on column dnase i digestion  (Qiagen)


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    Structured Review

    Qiagen on column dnase i digestion
    Summary of in vitro primer extension and <t>DNase</t> I and KMnO 4 footprinting. ( A ) Sequence of P vpsL from −60 to +30. Bold and underlined A with black arrow at +1 and bold G (+3) represent the TSS determined by primer extensions; the −10 element and the −35 region are labeled and boxed in green; sequences in bold and red denote the VpsR binding site. Protection sites from DNase I footprinting and hypersensitive sites are depicted as rectangular boxes and triangles, respectively, either above (non-template) or below (template) the sequences: gray, RNAP with or without c-di-GMP or VpsR; black, RNAP with VpsR and c-di-GMP; red, VpsR with or without c-di-GMP. The open transcription bubble detected using KMnO 4 footprinting is shown as separated ssDNA from position −11 to +2 with sites of KMnO 4 cleavage indicated as purple asterisks. ( B ) Summary of positions of protection and hypersensitive sites on non-template and template strand DNA.
    On Column Dnase I Digestion, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 30 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Images

    1) Product Images from "VpsR and cyclic di-GMP together drive transcription initiation to activate biofilm formation in Vibrio cholerae"

    Article Title: VpsR and cyclic di-GMP together drive transcription initiation to activate biofilm formation in Vibrio cholerae

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gky606

    Summary of in vitro primer extension and DNase I and KMnO 4 footprinting. ( A ) Sequence of P vpsL from −60 to +30. Bold and underlined A with black arrow at +1 and bold G (+3) represent the TSS determined by primer extensions; the −10 element and the −35 region are labeled and boxed in green; sequences in bold and red denote the VpsR binding site. Protection sites from DNase I footprinting and hypersensitive sites are depicted as rectangular boxes and triangles, respectively, either above (non-template) or below (template) the sequences: gray, RNAP with or without c-di-GMP or VpsR; black, RNAP with VpsR and c-di-GMP; red, VpsR with or without c-di-GMP. The open transcription bubble detected using KMnO 4 footprinting is shown as separated ssDNA from position −11 to +2 with sites of KMnO 4 cleavage indicated as purple asterisks. ( B ) Summary of positions of protection and hypersensitive sites on non-template and template strand DNA.
    Figure Legend Snippet: Summary of in vitro primer extension and DNase I and KMnO 4 footprinting. ( A ) Sequence of P vpsL from −60 to +30. Bold and underlined A with black arrow at +1 and bold G (+3) represent the TSS determined by primer extensions; the −10 element and the −35 region are labeled and boxed in green; sequences in bold and red denote the VpsR binding site. Protection sites from DNase I footprinting and hypersensitive sites are depicted as rectangular boxes and triangles, respectively, either above (non-template) or below (template) the sequences: gray, RNAP with or without c-di-GMP or VpsR; black, RNAP with VpsR and c-di-GMP; red, VpsR with or without c-di-GMP. The open transcription bubble detected using KMnO 4 footprinting is shown as separated ssDNA from position −11 to +2 with sites of KMnO 4 cleavage indicated as purple asterisks. ( B ) Summary of positions of protection and hypersensitive sites on non-template and template strand DNA.

    Techniques Used: In Vitro, Footprinting, Sequencing, Labeling, Binding Assay

    DNase I footprinting of P vpsL complexes on ( A ) nontemplate DNA and ( B ) template DNA. GA corresponds to G+A ladder. VpsR, c-di-GMP and/or RNAP are present as indicated. To the right of each gel image, a schematic indicates the −10 and −35 regions and the +1. The VpsR binding site is indicated as a dashed black line. DNase I protection regions and hypersensitive sites seen with the activated complex of RNAP, VpsR, c-di-GMP and DNA are depicted as black rectangles and horizontal arrows, respectively. The dashed red boxes indicate the regions of DNA where the protection/enhancement within and immediately adjacent to the VpsR binding site changes when comparing complexes containing RNAP with or without VpsR or c-di-GMP to the activated complex. (See text for details.)
    Figure Legend Snippet: DNase I footprinting of P vpsL complexes on ( A ) nontemplate DNA and ( B ) template DNA. GA corresponds to G+A ladder. VpsR, c-di-GMP and/or RNAP are present as indicated. To the right of each gel image, a schematic indicates the −10 and −35 regions and the +1. The VpsR binding site is indicated as a dashed black line. DNase I protection regions and hypersensitive sites seen with the activated complex of RNAP, VpsR, c-di-GMP and DNA are depicted as black rectangles and horizontal arrows, respectively. The dashed red boxes indicate the regions of DNA where the protection/enhancement within and immediately adjacent to the VpsR binding site changes when comparing complexes containing RNAP with or without VpsR or c-di-GMP to the activated complex. (See text for details.)

    Techniques Used: Footprinting, Binding Assay

    2) Product Images from "VpsR and cyclic di-GMP together drive transcription initiation to activate biofilm formation in Vibrio cholerae"

    Article Title: VpsR and cyclic di-GMP together drive transcription initiation to activate biofilm formation in Vibrio cholerae

