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33 results for “Proteobacteria”
Fig. 4 in Report of 29 unrecorded bacterial species from the phylum Proteobacteria
Fig. 4. Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences, showing the relationship between 7 unrecorded bacterial species and other representatives of the class Gammaproteobacteria. Bootstrap values (>70%) based on 1000 resamplings are shown at branching points. Filled circles indicate that the corresponding nodes were recovered by all treeing methods. Open circles indicate that the corresponding nodes were recovered by the neighbor-joining and maximum-likelihood methods. Flavobacterium aquatile LMG 4008T (AM230485) was used as an outgroup (not shown). Bar, 0.05 substitutions per nucleotide position.
Fig. 2 in A report of four unrecorded Proteobacteria species isolated from soil in Korea
Fig. 2. Neighbor-joining phylogenetic tree based on 16S rRNA sequences shows the relationship between the strains isolated in this study and their relatives in the genera Curvibacter (A), Massilia (B) and Pseudomonas (C). Bootstrap values (>70%) are shown above nodes for the neighbor-joining. Scale bar: 0.01 changes per nucleotide.
Supplementary data for the manuscript titled 'Energy metabolism and aerobic respiratory chain of Vitreoscilla sp. C1: Comparison with beta-proteobacteria'
<p>This dataset contains the supplementary data files for the manuscript titled, 'Energy metabolism and aerobic respiratory chain of Vitreoscilla sp. C1: Comparison with beta-proteobacteria.' </p>
Phylogenomic testing of root hypotheses - demonstrative datasets - Opisthokonta and Proteobacteria
<p>The determination of the last common ancestor (LCA) of a group of species plays a vital role in evolutionary theory. Traditionally, an LCA is inferred by the rooting of a fully resolved species tree. From a theoretical perspective, however, inference of the LCA amounts to the reconstruction of just one branch - the root branch - of the true species tree, and should therefore be a much easier task than the full resolution of the species tree. Discarding the reliance on a hypothesised species tree and its rooting leads us to re-evaluate what phylogenetic signal is directly relevant to LCA inference, and to recast the task as that of sampling the total evidence from all gene families at the genomic scope. Here we reformulate LCA and root inference in the framework of statistical hypothesis testing and outline an analytical procedure to formally test competing a-priori LCA hypotheses and to infer confidence sets for the earliest speciation events in the history of a group of species. Applying our methods to two demonstrative datasets we show that our inference of the opisthokonta LCA is well in agreement with the common knowledge. Inference of the proteobacteria LCA shows that it is most closely related to modern Epsilonproteobacteria, raising the possibility that it may have been characterized by a chemolithoautotrophic and anaerobic life-style. Our inference is based on data comprising between 43% (opisthokonta) and 86% (proteobacteria) of all gene families. Approaching LCA inference within a statistical framework renders the phylogenomic inference powerful and robust.</p>
Phylogenomic testing of root hypotheses - demonstrative datasets - Opisthokonta and Proteobacteria
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Table S1.- Occurrence analysis in alpha-proteobacteria, represented by number of copies of each gene on strain genome.
<p>Data set of 204 alphaproteobacteria to analyze for the presence and absence of 12 proteins related to the pantothenate synthesis and transport. The protein FASTA files (faa) for each of the genomes were downloaded from the RefSeq NCBI database. Protein sequences with an expectation value (E) of 10<sup>-3</sup>or less were considered as putative homologues. We used Proteinortho v5.15 to obtain the clusters of orthologous proteins from the 204 protein FASTA files. Next, we used the Pfam v31.0 database to determine which protein ortho clusters represent the 12 proteins of interest analyzed in this work. The proteins we searched for were: PYD1, PYD2, PYD3, GAD, KPHMT, PS, ADC, KPR, MRF, KAR, Aam and GabT.</p>
Fig. 2 in The first record of nine bacterial species belonging to the phylum Proteobacteria in Korea
Fig. 2. Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences shows the relationship between the strains isolated in this study and their relatives in the genera Methylobacterium (1) and Microvirga (2). Bootstrap values (>70%) are shown above nodes for the neighbor-joining methods. Bar: 0.01 substitutions per nucleotide position.
Fig. 1 in Report of 29 unrecorded bacterial species from the phylum Proteobacteria
Fig. 1. Transmission electron micrographs of the strains isolated in this study. Strains: 1, S1-08; 2, SS1-17; 3, SS1-22; 4, SH33; 5, BK16- 1; 6, SH41; 7, BES-63; 8, ES2-15; 9, AS5-06; 10, CS4-36; 11, BK-22; 12, BK-77; 13, BK-179; 14, SS1-70; 15, SS2-102; 16, BK-176; 17, SJ55; 18, BK-182; 19, BK-210; 20, ES1-46; 21, BK-219; 22, BK-438; 23, BK-128; 24, BK-213; 25, GS1-30; 26, 04KS1-07; 27, CS4-45; 28, BES3-108; 29, KS1-13.
Fig. 1 in A report of four unrecorded Proteobacteria species isolated from soil in Korea
Fig. 1. Transmission electron micrographs of the strains isolated in this study. Strains: (A) Curvibacter lanceolatus R-1-5; (B) Massilia brevitalea R-2-13; (C) Pseudomonas lini R-2-1; and (D) Pseudomonas vancouverensis R-1-8.
Data from: From β- to α-proteobacteria: the origin and evolution of rhizobial nodulation genes nodIJ
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Gut colonization by Proteobacteria alters host metabolism and modulates cocaine neurobehavioral responses
GEO Series GSE212421. Mus musculus. 9 samples. Type: Expression profiling by high throughput sequencing.
CceR and AkgR regulate of central carbon and energy metabolism in α-Proteobacteria
GEO Series GSE63450. Cereibacter sphaeroides; Cereibacter sphaeroides 2.4.1. 13 samples. Type: Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing.
Comparative analysis of bacterial communities in olive psyllids, Euphyllura straminea and Euphyllura pakistanica expose Proteobacteria dominance
<p>Comparative analysis of bacterial communities in olive psyllids, Euphyllura straminea and Euphyllura pakistanica expose Proteobacteria dominance<br> </p>
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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.