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  • 99
    Millipore ribonucleic acid rna extraction
    EPR analysis of Tau fibrils. Single cysteines in K18 and K19 monomers were spin-labeled with the nitroxide label MTSL and allowed to fibrillize in the presence of polyanionic cofactors. All spectra were taken at 150 G and normalized to the same number of spins. K18 and K19 fibrils were formed in the presence of (A) polyA, (B) <t>polyU,</t> polyAU, tRNA, and yeast <t>RNA</t> extract, and (C) polydA and polyGlu. The single-line EPR spectra observed for all fibrils indicate that, regardless of cofactor, β-strands in the proteins are aligned parallel and in-register.
    Ribonucleic Acid Rna Extraction, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 53 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 53 article reviews
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    99
    Millipore rna extraction
    EPR analysis of Tau fibrils. Single cysteines in K18 and K19 monomers were spin-labeled with the nitroxide label MTSL and allowed to fibrillize in the presence of polyanionic cofactors. All spectra were taken at 150 G and normalized to the same number of spins. K18 and K19 fibrils were formed in the presence of (A) polyA, (B) <t>polyU,</t> polyAU, tRNA, and yeast <t>RNA</t> extract, and (C) polydA and polyGlu. The single-line EPR spectra observed for all fibrils indicate that, regardless of cofactor, β-strands in the proteins are aligned parallel and in-register.
    Rna Extraction, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 1330 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rna extraction/product/Millipore
    Average 99 stars, based on 1330 article reviews
    Price from $9.99 to $1999.99
    rna extraction - by Bioz Stars, 2020-05
    99/100 stars
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    99
    Millipore qpcr rna extraction
    For figure legend see page . Figure 1. (see previous page) Lacto-rpoB and 23S methyl <t>RNA</t> elements are regulated by RNase III in S. <t>pyogenes.</t> A. Northern blot analysis (polyacrylamide gel electrophoresis) of Lacto-rpoB and 23S-methyl RNA expression in WT (SF370), ΔRNase III (Δ rnc ) and ΔRNase Y (Δ rny ) strains grown to early logarithmic (EL), mid logarithmic (ML) and early stationary (ES) phases. 5S rRNA is used as loading control. B. Expression profiles of Lacto-rpoB and the 23S-methyl motif with surrounding genes captured using the Integrative Genomics Viewer (IGV) software. The sequence coverage was calculated using BEDTools-Version-2.15.0 and the scale is given in number of reads per million. The distribution of reads starting (5') and ending (3') at each nucleotide position is represented in blue and orange, respectively. The position of the oligonucleotide probes (OLEC) used in Northern blot analysis is indicated. C. Prediction of RNA secondary structure using RNAfold (rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi). The arrows represent putative cleavages by RNase III (nucleotides determined by analyzing the 5' and 3' ends of the sRNAs in sRNA sequencing data).
    Qpcr Rna Extraction, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 216 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/qpcr rna extraction/product/Millipore
    Average 99 stars, based on 216 article reviews
    Price from $9.99 to $1999.99
    qpcr rna extraction - by Bioz Stars, 2020-05
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    95
    Millipore rna extraction kit
    For figure legend see page . Figure 1. (see previous page) Lacto-rpoB and 23S methyl <t>RNA</t> elements are regulated by RNase III in S. <t>pyogenes.</t> A. Northern blot analysis (polyacrylamide gel electrophoresis) of Lacto-rpoB and 23S-methyl RNA expression in WT (SF370), ΔRNase III (Δ rnc ) and ΔRNase Y (Δ rny ) strains grown to early logarithmic (EL), mid logarithmic (ML) and early stationary (ES) phases. 5S rRNA is used as loading control. B. Expression profiles of Lacto-rpoB and the 23S-methyl motif with surrounding genes captured using the Integrative Genomics Viewer (IGV) software. The sequence coverage was calculated using BEDTools-Version-2.15.0 and the scale is given in number of reads per million. The distribution of reads starting (5') and ending (3') at each nucleotide position is represented in blue and orange, respectively. The position of the oligonucleotide probes (OLEC) used in Northern blot analysis is indicated. C. Prediction of RNA secondary structure using RNAfold (rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi). The arrows represent putative cleavages by RNase III (nucleotides determined by analyzing the 5' and 3' ends of the sRNAs in sRNA sequencing data).
    Rna Extraction Kit, supplied by Millipore, used in various techniques. Bioz Stars score: 95/100, based on 174 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rna extraction kit/product/Millipore
    Average 95 stars, based on 174 article reviews
    Price from $9.99 to $1999.99
    rna extraction kit - by Bioz Stars, 2020-05
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      Buy from Supplier

    Image Search Results


    EPR analysis of Tau fibrils. Single cysteines in K18 and K19 monomers were spin-labeled with the nitroxide label MTSL and allowed to fibrillize in the presence of polyanionic cofactors. All spectra were taken at 150 G and normalized to the same number of spins. K18 and K19 fibrils were formed in the presence of (A) polyA, (B) polyU, polyAU, tRNA, and yeast RNA extract, and (C) polydA and polyGlu. The single-line EPR spectra observed for all fibrils indicate that, regardless of cofactor, β-strands in the proteins are aligned parallel and in-register.

