dnase-treated rna Search Results


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  • 99
    New England Biolabs dnase treated rna
    Dnase Treated Rna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 173 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher dnase treated rna
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    Millipore dnase treated rna
    Dnase Treated Rna, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 82 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore dnase treated phenol chloroform purified rna
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    Bio-Rad dnase treated rna
    NuMA interacts with proteins and nucleic acid components of ribosomal biogenesis. S1 cells were cultured for 8 days with complete medium followed by 2 days without EGF to induce proliferation arrest; T4–2 cells were cultured for 6 days. ( A ) Immunoprecipitation (IP) of nuclear extracts from S1 and T4–2 cells with NuMA antibodies (NuMA) or with non-specific immunoglobulins (IgG), followed by western blot analysis of the input and immunoprecipitated samples using NuMA and NM1 antibodies. ( B ) Immunoprecipitation of nuclear extracts from S1 cells followed by western blot analysis for NuMA and <t>RNA</t> polymerase I (RNA pol I). ( C ) ChIP from T4–2 cells with NuMA antibody ( n = 4) or RNA Polymerase I antibody ( n = 2), followed by RT-qPCR for coding (pro-1, H4, H8, H13) and non-coding (H18) regions of rDNA. The drawing shows the organization of the rDNA gene (IGS = intergenic sequence). Data are normalized to those obtained with IgG control (see ‘Materials and Methods’ section). ( D ) RNA immunoprecipitation fromT4–2 cells with NuMA antibody or with non-specific IgG of nuclear extracts and soluble extracts (the latter were treated with 50 μg/ml cycloheximide [CH]). Both the <t>DNAse</t> treated non-reverse transcribed RNA (nonRT RNA) and the DNAse treated reverse-transcribed cDNA (cDNA) samples were subjected to PCR using primers specific for human 18S and 28S rRNAs ( n = 2). ( E and F ) Immunoprecipitation of nuclear extracts from S1 cells followed by western blot analysis for NuMA, RPL26 and RPL24.
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    Thermo Fisher rna dnase treated
    NuMA interacts with proteins and nucleic acid components of ribosomal biogenesis. S1 cells were cultured for 8 days with complete medium followed by 2 days without EGF to induce proliferation arrest; T4–2 cells were cultured for 6 days. ( A ) Immunoprecipitation (IP) of nuclear extracts from S1 and T4–2 cells with NuMA antibodies (NuMA) or with non-specific immunoglobulins (IgG), followed by western blot analysis of the input and immunoprecipitated samples using NuMA and NM1 antibodies. ( B ) Immunoprecipitation of nuclear extracts from S1 cells followed by western blot analysis for NuMA and <t>RNA</t> polymerase I (RNA pol I). ( C ) ChIP from T4–2 cells with NuMA antibody ( n = 4) or RNA Polymerase I antibody ( n = 2), followed by RT-qPCR for coding (pro-1, H4, H8, H13) and non-coding (H18) regions of rDNA. The drawing shows the organization of the rDNA gene (IGS = intergenic sequence). Data are normalized to those obtained with IgG control (see ‘Materials and Methods’ section). ( D ) RNA immunoprecipitation fromT4–2 cells with NuMA antibody or with non-specific IgG of nuclear extracts and soluble extracts (the latter were treated with 50 μg/ml cycloheximide [CH]). Both the <t>DNAse</t> treated non-reverse transcribed RNA (nonRT RNA) and the DNAse treated reverse-transcribed cDNA (cDNA) samples were subjected to PCR using primers specific for human 18S and 28S rRNAs ( n = 2). ( E and F ) Immunoprecipitation of nuclear extracts from S1 cells followed by western blot analysis for NuMA, RPL26 and RPL24.
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    Thermo Fisher dnase treated rnas
    NuMA interacts with proteins and nucleic acid components of ribosomal biogenesis. S1 cells were cultured for 8 days with complete medium followed by 2 days without EGF to induce proliferation arrest; T4–2 cells were cultured for 6 days. ( A ) Immunoprecipitation (IP) of nuclear extracts from S1 and T4–2 cells with NuMA antibodies (NuMA) or with non-specific immunoglobulins (IgG), followed by western blot analysis of the input and immunoprecipitated samples using NuMA and NM1 antibodies. ( B ) Immunoprecipitation of nuclear extracts from S1 cells followed by western blot analysis for NuMA and <t>RNA</t> polymerase I (RNA pol I). ( C ) ChIP from T4–2 cells with NuMA antibody ( n = 4) or RNA Polymerase I antibody ( n = 2), followed by RT-qPCR for coding (pro-1, H4, H8, H13) and non-coding (H18) regions of rDNA. The drawing shows the organization of the rDNA gene (IGS = intergenic sequence). Data are normalized to those obtained with IgG control (see ‘Materials and Methods’ section). ( D ) RNA immunoprecipitation fromT4–2 cells with NuMA antibody or with non-specific IgG of nuclear extracts and soluble extracts (the latter were treated with 50 μg/ml cycloheximide [CH]). Both the <t>DNAse</t> treated non-reverse transcribed RNA (nonRT RNA) and the DNAse treated reverse-transcribed cDNA (cDNA) samples were subjected to PCR using primers specific for human 18S and 28S rRNAs ( n = 2). ( E and F ) Immunoprecipitation of nuclear extracts from S1 cells followed by western blot analysis for NuMA, RPL26 and RPL24.
    Dnase Treated Rnas, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 279 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher dnase ambion treated rna
    NuMA interacts with proteins and nucleic acid components of ribosomal biogenesis. S1 cells were cultured for 8 days with complete medium followed by 2 days without EGF to induce proliferation arrest; T4–2 cells were cultured for 6 days. ( A ) Immunoprecipitation (IP) of nuclear extracts from S1 and T4–2 cells with NuMA antibodies (NuMA) or with non-specific immunoglobulins (IgG), followed by western blot analysis of the input and immunoprecipitated samples using NuMA and NM1 antibodies. ( B ) Immunoprecipitation of nuclear extracts from S1 cells followed by western blot analysis for NuMA and <t>RNA</t> polymerase I (RNA pol I). ( C ) ChIP from T4–2 cells with NuMA antibody ( n = 4) or RNA Polymerase I antibody ( n = 2), followed by RT-qPCR for coding (pro-1, H4, H8, H13) and non-coding (H18) regions of rDNA. The drawing shows the organization of the rDNA gene (IGS = intergenic sequence). Data are normalized to those obtained with IgG control (see ‘Materials and Methods’ section). ( D ) RNA immunoprecipitation fromT4–2 cells with NuMA antibody or with non-specific IgG of nuclear extracts and soluble extracts (the latter were treated with 50 μg/ml cycloheximide [CH]). Both the <t>DNAse</t> treated non-reverse transcribed RNA (nonRT RNA) and the DNAse treated reverse-transcribed cDNA (cDNA) samples were subjected to PCR using primers specific for human 18S and 28S rRNAs ( n = 2). ( E and F ) Immunoprecipitation of nuclear extracts from S1 cells followed by western blot analysis for NuMA, RPL26 and RPL24.
