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