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1,076 results for “Metabarcoding”
Supplementary material 2 from: Okanishi M, Kohtsuka H, Wu Q, Shinji J, Shibata N, Tamada T, Nakano T, Minamoto T (2023) Development of two new sets of PCR primers for eDNA metabarcoding of brittle stars (Echinodermata, Ophiuroidea). Metabarcoding and Metagenomics 7: e94298. https://doi.org/10.3897/mbmg.7.94298
Taxonomic notes for detected taxa
Supplementary material 1 from: Okanishi M, Kohtsuka H, Wu Q, Shinji J, Shibata N, Tamada T, Nakano T, Minamoto T (2023) Development of two new sets of PCR primers for eDNA metabarcoding of brittle stars (Echinodermata, Ophiuroidea). Metabarcoding and Metagenomics 7: e94298. https://doi.org/10.3897/mbmg.7.94298
A fasta file of 1,340 mitochondrial 16S rRNA gene sequences
Supplementary material 5 from: Okanishi M, Kohtsuka H, Wu Q, Shinji J, Shibata N, Tamada T, Nakano T, Minamoto T (2023) Development of two new sets of PCR primers for eDNA metabarcoding of brittle stars (Echinodermata, Ophiuroidea). Metabarcoding and Metagenomics 7: e94298. https://doi.org/10.3897/mbmg.7.94298
Additional data
Data from Meta-IBD Project, metabarcoding for the diatom trophic indices evaluation, South West France
<p>These data were generated within the framework of the Meta-IBD project, led by the Laboratoires des Pyrénées et des Landes and financially supported by the Adour Garonne Water Agency, including two scientific partners, Scimabio Interface and Artemis.</p> <p>The objective of the project was to compare the evaluation of diatom trophic indices obtained by the reference method (microscopy) versus the metabarcoding method, at the local scale. This comparison is based on biofilm sampling in southwest France, in the Adour, Nives and Gaves regions, in 2021 and 2022. The project ran from May 2021 to September 2023.</p> <p>The directory contains the following files:</p> <p>756 (378 x 2 replicates) samples fastq files (file intituled MetaIBD_Biofilm2021et22_LPL.rar) - contains the 756 fastq files from the Laboratoires des Pyrénées et des Landes sequencing.</p> <p>Metadonnees_MetaIBD_20212022.csv - contains all the data available for each sample corresponding to the names of the sequencing fastq files.</p>
eDNA metabarcoding reveals submarine canyon biodiversity across depth gradient
<p>Dataset for thesis Chapter 5</p>
Supplementary material 1 from: Liu M, Burridge CP, Clarke LJ, Baker SC, Jordan GJ (2023) Does phylogeny explain bias in quantitative DNA metabarcoding? Metabarcoding and Metagenomics 7: e101266. https://doi.org/10.3897/mbmg.7.101266
The bioinformatic pipeline of processing metabarcoding data
Supplementary material 3 from: Liu M, Burridge CP, Clarke LJ, Baker SC, Jordan GJ (2023) Does phylogeny explain bias in quantitative DNA metabarcoding? Metabarcoding and Metagenomics 7: e101266. https://doi.org/10.3897/mbmg.7.101266
Scoring scheme for mismatch between DNA template and primers
Supplementary material 2 from: Liu M, Burridge CP, Clarke LJ, Baker SC, Jordan GJ (2023) Does phylogeny explain bias in quantitative DNA metabarcoding? Metabarcoding and Metagenomics 7: e101266. https://doi.org/10.3897/mbmg.7.101266
Composition and biomass of 24 studied samples, and HTS read abundance of studied species
Supplementary material 7 from: Kolter A, Husemann M, Podsiadlowski L, Gemeinholzer B (2023) Pollen metabarcoding of museum specimens and recently collected bumblebees (Bombus) indicates foraging shifts. Metabarcoding and Metagenomics 7: e86883. https://doi.org/10.3897/mbmg.7.86883
Raw ASV data
Supplementary material 1 from: Kolter A, Husemann M, Podsiadlowski L, Gemeinholzer B (2023) Pollen metabarcoding of museum specimens and recently collected bumblebees (Bombus) indicates foraging shifts. Metabarcoding and Metagenomics 7: e86883. https://doi.org/10.3897/mbmg.7.86883
Optimizations
Supplementary material 6 from: Kolter A, Husemann M, Podsiadlowski L, Gemeinholzer B (2023) Pollen metabarcoding of museum specimens and recently collected bumblebees (Bombus) indicates foraging shifts. Metabarcoding and Metagenomics 7: e86883. https://doi.org/10.3897/mbmg.7.86883