    Dnase Ambion Treated Rna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher rna free dnase treated rna
    NuMA interacts with proteins and nucleic acid components of ribosomal biogenesis. S1 cells were cultured for 8 days with complete medium followed by 2 days without EGF to induce proliferation arrest; T4–2 cells were cultured for 6 days. ( A ) Immunoprecipitation (IP) of nuclear extracts from S1 and T4–2 cells with NuMA antibodies (NuMA) or with non-specific immunoglobulins (IgG), followed by western blot analysis of the input and immunoprecipitated samples using NuMA and NM1 antibodies. ( B ) Immunoprecipitation of nuclear extracts from S1 cells followed by western blot analysis for NuMA and <t>RNA</t> polymerase I (RNA pol I). ( C ) ChIP from T4–2 cells with NuMA antibody ( n = 4) or RNA Polymerase I antibody ( n = 2), followed by RT-qPCR for coding (pro-1, H4, H8, H13) and non-coding (H18) regions of rDNA. The drawing shows the organization of the rDNA gene (IGS = intergenic sequence). Data are normalized to those obtained with IgG control (see ‘Materials and Methods’ section). ( D ) RNA immunoprecipitation fromT4–2 cells with NuMA antibody or with non-specific IgG of nuclear extracts and soluble extracts (the latter were treated with 50 μg/ml cycloheximide [CH]). Both the <t>DNAse</t> treated non-reverse transcribed RNA (nonRT RNA) and the DNAse treated reverse-transcribed cDNA (cDNA) samples were subjected to PCR using primers specific for human 18S and 28S rRNAs ( n = 2). ( E and F ) Immunoprecipitation of nuclear extracts from S1 cells followed by western blot analysis for NuMA, RPL26 and RPL24.
    Rna Free Dnase Treated Rna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 98/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore dnase i
    Absence of TLR9 combined with HMGB1 blockade increases hepatic resistance to I/R injury WT and TLR9 −/− (A) CD45 + NPCs or (B) neutrophils were cultured in conditioned (Con) media from necrotic hepatocytes and αHMGB1. Certain wells containing αHMGB1 were pre-treated with <t>DNAse</t> I for 2 h. After 12 h or 24 h, supernatant cytokines were measured. (C) WT and TLR9 −/− mice were injected with αHMGB1 or isotype control 1 h prior to I/R. Serum ALT was measured 12 h later. (D) The percentage of neutrophils in the ischemic livers of mice subjected to 12 h of I/R following treatment with αHMGB1 or isotype is shown. (E) WT mice were pre-treated with iCpG, αHMGB1 or both just prior to I/R. Serum ALT was measured 12 h later. Data represent means ± SEM and are representative of 3 (A, B) or 2 (C, D, E) independent experiments (4–6 mice/group). *p
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    Roche dnase treated rna
    Absence of TLR9 combined with HMGB1 blockade increases hepatic resistance to I/R injury WT and TLR9 −/− (A) CD45 + NPCs or (B) neutrophils were cultured in conditioned (Con) media from necrotic hepatocytes and αHMGB1. Certain wells containing αHMGB1 were pre-treated with <t>DNAse</t> I for 2 h. After 12 h or 24 h, supernatant cytokines were measured. (C) WT and TLR9 −/− mice were injected with αHMGB1 or isotype control 1 h prior to I/R. Serum ALT was measured 12 h later. (D) The percentage of neutrophils in the ischemic livers of mice subjected to 12 h of I/R following treatment with αHMGB1 or isotype is shown. (E) WT mice were pre-treated with iCpG, αHMGB1 or both just prior to I/R. Serum ALT was measured 12 h later. Data represent means ± SEM and are representative of 3 (A, B) or 2 (C, D, E) independent experiments (4–6 mice/group). *p
    Dnase Treated Rna, supplied by Roche, used in various techniques. Bioz Stars score: 92/100, based on 383 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TaKaRa dnase treated rna
    Absence of TLR9 combined with HMGB1 blockade increases hepatic resistance to I/R injury WT and TLR9 −/− (A) CD45 + NPCs or (B) neutrophils were cultured in conditioned (Con) media from necrotic hepatocytes and αHMGB1. Certain wells containing αHMGB1 were pre-treated with <t>DNAse</t> I for 2 h. After 12 h or 24 h, supernatant cytokines were measured. (C) WT and TLR9 −/− mice were injected with αHMGB1 or isotype control 1 h prior to I/R. Serum ALT was measured 12 h later. (D) The percentage of neutrophils in the ischemic livers of mice subjected to 12 h of I/R following treatment with αHMGB1 or isotype is shown. (E) WT mice were pre-treated with iCpG, αHMGB1 or both just prior to I/R. Serum ALT was measured 12 h later. Data represent means ± SEM and are representative of 3 (A, B) or 2 (C, D, E) independent experiments (4–6 mice/group). *p
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    Agilent technologies dnase treated rna
    Nanodrop spectrophotometry measurements of HTP96-extracted <t>RNA</t> . HTP96 RNA extracts are of high quality and are free from appreciable levels of organic contaminants. A . HTP96 RNA measured immediately after extraction (five-fold dilution). B . HTP96 RNA measured after <t>DNase</t> treatment (five-fold dilution).
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    Promega dnase treated rna
    Nanodrop spectrophotometry measurements of HTP96-extracted <t>RNA</t> . HTP96 RNA extracts are of high quality and are free from appreciable levels of organic contaminants. A . HTP96 RNA measured immediately after extraction (five-fold dilution). B . HTP96 RNA measured after <t>DNase</t> treatment (five-fold dilution).
    Dnase Treated Rna, supplied by Promega, used in various techniques. Bioz Stars score: 93/100, based on 1208 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc dnase treated rna