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gky606

    Summary of in vitro primer extension and DNase I and KMnO 4 footprinting. ( A ) Sequence of P vpsL from −60 to +30. Bold and underlined A with black arrow at +1 and bold G (+3) represent the TSS determined by primer extensions; the −10 element and the −35 region are labeled and boxed in green; sequences in bold and red denote the VpsR binding site. Protection sites from DNase I footprinting and hypersensitive sites are depicted as rectangular boxes and triangles, respectively, either above (non-template) or below (template) the sequences: gray, RNAP with or without c-di-GMP or VpsR; black, RNAP with VpsR and c-di-GMP; red, VpsR with or without c-di-GMP. The open transcription bubble detected using KMnO 4 footprinting is shown as separated ssDNA from position −11 to +2 with sites of KMnO 4 cleavage indicated as purple asterisks. ( B ) Summary of positions of protection and hypersensitive sites on non-template and template strand DNA.
    Figure Legend Snippet: Summary of in vitro primer extension and DNase I and KMnO 4 footprinting. ( A ) Sequence of P vpsL from −60 to +30. Bold and underlined A with black arrow at +1 and bold G (+3) represent the TSS determined by primer extensions; the −10 element and the −35 region are labeled and boxed in green; sequences in bold and red denote the VpsR binding site. Protection sites from DNase I footprinting and hypersensitive sites are depicted as rectangular boxes and triangles, respectively, either above (non-template) or below (template) the sequences: gray, RNAP with or without c-di-GMP or VpsR; black, RNAP with VpsR and c-di-GMP; red, VpsR with or without c-di-GMP. The open transcription bubble detected using KMnO 4 footprinting is shown as separated ssDNA from position −11 to +2 with sites of KMnO 4 cleavage indicated as purple asterisks. ( B ) Summary of positions of protection and hypersensitive sites on non-template and template strand DNA.

    Techniques Used: In Vitro, Footprinting, Sequencing, Labeling, Binding Assay

    DNase I footprinting of P vpsL complexes on ( A ) nontemplate DNA and ( B ) template DNA. GA corresponds to G+A ladder. VpsR, c-di-GMP and/or RNAP are present as indicated. To the right of each gel image, a schematic indicates the −10 and −35 regions and the +1. The VpsR binding site is indicated as a dashed black line. DNase I protection regions and hypersensitive sites seen with the activated complex of RNAP, VpsR, c-di-GMP and DNA are depicted as black rectangles and horizontal arrows, respectively. The dashed red boxes indicate the regions of DNA where the protection/enhancement within and immediately adjacent to the VpsR binding site changes when comparing complexes containing RNAP with or without VpsR or c-di-GMP to the activated complex. (See text for details.)
    Figure Legend Snippet: DNase I footprinting of P vpsL complexes on ( A ) nontemplate DNA and ( B ) template DNA. GA corresponds to G+A ladder. VpsR, c-di-GMP and/or RNAP are present as indicated. To the right of each gel image, a schematic indicates the −10 and −35 regions and the +1. The VpsR binding site is indicated as a dashed black line. DNase I protection regions and hypersensitive sites seen with the activated complex of RNAP, VpsR, c-di-GMP and DNA are depicted as black rectangles and horizontal arrows, respectively. The dashed red boxes indicate the regions of DNA where the protection/enhancement within and immediately adjacent to the VpsR binding site changes when comparing complexes containing RNAP with or without VpsR or c-di-GMP to the activated complex. (See text for details.)

    Techniques Used: Footprinting, Binding Assay

    Related Articles

    Centrifugation:

    Article Title: VpsR and cyclic di-GMP together drive transcription initiation to activate biofilm formation in Vibrio cholerae
    Article Snippet: .. Cells were harvested by centrifugation and RNA was extracted using the RNeasy kit (Qiagen), and an on-column DNase I digestion (Qiagen) was performed according to manufacturer's instructions. ..

    Synthesized:

    Article Title: Inhibitory Effects of iPSC-MSCs and Their Extracellular Vesicles on the Onset of Sialadenitis in a Mouse Model of Sjögren's Syndrome
    Article Snippet: Reverse Transcription and Quantitative PCR Total RNAs were extracted with the RNeasy Plus Mini Kit with on-column DNase I digestion (Qiagen, 74136). .. The primers were synthesized by Thermo Fisher with sequences retrieved from PrimerBank ( https://pga.mgh.harvard.edu/primerbank ).

    Article Title: Critical Role of TGF-β and IL-2 Receptor Signaling in Foxp3 Induction by an Inhibitor of DNA Methylation
    Article Snippet: Gene Expression Analysis Total populations of viable cells were FACS purified from TCR stimulation cultures at indicated time points, and total RNA was extracted using the RNeasy® Mini Kit and on-column DNase I digestion (QIAGEN). .. For real-time RT-PCR, cDNA was synthesized using SuperScript II reverse transcriptase (Invitrogen) according to the manufacturer’s recommendations.

    Article Title: Critical Role of TGF-β and IL-2 Receptor Signaling in Foxp3 Induction by an Inhibitor of DNA Methylation
    Article Snippet: Total populations of viable cells were FACS purified from TCR stimulation cultures at indicated time points, and total RNA was extracted using the RNeasy® Mini Kit and on-column DNase I digestion (QIAGEN). .. For real-time RT-PCR, cDNA was synthesized using SuperScript II reverse transcriptase (Invitrogen) according to the manufacturer’s recommendations.

    Quantitative RT-PCR:

    Article Title: Critical Role of TGF-β and IL-2 Receptor Signaling in Foxp3 Induction by an Inhibitor of DNA Methylation
    Article Snippet: Gene Expression Analysis Total populations of viable cells were FACS purified from TCR stimulation cultures at indicated time points, and total RNA was extracted using the RNeasy® Mini Kit and on-column DNase I digestion (QIAGEN). .. For real-time RT-PCR, cDNA was synthesized using SuperScript II reverse transcriptase (Invitrogen) according to the manufacturer’s recommendations.

    Article Title: CXCL8 and CCL20 Enhance Osteoclastogenesis via Modulation of Cytokine Production by Human Primary Osteoblasts
    Article Snippet: .. RNA Isolation and Real-time RT-PCR Total RNA of primary osteoblasts was isolated using an RNeasy Micro kit with an on-column DNase I digestion (Qiagen, Basel, Switzerland). .. Total RNA concentrations were measured with a Nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE). cDNA synthesis was performed in a thermocycler GeneAmp PCR System 9700 PE (Applied Biosystems, Foster City, CA), using a SuperScript VILO cDNA Synthesis Kit (LifeTechnologies, Inchinnan, UK), with 0.1 μg of total RNA in 20 μl reaction mixture consisting of VILO Reaction Mix and SuperScript Enzyme Mix.