    Journal: Biochemistry

    Article Title: RNA Binds to Tau Fibrils and Sustains Template-Assisted Growth

    doi: 10.1021/acs.biochem.5b00453

    Figure Lengend Snippet: EPR analysis of Tau fibrils. Single cysteines in K18 and K19 monomers were spin-labeled with the nitroxide label MTSL and allowed to fibrillize in the presence of polyanionic cofactors. All spectra were taken at 150 G and normalized to the same number of spins. K18 and K19 fibrils were formed in the presence of (A) polyA, (B) polyU, polyAU, tRNA, and yeast RNA extract, and (C) polydA and polyGlu. The single-line EPR spectra observed for all fibrils indicate that, regardless of cofactor, β-strands in the proteins are aligned parallel and in-register.

    Article Snippet: Fibrils were also prepared with 30–65 μM spin-labeled Tau with polyU (Sigma P9528), double-stranded polyAU (Sigma P1537), tRNA (Sigma R8759), or RNA extract from baker’s yeast (Sigma R650) at concentration ranges of 140–200 μg/mL or with polydA (Sigma P0887) at 36 μg/mL.

    Techniques: Electron Paramagnetic Resonance, Labeling

    Subsampling of RNA-seq data. The effect of subsampling on the number and concordance of the RNA-seq SNVs. Here, decreasing subsets of a single replicate of HCT116a (corresponding to a total of 32 million read pairs) is shown. The concordance of each subset is annotated next to the corresponding data point. For data on additional cell lines, see S1 Fig .

    Journal: PLoS ONE

    Article Title: A novel RNA sequencing data analysis method for cell line authentication

    doi: 10.1371/journal.pone.0171435

    Figure Lengend Snippet: Subsampling of RNA-seq data. The effect of subsampling on the number and concordance of the RNA-seq SNVs. Here, decreasing subsets of a single replicate of HCT116a (corresponding to a total of 32 million read pairs) is shown. The concordance of each subset is annotated next to the corresponding data point. For data on additional cell lines, see S1 Fig .

    Article Snippet: Cell line cultivations and RNA extractions The HCT116a and RKO cell lines were cultivated in standard McCoy medium with 10% Foetal Bovine Serum and were split 1:5 every third or fourth day (Sigma Aldrich).

    Techniques: RNA Sequencing Assay

    BEX1 directly controls A + U-rich element containing mRNAs. a Comparison of RNAseq and RIP-seq list showing 91 overlapping mRNAs due to BEX1 overexpression or BEX1-dependent pull-down, respectively, 17.58% of which contains AU-rich elements (ARE). b RNA EMSA showing an ARE-ribonucleoprotein cardiac complex shift from heart protein extract at 4 and 8 μg, which is shifted even higher by addition or recombinant BEX1-GST (blue arrows). GST was used as negative control. c qPCR for β-globin mRNA at 0, 45, 90, 135 and 180 min post-tetracycline addition in stable cell lines (control, GM-CSF ARE or c-fos ARE) transfected with BEX1 or GFP control plasmid. A synthetic poly A (SPA) is present in all 3 constructs. Results reflect 3 separate experiments. d Level of β-globin mRNA following RNA immunoprecipitation using Flag antibodies from Flag-BEX1 or GFP expressing stable cell lines (control, GM-CSF ARE and c-fos ARE) by qPCR. The results are from 3 separate experiments. e qPCR analysis for TNFα and CCL5 mRNA immunoprecipitated with BEX1 antibody from BEX1 transgenic hearts. Number of experiments conducted is shown in the graph for each condition. * P