    Depletion of rRNA from <t>RNA</t> samples isolated from dual species P. aeruginosa / S. aureus cultures. A total of 2 μg of <t>DNAse-treated</t> RNA, isolated form a dual species P. aeruginosa PAO1 and S. aureus ATCC6538 culture, was subjected to treatment with the Illumina Ribo-Zero rRNA Removal Kit (Bacteria) or Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit. Following rRNA depletion and ethanol/acetate precipitation and resuspension in equal volumes of water, the RNA was assessed using the Bioanalyzer RNA 6000 Pico kit. Representative electropherograms of ( A ) starting total RNA material and aliquots of the RNA samples that have been processed using the ( B ) MICROBExpress or ( C ) Ribo-Zero kits are shown. ( D ) Percent of rRNA contamination as reported by the Agilent Bioanalyzer 2100 Expert Software in RNA samples from single and dual species cultures of P. aeruginosa and/or S. aureus treated with the Ribo-Zero or MICROBExpress kits. Untreated input RNA (Total) or RNA processed via Ribo-Zero or MICROBExpress treatment was subjected to qPCR analysis of P. aeruginosa ( E , G ) or S. aureus ( F , H ) rRNA transcript abundance. ( E , F ) qPCR threshold cycle (Cq) for the indicated rRNA transcripts. ( G , H ) Copy numbers of P. aeruginosa or S. aureus 16S, 23 s, and 5S rRNA transcripts were calculated using respective qPCR standard curves. cDNA synthesis for the qPCR reactions was performed using 10 ng of indicated RNA samples as input. Experiments were repeated using two biological replicates. Error bars indicate standard deviation.
    Dnase Treated Rna, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 189 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Novogene dnase treated rna
    Depletion of rRNA from <t>RNA</t> samples isolated from dual species P. aeruginosa / S. aureus cultures. A total of 2 μg of <t>DNAse-treated</t> RNA, isolated form a dual species P. aeruginosa PAO1 and S. aureus ATCC6538 culture, was subjected to treatment with the Illumina Ribo-Zero rRNA Removal Kit (Bacteria) or Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit. Following rRNA depletion and ethanol/acetate precipitation and resuspension in equal volumes of water, the RNA was assessed using the Bioanalyzer RNA 6000 Pico kit. Representative electropherograms of ( A ) starting total RNA material and aliquots of the RNA samples that have been processed using the ( B ) MICROBExpress or ( C ) Ribo-Zero kits are shown. ( D ) Percent of rRNA contamination as reported by the Agilent Bioanalyzer 2100 Expert Software in RNA samples from single and dual species cultures of P. aeruginosa and/or S. aureus treated with the Ribo-Zero or MICROBExpress kits. Untreated input RNA (Total) or RNA processed via Ribo-Zero or MICROBExpress treatment was subjected to qPCR analysis of P. aeruginosa ( E , G ) or S. aureus ( F , H ) rRNA transcript abundance. ( E , F ) qPCR threshold cycle (Cq) for the indicated rRNA transcripts. ( G , H ) Copy numbers of P. aeruginosa or S. aureus 16S, 23 s, and 5S rRNA transcripts were calculated using respective qPCR standard curves. cDNA synthesis for the qPCR reactions was performed using 10 ng of indicated RNA samples as input. Experiments were repeated using two biological replicates. Error bars indicate standard deviation.
    Dnase Treated Rna, supplied by Novogene, used in various techniques. Bioz Stars score: 91/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs dnase treated total rnas
    Depletion of rRNA from <t>RNA</t> samples isolated from dual species P. aeruginosa / S. aureus cultures. A total of 2 μg of <t>DNAse-treated</t> RNA, isolated form a dual species P. aeruginosa PAO1 and S. aureus ATCC6538 culture, was subjected to treatment with the Illumina Ribo-Zero rRNA Removal Kit (Bacteria) or Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit. Following rRNA depletion and ethanol/acetate precipitation and resuspension in equal volumes of water, the RNA was assessed using the Bioanalyzer RNA 6000 Pico kit. Representative electropherograms of ( A ) starting total RNA material and aliquots of the RNA samples that have been processed using the ( B ) MICROBExpress or ( C ) Ribo-Zero kits are shown. ( D ) Percent of rRNA contamination as reported by the Agilent Bioanalyzer 2100 Expert Software in RNA samples from single and dual species cultures of P. aeruginosa and/or S. aureus treated with the Ribo-Zero or MICROBExpress kits. Untreated input RNA (Total) or RNA processed via Ribo-Zero or MICROBExpress treatment was subjected to qPCR analysis of P. aeruginosa ( E , G ) or S. aureus ( F , H ) rRNA transcript abundance. ( E , F ) qPCR threshold cycle (Cq) for the indicated rRNA transcripts. ( G , H ) Copy numbers of P. aeruginosa or S. aureus 16S, 23 s, and 5S rRNA transcripts were calculated using respective qPCR standard curves. cDNA synthesis for the qPCR reactions was performed using 10 ng of indicated RNA samples as input. Experiments were repeated using two biological replicates. Error bars indicate standard deviation.
    Dnase Treated Total Rnas, supplied by New England Biolabs, 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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    CapitalBio Corporation dnase treated rna
    Depletion of rRNA from <t>RNA</t> samples isolated from dual species P. aeruginosa / S. aureus cultures. A total of 2 μg of <t>DNAse-treated</t> RNA, isolated form a dual species P. aeruginosa PAO1 and S. aureus ATCC6538 culture, was subjected to treatment with the Illumina Ribo-Zero rRNA Removal Kit (Bacteria) or Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit. Following rRNA depletion and ethanol/acetate precipitation and resuspension in equal volumes of water, the RNA was assessed using the Bioanalyzer RNA 6000 Pico kit. Representative electropherograms of ( A ) starting total RNA material and aliquots of the RNA samples that have been processed using the ( B ) MICROBExpress or ( C ) Ribo-Zero kits are shown. ( D ) Percent of rRNA contamination as reported by the Agilent Bioanalyzer 2100 Expert Software in RNA samples from single and dual species cultures of P. aeruginosa and/or S. aureus treated with the Ribo-Zero or MICROBExpress kits. Untreated input RNA (Total) or RNA processed via Ribo-Zero or MICROBExpress treatment was subjected to qPCR analysis of P. aeruginosa ( E , G ) or S. aureus ( F , H ) rRNA transcript abundance. ( E , F ) qPCR threshold cycle (Cq) for the indicated rRNA transcripts. ( G , H ) Copy numbers of P. aeruginosa or S. aureus 16S, 23 s, and 5S rRNA transcripts were calculated using respective qPCR standard curves. cDNA synthesis for the qPCR reactions was performed using 10 ng of indicated RNA samples as input. Experiments were repeated using two biological replicates. Error bars indicate standard deviation.
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    Image Search Results


