dnaase i  (Qiagen)


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    Structured Review

    Qiagen dnaase i
    Dnaase I, supplied by Qiagen, used in various techniques. Bioz Stars score: 93/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dnaase i/product/Qiagen
    Average 93 stars, based on 6 article reviews
    Price from $9.99 to $1999.99
    dnaase i - by Bioz Stars, 2020-04
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    Clone Assay:

    Article Title: A noncoding antisense RNA in tie-1 locus regulates tie-1 function in vivo
    Article Snippet: Paragraph title: Molecular biology: cloning of tie-1AS lncRNA ... The RNA was treated with DNase I for 30 minutes and recovered by RNeasy kit (QIAGEN).

    Article Title: Ultra-sensitive chemiluminescence imaging DNA hybridization method in the detection of mosquito-borne viruses and parasites
    Article Snippet: First, plasmids were constructed by cloning target gene fragments to PGM-T vector as described in the manufacturer’s protocol (Tiangen Biotech Beijing Co., Ltd.). .. Further, in vitro transcribed RNAs were purified and digested by DNase I using RNeasy Mini Kit (QIAGEN, Mississauga, Canada) as described in the manufacturer’s protocol.

    Centrifugation:

    Article Title: Bradyrhizobium diazoefficiens USDA110 PhaR functions for pleiotropic regulation of cellular processes besides PHB accumulation
    Article Snippet: After centrifugation, 1 mL of the upper aqueous layer was mixed with 1 mL of phenol-chloroform for 30 s. After another centrifugation, 0.75 mL of the upper aqueous layer was mixed with 0.1 mL of 1 M LiCl and 2.5 mL of ethanol and centrifuged. .. The RNA precipitate was dissolved in distilled water, and treated with DNase I at 37 °C for 1 h. Then DNA-free RNA was purified using RNeasy Mini Kit (Qiagen).

    Amplification:

    Article Title: A noncoding antisense RNA in tie-1 locus regulates tie-1 function in vivo
    Article Snippet: Rapid amplification of cDNA ends (RACEs) was performed by the RLM-RACE Kit (Ambion) and SMART RACE cDNA Amplification Kit (Clontech). .. The RNA was treated with DNase I for 30 minutes and recovered by RNeasy kit (QIAGEN).

    Article Title: Induction of Dedifferentiation, Genomewide Transcriptional Programming, and Epigenetic Reprogramming by Extracts of Carcinoma and Embryonic Stem Cells D⃞
    Article Snippet: Total RNA was isolated using a Stratagene RNA Nanoprep isolation kit, treated with DNAse I, and purified with RNeasy Mini columns (QIAGEN, Valencia, CA). .. Briefly, total RNA was reverse transcribed using Superscript II reverse transcriptase (Invitrogen). cDNA was amplified by PCR as follows: 95°C for 1 min, 20–30 cycles of 95°C for 15 s, 65°C for 30 s, and 68°C for 3 min. PCRcDNA was purified with QIAquick columns (QIAGEN) and ethanol precipitation and dissolved in H2 O. Biotin-labeling of cRNA.

    Article Title: IFN? Inhibits the Cytosolic Replication of Shigella flexneri via the Cytoplasmic RNA Sensor RIG-I
    Article Snippet: .. RNA samples were treated with DNase I prior to reverse transcription and amplification with SYBR Green One-Step Quantitative RT-PCR kit (Qiagen). ..

    Quantitative RT-PCR:

    Article Title: Characterization of the Neisseria gonorrhoeae Iron and Fur Regulatory Network
    Article Snippet: .. For quantitative real-time PCR (qRT-PCR), RNA was purified from these pellets using an RNeasy kit (Qiagen, Hilden, Germany) and treated with DNase I ( ). qRT-PCR was performed using the QuantiTect SYBR green RT-PCR kit (Qiagen) and analyzed using an ABI Prism 7700 sequence detection system (Applied Biosystems, Foster City, CA) with the primers listed in . .. Each reaction mixture contained 25 ng of purified total RNA.

    Article Title: ESCRT-I Protein Tsg101 Plays a Role in the Post-macropinocytic Trafficking and Infection of Endothelial Cells by Kaposi’s Sarcoma-Associated Herpesvirus
    Article Snippet: .. After 48h, cells were washed, treated with DNAse I for 10 min at 37°C, washed, total RNA was extracted from cell lysates using an RNeasy kit (QIAGEN), quantified and subjected to one step real-time RT-PCR (EZ RT-PCR core reagents, Applied Biosystems, Branchburg, NJ) for the ORF73 gene using gene specific primers and TaqMan probes as described previously [ ]. .. A standard curve was derived using the Ct values for different dilutions of in vitro transcribed transcripts to obtain the relative copy numbers of the transcripts [ ].

    Article Title: IFN? Inhibits the Cytosolic Replication of Shigella flexneri via the Cytoplasmic RNA Sensor RIG-I
    Article Snippet: .. RNA samples were treated with DNase I prior to reverse transcription and amplification with SYBR Green One-Step Quantitative RT-PCR kit (Qiagen). ..