    Journal: Nature Communications

    Article Title: BEX1 is an RNA-dependent mediator of cardiomyopathy

    doi: 10.1038/s41467-017-02005-1

    Figure Lengend Snippet: BEX1 directly controls A + U-rich element containing mRNAs. a Comparison of RNAseq and RIP-seq list showing 91 overlapping mRNAs due to BEX1 overexpression or BEX1-dependent pull-down, respectively, 17.58% of which contains AU-rich elements (ARE). b RNA EMSA showing an ARE-ribonucleoprotein cardiac complex shift from heart protein extract at 4 and 8 μg, which is shifted even higher by addition or recombinant BEX1-GST (blue arrows). GST was used as negative control. c qPCR for β-globin mRNA at 0, 45, 90, 135 and 180 min post-tetracycline addition in stable cell lines (control, GM-CSF ARE or c-fos ARE) transfected with BEX1 or GFP control plasmid. A synthetic poly A (SPA) is present in all 3 constructs. Results reflect 3 separate experiments. d Level of β-globin mRNA following RNA immunoprecipitation using Flag antibodies from Flag-BEX1 or GFP expressing stable cell lines (control, GM-CSF ARE and c-fos ARE) by qPCR. The results are from 3 separate experiments. e qPCR analysis for TNFα and CCL5 mRNA immunoprecipitated with BEX1 antibody from BEX1 transgenic hearts. Number of experiments conducted is shown in the graph for each condition. * P

    Article Snippet: For RIP-sequencing, Magna RIP kit (Millipore) was used to extract RNA, and anti-Flag M2 magnetic beads (M8823, Sigma) were used to immunoprecipitate ribonucleoprotein complexes from neonatal rat cardiomyocytes overexpressing Flag-tagged BEX1 or β-galactosidase control.

    Techniques: Over Expression, Recombinant, Negative Control, Real-time Polymerase Chain Reaction, Stable Transfection, Transfection, Plasmid Preparation, Construct, Immunoprecipitation, Expressing, Transgenic Assay

    Radioactive signal for increasing amounts of DNA added to 10 ng of radiolabeled RNA and for DNA alone. The signal is expressed as the SAB.

    Journal: Applied and Environmental Microbiology

    Article Title: The Presence of Humic Substances and DNA in RNA Extracts Affects Hybridization Results

    doi:

    Figure Lengend Snippet: Radioactive signal for increasing amounts of DNA added to 10 ng of radiolabeled RNA and for DNA alone. The signal is expressed as the SAB.

    Article Snippet: To evaluate the effect of the presence of DNA in RNA extracts on membrane hybridizations, RNA was removed from E. coli DNA (catalog no. D-2001; Sigma, St. Louis, Mo.) by RNase digestion (Ribonuclease 1 A; Pharmacia).

    Techniques:

    Hybridization response for RNA amended with DNA and for DNA alone. The hybridization response is expressed as a percentage of the hybridization response obtained with RNA only.

    Journal: Applied and Environmental Microbiology

    Article Title: The Presence of Humic Substances and DNA in RNA Extracts Affects Hybridization Results

    doi:

    Figure Lengend Snippet: Hybridization response for RNA amended with DNA and for DNA alone. The hybridization response is expressed as a percentage of the hybridization response obtained with RNA only.

    Article Snippet: To evaluate the effect of the presence of DNA in RNA extracts on membrane hybridizations, RNA was removed from E. coli DNA (catalog no. D-2001; Sigma, St. Louis, Mo.) by RNase digestion (Ribonuclease 1 A; Pharmacia).

    Techniques: Hybridization

    DNA synthesis catalyzed by RT-KTQ-LSIM is hampered by 2′-O-methylation of RNA templates. ( A ) Structures of relevant nucleotides. ( B ) Primer extension in presence of methylated or unmethylated RNA templates catalyzed by RT-KTQ-LSIM. ( C ) qRT-PCR amplification of methylated and unmethylated RNA oligonucleotides catalyzed by RT-KTQ-LSIM.

    Journal: Nucleic Acids Research

    Article Title: Direct and site-specific quantification of RNA 2′-O-methylation by PCR with an engineered DNA polymerase

    doi: 10.1093/nar/gkw200

    Figure Lengend Snippet: DNA synthesis catalyzed by RT-KTQ-LSIM is hampered by 2′-O-methylation of RNA templates. ( A ) Structures of relevant nucleotides. ( B ) Primer extension in presence of methylated or unmethylated RNA templates catalyzed by RT-KTQ-LSIM. ( C ) qRT-PCR amplification of methylated and unmethylated RNA oligonucleotides catalyzed by RT-KTQ-LSIM.

    Article Snippet: qRT-PCR with human RNA extracts and in vitro transcribed 18s rRNA qRT-PCRs were conducted in a total volume of 20 μl reaction mixture containing 100 nM forward primer, 100 nM reverse primer, 200 μM dNTPs (each), 0.5 M betaine, 1x SYBR® green I (sigma), 100 nM Taq DNA polymerase aptamer ( ) and 100 nM of either RT-KTQ-LSIM or RT-KTQ-LSIM V669L in KlenTaq reaction buffer.