    NuMA interacts with proteins and nucleic acid components of ribosomal biogenesis. S1 cells were cultured for 8 days with complete medium followed by 2 days without EGF to induce proliferation arrest; T4–2 cells were cultured for 6 days. ( A ) Immunoprecipitation (IP) of nuclear extracts from S1 and T4–2 cells with NuMA antibodies (NuMA) or with non-specific immunoglobulins (IgG), followed by western blot analysis of the input and immunoprecipitated samples using NuMA and NM1 antibodies. ( B ) Immunoprecipitation of nuclear extracts from S1 cells followed by western blot analysis for NuMA and RNA polymerase I (RNA pol I). ( C ) ChIP from T4–2 cells with NuMA antibody ( n = 4) or RNA Polymerase I antibody ( n = 2), followed by RT-qPCR for coding (pro-1, H4, H8, H13) and non-coding (H18) regions of rDNA. The drawing shows the organization of the rDNA gene (IGS = intergenic sequence). Data are normalized to those obtained with IgG control (see ‘Materials and Methods’ section). ( D ) RNA immunoprecipitation fromT4–2 cells with NuMA antibody or with non-specific IgG of nuclear extracts and soluble extracts (the latter were treated with 50 μg/ml cycloheximide [CH]). Both the DNAse treated non-reverse transcribed RNA (nonRT RNA) and the DNAse treated reverse-transcribed cDNA (cDNA) samples were subjected to PCR using primers specific for human 18S and 28S rRNAs ( n = 2). ( E and F ) Immunoprecipitation of nuclear extracts from S1 cells followed by western blot analysis for NuMA, RPL26 and RPL24.