    SYBR Green Assay:

    Article Title: Characterization of the Neisseria gonorrhoeae Iron and Fur Regulatory Network
    Article Snippet: .. For quantitative real-time PCR (qRT-PCR), RNA was purified from these pellets using an RNeasy kit (Qiagen, Hilden, Germany) and treated with DNase I ( ). qRT-PCR was performed using the QuantiTect SYBR green RT-PCR kit (Qiagen) and analyzed using an ABI Prism 7700 sequence detection system (Applied Biosystems, Foster City, CA) with the primers listed in . .. Each reaction mixture contained 25 ng of purified total RNA.

    Article Title: IFN? Inhibits the Cytosolic Replication of Shigella flexneri via the Cytoplasmic RNA Sensor RIG-I
    Article Snippet: .. RNA samples were treated with DNase I prior to reverse transcription and amplification with SYBR Green One-Step Quantitative RT-PCR kit (Qiagen). ..

    Microarray:

    Article Title: Induction of Dedifferentiation, Genomewide Transcriptional Programming, and Epigenetic Reprogramming by Extracts of Carcinoma and Embryonic Stem Cells D⃞
    Article Snippet: Paragraph title: Microarray Analysis of Gene Expression ... Total RNA was isolated using a Stratagene RNA Nanoprep isolation kit, treated with DNAse I, and purified with RNeasy Mini columns (QIAGEN, Valencia, CA).

    Incubation:

    Article Title: Bradyrhizobium diazoefficiens USDA110 PhaR functions for pleiotropic regulation of cellular processes besides PHB accumulation
    Article Snippet: The supernatant was discarded, and the precipitate was dissolved in 0.175 mL of distilled water, mixed with 3.5-fold volume of 4 M sodium acetate (pH 6.0), incubated at − 20 °C for a minimum of 1 h, and centrifuged. .. The RNA precipitate was dissolved in distilled water, and treated with DNase I at 37 °C for 1 h. Then DNA-free RNA was purified using RNeasy Mini Kit (Qiagen).

    Article Title: Characterization of the Neisseria gonorrhoeae Iron and Fur Regulatory Network
    Article Snippet: All strains were plated on GCB plates, grown overnight at 37°C with 5% CO2 , and inoculated into chemically defined medium (CDM) ( ) containing 0.042% Na2 HCO3 with shaking for 2 h. Cultures were diluted into fresh CDM to an optical density at 600 nm (OD600 ) of 0.1 and incubated for an additional 2 h. Subsequently, 100 μM ferric nitrate (for iron-replete [+Fe] conditions) or 100 μM desferal (for iron-depleted [−Fe] conditions) was added to the culture. .. For quantitative real-time PCR (qRT-PCR), RNA was purified from these pellets using an RNeasy kit (Qiagen, Hilden, Germany) and treated with DNase I ( ). qRT-PCR was performed using the QuantiTect SYBR green RT-PCR kit (Qiagen) and analyzed using an ABI Prism 7700 sequence detection system (Applied Biosystems, Foster City, CA) with the primers listed in .

    Article Title: Systematic Comparison and Validation of Quantitative Real-Time PCR Methods for the Quantitation of Adeno-Associated Viral Products
    Article Snippet: After the inactivation of DNase I at 65°C for 10 min, proteinase K (0.4 unit) was then added and incubated at 50°C for 1 hr to release vector DNA from AAV capsids before being inactivated at 95°C for 20 min. .. Method B consisted of the removal of residual plasmid DNA with DNase I and proteinase K, followed by the extraction of vector DNA using a spin column (DNeasy blood and tissue kit; Qiagen, Manchester, UK).

    Article Title: DIG-seq: a genome-wide CRISPR off-target profiling method using chromatin DNA
    Article Snippet: We washed 2 × 107 cells twice with PBS and incubated them with DNase I (4–32 units) in a reaction volume of 120 µL (10 mM NaCl, 10 mM Tris-HCl, 3 mM MgCl2 , and 0.1% NP-40, at pH 7.4) for 30 min at 37°C. .. DNase I–digested DNA was purified with a DNeasy tissue kit (Qiagen).

    Article Title: Identification and characterization of DNA sequences that prevent glucocorticoid receptor binding to nearby response elements
    Article Snippet: .. Nuclei were resuspended in 200 μl DNase I buffer and 50 μl aliquots were DNase I treated (or mock treated to normalize for the amount of chromatin in input) by the addition of 25 μl of DNase I buffer containing 1.5 μl DNase I (Qiagen, 2.7 u/μl) and then incubated at 37°C for 8 min. .. The reaction was stopped by addition of an equal volume of 2x stop buffer (50 mM Tris pH 7.4; 200 mM NaCl; 100 mM EDTA; 2% SDS, 200 μg/ml proteinase K) and samples were incubated at 65°C for 4 h to remove proteins.