    Article Title: Critical Role of TGF-β and IL-2 Receptor Signaling in Foxp3 Induction by an Inhibitor of DNA Methylation
    Article Snippet: Total populations of viable cells were FACS purified from TCR stimulation cultures at indicated time points, and total RNA was extracted using the RNeasy® Mini Kit and on-column DNase I digestion (QIAGEN). .. For real-time RT-PCR, cDNA was synthesized using SuperScript II reverse transcriptase (Invitrogen) according to the manufacturer’s recommendations.

    Article Title: Mechanical Loading Reduces Inflammation-Induced Human Osteocyte-to-Osteoclast Communication
    Article Snippet: .. RNA Isolation and Real-Time RT-PCR Total RNA from osteocytes was isolated using an RNeasy® Micro kit with an on-column DNase I digestion (Qiagen, Basel, Switzerland). .. Total RNA concentrations were measured with a Nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE). cDNA synthesis was performed in a thermocycler GeneAmp® PCR System 9700 PE (Applied Biosystems, Foster City, CA), using aSuperScript® VILO™ cDNA Synthesis Kit (LifeTechnologies, Inchinnan, UK), with 0.1 μg of total RNA in 20 μl reaction mixture consisting of VILO Reaction Mix and SuperScript Enzyme Mix. cDNA was stored at −20 °C until real-time PCR analysis.

    Article Title: CNBP controls IL-12 gene transcription and Th1 immunity
    Article Snippet: Paragraph title: RNA extraction and qRT-PCR ... Genomic DNA in RNA purifications was eliminated using on-column DNase I digestion (Qiagen).

    SYBR Green Assay:

    Article Title: Inhibitory Effects of iPSC-MSCs and Their Extracellular Vesicles on the Onset of Sialadenitis in a Mouse Model of Sjögren's Syndrome
    Article Snippet: Reverse Transcription and Quantitative PCR Total RNAs were extracted with the RNeasy Plus Mini Kit with on-column DNase I digestion (Qiagen, 74136). .. Quantitative PCR (qPCR) was performed with SYBR Green master mix on a 7900HT Fast Real-Time PCR System (Applied Biosystems).

    Article Title: Critical Role of TGF-β and IL-2 Receptor Signaling in Foxp3 Induction by an Inhibitor of DNA Methylation
    Article Snippet: Gene Expression Analysis Total populations of viable cells were FACS purified from TCR stimulation cultures at indicated time points, and total RNA was extracted using the RNeasy® Mini Kit and on-column DNase I digestion (QIAGEN). .. The QuantiFast SYBR Green PCR kit (Qiagen) and a Mastercycler ep realplex thermal cycler (Eppendorf) were used to analyze cDNA in replicates.

    Article Title: CXCL8 and CCL20 Enhance Osteoclastogenesis via Modulation of Cytokine Production by Human Primary Osteoblasts
    Article Snippet: RNA Isolation and Real-time RT-PCR Total RNA of primary osteoblasts was isolated using an RNeasy Micro kit with an on-column DNase I digestion (Qiagen, Basel, Switzerland). .. Real-time PCR reactions were performed using 2.5 μl cDNA and SYBR Green Supermix (Roche Laboratories, Indianapolis, IN) in a LightCycler (Roche Diagnostics).

    Article Title: Critical Role of TGF-β and IL-2 Receptor Signaling in Foxp3 Induction by an Inhibitor of DNA Methylation
    Article Snippet: Total populations of viable cells were FACS purified from TCR stimulation cultures at indicated time points, and total RNA was extracted using the RNeasy® Mini Kit and on-column DNase I digestion (QIAGEN). .. The QuantiFast SYBR Green PCR kit (Qiagen) and a Mastercycler ep realplex thermal cycler (Eppendorf) were used to analyze cDNA in replicates.

    Article Title: Mechanical Loading Reduces Inflammation-Induced Human Osteocyte-to-Osteoclast Communication
    Article Snippet: RNA Isolation and Real-Time RT-PCR Total RNA from osteocytes was isolated using an RNeasy® Micro kit with an on-column DNase I digestion (Qiagen, Basel, Switzerland). .. Real-time PCR reactions were performed using 2.0 μl cDNA and SYBR® Green Supermix (Roche Laboratories, Indianapolis, IN) in a LightCycler® (Roche Diagnostics, Switzerland).

    Article Title: CNBP controls IL-12 gene transcription and Th1 immunity
    Article Snippet: Genomic DNA in RNA purifications was eliminated using on-column DNase I digestion (Qiagen). .. Diluted cDNAs (1:100 final) were subjected to qPCR analysis using iQ SYBR Green Supermix reagent (Bio-Rad).

    Microarray:

    Article Title: Glucocorticoid therapy regulates podocyte motility by inhibition of Rac1
    Article Snippet: Paragraph title: Microarray analysis ... Total cellular RNA was isolated using the RNeasy mini kit with on-column DNase I digestion (Qiagen).

    Random Hexamer Labeling:

    Article Title: The combinatorial approach of laser-captured microdissection and reverse transcription quantitative polymerase chain reaction accurately determines HER2 status in breast cancer
    Article Snippet: The RNeasy FFPE kit including an on-column DNase I digestion (Qiagen; version 09/2011) was used for RNA extraction according to the manufacturer’s instructions. .. Reverse transcription was performed using total RNA according to the combined random hexamer and oligo(dT) priming protocol of the Transcriptor First Strand cDNA Synthesis Kit (Roche) in a final volume of 20 μl.

