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.
26
datasets available to search
ShareScore release 0.9.0
Dataset results
26 results for “bacterial networks”
Bacterial training dataset for Galaxy training network tutorials on Genome assembly
<p>This training dataset is from an imaginary <em>Staphylococcus aureus</em> bacterium with a miniature genome. There is a reference genome in various formats as well as some fastq reads of a closely related but also imaginary mutant strain.</p> <p>It is a useful dataset for demonstrating:</p> <ul> <li>de novo genome assembly</li> <li>read mapping and variant calling</li> <li>genome annotation</li> </ul> <p>The files included are:</p> <ul> <li><strong>wildtype.fna</strong>: the reference genome sequence of the wildtype strain in fasta format (a header line, then the nucleotide sequence of the genome.)</li> <li><strong>wildtype.gff</strong>: the reference genome sequence of the wildtype strain in general feature format (a list of features - one feature per line, then the nucleotide sequence of the genome.)</li> <li><strong>wildtype.gbk</strong>: the reference genome sequence in genbank format.</li> <li><strong>mutant_R1.fastq</strong> and <strong>mutant_R2.fastq</strong>: Fastq sequence reads of a closely related mutant strain. <ul> <li>The reads are paired-end.</li> <li>Each read is 150 bases long.</li> <li>The number of bases sequenced is equivalent to 19x the genome sequence of the wildtype strain. (Read coverage 19x - rather low!).</li> </ul> </li> </ul>
Data for: Irreversibility in bacterial regulatory networks
Open the record for dataset details and reuse information.
Untargeted metabolomics data for the publication Weiss et al. 2022 "In vitro interaction network of a synthetic gut bacterial community"
<p>This dataset contains the untargeted metabolomics data for the publication Weiss et al. 2022 "In vitro interaction network of a synthetic gut bacterial community". The dataset has also been submitted to MetaboLights repository with ID "MTBLS3535". Please refer to the MetaboLights repository for the most up-to-date datasets. </p> <p>Publication abstract:</p> <p>A key challenge in microbiome research is to predict the functionality of microbial communities based on community membership and (meta)-genomic data. As central microbiota functions are determined by bacterial community networks, it is important to gain insight into the principles that govern bacteria-bacteria interactions. Here, we focused on the growth and metabolic interactions of the Oligo-Mouse-Microbiota (OMM<sup>12</sup>) synthetic bacterial community, which is increasingly used as a model system in gut microbiome research. Using a bottom-up approach, we uncovered the directionality of strain-strain interactions in mono- and pairwise co-culture experiments as well as in community batch culture. Metabolic network reconstruction in combination with metabolomics analysis of bacterial culture supernatants provided insights into the metabolic potential and activity of the individual community members. Thereby, we could show that the OMM<sup>12</sup> interaction network is shaped by both exploitative and interference competition in vitro in nutrient-rich culture media and demonstrate how community structure can be shifted by changing the nutritional environment. In particular, <em>Enterococcus faecalis</em> KB1 was identified as an important driver of community composition by affecting the abundance of several other consortium members in vitro. As a result, this study gives fundamental insight into key drivers and mechanistic basis of the OMM<sup>12</sup> interaction network in vitro, which serves as a knowledge base for future mechanistic in vivo studies.</p>
Dataset for: Synthetic Micrographs of Bacteria (SyMBac) Allows Accurate Segmentation of Bacterial Cells Using Deep Neural Networks
<p>Datasets for the paper Synthetic Micrographs of Bacteria (SyMBac) Allows Accurate Segmentation of Bacterial Cells Using Deep Neural Networks, published in BMC Biology.</p>
Bacterial Community Diversity and Bacterial Interaction Network in Eight Mosquito Species
<p>Sequences of the V4 region of 16S rRNA from 111 mosquito samples. </p> <p>This dataset was used for analysis of bacterial diversity and bacterial interaction network in eight mosquito species. Result of the analysis is in the article "Bacterial Community Diversity and Bacterial Interaction Network in Eight Mosquito Species" (Genes 2022, 13(11), 2052; https://doi.org/10.3390/genes13112052).</p>
Data from: Integrating variation in bacterial-fungal co-occurrence network with soil carbon dynamics