    Article Title: Enhanced efficiency of P-element mediated transgenesis in Drosophila: Microinjection of DNA complexed with nanomaterial
    Article Snippet: .. Subsequently, these LPN-pDNA complexes (10 μl) were mixed with RNase free DNase I (Qiagen, USA) (10 μl, equivalent to one kunitz unit of DNase I in RDD buffer from Qiagen RNAse free DNase I set) and incubated for 2 h at 37°C. ..

    Expressing:

    Article Title: Characterization of the Neisseria gonorrhoeae Iron and Fur Regulatory Network
    Article Snippet: For quantitative real-time PCR (qRT-PCR), RNA was purified from these pellets using an RNeasy kit (Qiagen, Hilden, Germany) and treated with DNase I ( ). qRT-PCR was performed using the QuantiTect SYBR green RT-PCR kit (Qiagen) and analyzed using an ABI Prism 7700 sequence detection system (Applied Biosystems, Foster City, CA) with the primers listed in . .. The relative expression level of each gene was normalized to the endogenous 16S rRNA gene and represented as the ratio to that of the WT strain grown under iron-replete conditions.

    Article Title: Induction of Dedifferentiation, Genomewide Transcriptional Programming, and Epigenetic Reprogramming by Extracts of Carcinoma and Embryonic Stem Cells D⃞
    Article Snippet: Paragraph title: Microarray Analysis of Gene Expression ... Total RNA was isolated using a Stratagene RNA Nanoprep isolation kit, treated with DNAse I, and purified with RNeasy Mini columns (QIAGEN, Valencia, CA).

    Article Title: ESCRT-I Protein Tsg101 Plays a Role in the Post-macropinocytic Trafficking and Infection of Endothelial Cells by Kaposi’s Sarcoma-Associated Herpesvirus
    Article Snippet: Paragraph title: Measurement of KSHV gene expression by real-time reverse transcription PCR (RT-PCR) ... After 48h, cells were washed, treated with DNAse I for 10 min at 37°C, washed, total RNA was extracted from cell lysates using an RNeasy kit (QIAGEN), quantified and subjected to one step real-time RT-PCR (EZ RT-PCR core reagents, Applied Biosystems, Branchburg, NJ) for the ORF73 gene using gene specific primers and TaqMan probes as described previously [ ].

    Derivative Assay:

    Article Title: ESCRT-I Protein Tsg101 Plays a Role in the Post-macropinocytic Trafficking and Infection of Endothelial Cells by Kaposi’s Sarcoma-Associated Herpesvirus
    Article Snippet: After 48h, cells were washed, treated with DNAse I for 10 min at 37°C, washed, total RNA was extracted from cell lysates using an RNeasy kit (QIAGEN), quantified and subjected to one step real-time RT-PCR (EZ RT-PCR core reagents, Applied Biosystems, Branchburg, NJ) for the ORF73 gene using gene specific primers and TaqMan probes as described previously [ ]. .. A standard curve was derived using the Ct values for different dilutions of in vitro transcribed transcripts to obtain the relative copy numbers of the transcripts [ ].

    High Performance Liquid Chromatography:

    Article Title: Systematic Comparison and Validation of Quantitative Real-Time PCR Methods for the Quantitation of Adeno-Associated Viral Products
    Article Snippet: Method B consisted of the removal of residual plasmid DNA with DNase I and proteinase K, followed by the extraction of vector DNA using a spin column (DNeasy blood and tissue kit; Qiagen, Manchester, UK). .. To test the efficiency of DNase I and proteinase K treatments, replicates of a crude sample (before HPLC) and HPLC-purified AAV sample were spiked with 1.25×10 copies of the AAV-independent plasmid pRRLSIN.cPPT.PGK-GFP.WPRE (plasmid 12252; Addgene, Cambridge, MA) encoding lentiviral vector sequences.

    Infection:

    Article Title: ESCRT-I Protein Tsg101 Plays a Role in the Post-macropinocytic Trafficking and Infection of Endothelial Cells by Kaposi’s Sarcoma-Associated Herpesvirus
    Article Snippet: Measurement of KSHV gene expression by real-time reverse transcription PCR (RT-PCR) HMVEC-d and HUVEC cells were infected with KSHV (30 DNA copies/cell) for 2 h at 37°C, washed twice with HBSS, treated with 0.25% trypsin-EDTA for 5 min at 37°C to remove the bound but noninternalized virus. .. After 48h, cells were washed, treated with DNAse I for 10 min at 37°C, washed, total RNA was extracted from cell lysates using an RNeasy kit (QIAGEN), quantified and subjected to one step real-time RT-PCR (EZ RT-PCR core reagents, Applied Biosystems, Branchburg, NJ) for the ORF73 gene using gene specific primers and TaqMan probes as described previously [ ].