    Journal: Nucleic Acids Research

    Article Title: The nuclear mitotic apparatus protein NuMA controls rDNA transcription and mediates the nucleolar stress response in a p53-independent manner

    doi: 10.1093/nar/gkx782

    Figure Lengend Snippet: NuMA interacts with proteins and nucleic acid components of ribosomal biogenesis. S1 cells were cultured for 8 days with complete medium followed by 2 days without EGF to induce proliferation arrest; T4–2 cells were cultured for 6 days. ( A ) Immunoprecipitation (IP) of nuclear extracts from S1 and T4–2 cells with NuMA antibodies (NuMA) or with non-specific immunoglobulins (IgG), followed by western blot analysis of the input and immunoprecipitated samples using NuMA and NM1 antibodies. ( B ) Immunoprecipitation of nuclear extracts from S1 cells followed by western blot analysis for NuMA and RNA polymerase I (RNA pol I). ( C ) ChIP from T4–2 cells with NuMA antibody ( n = 4) or RNA Polymerase I antibody ( n = 2), followed by RT-qPCR for coding (pro-1, H4, H8, H13) and non-coding (H18) regions of rDNA. The drawing shows the organization of the rDNA gene (IGS = intergenic sequence). Data are normalized to those obtained with IgG control (see ‘Materials and Methods’ section). ( D ) RNA immunoprecipitation fromT4–2 cells with NuMA antibody or with non-specific IgG of nuclear extracts and soluble extracts (the latter were treated with 50 μg/ml cycloheximide [CH]). Both the DNAse treated non-reverse transcribed RNA (nonRT RNA) and the DNAse treated reverse-transcribed cDNA (cDNA) samples were subjected to PCR using primers specific for human 18S and 28S rRNAs ( n = 2). ( E and F ) Immunoprecipitation of nuclear extracts from S1 cells followed by western blot analysis for NuMA, RPL26 and RPL24.

    Article Snippet: The DNAse-treated RNA sample was reverse-transcribed into cDNA using the Iscript™ DNA synthesis kit (Bio-Rad).

    Techniques: Cell Culture, Immunoprecipitation, Western Blot, Chromatin Immunoprecipitation, Quantitative RT-PCR, Sequencing, Polymerase Chain Reaction

    Absence of TLR9 combined with HMGB1 blockade increases hepatic resistance to I/R injury WT and TLR9 −/− (A) CD45 + NPCs or (B) neutrophils were cultured in conditioned (Con) media from necrotic hepatocytes and αHMGB1. Certain wells containing αHMGB1 were pre-treated with DNAse I for 2 h. After 12 h or 24 h, supernatant cytokines were measured. (C) WT and TLR9 −/− mice were injected with αHMGB1 or isotype control 1 h prior to I/R. Serum ALT was measured 12 h later. (D) The percentage of neutrophils in the ischemic livers of mice subjected to 12 h of I/R following treatment with αHMGB1 or isotype is shown. (E) WT mice were pre-treated with iCpG, αHMGB1 or both just prior to I/R. Serum ALT was measured 12 h later. Data represent means ± SEM and are representative of 3 (A, B) or 2 (C, D, E) independent experiments (4–6 mice/group). *p

    Journal: Hepatology (Baltimore, Md.)

    Article Title: Toll-like receptor 9 inhibition confers protection from liver ischemia-reperfusion injury

    doi: 10.1002/hep.23365

    Figure Lengend Snippet: Absence of TLR9 combined with HMGB1 blockade increases hepatic resistance to I/R injury WT and TLR9 −/− (A) CD45 + NPCs or (B) neutrophils were cultured in conditioned (Con) media from necrotic hepatocytes and αHMGB1. Certain wells containing αHMGB1 were pre-treated with DNAse I for 2 h. After 12 h or 24 h, supernatant cytokines were measured. (C) WT and TLR9 −/− mice were injected with αHMGB1 or isotype control 1 h prior to I/R. Serum ALT was measured 12 h later. (D) The percentage of neutrophils in the ischemic livers of mice subjected to 12 h of I/R following treatment with αHMGB1 or isotype is shown. (E) WT mice were pre-treated with iCpG, αHMGB1 or both just prior to I/R. Serum ALT was measured 12 h later. Data represent means ± SEM and are representative of 3 (A, B) or 2 (C, D, E) independent experiments (4–6 mice/group). *p

    Article Snippet: In additional experiments, conditioned media was pre-treated for 2 h with DNAse I (100 μg/ml; Sigma-Aldrich) at 25 °C.