    Formalin-fixed Paraffin-Embedded:

    Article Title: Increased Wnt and Notch signaling: a clue to the renal disease in Schimke immuno-osseous dysplasia?
    Article Snippet: Total RNA from formalin-fixed paraffin-embedded (FFPE) fetal kidney was isolated using the RNeasy FFPE Kit (Qiagen, Toronto, ON, Canada). .. Genomic DNA was removed by on-column DNase I digestion (Qiagen, Toronto, ON, Canada).

    Article Title: The combinatorial approach of laser-captured microdissection and reverse transcription quantitative polymerase chain reaction accurately determines HER2 status in breast cancer
    Article Snippet: .. The RNeasy FFPE kit including an on-column DNase I digestion (Qiagen; version 09/2011) was used for RNA extraction according to the manufacturer’s instructions. .. For deparaffinization the FFPE tissue sections were treated with xylene.

    Expressing:

    Article Title: Critical Role of TGF-β and IL-2 Receptor Signaling in Foxp3 Induction by an Inhibitor of DNA Methylation
    Article Snippet: .. Gene Expression Analysis Total populations of viable cells were FACS purified from TCR stimulation cultures at indicated time points, and total RNA was extracted using the RNeasy® Mini Kit and on-column DNase I digestion (QIAGEN). .. For real-time RT-PCR, cDNA was synthesized using SuperScript II reverse transcriptase (Invitrogen) according to the manufacturer’s recommendations.

    Article Title: Glucocorticoid therapy regulates podocyte motility by inhibition of Rac1
    Article Snippet: Total cellular RNA was isolated using the RNeasy mini kit with on-column DNase I digestion (Qiagen). .. Total RNA from each sample was used to prepare biotinylated fragmented complementary RNA according to the GeneChip® Expression Analysis Protocol (Affymetrix).

    Article Title: Critical Role of TGF-β and IL-2 Receptor Signaling in Foxp3 Induction by an Inhibitor of DNA Methylation
    Article Snippet: Paragraph title: Gene Expression Analysis ... Total populations of viable cells were FACS purified from TCR stimulation cultures at indicated time points, and total RNA was extracted using the RNeasy® Mini Kit and on-column DNase I digestion (QIAGEN).

    Article Title: CNBP controls IL-12 gene transcription and Th1 immunity
    Article Snippet: Genomic DNA in RNA purifications was eliminated using on-column DNase I digestion (Qiagen). .. Gene expression levels were normalized to Gapdh as housekeeping genes.

    Cell Culture:

    Article Title: Glucocorticoid therapy regulates podocyte motility by inhibition of Rac1
    Article Snippet: Microarray analysis Fully differentiated human wild type podocytes cultured in RPMI 1640 medium were treated with 1 µM prednisolone or an equal volume (0.001%,v/v) of methanol as a vehicle control for 5 hours at 37 °C. .. Total cellular RNA was isolated using the RNeasy mini kit with on-column DNase I digestion (Qiagen).

    Generated:

    Article Title: VpsR and cyclic di-GMP together drive transcription initiation to activate biofilm formation in Vibrio cholerae
    Article Snippet: Primer extension analyses of RNA generated in vitro were performed according to manufacturer’s instructions (Promega) by using AMV Reverse Transcriptase. .. Cells were harvested by centrifugation and RNA was extracted using the RNeasy kit (Qiagen), and an on-column DNase I digestion (Qiagen) was performed according to manufacturer's instructions.

    Sequencing:

    Article Title: RNA-Seq study reveals genetic responses of diverse wild soybean accessions to increased ozone levels
    Article Snippet: .. Isolation of RNA and sequencing Total RNA was isolated using Plant RNeasy kits with on-column DNase I digestion (Qiagen, CA). .. Isolated samples were sent to the Genomic Sciences Laboratory (GSL) at North Carolina State University in Raleigh, NC where RNA quality was assured with Bioanalyzer RNA nano chips (Agilent, CA); Truseq libraries (Illumina, CA) were prepared; and libraries were sequenced using the HiSeq 2500 (Illumina, CA).

    Binding Assay:

    Article Title: Identification of candidate long non-coding RNAs in response to myocardial infarction
    Article Snippet: Heart was excised and immediately homogenized in Lysis Binding Buffer (mirVana isolation kit, Life technologies) for extraction of total RNA using the mirVana isolation kit (Life technologies, Merelbeke, Belgium) according to manufacturer’s instructions. .. On-column DNase I digestion (Qiagen, Venlo, The Netherlands) was performed to eliminate potential contamination with genomic DNA.

    In Vivo:

    Article Title: VpsR and cyclic di-GMP together drive transcription initiation to activate biofilm formation in Vibrio cholerae
    Article Snippet: In vivo RNA was obtained from WN310 containing pMLH17 and pCMW75 or pCMW98 grown in LB with 100 μg/ml ampicillin and 100 μg/ml kanamycin at 37°C with shaking at 220 rpm to an OD600 of ∼0.5. .. Cells were harvested by centrifugation and RNA was extracted using the RNeasy kit (Qiagen), and an on-column DNase I digestion (Qiagen) was performed according to manufacturer's instructions.

    RNA Sequencing Assay:

    Article Title: Non-exhaustive DNA methylation-mediated transposon silencing in the black truffle genome, a complex fungal genome with massive repeat element content
    Article Snippet: .. RNA-seq library preparation and data analysis Total RNA was extracted as described above, dissolved in H2 O after LiCl precipitation and purified with the RNeasy Plant Mini kit followed by on-column DNase I digestion (QIAGEN) as per the manufacturer’s instructions. ..