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: Characterization of the Neisseria gonorrhoeae Iron and Fur Regulatory Network
    Article Snippet: .. For quantitative real-time PCR (qRT-PCR), RNA was purified from these pellets using an RNeasy kit (Qiagen, Hilden, Germany) and treated with DNase I ( ). qRT-PCR was performed using the QuantiTect SYBR green RT-PCR kit (Qiagen) and analyzed using an ABI Prism 7700 sequence detection system (Applied Biosystems, Foster City, CA) with the primers listed in . .. Each reaction mixture contained 25 ng of purified total RNA.

    Article Title: ESCRT-I Protein Tsg101 Plays a Role in the Post-macropinocytic Trafficking and Infection of Endothelial Cells by Kaposi’s Sarcoma-Associated Herpesvirus
    Article Snippet: .. After 48h, cells were washed, treated with DNAse I for 10 min at 37°C, washed, total RNA was extracted from cell lysates using an RNeasy kit (QIAGEN), quantified and subjected to one step real-time RT-PCR (EZ RT-PCR core reagents, Applied Biosystems, Branchburg, NJ) for the ORF73 gene using gene specific primers and TaqMan probes as described previously [ ]. .. A standard curve was derived using the Ct values for different dilutions of in vitro transcribed transcripts to obtain the relative copy numbers of the transcripts [ ].

    Generated:

    Article Title: Characterization of the Neisseria gonorrhoeae Iron and Fur Regulatory Network
    Article Snippet: N. gonorrhoeae fur and fur -complemented strains were generated in a previous study ( ). .. For quantitative real-time PCR (qRT-PCR), RNA was purified from these pellets using an RNeasy kit (Qiagen, Hilden, Germany) and treated with DNase I ( ). qRT-PCR was performed using the QuantiTect SYBR green RT-PCR kit (Qiagen) and analyzed using an ABI Prism 7700 sequence detection system (Applied Biosystems, Foster City, CA) with the primers listed in .

    Polymerase Chain Reaction:

    Article Title: Identification and characterization of DNA sequences that prevent glucocorticoid receptor binding to nearby response elements
    Article Snippet: Nuclei were resuspended in 200 μl DNase I buffer and 50 μl aliquots were DNase I treated (or mock treated to normalize for the amount of chromatin in input) by the addition of 25 μl of DNase I buffer containing 1.5 μl DNase I (Qiagen, 2.7 u/μl) and then incubated at 37°C for 8 min. .. Finally, DNA was purified using the PCR purification kit (Qiagen) and regions of interest were analyzed by qPCR (primers listed in Supplementary Table S2).

    Article Title: Induction of Dedifferentiation, Genomewide Transcriptional Programming, and Epigenetic Reprogramming by Extracts of Carcinoma and Embryonic Stem Cells D⃞
    Article Snippet: Total RNA was isolated using a Stratagene RNA Nanoprep isolation kit, treated with DNAse I, and purified with RNeasy Mini columns (QIAGEN, Valencia, CA). .. Briefly, total RNA was reverse transcribed using Superscript II reverse transcriptase (Invitrogen). cDNA was amplified by PCR as follows: 95°C for 1 min, 20–30 cycles of 95°C for 15 s, 65°C for 30 s, and 68°C for 3 min. PCRcDNA was purified with QIAquick columns (QIAGEN) and ethanol precipitation and dissolved in H2 O. Biotin-labeling of cRNA.

    Article Title: ESCRT-I Protein Tsg101 Plays a Role in the Post-macropinocytic Trafficking and Infection of Endothelial Cells by Kaposi’s Sarcoma-Associated Herpesvirus
    Article Snippet: Paragraph title: Measurement of KSHV gene expression by real-time reverse transcription PCR (RT-PCR) ... After 48h, cells were washed, treated with DNAse I for 10 min at 37°C, washed, total RNA was extracted from cell lysates using an RNeasy kit (QIAGEN), quantified and subjected to one step real-time RT-PCR (EZ RT-PCR core reagents, Applied Biosystems, Branchburg, NJ) for the ORF73 gene using gene specific primers and TaqMan probes as described previously [ ].

    Isolation:

    Article Title: Induction of Dedifferentiation, Genomewide Transcriptional Programming, and Epigenetic Reprogramming by Extracts of Carcinoma and Embryonic Stem Cells D⃞
    Article Snippet: .. Total RNA was isolated using a Stratagene RNA Nanoprep isolation kit, treated with DNAse I, and purified with RNeasy Mini columns (QIAGEN, Valencia, CA). ..

    Purification:

    Article Title: Bradyrhizobium diazoefficiens USDA110 PhaR functions for pleiotropic regulation of cellular processes besides PHB accumulation
    Article Snippet: .. The RNA precipitate was dissolved in distilled water, and treated with DNase I at 37 °C for 1 h. Then DNA-free RNA was purified using RNeasy Mini Kit (Qiagen). .. Concentrations of the purified RNA samples were determined with Nano Vue Plus (GE Healthcare), and the samples were stored in aliquots at − 80 °C prior to the usage.