    Techniques: Cell Culture, Mouse Assay, Injection

    Liver NPCs are activated by endogenous hepatocyte DNA through TLR9 WT and TLR9 −/− (A) CD45 + NPCs or (B) neutrophils were cultured in media alone or with conditioned (Con) media from 10 6 or 5 × 10 6 necrotic hepatocytes. Some wells containing conditioned media (from 5 × 10 6 necrotic hepatocytes) were pre-treated with DNAse I for 2 h prior to co-culture with NPCs or neutrophils. Supernatant cytokines were measured 24 (NPCs) or 12 h (neutrophils) later. Levels of MCP-1 were undetectable for neutrophil cultures in (B) (unpublished data). Data represent means ± SEM and are representative of 3 independent experiments. *p

    Journal: Hepatology (Baltimore, Md.)

    Article Title: Toll-like receptor 9 inhibition confers protection from liver ischemia-reperfusion injury

    doi: 10.1002/hep.23365

    Figure Lengend Snippet: Liver NPCs are activated by endogenous hepatocyte DNA through TLR9 WT and TLR9 −/− (A) CD45 + NPCs or (B) neutrophils were cultured in media alone or with conditioned (Con) media from 10 6 or 5 × 10 6 necrotic hepatocytes. Some wells containing conditioned media (from 5 × 10 6 necrotic hepatocytes) were pre-treated with DNAse I for 2 h prior to co-culture with NPCs or neutrophils. Supernatant cytokines were measured 24 (NPCs) or 12 h (neutrophils) later. Levels of MCP-1 were undetectable for neutrophil cultures in (B) (unpublished data). Data represent means ± SEM and are representative of 3 independent experiments. *p

    Article Snippet: In additional experiments, conditioned media was pre-treated for 2 h with DNAse I (100 μg/ml; Sigma-Aldrich) at 25 °C.

    Techniques: Cell Culture, Co-Culture Assay

    Nanodrop spectrophotometry measurements of HTP96-extracted RNA . HTP96 RNA extracts are of high quality and are free from appreciable levels of organic contaminants. A . HTP96 RNA measured immediately after extraction (five-fold dilution). B . HTP96 RNA measured after DNase treatment (five-fold dilution).

    Journal: Plant Methods

    Article Title: Protocol: A simple phenol-based method for 96-well extraction of high quality RNA from Arabidopsis

    doi: 10.1186/1746-4811-7-7

    Figure Lengend Snippet: Nanodrop spectrophotometry measurements of HTP96-extracted RNA . HTP96 RNA extracts are of high quality and are free from appreciable levels of organic contaminants. A . HTP96 RNA measured immediately after extraction (five-fold dilution). B . HTP96 RNA measured after DNase treatment (five-fold dilution).

    Article Snippet: 4 μL of DNase treated RNA (300 ng μCL-1 ) were run on an Agilent 2100 Bioanalyzer microfluidic electrophoresis chip according to the manufacturer's instructions.

    Techniques: Spectrophotometry

    Microfluidic electrophoresis of HTP96-extracted RNA . The quality of HTP96 RNA (4 μL at 300 ng μL -1 ) was measured on an Agilent 2100 Bioanalyzer microfluidic electrophoresis chip following treatment with DNase. The microfluidic electrophoresis image (inset) and electropherogram are typical of high quality Arabidopsis RNA showing the clear cytosolic and plastidic (Cp, asterisks) ribosomal bands. RNA species of low molecular weight are also apparent. gDNA contamination is effectively removed by DNase treatment.

    Journal: Plant Methods

    Article Title: Protocol: A simple phenol-based method for 96-well extraction of high quality RNA from Arabidopsis

    doi: 10.1186/1746-4811-7-7

    Figure Lengend Snippet: Microfluidic electrophoresis of HTP96-extracted RNA . The quality of HTP96 RNA (4 μL at 300 ng μL -1 ) was measured on an Agilent 2100 Bioanalyzer microfluidic electrophoresis chip following treatment with DNase. The microfluidic electrophoresis image (inset) and electropherogram are typical of high quality Arabidopsis RNA showing the clear cytosolic and plastidic (Cp, asterisks) ribosomal bands. RNA species of low molecular weight are also apparent. gDNA contamination is effectively removed by DNase treatment.

    Article Snippet: 4 μL of DNase treated RNA (300 ng μCL-1 ) were run on an Agilent 2100 Bioanalyzer microfluidic electrophoresis chip according to the manufacturer's instructions.