    Techniques: DNA Synthesis, Methylation, Quantitative RT-PCR, Amplification

    RT-KTQ-LSIM V669L features increased discrimination between 2′-O-methylated and unmethlyated RNA templates and enables quantification of 2′-O-methylation by qRT-PCR. ( A ) Primer extension in the presence of methylated or unmethlyated RNA templates catalyzed by RT-KTQ-LSIM V669L. ( B ) qRT-PCR amplification of methylated and unmethylated RNA oligonucleotides catalyzed by RT-KTQ-LSIM V669L. ( C ) RT-PCR reactions were stopped after 25 cycles (top) or 30 cycles (bottom) and analyzed by agarose gel electrophoresis. ( D ) The ΔC T -method was used to calculate methylation ratio of RNA template at 100 pM concentration with varied fractions of 2′OmeA/A at the target position. Error bars describe SD (n = 3).

    Journal: Nucleic Acids Research

    Article Title: Direct and site-specific quantification of RNA 2′-O-methylation by PCR with an engineered DNA polymerase

    doi: 10.1093/nar/gkw200

    Figure Lengend Snippet: RT-KTQ-LSIM V669L features increased discrimination between 2′-O-methylated and unmethlyated RNA templates and enables quantification of 2′-O-methylation by qRT-PCR. ( A ) Primer extension in the presence of methylated or unmethlyated RNA templates catalyzed by RT-KTQ-LSIM V669L. ( B ) qRT-PCR amplification of methylated and unmethylated RNA oligonucleotides catalyzed by RT-KTQ-LSIM V669L. ( C ) RT-PCR reactions were stopped after 25 cycles (top) or 30 cycles (bottom) and analyzed by agarose gel electrophoresis. ( D ) The ΔC T -method was used to calculate methylation ratio of RNA template at 100 pM concentration with varied fractions of 2′OmeA/A at the target position. Error bars describe SD (n = 3).

    Article Snippet: qRT-PCR with human RNA extracts and in vitro transcribed 18s rRNA qRT-PCRs were conducted in a total volume of 20 μl reaction mixture containing 100 nM forward primer, 100 nM reverse primer, 200 μM dNTPs (each), 0.5 M betaine, 1x SYBR® green I (sigma), 100 nM Taq DNA polymerase aptamer ( ) and 100 nM of either RT-KTQ-LSIM or RT-KTQ-LSIM V669L in KlenTaq reaction buffer.

    Techniques: Methylation, Quantitative RT-PCR, Amplification, Reverse Transcription Polymerase Chain Reaction, Agarose Gel Electrophoresis, Concentration Assay

    Quantification of ribosomal methylation directly from total RNA by qRT-PCR. ( A ) Analysis of the methylation status of A27, A99, U428, G1490 and C1703 in 18s rRNA from total RNA extracts of various human cell lines. Error bars describe SD. ( B ) qRT-PCR data of methylation site A99 in HEK-293 and Caco2 cells. ΔC T values indicate higher degree of methylation in HEK-293 cells than in Caco2 cells.

    Journal: Nucleic Acids Research

    Article Title: Direct and site-specific quantification of RNA 2′-O-methylation by PCR with an engineered DNA polymerase

    doi: 10.1093/nar/gkw200

    Figure Lengend Snippet: Quantification of ribosomal methylation directly from total RNA by qRT-PCR. ( A ) Analysis of the methylation status of A27, A99, U428, G1490 and C1703 in 18s rRNA from total RNA extracts of various human cell lines. Error bars describe SD. ( B ) qRT-PCR data of methylation site A99 in HEK-293 and Caco2 cells. ΔC T values indicate higher degree of methylation in HEK-293 cells than in Caco2 cells.

    Article Snippet: qRT-PCR with human RNA extracts and in vitro transcribed 18s rRNA qRT-PCRs were conducted in a total volume of 20 μl reaction mixture containing 100 nM forward primer, 100 nM reverse primer, 200 μM dNTPs (each), 0.5 M betaine, 1x SYBR® green I (sigma), 100 nM Taq DNA polymerase aptamer ( ) and 100 nM of either RT-KTQ-LSIM or RT-KTQ-LSIM V669L in KlenTaq reaction buffer.