    Article Title: Characterization of the Neisseria gonorrhoeae Iron and Fur Regulatory Network
    Article Snippet: .. For quantitative real-time PCR (qRT-PCR), RNA was purified from these pellets using an RNeasy kit (Qiagen, Hilden, Germany) and treated with DNase I ( ). qRT-PCR was performed using the QuantiTect SYBR green RT-PCR kit (Qiagen) and analyzed using an ABI Prism 7700 sequence detection system (Applied Biosystems, Foster City, CA) with the primers listed in . .. Each reaction mixture contained 25 ng of purified total RNA.

    Article Title: Systematic Comparison and Validation of Quantitative Real-Time PCR Methods for the Quantitation of Adeno-Associated Viral Products
    Article Snippet: Viral genome extraction Two methods were used to extract AAV vector DNA from purified AAV vectors. .. Method B consisted of the removal of residual plasmid DNA with DNase I and proteinase K, followed by the extraction of vector DNA using a spin column (DNeasy blood and tissue kit; Qiagen, Manchester, UK).

    Article Title: DIG-seq: a genome-wide CRISPR off-target profiling method using chromatin DNA
    Article Snippet: .. DNase I–digested DNA was purified with a DNeasy tissue kit (Qiagen). .. Digested DNA was mixed with KAPA SYBR FAST qPCR master mix (Kapa Biosystems) and analyzed by real-time qPCR.

    Article Title: Identification and characterization of DNA sequences that prevent glucocorticoid receptor binding to nearby response elements
    Article Snippet: Nuclei were resuspended in 200 μl DNase I buffer and 50 μl aliquots were DNase I treated (or mock treated to normalize for the amount of chromatin in input) by the addition of 25 μl of DNase I buffer containing 1.5 μl DNase I (Qiagen, 2.7 u/μl) and then incubated at 37°C for 8 min. .. Finally, DNA was purified using the PCR purification kit (Qiagen) and regions of interest were analyzed by qPCR (primers listed in Supplementary Table S2).

    Article Title: Induction of Dedifferentiation, Genomewide Transcriptional Programming, and Epigenetic Reprogramming by Extracts of Carcinoma and Embryonic Stem Cells D⃞
    Article Snippet: .. Total RNA was isolated using a Stratagene RNA Nanoprep isolation kit, treated with DNAse I, and purified with RNeasy Mini columns (QIAGEN, Valencia, CA). ..

    Article Title: Ultra-sensitive chemiluminescence imaging DNA hybridization method in the detection of mosquito-borne viruses and parasites
    Article Snippet: .. Further, in vitro transcribed RNAs were purified and digested by DNase I using RNeasy Mini Kit (QIAGEN, Mississauga, Canada) as described in the manufacturer’s protocol. .. The purified RNAs were mixed with 2 × RNA Loading Dye Solution (ThermoFisher) and resolved by 2% agarose gel electrophoresis.

    Sequencing:

    Article Title: Characterization of the Neisseria gonorrhoeae Iron and Fur Regulatory Network
    Article Snippet: .. For quantitative real-time PCR (qRT-PCR), RNA was purified from these pellets using an RNeasy kit (Qiagen, Hilden, Germany) and treated with DNase I ( ). qRT-PCR was performed using the QuantiTect SYBR green RT-PCR kit (Qiagen) and analyzed using an ABI Prism 7700 sequence detection system (Applied Biosystems, Foster City, CA) with the primers listed in . .. Each reaction mixture contained 25 ng of purified total RNA.

    Construct:

    Article Title: Ultra-sensitive chemiluminescence imaging DNA hybridization method in the detection of mosquito-borne viruses and parasites
    Article Snippet: First, plasmids were constructed by cloning target gene fragments to PGM-T vector as described in the manufacturer’s protocol (Tiangen Biotech Beijing Co., Ltd.). .. Further, in vitro transcribed RNAs were purified and digested by DNase I using RNeasy Mini Kit (QIAGEN, Mississauga, Canada) as described in the manufacturer’s protocol.

    Rapid Amplification of cDNA Ends:

    Article Title: A noncoding antisense RNA in tie-1 locus regulates tie-1 function in vivo
    Article Snippet: Rapid amplification of cDNA ends (RACEs) was performed by the RLM-RACE Kit (Ambion) and SMART RACE cDNA Amplification Kit (Clontech). .. The RNA was treated with DNase I for 30 minutes and recovered by RNeasy kit (QIAGEN).

    Plasmid Preparation:

    Article Title: A noncoding antisense RNA in tie-1 locus regulates tie-1 function in vivo
    Article Snippet: The RNA was treated with DNase I for 30 minutes and recovered by RNeasy kit (QIAGEN). .. The RACE products were cloned into pCR4-TOPO vector (Invitrogen) and sequenced.

