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    Qiagen qiagen qiashredder columns
    Analysis of technical bias to perceived community composition. (A) NMDS of the 16S rRNA gene amplicon sequencing data based on a Bray-Curtis dissimilarity matrix generated after random subsampling of 2,800 sequences from each sample. Bars indicate the range of coordinates for the three replicate extractions/sequencing datasets per treatment. (B) Phylum level data (top 10 most abundant phyla, fractions of all reads). Number 1–3 between parentheses indicates the sequencing run from which each dataset is derived. APO combines three slightly different treatments that did not result in significantly different taxonomic representations ( S2 Fig .). Acronyms: Extraction protocols: APS (standard AllPrep protocol), APO (optimized AllPrep protocol), Enz (Enzymatic protocol), Bead (Bead-beating protocol); Preservation methods: NT (none), RL (RNAlater), RP (RNAprotect), BU (Qiagen Lysis Buffer RLT+); Other modifications: LYS (lysozyme), NQ (No <t>QIAshredder</t> column), TL (bead-beating with TissueLyser). Except for the APO samples, none of the Douglas Lake filters were preserved in RNA protection agents.
    Qiagen Qiashredder Columns, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 4228 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Analysis of technical bias to perceived community composition. (A) NMDS of the 16S rRNA gene amplicon sequencing data based on a Bray-Curtis dissimilarity matrix generated after random subsampling of 2,800 sequences from each sample. Bars indicate the range of coordinates for the three replicate extractions/sequencing datasets per treatment. (B) Phylum level data (top 10 most abundant phyla, fractions of all reads). Number 1–3 between parentheses indicates the sequencing run from which each dataset is derived. APO combines three slightly different treatments that did not result in significantly different taxonomic representations ( S2 Fig .). Acronyms: Extraction protocols: APS (standard AllPrep protocol), APO (optimized AllPrep protocol), Enz (Enzymatic protocol), Bead (Bead-beating protocol); Preservation methods: NT (none), RL (RNAlater), RP (RNAprotect), BU (Qiagen Lysis Buffer RLT+); Other modifications: LYS (lysozyme), NQ (No QIAshredder column), TL (bead-beating with TissueLyser). Except for the APO samples, none of the Douglas Lake filters were preserved in RNA protection agents.

    Journal: PLoS ONE

    Article Title: RNA Preservation Agents and Nucleic Acid Extraction Method Bias Perceived Bacterial Community Composition

    doi: 10.1371/journal.pone.0121659

    Figure Lengend Snippet: Analysis of technical bias to perceived community composition. (A) NMDS of the 16S rRNA gene amplicon sequencing data based on a Bray-Curtis dissimilarity matrix generated after random subsampling of 2,800 sequences from each sample. Bars indicate the range of coordinates for the three replicate extractions/sequencing datasets per treatment. (B) Phylum level data (top 10 most abundant phyla, fractions of all reads). Number 1–3 between parentheses indicates the sequencing run from which each dataset is derived. APO combines three slightly different treatments that did not result in significantly different taxonomic representations ( S2 Fig .). Acronyms: Extraction protocols: APS (standard AllPrep protocol), APO (optimized AllPrep protocol), Enz (Enzymatic protocol), Bead (Bead-beating protocol); Preservation methods: NT (none), RL (RNAlater), RP (RNAprotect), BU (Qiagen Lysis Buffer RLT+); Other modifications: LYS (lysozyme), NQ (No QIAshredder column), TL (bead-beating with TissueLyser). Except for the APO samples, none of the Douglas Lake filters were preserved in RNA protection agents.

    Article Snippet: The lysate was transferred to a QIAshredder column (Qiagen) and the remainder of the protocol was performed according to the manufacturer’s instructions, performing two elution steps with of 30 μl elution buffer for both RNA and DNA.

    Techniques: Amplification, Sequencing, Generated, Derivative Assay, Preserving, Lysis

    View of threshold (Ct) values derived from real-time PCR. Ct values were compared among PCR amplifications using three preparation methods and two primer sets. In each of 11 Las-infected citrus leaf samples, real-time PCR using Las606/LSS and OI1/OI2c primer sets with templates obtained from Extracted DNA , Biomasher-pellet , and QIAshredder-pellet was performed to derive each Ct value. The numbers in each graph are Ct values.

    Journal: PLoS ONE

    Article Title: Convenient Detection of the Citrus Greening (Huanglongbing) Bacterium 'Candidatus Liberibacter asiaticus' by Direct PCR from the Midrib Extract

    doi: 10.1371/journal.pone.0057011

    Figure Lengend Snippet: View of threshold (Ct) values derived from real-time PCR. Ct values were compared among PCR amplifications using three preparation methods and two primer sets. In each of 11 Las-infected citrus leaf samples, real-time PCR using Las606/LSS and OI1/OI2c primer sets with templates obtained from Extracted DNA , Biomasher-pellet , and QIAshredder-pellet was performed to derive each Ct value. The numbers in each graph are Ct values.

    Article Snippet: However, when the preparation using QIAshredder spin column will be modified, the sensitivity of detection may be improved.

    Techniques: Derivative Assay, Real-time Polymerase Chain Reaction, Polymerase Chain Reaction, Infection