    Isolation:

    Article Title: CXCL8 and CCL20 Enhance Osteoclastogenesis via Modulation of Cytokine Production by Human Primary Osteoblasts
    Article Snippet: .. RNA Isolation and Real-time RT-PCR Total RNA of primary osteoblasts was isolated using an RNeasy Micro kit with an on-column DNase I digestion (Qiagen, Basel, Switzerland). .. Total RNA concentrations were measured with a Nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE). cDNA synthesis was performed in a thermocycler GeneAmp PCR System 9700 PE (Applied Biosystems, Foster City, CA), using a SuperScript VILO cDNA Synthesis Kit (LifeTechnologies, Inchinnan, UK), with 0.1 μg of total RNA in 20 μl reaction mixture consisting of VILO Reaction Mix and SuperScript Enzyme Mix.

    Article Title: Identification of candidate long non-coding RNAs in response to myocardial infarction
    Article Snippet: Heart was excised and immediately homogenized in Lysis Binding Buffer (mirVana isolation kit, Life technologies) for extraction of total RNA using the mirVana isolation kit (Life technologies, Merelbeke, Belgium) according to manufacturer’s instructions. .. On-column DNase I digestion (Qiagen, Venlo, The Netherlands) was performed to eliminate potential contamination with genomic DNA.

    Article Title: Increased Wnt and Notch signaling: a clue to the renal disease in Schimke immuno-osseous dysplasia?
    Article Snippet: Total RNA from formalin-fixed paraffin-embedded (FFPE) fetal kidney was isolated using the RNeasy FFPE Kit (Qiagen, Toronto, ON, Canada). .. Genomic DNA was removed by on-column DNase I digestion (Qiagen, Toronto, ON, Canada).

    Article Title: Glucocorticoid therapy regulates podocyte motility by inhibition of Rac1
    Article Snippet: .. Total cellular RNA was isolated using the RNeasy mini kit with on-column DNase I digestion (Qiagen). .. RNA integrity was assessed by a Nanodrop ND100 ultralow volume-spectrophotometer (Lab Tech) followed by a 2100 Bioanalyser (Agilent).

    Article Title: Unravelling Endogenous MicroRNA System Dysfunction as a New Pathophysiological Mechanism in Machado-Joseph Disease
    Article Snippet: .. All samples were submitted to on-column DNase I digestion (QIAGEN) during isolation. .. Total amount of RNA was quantified by optical density (OD) using a NanoDrop 2000 Spectrophotometer (Thermo Scientific) and RNA was stored at −80°C.

    Article Title: Mechanical Loading Reduces Inflammation-Induced Human Osteocyte-to-Osteoclast Communication
    Article Snippet: .. RNA Isolation and Real-Time RT-PCR Total RNA from osteocytes was isolated using an RNeasy® Micro kit with an on-column DNase I digestion (Qiagen, Basel, Switzerland). .. Total RNA concentrations were measured with a Nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE). cDNA synthesis was performed in a thermocycler GeneAmp® PCR System 9700 PE (Applied Biosystems, Foster City, CA), using aSuperScript® VILO™ cDNA Synthesis Kit (LifeTechnologies, Inchinnan, UK), with 0.1 μg of total RNA in 20 μl reaction mixture consisting of VILO Reaction Mix and SuperScript Enzyme Mix. cDNA was stored at −20 °C until real-time PCR analysis.

    Article Title: RNA-Seq study reveals genetic responses of diverse wild soybean accessions to increased ozone levels
    Article Snippet: .. Isolation of RNA and sequencing Total RNA was isolated using Plant RNeasy kits with on-column DNase I digestion (Qiagen, CA). .. Isolated samples were sent to the Genomic Sciences Laboratory (GSL) at North Carolina State University in Raleigh, NC where RNA quality was assured with Bioanalyzer RNA nano chips (Agilent, CA); Truseq libraries (Illumina, CA) were prepared; and libraries were sequenced using the HiSeq 2500 (Illumina, CA).

    Negative Control:

    Article Title: CXCL8 and CCL20 Enhance Osteoclastogenesis via Modulation of Cytokine Production by Human Primary Osteoblasts
    Article Snippet: RNA Isolation and Real-time RT-PCR Total RNA of primary osteoblasts was isolated using an RNeasy Micro kit with an on-column DNase I digestion (Qiagen, Basel, Switzerland). .. In each PCR run, the reaction mixture without cDNA was used as a negative control.

    Article Title: Mechanical Loading Reduces Inflammation-Induced Human Osteocyte-to-Osteoclast Communication
    Article Snippet: RNA Isolation and Real-Time RT-PCR Total RNA from osteocytes was isolated using an RNeasy® Micro kit with an on-column DNase I digestion (Qiagen, Basel, Switzerland). .. In each PCR run, the reaction mixture without cDNA was used as a negative control.

    Purification:

    Article Title: Critical Role of TGF-β and IL-2 Receptor Signaling in Foxp3 Induction by an Inhibitor of DNA Methylation
    Article Snippet: .. Gene Expression Analysis Total populations of viable cells were FACS purified from TCR stimulation cultures at indicated time points, and total RNA was extracted using the RNeasy® Mini Kit and on-column DNase I digestion (QIAGEN). .. For real-time RT-PCR, cDNA was synthesized using SuperScript II reverse transcriptase (Invitrogen) according to the manufacturer’s recommendations.

    Article Title: Non-exhaustive DNA methylation-mediated transposon silencing in the black truffle genome, a complex fungal genome with massive repeat element content
    Article Snippet: .. RNA-seq library preparation and data analysis Total RNA was extracted as described above, dissolved in H2 O after LiCl precipitation and purified with the RNeasy Plant Mini kit followed by on-column DNase I digestion (QIAGEN) as per the manufacturer’s instructions. ..