    Article Title: Systematic Comparison and Validation of Quantitative Real-Time PCR Methods for the Quantitation of Adeno-Associated Viral Products
    Article Snippet: .. Method B consisted of the removal of residual plasmid DNA with DNase I and proteinase K, followed by the extraction of vector DNA using a spin column (DNeasy blood and tissue kit; Qiagen, Manchester, UK). .. To test the efficiency of DNase I and proteinase K treatments, replicates of a crude sample (before HPLC) and HPLC-purified AAV sample were spiked with 1.25×10 copies of the AAV-independent plasmid pRRLSIN.cPPT.PGK-GFP.WPRE (plasmid 12252; Addgene, Cambridge, MA) encoding lentiviral vector sequences.

    Article Title: Ultra-sensitive chemiluminescence imaging DNA hybridization method in the detection of mosquito-borne viruses and parasites
    Article Snippet: First, plasmids were constructed by cloning target gene fragments to PGM-T vector as described in the manufacturer’s protocol (Tiangen Biotech Beijing Co., Ltd.). .. Further, in vitro transcribed RNAs were purified and digested by DNase I using RNeasy Mini Kit (QIAGEN, Mississauga, Canada) as described in the manufacturer’s protocol.

    Article Title: Enhanced efficiency of P-element mediated transgenesis in Drosophila: Microinjection of DNA complexed with nanomaterial
    Article Snippet: Paragraph title: Determination of Nanoparticle to plasmid ratio (N/P ratio) based on DNA retardation assay and DNase I protection assay ... Subsequently, these LPN-pDNA complexes (10 μl) were mixed with RNase free DNase I (Qiagen, USA) (10 μl, equivalent to one kunitz unit of DNase I in RDD buffer from Qiagen RNAse free DNase I set) and incubated for 2 h at 37°C.

    Software:

    Article Title: Enhanced efficiency of P-element mediated transgenesis in Drosophila: Microinjection of DNA complexed with nanomaterial
    Article Snippet: Subsequently, these LPN-pDNA complexes (10 μl) were mixed with RNase free DNase I (Qiagen, USA) (10 μl, equivalent to one kunitz unit of DNase I in RDD buffer from Qiagen RNAse free DNase I set) and incubated for 2 h at 37°C. .. Subsequently, samples were electrophoresed on 0.8% agarose gels and the relative intensity of pDNA released from complexes was estimated by densitometry using quantity one software (Bio-Rad, USA).

    Real-time Polymerase Chain Reaction:

    Article Title: Characterization of the Neisseria gonorrhoeae Iron and Fur Regulatory Network
    Article Snippet: .. For quantitative real-time PCR (qRT-PCR), RNA was purified from these pellets using an RNeasy kit (Qiagen, Hilden, Germany) and treated with DNase I ( ). qRT-PCR was performed using the QuantiTect SYBR green RT-PCR kit (Qiagen) and analyzed using an ABI Prism 7700 sequence detection system (Applied Biosystems, Foster City, CA) with the primers listed in . .. Each reaction mixture contained 25 ng of purified total RNA.

    Article Title: DIG-seq: a genome-wide CRISPR off-target profiling method using chromatin DNA
    Article Snippet: Paragraph title: DNase I digestion assays and qPCR ... DNase I–digested DNA was purified with a DNeasy tissue kit (Qiagen).

    Article Title: Identification and characterization of DNA sequences that prevent glucocorticoid receptor binding to nearby response elements
    Article Snippet: Nuclei were resuspended in 200 μl DNase I buffer and 50 μl aliquots were DNase I treated (or mock treated to normalize for the amount of chromatin in input) by the addition of 25 μl of DNase I buffer containing 1.5 μl DNase I (Qiagen, 2.7 u/μl) and then incubated at 37°C for 8 min. .. Finally, DNA was purified using the PCR purification kit (Qiagen) and regions of interest were analyzed by qPCR (primers listed in Supplementary Table S2).

    Agarose Gel Electrophoresis:

    Article Title: Ultra-sensitive chemiluminescence imaging DNA hybridization method in the detection of mosquito-borne viruses and parasites
    Article Snippet: Following digestion with FastDigest Sal I restriction endonuclease (ThermoFisher, Waltham, USA), the plasmids were purified by agarose gel and retrieved. .. Further, in vitro transcribed RNAs were purified and digested by DNase I using RNeasy Mini Kit (QIAGEN, Mississauga, Canada) as described in the manufacturer’s protocol.

    In Vitro:

    Article Title: ESCRT-I Protein Tsg101 Plays a Role in the Post-macropinocytic Trafficking and Infection of Endothelial Cells by Kaposi’s Sarcoma-Associated Herpesvirus
    Article Snippet: After 48h, cells were washed, treated with DNAse I for 10 min at 37°C, washed, total RNA was extracted from cell lysates using an RNeasy kit (QIAGEN), quantified and subjected to one step real-time RT-PCR (EZ RT-PCR core reagents, Applied Biosystems, Branchburg, NJ) for the ORF73 gene using gene specific primers and TaqMan probes as described previously [ ]. .. A standard curve was derived using the Ct values for different dilutions of in vitro transcribed transcripts to obtain the relative copy numbers of the transcripts [ ].

