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8 results for “16S primer”
Santa Barbara Channel Marine BON: genomics study on 16S primer comparison
This project examined the effects of 16S rRNA gene primer selection on population representation and community ecology of bacteria and archaea in the Santa Barbara Channel. Four 16S rRNA primer sets targeting different hypervariable regions of the gene were compared using both mock communities of known composition constructed from cloned 16S rRNA genes and field samples covering the annual cycle. Amplicon results were compared with shotgun metagenomes prepared from a subset of the field samples. The field samples included in the comparison study are subsets of two more extensive field programs in the Santa Barbara Channel. Samples included from the Plumes and Blooms transect times-series program were collected between February 2012 and August 2014. Samples from University-National Oceanographic Laboratory Systems cruise PS1103 (Wear et al. 2015; DOI: 10.1002/lno.10042) were collected in May 2011. All datasheets represent curated, processed output of the bioinformatics pipeline. Unprocessed sequencing data are archived with the National Center for Biotechnology Information, with accession numbers specified in the individual datasheets. Four dataset entities included primer testing on a known mock community (Entity #1 and #2) as well as the application of the primers to field samples (Entity #3) and shotgun metagenomes from a subset of field samples (Entity #4): 1) Cloned 16S genes used to construct the mock community. 2) Mock community sequencing results - relative abundance of each clone with each of 4 primer sets. 3) Field sequencing results - relative abundance of operational taxonomic units (OTUs) and weighted UniFrac distance matrices. 4) Metagenome results – taxonomic identities of individual 16S rRNA sequences identified in each metagenome. The funding source for this project is: the National Aeronautics and Space Administration Biodiversity and Ecological Forecasting program (Grant NNX14AR62A), the Bureau of Ocean and Energy Management Ecosystem Studies progr
KuafuPrimer: Machine learning facilitates the design of 16S rRNA gene primers with minimal bias in bacterial communities
<p>KuafuPrimer is a machine learning-aided method that learns community characteristics from several samples to design 16S rRNA gene primers with minimal bias for microbial communities. It is built on <strong>Python 3.9.0</strong>, <strong>Pytorch 1.12.0</strong>. Here are some large size files required to run KuafuPrimer, and users need to download and put them in correct directories before running the program.</p> <ol> <li>Silva_ref_data.zip: processed files of silva dataset that should be put in <code>Model_data/Silva_ref_data/</code>.</li> <li>DeepAnno16_publicated_model.zip: parameters of the trained DeepAnno16 model that should be put in <code>Model_data/DeepAnno16_publicated_model/</code> .</li> </ol> <p>For more information, please refer to https://github.com/zhanghaoyu9931/KuafuPrimer.</p>
Supplementary material 4 from: Hintikka S, Carlsson JE, Carlsson J (2022) The bacterial hitchhiker's guide to COI: Universal primer-based COI capture probes fail to exclude bacterial DNA, but 16S capture leaves metazoa behind. Metabarcoding and Metagenomics 6: e80416. https://doi.org/10.3897/mbmg.6.80416
COI library ASV tax
Supplementary material 1 from: Hintikka S, Carlsson JE, Carlsson J (2022) The bacterial hitchhiker's guide to COI: Universal primer-based COI capture probes fail to exclude bacterial DNA, but 16S capture leaves metazoa behind. Metabarcoding and Metagenomics 6: e80416. https://doi.org/10.3897/mbmg.6.80416
File S1
Supplementary material 3 from: Hintikka S, Carlsson JE, Carlsson J (2022) The bacterial hitchhiker's guide to COI: Universal primer-based COI capture probes fail to exclude bacterial DNA, but 16S capture leaves metazoa behind. Metabarcoding and Metagenomics 6: e80416. https://doi.org/10.3897/mbmg.6.80416
16S library ASV tax
Supplementary material 5 from: Hintikka S, Carlsson JE, Carlsson J (2022) The bacterial hitchhiker's guide to COI: Universal primer-based COI capture probes fail to exclude bacterial DNA, but 16S capture leaves metazoa behind. Metabarcoding and Metagenomics 6: e80416. https://doi.org/10.3897/mbmg.6.80416
Unassigned COIASVs krona
Supplementary material 2 from: Hintikka S, Carlsson JE, Carlsson J (2022) The bacterial hitchhiker's guide to COI: Universal primer-based COI capture probes fail to exclude bacterial DNA, but 16S capture leaves metazoa behind. Metabarcoding and Metagenomics 6: e80416. https://doi.org/10.3897/mbmg.6.80416
Metadata all
New 16S rRNA primers to uncover Bdellovibrio and like organisms diversity and abundance
<p>Alignment files and OTU tables</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.
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.