Title: Application of high-throughput sequencing (HTS) metabarcoding to diatom biomonitoring: Do DNA extraction methods matter?

Type Dataset Vasselon, Valentin, Domaizon, Isabelle, Rimet, Frédéric, Kahlert, Maria, Bouchez, Agnès (2016): Application of high-throughput sequencing (HTS) metabarcoding to diatom biomonitoring: Do DNA extraction methods matter?. Zenodo. Dataset. https://zenodo.org/record/166859

Authors: Vasselon, Valentin (INRA, France) ; Domaizon, Isabelle (INRA, France) ; Rimet, Frédéric (INRA, France) ; Kahlert, Maria (SLU, Sweden) ; Bouchez, Agnès (INRA, France) ;

Links

• Item record in Zenodo
• Digital object URL

Summary

The 8 benthic samples from Mainland France (stream Edian, stream Aire, lake Geneva), Sweden (stream Dåmman, Agricultural stream, lake Båtkåjaure) and Mayotte (stream Dapani, stream Majimbini) were collected by scraping material from the surface of stones, following the French standard (AFNOR 2007) used in routine biomonitoring programs.DNA was extracted from each sample (2 replicates) using five DNA extraction methods, followed by the amplification of a short rbcL DNA barcode (312bp) specific to diatoms. PCR products were then sequenced in one random direction using the Ion Torrent™ Personal Genome Machine® (PGM) System according to the manufacturer’s instructions. The data file contains one fastq file per library sequenced with the raw DNA reads, as provided by the sequencing platform (demultiplexing performed by the sequencing platform). An excel file is also provided to make the link between the fastq file number and the sample information (sample origin, DNA extraction method used, number of raw reads).

More information

• DOI: 10.5281/zenodo.166859

Subjects

• next-generation biomonitoring, DNA extraction methods, metabarcoding, high-throughput sequencing, diatom communities

Dates

• Publication date: 2016
• Issued: November 16, 2016

Rights

• https://creativecommons.org/licenses/by/4.0/legalcode Creative Commons Attribution 4.0 International
• info:eu-repo/semantics/openAccess Open Access

Format

electronic resource

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