    Article Title: Ultra-sensitive chemiluminescence imaging DNA hybridization method in the detection of mosquito-borne viruses and parasites
    Article Snippet: .. Further, in vitro transcribed RNAs were purified and digested by DNase I using RNeasy Mini Kit (QIAGEN, Mississauga, Canada) as described in the manufacturer’s protocol. .. The purified RNAs were mixed with 2 × RNA Loading Dye Solution (ThermoFisher) and resolved by 2% agarose gel electrophoresis.

    Ethanol Precipitation:

    Article Title: Induction of Dedifferentiation, Genomewide Transcriptional Programming, and Epigenetic Reprogramming by Extracts of Carcinoma and Embryonic Stem Cells D⃞
    Article Snippet: Total RNA was isolated using a Stratagene RNA Nanoprep isolation kit, treated with DNAse I, and purified with RNeasy Mini columns (QIAGEN, Valencia, CA). .. Briefly, total RNA was reverse transcribed using Superscript II reverse transcriptase (Invitrogen). cDNA was amplified by PCR as follows: 95°C for 1 min, 20–30 cycles of 95°C for 15 s, 65°C for 30 s, and 68°C for 3 min. PCRcDNA was purified with QIAquick columns (QIAGEN) and ethanol precipitation and dissolved in H2 O. Biotin-labeling of cRNA.

    Spectrophotometry:

    Article Title: Ultra-sensitive chemiluminescence imaging DNA hybridization method in the detection of mosquito-borne viruses and parasites
    Article Snippet: Further, in vitro transcribed RNAs were purified and digested by DNase I using RNeasy Mini Kit (QIAGEN, Mississauga, Canada) as described in the manufacturer’s protocol. .. Finally, in vitro transcribed RNAs were quantified by UV spectrophotometry and subject to serial dilutions at a magnitude of 10 and stored at -70 °C until use.

    Concentration Assay:

    Article Title: Ultra-sensitive chemiluminescence imaging DNA hybridization method in the detection of mosquito-borne viruses and parasites
    Article Snippet: Preparation of in vitro transcript RNA To verify the LOD of this strategy and calibrate the concentration of virus-like particles (VLPs), in vitro transcribed RNAs of these MBVs were prepared. .. Further, in vitro transcribed RNAs were purified and digested by DNase I using RNeasy Mini Kit (QIAGEN, Mississauga, Canada) as described in the manufacturer’s protocol.

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    Qiagen dnase i
    S. flexneri  nucleic acids are sufficient to induce type I IFN production via RIG-I. Low molecular weight poly (I∶C), extracted  S. flexneri  RNA treated with DNase I, or  S. flexneri  DNA treated with RNase were transfected into MEFs at 0.4 µg ligand/well. Eight hours post transfection, supernatants were added to L929-ISRE cells, which harbor an IFNβ-responsive luciferase reporter. Where appropriate, significant statistical differences are indicated as follows: ns, not significant; *, p
    Dnase I, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 1086 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 1086 article reviews
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    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.
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    Image Search Results


    S. flexneri  nucleic acids are sufficient to induce type I IFN production via RIG-I. Low molecular weight poly (I∶C), extracted  S. flexneri  RNA treated with DNase I, or  S. flexneri  DNA treated with RNase were transfected into MEFs at 0.4 µg ligand/well. Eight hours post transfection, supernatants were added to L929-ISRE cells, which harbor an IFNβ-responsive luciferase reporter. Where appropriate, significant statistical differences are indicated as follows: ns, not significant; *, p

    Journal: PLoS Pathogens

    Article Title: IFN? Inhibits the Cytosolic Replication of Shigella flexneri via the Cytoplasmic RNA Sensor RIG-I

    doi: 10.1371/journal.ppat.1002809

    Figure Lengend Snippet: S. flexneri nucleic acids are sufficient to induce type I IFN production via RIG-I. Low molecular weight poly (I∶C), extracted S. flexneri RNA treated with DNase I, or S. flexneri DNA treated with RNase were transfected into MEFs at 0.4 µg ligand/well. Eight hours post transfection, supernatants were added to L929-ISRE cells, which harbor an IFNβ-responsive luciferase reporter. Where appropriate, significant statistical differences are indicated as follows: ns, not significant; *, p

    Article Snippet: RNA samples were treated with DNase I prior to reverse transcription and amplification with SYBR Green One-Step Quantitative RT-PCR kit (Qiagen).