    Techniques: Electrophoresis, Chromatin Immunoprecipitation, Molecular Weight

    Depletion of rRNA from RNA samples isolated from dual species P. aeruginosa / S. aureus cultures. A total of 2 μg of DNAse-treated RNA, isolated form a dual species P. aeruginosa PAO1 and S. aureus ATCC6538 culture, was subjected to treatment with the Illumina Ribo-Zero rRNA Removal Kit (Bacteria) or Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit. Following rRNA depletion and ethanol/acetate precipitation and resuspension in equal volumes of water, the RNA was assessed using the Bioanalyzer RNA 6000 Pico kit. Representative electropherograms of ( A ) starting total RNA material and aliquots of the RNA samples that have been processed using the ( B ) MICROBExpress or ( C ) Ribo-Zero kits are shown. ( D ) Percent of rRNA contamination as reported by the Agilent Bioanalyzer 2100 Expert Software in RNA samples from single and dual species cultures of P. aeruginosa and/or S. aureus treated with the Ribo-Zero or MICROBExpress kits. Untreated input RNA (Total) or RNA processed via Ribo-Zero or MICROBExpress treatment was subjected to qPCR analysis of P. aeruginosa ( E , G ) or S. aureus ( F , H ) rRNA transcript abundance. ( E , F ) qPCR threshold cycle (Cq) for the indicated rRNA transcripts. ( G , H ) Copy numbers of P. aeruginosa or S. aureus 16S, 23 s, and 5S rRNA transcripts were calculated using respective qPCR standard curves. cDNA synthesis for the qPCR reactions was performed using 10 ng of indicated RNA samples as input. Experiments were repeated using two biological replicates. Error bars indicate standard deviation.

    Journal: Scientific Reports

    Article Title: Comparative evaluation of rRNA depletion procedures for the improved analysis of bacterial biofilm and mixed pathogen culture transcriptomes

    doi: 10.1038/srep41114

    Figure Lengend Snippet: Depletion of rRNA from RNA samples isolated from dual species P. aeruginosa / S. aureus cultures. A total of 2 μg of DNAse-treated RNA, isolated form a dual species P. aeruginosa PAO1 and S. aureus ATCC6538 culture, was subjected to treatment with the Illumina Ribo-Zero rRNA Removal Kit (Bacteria) or Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit. Following rRNA depletion and ethanol/acetate precipitation and resuspension in equal volumes of water, the RNA was assessed using the Bioanalyzer RNA 6000 Pico kit. Representative electropherograms of ( A ) starting total RNA material and aliquots of the RNA samples that have been processed using the ( B ) MICROBExpress or ( C ) Ribo-Zero kits are shown. ( D ) Percent of rRNA contamination as reported by the Agilent Bioanalyzer 2100 Expert Software in RNA samples from single and dual species cultures of P. aeruginosa and/or S. aureus treated with the Ribo-Zero or MICROBExpress kits. Untreated input RNA (Total) or RNA processed via Ribo-Zero or MICROBExpress treatment was subjected to qPCR analysis of P. aeruginosa ( E , G ) or S. aureus ( F , H ) rRNA transcript abundance. ( E , F ) qPCR threshold cycle (Cq) for the indicated rRNA transcripts. ( G , H ) Copy numbers of P. aeruginosa or S. aureus 16S, 23 s, and 5S rRNA transcripts were calculated using respective qPCR standard curves. cDNA synthesis for the qPCR reactions was performed using 10 ng of indicated RNA samples as input. Experiments were repeated using two biological replicates. Error bars indicate standard deviation.

    Article Snippet: Comparison of three commercially available rRNA depletion methods In order to evaluate the efficiency of commercially available kits in the depletion of rRNA from P. aeruginosa biofilm samples, we have subjected 4 μg of DNAse-treated RNA isolated form 3-day-old PAO1 biofilms to treatment with the Illumina Ribo-Zero rRNA Removal Kit (Bacteria), Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit and the Life Technologies RiboMinus Transcriptome Isolation Kit, Bacteria.

    Techniques: Isolation, Software, Real-time Polymerase Chain Reaction, Standard Deviation

    Quantitative and qualitative comparison of RNA recovered following rRNA depletion. A total of 4 μg of DNAse-treated RNA, isolated form 3-day-old P. aeruginosa PAO1 biofilms, was subjected to treatment with the Illumina Ribo-Zero rRNA Removal Kit (Bacteria), Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit and the Life Technologies RiboMinus Transcriptome Isolation Kit, Bacteria. Following rRNA depletion and ethanol/acetate precipitation and resuspension in equal volumes of water, the RNA was assessed using Qubit fluorimetric quantitation with the Qubit RNA HS Assay Kit. Yields are reported as total RNA recovered ( A ) and as percentage of the input RNA ( B ). The RNA samples were also assessed using the Bioanalyzer RNA 6000 Pico kit. Representative electropherograms of ( C ) starting total RNA material and aliquots of the RNA samples that have been processed using the ( D ) MICROBExpress, ( E ) RiboMinus, or ( F ) Ribo-Zero kits are shown. Dashed lines indicate peaks corresponding to 16S and 23S RNA traces, which were detected in total RNA, MICROBExpress, and RiboMins samples. ( G ) The area of 16S and 23S rRNA peaks as percent of the total detected RNA was estimated, as determined using the 2100 Expert Software. RFU, relative fluorescence units. Experiments were repeated using three biological replicates.