    Article Title: Critical Role of TGF-β and IL-2 Receptor Signaling in Foxp3 Induction by an Inhibitor of DNA Methylation
    Article Snippet: .. Total populations of viable cells were FACS purified from TCR stimulation cultures at indicated time points, and total RNA was extracted using the RNeasy® Mini Kit and on-column DNase I digestion (QIAGEN). .. For real-time RT-PCR, cDNA was synthesized using SuperScript II reverse transcriptase (Invitrogen) according to the manufacturer’s recommendations.

    Polymerase Chain Reaction:

    Article Title: Critical Role of TGF-β and IL-2 Receptor Signaling in Foxp3 Induction by an Inhibitor of DNA Methylation
    Article Snippet: Gene Expression Analysis Total populations of viable cells were FACS purified from TCR stimulation cultures at indicated time points, and total RNA was extracted using the RNeasy® Mini Kit and on-column DNase I digestion (QIAGEN). .. The QuantiFast SYBR Green PCR kit (Qiagen) and a Mastercycler ep realplex thermal cycler (Eppendorf) were used to analyze cDNA in replicates.

    Article Title: CXCL8 and CCL20 Enhance Osteoclastogenesis via Modulation of Cytokine Production by Human Primary Osteoblasts
    Article Snippet: RNA Isolation and Real-time RT-PCR Total RNA of primary osteoblasts was isolated using an RNeasy Micro kit with an on-column DNase I digestion (Qiagen, Basel, Switzerland). .. Total RNA concentrations were measured with a Nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE). cDNA synthesis was performed in a thermocycler GeneAmp PCR System 9700 PE (Applied Biosystems, Foster City, CA), using a SuperScript VILO cDNA Synthesis Kit (LifeTechnologies, Inchinnan, UK), with 0.1 μg of total RNA in 20 μl reaction mixture consisting of VILO Reaction Mix and SuperScript Enzyme Mix.

    Article Title: Critical Role of TGF-β and IL-2 Receptor Signaling in Foxp3 Induction by an Inhibitor of DNA Methylation
    Article Snippet: Total populations of viable cells were FACS purified from TCR stimulation cultures at indicated time points, and total RNA was extracted using the RNeasy® Mini Kit and on-column DNase I digestion (QIAGEN). .. The QuantiFast SYBR Green PCR kit (Qiagen) and a Mastercycler ep realplex thermal cycler (Eppendorf) were used to analyze cDNA in replicates.

    Article Title: Mechanical Loading Reduces Inflammation-Induced Human Osteocyte-to-Osteoclast Communication
    Article Snippet: RNA Isolation and Real-Time RT-PCR Total RNA from osteocytes was isolated using an RNeasy® Micro kit with an on-column DNase I digestion (Qiagen, Basel, Switzerland). .. Total RNA concentrations were measured with a Nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE). cDNA synthesis was performed in a thermocycler GeneAmp® PCR System 9700 PE (Applied Biosystems, Foster City, CA), using aSuperScript® VILO™ cDNA Synthesis Kit (LifeTechnologies, Inchinnan, UK), with 0.1 μg of total RNA in 20 μl reaction mixture consisting of VILO Reaction Mix and SuperScript Enzyme Mix. cDNA was stored at −20 °C until real-time PCR analysis.

    Lysis:

    Article Title: Identification of candidate long non-coding RNAs in response to myocardial infarction
    Article Snippet: Heart was excised and immediately homogenized in Lysis Binding Buffer (mirVana isolation kit, Life technologies) for extraction of total RNA using the mirVana isolation kit (Life technologies, Merelbeke, Belgium) according to manufacturer’s instructions. .. On-column DNase I digestion (Qiagen, Venlo, The Netherlands) was performed to eliminate potential contamination with genomic DNA.

    Chloramphenicol Acetyltransferase Assay:

    Article Title: Critical Role of TGF-β and IL-2 Receptor Signaling in Foxp3 Induction by an Inhibitor of DNA Methylation
    Article Snippet: Gene Expression Analysis Total populations of viable cells were FACS purified from TCR stimulation cultures at indicated time points, and total RNA was extracted using the RNeasy® Mini Kit and on-column DNase I digestion (QIAGEN). .. The following primers were used: HPRT: 5′-GTC AAC GGG GGA CAT AAA AG-3′ and 5′-AGG GCA TAT CCA ACA ACA AAC-3′; Foxp3: 5′-CCC AGG AAA GAC AGC AAC CTT-3′ and 5′-CAA ACA GGC CGC CGT CTG GAG CC-3′; Smad7: 5′-AAG AGG CTG TGT TGC TGT GA-3′ and 5′-CAG CCT GCA GTT GGT TTG AGA-3′.

    Article Title: Critical Role of TGF-β and IL-2 Receptor Signaling in Foxp3 Induction by an Inhibitor of DNA Methylation
    Article Snippet: Total populations of viable cells were FACS purified from TCR stimulation cultures at indicated time points, and total RNA was extracted using the RNeasy® Mini Kit and on-column DNase I digestion (QIAGEN). .. The following primers were used: HPRT: 5′-GTC AAC GGG GGA CAT AAA AG-3′ and 5′-AGG GCA TAT CCA ACA ACA AAC-3′; Foxp3: 5′-CCC AGG AAA GAC AGC AAC CTT-3′ and 5′-CAA ACA GGC CGC CGT CTG GAG CC-3′; Smad7: 5′-AAG AGG CTG TGT TGC TGT GA-3′ and 5′-CAG CCT GCA GTT GGT TTG AGA-3′.

    Mouse Assay:

    Article Title: Identification of candidate long non-coding RNAs in response to myocardial infarction
    Article Snippet: Mice were sacrificed with an overdose of isoflurane/oxygen mixture. .. On-column DNase I digestion (Qiagen, Venlo, The Netherlands) was performed to eliminate potential contamination with genomic DNA.