    Techniques: Molecular Weight, Transfection, Luciferase

    The role of cell lysis and eDNA in  S. aureus  biofilm adherence. UAMS-1 (filled bars) and KB1050 ( cid A mutant; striped bars) were grown for 24 hr in a static biofilm assay as described in  Materials and Methods . Where indicated, DNase I, RNase A, or PAS

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    Article Title: The cidA murein hydrolase regulator contributes to DNA release and biofilm development in Staphylococcus aureus

    doi: 10.1073/pnas.0610226104

    Figure Lengend Snippet: The role of cell lysis and eDNA in S. aureus biofilm adherence. UAMS-1 (filled bars) and KB1050 ( cid A mutant; striped bars) were grown for 24 hr in a static biofilm assay as described in Materials and Methods . Where indicated, DNase I, RNase A, or PAS

    Article Snippet: Where indicated, 28 units of DNase I was added to the wells at the time of inoculation.

    Techniques: Lysis, Mutagenesis, Biofilm Production Assay

    CLSM of static biofilm. UAMS-1 and KB1050 ( cid A mutant) were grown as static biofilm as described in Materials and Methods . Where indicated, 28 units of DNase I was added to each well at the time of inoculation. After 24-h growth, the biofilms were washed

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    Article Title: The cidA murein hydrolase regulator contributes to DNA release and biofilm development in Staphylococcus aureus

    doi: 10.1073/pnas.0610226104

    Figure Lengend Snippet: CLSM of static biofilm. UAMS-1 and KB1050 ( cid A mutant) were grown as static biofilm as described in Materials and Methods . Where indicated, 28 units of DNase I was added to each well at the time of inoculation. After 24-h growth, the biofilms were washed

    Article Snippet: Where indicated, 28 units of DNase I was added to the wells at the time of inoculation.

    Techniques: Confocal Laser Scanning Microscopy, Mutagenesis

    BRG1 mediates RUNX2 promoter accessibility. (A) The active chromatin modification, H3K27ac, is enriched at the RUNX2 promoter in anaplastic thyroid cancer cells (SW 1736) but not in nonmalignant thyroid cells (Nthy-ORI). Values were calculated as fold enrichment compared with the matched IgG antibody control. Error bars are SD; significance compared with IgG is indicated. (B) The RUNX2 promoter is more accessible in anaplastic thyroid cancer cells (SW 1736) than nonmalignant (Nthy-ORI) by the DNase I hypersensitivity assay. Values were calculated as relative sensitivity to DNase digestion compared with a known heterochromatinized site. Error bars are SD; significance compared with nonmalignant cells is indicated. (C) Treatment with a BRG1 inhibitor (PF1-3, 30 µM) for 6 hours results in an increase in sensitivity to DNase I digestion of the RUNX2 promoter in nonmalignant cells (Nthy-ORI). Error bars are SD; significance compared with vehicle control is indicated. (D) Treatment with PFI-3 results in a loss of H1.2 enrichment at the RUNX2 promoter detected by ChIP. Values were calculated as fold enrichment compared with the matched IgG antibody control. Error bars are SD; significance compared with vehicle control is indicated. * P

    Journal: Endocrinology

    Article Title: Thyroid Hormone Receptor β Suppression of RUNX2 Is Mediated by Brahma-Related Gene 1–Dependent Chromatin Remodeling

    doi: 10.1210/en.2018-00128

    Figure Lengend Snippet: BRG1 mediates RUNX2 promoter accessibility. (A) The active chromatin modification, H3K27ac, is enriched at the RUNX2 promoter in anaplastic thyroid cancer cells (SW 1736) but not in nonmalignant thyroid cells (Nthy-ORI). Values were calculated as fold enrichment compared with the matched IgG antibody control. Error bars are SD; significance compared with IgG is indicated. (B) The RUNX2 promoter is more accessible in anaplastic thyroid cancer cells (SW 1736) than nonmalignant (Nthy-ORI) by the DNase I hypersensitivity assay. Values were calculated as relative sensitivity to DNase digestion compared with a known heterochromatinized site. Error bars are SD; significance compared with nonmalignant cells is indicated. (C) Treatment with a BRG1 inhibitor (PF1-3, 30 µM) for 6 hours results in an increase in sensitivity to DNase I digestion of the RUNX2 promoter in nonmalignant cells (Nthy-ORI). Error bars are SD; significance compared with vehicle control is indicated. (D) Treatment with PFI-3 results in a loss of H1.2 enrichment at the RUNX2 promoter detected by ChIP. Values were calculated as fold enrichment compared with the matched IgG antibody control. Error bars are SD; significance compared with vehicle control is indicated. * P

    Article Snippet: Chromatin (2 μg) was treated with 0.5 unit DNase I (Qiagen) for 15 minutes at room temperature in 1× DNase Incubation Buffer (10 mM Tris-HCl, pH 7.6, 2.5 mM MgCl2 , 0.5 mM CaCl2 ).

    Techniques: Modification, Chromatin Immunoprecipitation

    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.

    Journal: Nucleic Acids Research

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

    doi: 10.1093/nar/gky606

    Figure Lengend 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.

    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.

    Techniques: 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.)

    Journal: Nucleic Acids Research

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

    doi: 10.1093/nar/gky606

    Figure Lengend 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.)

    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.

    Techniques: Footprinting, Binding Assay