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14 results for “Flavobacterium”
Shine Dalgarno strength data for manuscript "Occlusion of the anti-Shine-Dalgarno on the 30S platform reduces the efficiency of prfB programmed frameshifting in Flavobacterium johnsoniae"
<p>This data set contains Shine Dalgarno strengths for every gene in 4362 bacterial genomes that were analyzed in the manuscript titled "Analysis of programmed frameshifting during translation of prfB in Flavobacterium johnsoniae". There is one comma separated file per genome. They are split between six zip archives. Each line in these files represents one gene. The columns are the genome ID, the name of the gene, the SD strength in kcal/mol as determined by free_scan, the mock SD strength in kcal/mol as determined by free_scan, the anti Shine Dalgarno sequence identified from the 16S ribosomal RNAs of the organism, the sequence of the SD region that was scanned, and the sequence of the mock SD region that was scanned. The mock SD region is further upstream of the gene and should not contain a true SD sequence and is provided as a control.</p>
Fig. 1 in Flavobacterium niveum sp. nov., isolated from a freshwater creek
Fig. 1. Neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showing the position of Flavobacterium niveum TAPW14T and other Flavobacterium species. Numbers at nodes are bootstrap percentages (>70 %) based on the neighbour-joining (above nodes) and maximum-parsimony (below nodes) tree-making algorithms. Filled circles indicate branches of the tree that were also recovered using the maximum-likelihood and maximum-parsimony tree-making algorithms. Open circles indicate that the corresponding nodes were also recovered in the tree generated with the maximum-parsimony algorithm. Myroides odoratus ATCC 4651T was used as an outgroup. Bar, 0.01 substitutions per nucleotide position.
Fig. 1 in Flavobacterium tibetense sp. nov., isolated from a wetland
Fig. 1. Phylogenetic tree of strain YH5T and related type strains within the genus Flavobacterium based on almost-complete 16S rRNA gene sequences. The tree was calculated using the neighbour-joining algorithm in MEGA 5 software. Numbers at nodes indicate the percentages of bootstrap support based on 1000 resampled datasets; only values>50 % are shown. Zobellia galactanivorans DsijT (FP476056) was used as outgroup. Bar, 0.01 substitutions per nucleotide position.
Fig. 1 in Flavobacterium eburneum sp. nov., isolated from reclaimed saline land soil
Fig. 1. Phylogenetic tree reconstructed using the neighbour-joining method based on 16S rRNA gene sequences, and showings the position of strain SA31T and its closely related species. Escherichia coli ATCC 11775T (GenBank accession no. JMST01000030) was used as an outgroup. Evolutionary distances were computed using Kimura's 2-parameter method [21] and are given in units of number of base substitutions per site. Bootstrap values (expressed as percentages of 1000 iterations)>50 % are shown at branch points. Filled circles indicate branches found in phylogenetic consensus trees generated with the maximum-likelihood method. Bar, 0.02 nucleotide substitutions per nucleotide position.
Gene expression analysis between planktonic and biofilm states of Flavobacterium columnare
GEO Series GSE109937. Flavobacterium columnare. 12 samples. Type: Expression profiling by high throughput sequencing.
Transcriptional responses of resistant and susceptible fish clones to the bacterial pathogen Flavobacterium psychrophilum
GEO Series GSE35448. Oncorhynchus mykiss. 23 samples. Type: Expression profiling by array.
Immunoprotective effects of two histone H2A variants in the grass carp against Flavobacterium columnare infection
GEO Series GSE201422. Ctenopharyngodon idella. 9 samples. Type: Expression profiling by high throughput sequencing.
Gene expression profiling of catfish after treatment with Flavobacterium columnare DnaK protein
GEO Series GSE121116. Ictalurus punctatus. 18 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome architecture and regulation at environmental transitions of the fish pathogen Flavobacterium psychrophilum: Global RNA-Seq
GEO Series GSE164190. Flavobacterium psychrophilum. 1 samples. Type: Expression profiling by high throughput sequencing.
Gene expression analysis comparing a selected strain of rainbow trout with superior growth and immune performance to a commercial reference strain during baterial infection with Flavobacterium psychro
GEO Series GSE156930. Oncorhynchus mykiss. 28 samples. Type: Expression profiling by high throughput sequencing.
Gene expression profiles of white bass (Morone chrysops) and hybrid striped bass (M. chrysops x M. saxatilis) gill tissue over time following Flavobacterium covae exposure
GEO Series GSE246056. Morone chrysops x Morone saxatilis; Morone chrysops. 48 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome architecture and regulation at environmental transitions of the fish pathogen Flavobacterium psychrophilum: 5’-end RNA-Seq
GEO Series GSE164189. Flavobacterium psychrophilum. 1 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome architecture and regulation at environmental transitions of the fish pathogen Flavobacterium psychrophilum
GEO Series GSE163842. Flavobacterium psychrophilum. 64 samples. Type: Expression profiling by array.
Validation of a QTL for Flavobacterium psychrophilum resistance in rainbow trout Oncorhynchus mykiss
GEO Series GSE216505. Oncorhynchus mykiss. 270 samples. Type: Expression profiling by RT-PCR.
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)
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.