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A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities.
Shaffer, Justin P; Marotz, Clarisse; Belda-Ferre, Pedro; Martino, Cameron; Wandro, Stephen; Estaki, Mehrbod; Salido, Rodolfo A; Carpenter, Carolina S; Zaramela, Livia S; Minich, Jeremiah J; Bryant, MacKenzie; Sanders, Karenina; Fraraccio, Serena; Ackermann, Gail; Humphrey, Gregory; Swafford, Austin D; Miller-Montgomery, Sandrine; Knight, Rob.
  • Shaffer JP; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
  • Marotz C; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
  • Belda-Ferre P; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
  • Martino C; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
  • Wandro S; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
  • Estaki M; Bioinformatics & Systems Biology Program, University of California San Diego, La Jolla, CA, USA.
  • Salido RA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
  • Carpenter CS; Micronoma Inc., San Diego, CA, USA.
  • Zaramela LS; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
  • Minich JJ; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
  • Bryant M; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
  • Sanders K; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
  • Fraraccio S; Marine Biology Research Division, University of California, San Diego, La Jolla, CA, USA.
  • Ackermann G; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
  • Humphrey G; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
  • Swafford AD; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
  • Miller-Montgomery S; Micronoma Inc., San Diego, CA, USA.
  • Knight R; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
Biotechniques ; 70(3): 149-159, 2021 03.
Article in English | MEDLINE | ID: covidwho-1054921
Preprint
This scientific journal article is probably based on a previously available preprint. It has been identified through a machine matching algorithm, human confirmation is still pending.
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ABSTRACT
One goal of microbial ecology researchers is to capture the maximum amount of information from all organisms in a sample. The recent COVID-19 pandemic, caused by the RNA virus SARS-CoV-2, has highlighted a gap in traditional DNA-based protocols, including the high-throughput methods the authors previously established as field standards. To enable simultaneous SARS-CoV-2 and microbial community profiling, the authors compared the relative performance of two total nucleic acid extraction protocols with the authors' previously benchmarked protocol. The authors included a diverse panel of environmental and host-associated sample types, including body sites commonly swabbed for COVID-19 testing. Here the authors present results comparing the cost, processing time, DNA and RNA yield, microbial community composition, limit of detection and well-to-well contamination between these protocols.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: DNA, Viral / RNA, Ribosomal, 16S / High-Throughput Nucleotide Sequencing / Microbiota / SARS-CoV-2 Limits: Animals / Female / Humans / Male Language: English Journal: Biotechniques Year: 2021 Document Type: Article Affiliation country: Btn-2020-0153

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Full text: Available Collection: International databases Database: MEDLINE Main subject: DNA, Viral / RNA, Ribosomal, 16S / High-Throughput Nucleotide Sequencing / Microbiota / SARS-CoV-2 Limits: Animals / Female / Humans / Male Language: English Journal: Biotechniques Year: 2021 Document Type: Article Affiliation country: Btn-2020-0153