Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
2
datasets available to search
ShareScore release 0.7.1
Dataset results
2 results for “mouse gut metagenome”
iMGMC - integrated Mouse Gut Metagenomic Catalog
<p><em>Creation of an new mouse gut gene catalog with special features:</em></p> <ul> <li>more diverse samples from different studies (12 Vendors incl. wild mice and various gut locations)</li> <li>clustering-free approach: all-in-one assembly, keeping track of each ORF to contigs to bins</li> <li>higher taxonomic resolution and more accuracy by using contigs for annotation</li> <li>16S rRNA gene integration via linkage to bins</li> <li>expansion by 20,927 MAGs from sample-wise assembly of 871 mouse gut metagenomic samples, representing 1,296 species</li> </ul> <p>Code used: <a href="https://github.com/tillrobin/iMGMC">https://github.com/tillrobin/iMGMC</a></p> <p>The vast complexity of host-associated microbial ecosystems requires host-specific reference catalogs to survey the functions and diversity of these communities. We generated a comprehensive resource, the integrated mouse gut metagenome catalog (iMGMC), comprising 4.6 million unique genes and 660 metagenome-assembled genomes (MAGs) with many of them (485 MAGs, 73%) linked to reconstructed full-length 16S rRNA gene sequences. iMGMC enables unprecedented coverage and taxonomic resolution of the mouse gut microbiota, i.e. more than 92% of MAGs lack species-level representatives in public repositories (<95% ANI match). The integration of MAGs and 16S rRNA gene data allows a more accurate prediction of functional profiles of communities than based on 16S rRNA amplicons alone. Accompanying iMGMC we provide a set of MAGs representing 1,296 gut bacteria obtained through complementary assembly strategies. We envision that integrated resources such as iMGMC together with MAG collections will enhance the resolution of numerous existing and future sequencing-based studies.</p> <p>Genecatalog:</p> <p>Description Size Filename<br> Catalog ORF sequences 1 GB iMGMC-GeneID.fasta.gz<br> Full assembly contigs 1.3 GB iMGMC-ConitgID.fasta.gz<br> Mapping File (GeneID->ContigID->BinID) 30 MB iMGMC-map-Gene-Contig-Bin.tab.gz<br> Taxonomic annotations 40 MB iMGMC_map_taxonomy.tar.gz<br> Functional annotations 36 MB iMGMC_map_functionality.tar.gz<br> 16S rRNA sequences 2 MB iMGMC-16SrRNAgenes.fasta</p> <p>Metagenome-assembled genomes (MAGs) :</p> <p>Description Size Filename<br> integrated MAGs 0.5 GB iMGMC_MAGs.tar.gz<br> representave mMAGs (n=1296) 1 GB iMGMC-mMAGs-dereplicated_genomes.tar.gz<br> representave hqMAGs (n=830) 0.7 GB iMGMC-hqMAGs-dereplicated_genomes.tar.gz<br> all mMAGs (n=20,927) 15 GB iMGMC-mMAGs.tar.gz<br> Annotations by CheckM, dRep-Clustering, GTDB-Tk 2 MB MAG-annotation_CheckM_dRep_GTDB-Tk.tar.gz<br> Functional annotations (hqMAGs by eggNOG mapper v2) 187 MB hqMAGs.emapper.annotations.gz</p> <p> </p>
Metagenome assembled genomes from mouse gut microbiota
Open the record for dataset details and reuse information.
ScienceDex guides
Understand access before you commit
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)
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.