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    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 1983 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    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

    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

    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

    Estimating the effect of the tissue heterogenity. Normalized gene expressions levels comparing diapausing and non-diapausing D . montana females A) from the RNAseq analysis (for comparison), and B) from the qPCR using the females whose ovaries had been removed before RNA extractions. Both data sets present the combined data for all the three isofemales strains (see text for details). CPM = counts per million. Significance levels for qPCR: • 0.1 > P > 0.05, **0.01 > P > 0.001, ***P

    Journal: PLoS ONE

    Article Title: Transcriptional Differences between Diapausing and Non-Diapausing D. montana Females Reared under the Same Photoperiod and Temperature

    doi: 10.1371/journal.pone.0161852

    Figure Lengend Snippet: Estimating the effect of the tissue heterogenity. Normalized gene expressions levels comparing diapausing and non-diapausing D . montana females A) from the RNAseq analysis (for comparison), and B) from the qPCR using the females whose ovaries had been removed before RNA extractions. Both data sets present the combined data for all the three isofemales strains (see text for details). CPM = counts per million. Significance levels for qPCR: • 0.1 > P > 0.05, **0.01 > P > 0.001, ***P

    Article Snippet: RNA extraction and RNAseq RNA extraction was performed using a Tri Reagent (Sigma-Aldrich) extraction kit followed by a RNeasy Mini (Qiagen) kit with DNase treatment.

    Techniques: Real-time Polymerase Chain Reaction