R pipeline and reference database
Supplementary material 3 from: Kolter A, Husemann M, Podsiadlowski L, Gemeinholzer B (2023) Pollen metabarcoding of museum specimens and recently collected bumblebees (Bombus) indicates foraging shifts. Metabarcoding and Metagenomics 7: e86883. https://doi.org/10.3897/mbmg.7.86883
trnL-P6 protocol - primer sequences
Supplementary material 4 from: Kolter A, Husemann M, Podsiadlowski L, Gemeinholzer B (2023) Pollen metabarcoding of museum specimens and recently collected bumblebees (Bombus) indicates foraging shifts. Metabarcoding and Metagenomics 7: e86883. https://doi.org/10.3897/mbmg.7.86883
Reference database protocol
Supplementary material 2 from: Kolter A, Husemann M, Podsiadlowski L, Gemeinholzer B (2023) Pollen metabarcoding of museum specimens and recently collected bumblebees (Bombus) indicates foraging shifts. Metabarcoding and Metagenomics 7: e86883. https://doi.org/10.3897/mbmg.7.86883
DNA extraction protocol
Supplementary material 5 from: Kolter A, Husemann M, Podsiadlowski L, Gemeinholzer B (2023) Pollen metabarcoding of museum specimens and recently collected bumblebees (Bombus) indicates foraging shifts. Metabarcoding and Metagenomics 7: e86883. https://doi.org/10.3897/mbmg.7.86883
Sequence processing workflow
Supplementary material 1 from: Röder N, Schwenk K (2023) Direct PCR meets high-throughput sequencing – metabarcoding of chironomid communities without DNA extraction. Metabarcoding and Metagenomics 7: e102455. https://doi.org/10.3897/mbmg.7.102455
Overview of chironomid size classes
Supplementary material 2 from: Röder N, Schwenk K (2023) Direct PCR meets high-throughput sequencing – metabarcoding of chironomid communities without DNA extraction. Metabarcoding and Metagenomics 7: e102455. https://doi.org/10.3897/mbmg.7.102455
Composition of the two artificial chironomid communities
Supplementary material 1 from: Hubancheva A, Bozicevic V, Morinière J, Goerlitz HR (2023) DNA metabarcoding data from faecal samples of the lesser (Myotis blythii) and the greater (Myotis myotis) mouse-eared bats from Bulgaria. Metabarcoding and Metagenomics 7: e106844. https://doi.org/10.3897/mbmg.7.106844
Metabarcoding data from M. myotis and M. blythii from Bulgaria
Reference sequence database for eDNA metabarcoding of San Francisco estuary fishes and invertebrates
<p>Environmental DNA (eDNA) methods complement traditional monitoring and can be configured to detect multiple species simultaneously. One such approach, eDNA metabarcoding, uses high-throughput DNA sequencing to indirectly detect many different organisms, spanning broad taxonomic boundaries, from water samples. We are optimizing a non-invasive, low cost eDNA metabarcoding protocol to be used in conjunction with existing monitoring programs. One resource that is currently lacking for metabarcoding studies in general, including those in the San Francisco Estuary (SFE), is a comprehensive database of DNA barcode reference sequences. Without this foundational data, many species go undetected or misidentified in metabarcoding studies. To meet this need, we generated a custom barcode sequence database for the SFE by DNA sequencing and mining of public DNA seqeunce data for estuarine and freshwater species of interest to monitoring programs and ecological studies. Here we present custom reference sequence databases for three barcodes: Cytochrome C Oxidase I (COI), 12S MiFish and 16S.</p>
Supplementary material 2 from: Parisy B, Schmidt NM, Wirta H, Stewart L, Pellissier L, Holben WE, Pannoni S, Somervuo P, Jones MM, Siren J, Vesterinen E, Ovaskainen O, Roslin T (2023) Ecological signals of arctic plant-microbe associations are consistent across eDNA and vegetation surveys. Metabarcoding and Metagenomics 7: e99979. https://doi.org/10.3897/mbmg.7.99979
Key to taxa for Figure 5, figures S11A and S11B
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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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.
International Brain Laboratory public data
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.