<p>Bacteria and fungi are core microorganisms in diverse ecosystems, and their cross-kingdom interactions are considered key determinants of microbiome structure and ecosystem functioning. However, how bacterial-fungal interactions mediate soil organic carbon (SOC) dynamics remains largely unexplored in the context of artificial forest ecosystems. Here, we characterized soil bacterial and fungal communities in four successive planting of Eucalyptus and compared them to a neighboring evergreen broadleaf forest. Carbon (C) mineralization combined with five C-degrading enzymatic activities was investigated to determine the effects of successive planting of Eucalyptus on SOC dynamics. Our results indicated that successive planting of Eucalyptus significantly altered the diversity and structure of soil bacterial and fungal communities and increased the negative bacterial-fungal associations. The bacterial diversity significantly decreased in all Eucalyptus plantations compared to the evergreen forest, while the fungal diversity showed the opposite trend. The ratio of negative bacterial-fungal associations increased with successive planting of Eucalyptus due to the decrease in SOC, ammonia nitrogen (NH4+−N), nitrate nitrogen (NO3−−N), and available phosphorus (AP). Structural equation modeling indicated that the potential cross-kingdom competition, based on the ratio of negative bacterial-fungal correlations, was significantly negatively associated with the diversity of total bacteria and keystone bacteria, thereby increasing C-degrading enzymatic activities and C mineralization.</p> <p>Synthesis and applications: Our results highlight the regulatory role of the negative bacterial-fungal association in enhancing the correlation between bacterial diversity and C mineralization. This suggests that promoting short-term successive planting in the management of Eucalyptus plantations can mitigate the impact of this association on SOC decomposition. Taken together, our study advances the understanding of bacterial-fungal negative associations to mediate carbon mineralization in Eucalyptus plantations, giving us a new insight into SOC cycling dynamics in artificial forests.</p>
Data from: Integrating variation in bacterial-fungal co-occurrence network with soil carbon dynamics
Open the record for dataset details and reuse information.
Siderophore synthetase-receptor gene coevolution reveals habitat and pathogen-specific bacterial iron interaction networks
Open the record for dataset details and reuse information.
Emergence of Supercoiling-Mediated Regulatory Networks through the Evolution of Bacterial Chromosome Organization
<p>Data generated using <a href="https://gitlab.inria.fr/tgrohens/evotsc">EvoTSC</a> and used in the <a href="https://doi.org/10.24072/pci.mcb.100198">Emergence of Supercoiling-Mediated Regulatory Networks through the Evolution of Bacterial Chromosome Organization</a> paper.</p> <p>This data is also used in Chapter 5 of my <a href="https://gitlab.inria.fr/tgrohens/phd">PhD thesis</a>.</p>
Data and results for Cochrane systematic review and network meta-analysis on treatment of spontaneous bacterial peritonitis
<p>This contains the data and the raw results for the Cochrane systematic review and network meta-analysis on the treatment of spontaneous bacterial peritonitis (https://doi.org/10.1002/14651858.CD013120). Please unzip the file and read the instructions before using the data.</p>
Calcium-rich parent materials enhance multiple soil functions and bacterial network complexity
Open the record for dataset details and reuse information.
Linked networks reveal dual roles of insect dispersal and species sorting for bacterial communities in flowers
Open the record for dataset details and reuse information.
Data from: The index case is not enough: variation among individuals, groups, and social networks modify bacterial transmission dynamics
Open the record for dataset details and reuse information.
Determination of an Interaction Network between an Extracellular Bacterial Pathogen and the Human Host
GEO Series GSE130901. [Haemophilus] ducreyi; Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Paired single-cell host profiling with multiplex-tagged bacterial mutants reveals intracellular virulence-immune networks [CEL-Seq]
GEO Series GSE230533. Mus musculus. 21 samples. Type: Expression profiling by high throughput sequencing.
Paired single-cell host profiling with multiplex-tagged bacterial mutants reveals intracellular virulence-immune networks III
GEO Series GSE198448. synthetic construct. 4 samples. Type: Other.
Paired single-cell host profiling with multiplex-tagged bacterial mutants reveals intracellular virulence-immune networks II
GEO Series GSE198436. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
Paired single-cell host profiling with multiplex-tagged bacterial mutants reveals intracellular virulence-immune networks IV
GEO Series GSE198724. synthetic construct. 38 samples. Type: Expression profiling by high throughput sequencing.
Paired single-cell host profiling with multiplex-tagged bacterial mutants reveals intracellular virulence-immune networks V
GEO Series GSE198726. Mus musculus. 34 samples. Type: Expression profiling by high throughput sequencing.
Paired single-cell host profiling with multiplex-tagged bacterial mutants reveals intracellular virulence-immune networks VI
GEO Series GSE198727. synthetic construct. 26 samples. Type: Other.
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.