    Article Title: Unravelling Endogenous MicroRNA System Dysfunction as a New Pathophysiological Mechanism in Machado-Joseph Disease
    Article Snippet: Striatum of mice were dissected and stored at −80°C until RNA isolation. .. All samples were submitted to on-column DNase I digestion (QIAGEN) during isolation.

    Software:

    Article Title: Identification of candidate long non-coding RNAs in response to myocardial infarction
    Article Snippet: Left ventricular (LV) end-diastolic volume (EDV), LV end-systolic volume (ESV) and LV ejection fraction (EF) were obtained from contiguous ECG-triggered short-axis slices using the QGS software. .. On-column DNase I digestion (Qiagen, Venlo, The Netherlands) was performed to eliminate potential contamination with genomic DNA.

    Real-time Polymerase Chain Reaction:

    Article Title: Inhibitory Effects of iPSC-MSCs and Their Extracellular Vesicles on the Onset of Sialadenitis in a Mouse Model of Sjögren's Syndrome
    Article Snippet: .. Reverse Transcription and Quantitative PCR Total RNAs were extracted with the RNeasy Plus Mini Kit with on-column DNase I digestion (Qiagen, 74136). .. Reverse transcription (RT) was carried out with the high-capacity cDNA reverse transcription kit (Thermo Fisher, 4374966).

    Article Title: CXCL8 and CCL20 Enhance Osteoclastogenesis via Modulation of Cytokine Production by Human Primary Osteoblasts
    Article Snippet: RNA Isolation and Real-time RT-PCR Total RNA of primary osteoblasts was isolated using an RNeasy Micro kit with an on-column DNase I digestion (Qiagen, Basel, Switzerland). .. Real-time PCR reactions were performed using 2.5 μl cDNA and SYBR Green Supermix (Roche Laboratories, Indianapolis, IN) in a LightCycler (Roche Diagnostics).

    Article Title: Mechanical Loading Reduces Inflammation-Induced Human Osteocyte-to-Osteoclast Communication
    Article Snippet: RNA Isolation and Real-Time RT-PCR Total RNA from osteocytes was isolated using an RNeasy® Micro kit with an on-column DNase I digestion (Qiagen, Basel, Switzerland). .. Total RNA concentrations were measured with a Nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE). cDNA synthesis was performed in a thermocycler GeneAmp® PCR System 9700 PE (Applied Biosystems, Foster City, CA), using aSuperScript® VILO™ cDNA Synthesis Kit (LifeTechnologies, Inchinnan, UK), with 0.1 μg of total RNA in 20 μl reaction mixture consisting of VILO Reaction Mix and SuperScript Enzyme Mix. cDNA was stored at −20 °C until real-time PCR analysis.

    Article Title: CNBP controls IL-12 gene transcription and Th1 immunity
    Article Snippet: Genomic DNA in RNA purifications was eliminated using on-column DNase I digestion (Qiagen). .. Diluted cDNAs (1:100 final) were subjected to qPCR analysis using iQ SYBR Green Supermix reagent (Bio-Rad).

    Article Title: The combinatorial approach of laser-captured microdissection and reverse transcription quantitative polymerase chain reaction accurately determines HER2 status in breast cancer
    Article Snippet: The RNeasy FFPE kit including an on-column DNase I digestion (Qiagen; version 09/2011) was used for RNA extraction according to the manufacturer’s instructions. .. Control reactions containing RNA but no reverse transcriptase were tested negative for genomic DNA contamination by qPCR.

    RNA Extraction:

    Article Title: Increased Wnt and Notch signaling: a clue to the renal disease in Schimke immuno-osseous dysplasia?
    Article Snippet: Paragraph title: RNA extraction ... Genomic DNA was removed by on-column DNase I digestion (Qiagen, Toronto, ON, Canada).

    Article Title: CNBP controls IL-12 gene transcription and Th1 immunity
    Article Snippet: Paragraph title: RNA extraction and qRT-PCR ... Genomic DNA in RNA purifications was eliminated using on-column DNase I digestion (Qiagen).

    Article Title: The combinatorial approach of laser-captured microdissection and reverse transcription quantitative polymerase chain reaction accurately determines HER2 status in breast cancer
    Article Snippet: .. The RNeasy FFPE kit including an on-column DNase I digestion (Qiagen; version 09/2011) was used for RNA extraction according to the manufacturer’s instructions. .. For deparaffinization the FFPE tissue sections were treated with xylene.

    Sample Prep:

    Article Title: Non-exhaustive DNA methylation-mediated transposon silencing in the black truffle genome, a complex fungal genome with massive repeat element content
    Article Snippet: RNA-seq library preparation and data analysis Total RNA was extracted as described above, dissolved in H2 O after LiCl precipitation and purified with the RNeasy Plant Mini kit followed by on-column DNase I digestion (QIAGEN) as per the manufacturer’s instructions. .. RNA was quantified with the Qubit RNA BR Assay Kit (Life technologies, Carlsbad, CA, USA) and 1 μg of purified RNA was utilized as starting material for library construction, which was carried out with the Illumina TruSeq RNA Sample Preparation kit as per the manufacturer's instructions.

    In Vitro:

    Article Title: VpsR and cyclic di-GMP together drive transcription initiation to activate biofilm formation in Vibrio cholerae
    Article Snippet: A sample (5 μl) of the in vitro transcription reaction was added to 6 μl of primer mixture containing 2 × AMV Primer Extension buffer and 2 pmol 32 P-labeled primer, which annealed +103 bp downstream of the +1 transcriptional start site. .. Cells were harvested by centrifugation and RNA was extracted using the RNeasy kit (Qiagen), and an on-column DNase I digestion (Qiagen) was performed according to manufacturer's instructions.

