N contents between FL and SL are shown for each time point (bottom panel). *P

    Article Snippet: qRT-PCR analyses After DNase (AM1906, ambion) treatment, cDNA was synthesized from approximately 400 ng of total RNA using an ImProm-II Reverse Transcription System (A3800, Promega).

    Techniques: Selection, Quantitative RT-PCR, Expressing

    Overview of EV-BEAMing. EVs from serum or CSF samples were pelleted at 100,000 g for 80 minutes and processed as follows: (1) RNA was extracted and (2) analyzed for total yield and quality using the Bioanalyzer (Agilent). (3) RNA was then reverse transcribed into cDNA and 1/2 of the sample was used to determine the IDH1 cDNA copy number inside EVs by (4) qPCR analysis. (5) The remaining sample was preamplified (14 cycles) and used as input for BEAMing PCR. The resulting DNA-coated beads were interrogated with sequence-specific fluorescent probes to produce beads with wild-type (green) and mutant (red) profiles. (6) The percentage of beads with mutant DNA was determined by FACS and used in conjunction with the qPCR data to determine the minimum number of copies present to allow reliable detection of the mutant message.

    Journal: Molecular Therapy. Nucleic Acids

    Article Title: BEAMing and Droplet Digital PCR Analysis of Mutant IDH1 mRNA in Glioma Patient Serum and Cerebrospinal Fluid Extracellular Vesicles

    doi: 10.1038/mtna.2013.28

    Figure Lengend Snippet: Overview of EV-BEAMing. EVs from serum or CSF samples were pelleted at 100,000 g for 80 minutes and processed as follows: (1) RNA was extracted and (2) analyzed for total yield and quality using the Bioanalyzer (Agilent). (3) RNA was then reverse transcribed into cDNA and 1/2 of the sample was used to determine the IDH1 cDNA copy number inside EVs by (4) qPCR analysis. (5) The remaining sample was preamplified (14 cycles) and used as input for BEAMing PCR. The resulting DNA-coated beads were interrogated with sequence-specific fluorescent probes to produce beads with wild-type (green) and mutant (red) profiles. (6) The percentage of beads with mutant DNA was determined by FACS and used in conjunction with the qPCR data to determine the minimum number of copies present to allow reliable detection of the mutant message.

    Article Snippet: External DNA on the EVs was removed using 2 µl of DNAse from the Turbo DNA-free kit (Ambion, Foster City, CA), according to manufacturer's recommendations.

    Techniques: Real-time Polymerase Chain Reaction, Polymerase Chain Reaction, Sequencing, Mutagenesis, FACS