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31 results for “Metabarcoding protocol”
Data from: Optimization of wetland environmental DNA metabarcoding protocols for Great Lakes region herpetofauna
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Tagsteady: a metabarcoding library preparation protocol to avoid false assignment of sequences to samples
Metabarcoding of environmental DNA (eDNA) and DNA extracted from bulk specimen samples is a powerful tool in studies of biodiversity, diet and ecological interactions as its inherent labelling of amplicons allows sequencing of taxonomically informative genetic markers from many samples in parallel. However, the occurrence of so-called 'tag-jumps' can cause incorrect assignment of sequences to samples and artificially inflate diversity. Two steps during library preparation of pools of 5' nucleotide-tagged amplicons have been suggested to cause tag-jumps; i) T4 DNA polymerase blunt-ending in the end-repair step and ii) post-ligation PCR amplification of amplicon libraries. The discovery of tag-jumps has led to recommendations to only carry out metabarcoding PCR amplifications with primers carrying twin-tags to ensure that tag-jumps cannot result in false assignments of sequences to samples. As this increases both cost and workload, a metabarcoding library preparation protocol which circumvents the two steps that causes tag-jumps is needed. Here, we demonstrate Tagsteady, a metabarcoding Illumina library preparation protocol for pools of nucleotide-tagged amplicons that enables efficient and cost-effective generation of metabarcoding data with virtually no tag-jumps. We use pools of twin-tagged amplicons to investigate the effect of T4 DNA polymerase blunt-ending and post-ligation PCR on the occurrence of tag-jumps. We demonstrate that both blunt-ending and post-ligation PCR, alone or together, can result in detrimental amounts of tag-jumps (here, up to ca. 49% of total sequences), while leaving both steps out (the Tagsteady protocol) results in amounts of sequences carrying new combinations of used tags (tag-jumps) comparable to background contamination.
Supplementary material 7 from: {"en": "Buchner D, Haase P, Leese F (2021) Wet grinding of invertebrate bulk samples – a scalable and cost-efficient protocol for metabarcoding and metagenomics. Metabarcoding and Metagenomics 5: e67533. https://doi.org/10.3897/mbmg.5.67533"}
Figure S2. Baseline-corrected amplification curves (left half) and melting -curves (right half) for A & B) kick-net samples and C & D) malaise trap samples
Data from: Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies
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Tagsteady: a metabarcoding library preparation protocol to avoid false assignment of sequences to samples
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Supplementary material 1 from: Marquina D, Roslin T, Łukasik P, Ronquist F (2022) Evaluation of non-destructive DNA extraction protocols for insect metabarcoding: gentler and shorter is better. Metabarcoding and Metagenomics 6: e78871. https://doi.org/10.3897/mbmg.6.78871
Community types
Supplementary material 6 from: Marquina D, Roslin T, Łukasik P, Ronquist F (2022) Evaluation of non-destructive DNA extraction protocols for insect metabarcoding: gentler and shorter is better. Metabarcoding and Metagenomics 6: e78871. https://doi.org/10.3897/mbmg.6.78871
16S MOTU table
Supplementary material 7 from: Marquina D, Roslin T, Łukasik P, Ronquist F (2022) Evaluation of non-destructive DNA extraction protocols for insect metabarcoding: gentler and shorter is better. Metabarcoding and Metagenomics 6: e78871. https://doi.org/10.3897/mbmg.6.78871
Tables and figures
Supplementary material 5 from: Marquina D, Roslin T, Łukasik P, Ronquist F (2022) Evaluation of non-destructive DNA extraction protocols for insect metabarcoding: gentler and shorter is better. Metabarcoding and Metagenomics 6: e78871. https://doi.org/10.3897/mbmg.6.78871
COI MOTU table
Supplementary material 3 from: Marquina D, Roslin T, Łukasik P, Ronquist F (2022) Evaluation of non-destructive DNA extraction protocols for insect metabarcoding: gentler and shorter is better. Metabarcoding and Metagenomics 6: e78871. https://doi.org/10.3897/mbmg.6.78871
16S reference library
Supplementary material 8 from: Marquina D, Roslin T, Łukasik P, Ronquist F (2022) Evaluation of non-destructive DNA extraction protocols for insect metabarcoding: gentler and shorter is better. Metabarcoding and Metagenomics 6: e78871. https://doi.org/10.3897/mbmg.6.78871
Lysis buffers and purification protocols
Supplementary material 4 from: Marquina D, Roslin T, Łukasik P, Ronquist F (2022) Evaluation of non-destructive DNA extraction protocols for insect metabarcoding: gentler and shorter is better. Metabarcoding and Metagenomics 6: e78871. https://doi.org/10.3897/mbmg.6.78871
Bioinformatic pipeline
Supplementary material 2 from: Marquina D, Roslin T, Łukasik P, Ronquist F (2022) Evaluation of non-destructive DNA extraction protocols for insect metabarcoding: gentler and shorter is better. Metabarcoding and Metagenomics 6: e78871. https://doi.org/10.3897/mbmg.6.78871
COI reference library
Supplementary material 9 from: Weigand AM, Macher J-N (2018) A DNA metabarcoding protocol for hyporheic freshwater meiofauna: Evaluating highly degenerate COI primers and replication strategy. Metabarcoding and Metagenomics 2: e26869. https://doi.org/10.3897/mbmg.2.26869
Table S6: Taxa identified based on morphology :
Supplementary material 8 from: Weigand AM, Macher J-N (2018) A DNA metabarcoding protocol for hyporheic freshwater meiofauna: Evaluating highly degenerate COI primers and replication strategy. Metabarcoding and Metagenomics 2: e26869. https://doi.org/10.3897/mbmg.2.26869
Table S5: MetazoaMOTU list with 2-out-of-3 replicate strategy and excluding site 61 :
Supplementary material 7 from: Weigand AM, Macher J-N (2018) A DNA metabarcoding protocol for hyporheic freshwater meiofauna: Evaluating highly degenerate COI primers and replication strategy. Metabarcoding and Metagenomics 2: e26869. https://doi.org/10.3897/mbmg.2.26869
Table S4: MetazoaMOTU list with all replicates and including site 61 :
Supplementary material 6 from: Weigand AM, Macher J-N (2018) A DNA metabarcoding protocol for hyporheic freshwater meiofauna: Evaluating highly degenerate COI primers and replication strategy. Metabarcoding and Metagenomics 2: e26869. https://doi.org/10.3897/mbmg.2.26869
Table S3: Overview of raw reads and quality filtered reads :
Supplementary material 3 from: Weigand AM, Macher J-N (2018) A DNA metabarcoding protocol for hyporheic freshwater meiofauna: Evaluating highly degenerate COI primers and replication strategy. Metabarcoding and Metagenomics 2: e26869. https://doi.org/10.3897/mbmg.2.26869
Figure S2: Taxonomic composition of hyporheic community with all metazoan MOTUs :
Supplementary material 5 from: Weigand AM, Macher J-N (2018) A DNA metabarcoding protocol for hyporheic freshwater meiofauna: Evaluating highly degenerate COI primers and replication strategy. Metabarcoding and Metagenomics 2: e26869. https://doi.org/10.3897/mbmg.2.26869
Table S2: Primer combinations :
Supplementary material 2 from: Weigand AM, Macher J-N (2018) A DNA metabarcoding protocol for hyporheic freshwater meiofauna: Evaluating highly degenerate COI primers and replication strategy. Metabarcoding and Metagenomics 2: e26869. https://doi.org/10.3897/mbmg.2.26869
Figure S1: Overview of sediment characteristics :
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.