    Spectrophotometry:

    Article Title: CXCL8 and CCL20 Enhance Osteoclastogenesis via Modulation of Cytokine Production by Human Primary Osteoblasts
    Article Snippet: RNA Isolation and Real-time RT-PCR Total RNA of primary osteoblasts was isolated using an RNeasy Micro kit with an on-column DNase I digestion (Qiagen, Basel, Switzerland). .. Total RNA concentrations were measured with a Nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE). cDNA synthesis was performed in a thermocycler GeneAmp PCR System 9700 PE (Applied Biosystems, Foster City, CA), using a SuperScript VILO cDNA Synthesis Kit (LifeTechnologies, Inchinnan, UK), with 0.1 μg of total RNA in 20 μl reaction mixture consisting of VILO Reaction Mix and SuperScript Enzyme Mix.

    Article Title: Identification of candidate long non-coding RNAs in response to myocardial infarction
    Article Snippet: On-column DNase I digestion (Qiagen, Venlo, The Netherlands) was performed to eliminate potential contamination with genomic DNA. .. Concentration and integrity of RNA were assessed using a Nanodrop spectrophotometer (Nanodrop products, Wilmington, USA) and a 2100 Bioanalyzer (Agilent technologies, Santa Clara, USA), respectively.

    Article Title: Unravelling Endogenous MicroRNA System Dysfunction as a New Pathophysiological Mechanism in Machado-Joseph Disease
    Article Snippet: All samples were submitted to on-column DNase I digestion (QIAGEN) during isolation. .. Total amount of RNA was quantified by optical density (OD) using a NanoDrop 2000 Spectrophotometer (Thermo Scientific) and RNA was stored at −80°C.

    Article Title: Mechanical Loading Reduces Inflammation-Induced Human Osteocyte-to-Osteoclast Communication
    Article Snippet: RNA Isolation and Real-Time RT-PCR Total RNA from osteocytes was isolated using an RNeasy® Micro kit with an on-column DNase I digestion (Qiagen, Basel, Switzerland). .. Total RNA concentrations were measured with a Nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE). cDNA synthesis was performed in a thermocycler GeneAmp® PCR System 9700 PE (Applied Biosystems, Foster City, CA), using aSuperScript® VILO™ cDNA Synthesis Kit (LifeTechnologies, Inchinnan, UK), with 0.1 μg of total RNA in 20 μl reaction mixture consisting of VILO Reaction Mix and SuperScript Enzyme Mix. cDNA was stored at −20 °C until real-time PCR analysis.

    Concentration Assay:

    Article Title: Identification of candidate long non-coding RNAs in response to myocardial infarction
    Article Snippet: On-column DNase I digestion (Qiagen, Venlo, The Netherlands) was performed to eliminate potential contamination with genomic DNA. .. Concentration and integrity of RNA were assessed using a Nanodrop spectrophotometer (Nanodrop products, Wilmington, USA) and a 2100 Bioanalyzer (Agilent technologies, Santa Clara, USA), respectively.

    CTG Assay:

    Article Title: Critical Role of TGF-β and IL-2 Receptor Signaling in Foxp3 Induction by an Inhibitor of DNA Methylation
    Article Snippet: Gene Expression Analysis Total populations of viable cells were FACS purified from TCR stimulation cultures at indicated time points, and total RNA was extracted using the RNeasy® Mini Kit and on-column DNase I digestion (QIAGEN). .. The following primers were used: HPRT: 5′-GTC AAC GGG GGA CAT AAA AG-3′ and 5′-AGG GCA TAT CCA ACA ACA AAC-3′; Foxp3: 5′-CCC AGG AAA GAC AGC AAC CTT-3′ and 5′-CAA ACA GGC CGC CGT CTG GAG CC-3′; Smad7: 5′-AAG AGG CTG TGT TGC TGT GA-3′ and 5′-CAG CCT GCA GTT GGT TTG AGA-3′.

    Article Title: Critical Role of TGF-β and IL-2 Receptor Signaling in Foxp3 Induction by an Inhibitor of DNA Methylation
    Article Snippet: Total populations of viable cells were FACS purified from TCR stimulation cultures at indicated time points, and total RNA was extracted using the RNeasy® Mini Kit and on-column DNase I digestion (QIAGEN). .. The following primers were used: HPRT: 5′-GTC AAC GGG GGA CAT AAA AG-3′ and 5′-AGG GCA TAT CCA ACA ACA AAC-3′; Foxp3: 5′-CCC AGG AAA GAC AGC AAC CTT-3′ and 5′-CAA ACA GGC CGC CGT CTG GAG CC-3′; Smad7: 5′-AAG AGG CTG TGT TGC TGT GA-3′ and 5′-CAG CCT GCA GTT GGT TTG AGA-3′.

    FACS:

    Article Title: Critical Role of TGF-β and IL-2 Receptor Signaling in Foxp3 Induction by an Inhibitor of DNA Methylation
    Article Snippet: .. Gene Expression Analysis Total populations of viable cells were FACS purified from TCR stimulation cultures at indicated time points, and total RNA was extracted using the RNeasy® Mini Kit and on-column DNase I digestion (QIAGEN). .. For real-time RT-PCR, cDNA was synthesized using SuperScript II reverse transcriptase (Invitrogen) according to the manufacturer’s recommendations.

    Article Title: Critical Role of TGF-β and IL-2 Receptor Signaling in Foxp3 Induction by an Inhibitor of DNA Methylation
    Article Snippet: .. Total populations of viable cells were FACS purified from TCR stimulation cultures at indicated time points, and total RNA was extracted using the RNeasy® Mini Kit and on-column DNase I digestion (QIAGEN). .. For real-time RT-PCR, cDNA was synthesized using SuperScript II reverse transcriptase (Invitrogen) according to the manufacturer’s recommendations.

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    Qiagen rnase free dnase set
    Rnase Free Dnase Set, supplied by Qiagen, used in various techniques. Bioz Stars score: 90/100, based on 962 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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