    Techniques: Methylation, Quantitative RT-PCR

    For figure legend see page . Figure 1. (see previous page) Lacto-rpoB and 23S methyl RNA elements are regulated by RNase III in S. pyogenes. A. Northern blot analysis (polyacrylamide gel electrophoresis) of Lacto-rpoB and 23S-methyl RNA expression in WT (SF370), ΔRNase III (Δ rnc ) and ΔRNase Y (Δ rny ) strains grown to early logarithmic (EL), mid logarithmic (ML) and early stationary (ES) phases. 5S rRNA is used as loading control. B. Expression profiles of Lacto-rpoB and the 23S-methyl motif with surrounding genes captured using the Integrative Genomics Viewer (IGV) software. The sequence coverage was calculated using BEDTools-Version-2.15.0 and the scale is given in number of reads per million. The distribution of reads starting (5') and ending (3') at each nucleotide position is represented in blue and orange, respectively. The position of the oligonucleotide probes (OLEC) used in Northern blot analysis is indicated. C. Prediction of RNA secondary structure using RNAfold (rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi). The arrows represent putative cleavages by RNase III (nucleotides determined by analyzing the 5' and 3' ends of the sRNAs in sRNA sequencing data).

    Journal: RNA Biology

    Article Title: RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes

    doi: 10.1080/15476286.2015.1110674

    Figure Lengend Snippet: For figure legend see page . Figure 1. (see previous page) Lacto-rpoB and 23S methyl RNA elements are regulated by RNase III in S. pyogenes. A. Northern blot analysis (polyacrylamide gel electrophoresis) of Lacto-rpoB and 23S-methyl RNA expression in WT (SF370), ΔRNase III (Δ rnc ) and ΔRNase Y (Δ rny ) strains grown to early logarithmic (EL), mid logarithmic (ML) and early stationary (ES) phases. 5S rRNA is used as loading control. B. Expression profiles of Lacto-rpoB and the 23S-methyl motif with surrounding genes captured using the Integrative Genomics Viewer (IGV) software. The sequence coverage was calculated using BEDTools-Version-2.15.0 and the scale is given in number of reads per million. The distribution of reads starting (5') and ending (3') at each nucleotide position is represented in blue and orange, respectively. The position of the oligonucleotide probes (OLEC) used in Northern blot analysis is indicated. C. Prediction of RNA secondary structure using RNAfold (rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi). The arrows represent putative cleavages by RNase III (nucleotides determined by analyzing the 5' and 3' ends of the sRNAs in sRNA sequencing data).

    Article Snippet: RNA extraction Total RNA from S. pyogenes SF370 wild type, deletion mutants and complemented strains was prepared using TRIzol (Sigma-Aldrich)/chloroform extraction and isopropanol precipitation from samples collected at several phases of growth (early logarithmic phase, EL; mid logarithmic phase, ML, and early stationary phrase, ES).

    Techniques: Polyacrylamide Gel Electrophoresis, Northern Blot, RNA Expression, Expressing, Software, Sequencing

    Effects of berberine on MCP-1 mRNA and IL-8 mRNA expression after stimulation with LPS in ARPE-19 cells in serum-free media were preincubated for 30 min with berberine or 0.05% DMSO. LPS (1 μg/ml) was added to the media and incubated for 3 h. After incubation, total RNA was extracted from the ARPE-19 cells, and semiquantitative real-time PCR was performed. Changes in MCP-1 mRNA ( a ) and IL-8 mRNA ( b ) in ARPE-19 cells after stimulation with LPS for 3 h are shown. The data are expressed as means ± standard errors of four independent experiments. * P

    Journal: International Ophthalmology

    Article Title: Effect of berberine on lipopolysaccharide-induced monocyte chemotactic protein-1 and interleukin-8 expression in a human retinal pigment epithelial cell line

    doi: 10.1007/s10792-017-0697-x

    Figure Lengend Snippet: Effects of berberine on MCP-1 mRNA and IL-8 mRNA expression after stimulation with LPS in ARPE-19 cells in serum-free media were preincubated for 30 min with berberine or 0.05% DMSO. LPS (1 μg/ml) was added to the media and incubated for 3 h. After incubation, total RNA was extracted from the ARPE-19 cells, and semiquantitative real-time PCR was performed. Changes in MCP-1 mRNA ( a ) and IL-8 mRNA ( b ) in ARPE-19 cells after stimulation with LPS for 3 h are shown. The data are expressed as means ± standard errors of four independent experiments. * P

    Article Snippet: Total RNA extraction and MCP-1 and IL-8 mRNA expression by real-time polymerase chain reaction Berberine was purchased from Sigma Chemicals (St. Louis, Mo., USA).

    Techniques: Expressing, Incubation, Real-time Polymerase Chain Reaction