    Journal: Scientific Reports

    Article Title: Comparative evaluation of rRNA depletion procedures for the improved analysis of bacterial biofilm and mixed pathogen culture transcriptomes

    doi: 10.1038/srep41114

    Figure Lengend Snippet: Quantitative and qualitative comparison of RNA recovered following rRNA depletion. A total of 4 μg of DNAse-treated RNA, isolated form 3-day-old P. aeruginosa PAO1 biofilms, was subjected to treatment with the Illumina Ribo-Zero rRNA Removal Kit (Bacteria), Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit and the Life Technologies RiboMinus Transcriptome Isolation Kit, Bacteria. Following rRNA depletion and ethanol/acetate precipitation and resuspension in equal volumes of water, the RNA was assessed using Qubit fluorimetric quantitation with the Qubit RNA HS Assay Kit. Yields are reported as total RNA recovered ( A ) and as percentage of the input RNA ( B ). The RNA samples were also assessed using the Bioanalyzer RNA 6000 Pico kit. Representative electropherograms of ( C ) starting total RNA material and aliquots of the RNA samples that have been processed using the ( D ) MICROBExpress, ( E ) RiboMinus, or ( F ) Ribo-Zero kits are shown. Dashed lines indicate peaks corresponding to 16S and 23S RNA traces, which were detected in total RNA, MICROBExpress, and RiboMins samples. ( G ) The area of 16S and 23S rRNA peaks as percent of the total detected RNA was estimated, as determined using the 2100 Expert Software. RFU, relative fluorescence units. Experiments were repeated using three biological replicates.

    Article Snippet: Comparison of three commercially available rRNA depletion methods In order to evaluate the efficiency of commercially available kits in the depletion of rRNA from P. aeruginosa biofilm samples, we have subjected 4 μg of DNAse-treated RNA isolated form 3-day-old PAO1 biofilms to treatment with the Illumina Ribo-Zero rRNA Removal Kit (Bacteria), Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit and the Life Technologies RiboMinus Transcriptome Isolation Kit, Bacteria.

    Techniques: Isolation, Quantitation Assay, RNA HS Assay, Software, Fluorescence

    rRNA depletion treatments of RNA derived from planktonic P. aeruginosa PAO1 and Staphylococcus aureus ATCC6538 cells. A total of 2 μg of DNAse-treated RNA, isolated from exponential phase P. aeruginosa PAO1 or Staphylococcus aureus ATCC6538 cells, was subjected to treatment with the Illumina Ribo-Zero rRNA Removal Kit (Bacteria) or Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit. Following rRNA depletion and ethanol/acetate precipitation and resuspension in equal volumes of water, the RNA was assessed using the Bioanalyzer RNA 6000 Pico kit. Representative electropherograms of starting total RNA material and aliquots of the RNA samples that have been processed using the MICROBExpress or Ribo-Zero kits are shown for the P. aeruginosa ( A ) and S. aureus ( B ) samples. The samples were subsequently subjected to qPCR analysis of rRNA transcript abundance, with qPCR threshold cycle (Cq) for the indicated rRNA transcripts shown for P. aeruginosa ( C ) and S. aureus ( E ). Copy numbers of P. aeruginosa ( D ) and S. aureus ( F ) 16S, 23 s, and 5S rRNA transcripts were calculated using respective qPCR standard curves. cDNA synthesis for the qPCR reactions was performed using 10 ng of indicated RNA samples as input. Experiments were repeated using two biological replicates. Error bars indicate standard deviation.

    Journal: Scientific Reports

    Article Title: Comparative evaluation of rRNA depletion procedures for the improved analysis of bacterial biofilm and mixed pathogen culture transcriptomes

    doi: 10.1038/srep41114

    Figure Lengend Snippet: rRNA depletion treatments of RNA derived from planktonic P. aeruginosa PAO1 and Staphylococcus aureus ATCC6538 cells. A total of 2 μg of DNAse-treated RNA, isolated from exponential phase P. aeruginosa PAO1 or Staphylococcus aureus ATCC6538 cells, was subjected to treatment with the Illumina Ribo-Zero rRNA Removal Kit (Bacteria) or Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit. Following rRNA depletion and ethanol/acetate precipitation and resuspension in equal volumes of water, the RNA was assessed using the Bioanalyzer RNA 6000 Pico kit. Representative electropherograms of starting total RNA material and aliquots of the RNA samples that have been processed using the MICROBExpress or Ribo-Zero kits are shown for the P. aeruginosa ( A ) and S. aureus ( B ) samples. The samples were subsequently subjected to qPCR analysis of rRNA transcript abundance, with qPCR threshold cycle (Cq) for the indicated rRNA transcripts shown for P. aeruginosa ( C ) and S. aureus ( E ). Copy numbers of P. aeruginosa ( D ) and S. aureus ( F ) 16S, 23 s, and 5S rRNA transcripts were calculated using respective qPCR standard curves. cDNA synthesis for the qPCR reactions was performed using 10 ng of indicated RNA samples as input. Experiments were repeated using two biological replicates. Error bars indicate standard deviation.

    Article Snippet: Comparison of three commercially available rRNA depletion methods In order to evaluate the efficiency of commercially available kits in the depletion of rRNA from P. aeruginosa biofilm samples, we have subjected 4 μg of DNAse-treated RNA isolated form 3-day-old PAO1 biofilms to treatment with the Illumina Ribo-Zero rRNA Removal Kit (Bacteria), Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit and the Life Technologies RiboMinus Transcriptome Isolation Kit, Bacteria.

    Techniques: Derivative Assay, Isolation, Real-time Polymerase Chain Reaction, Standard Deviation