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.
1,154
datasets available to search
ShareScore release 0.9.0
Dataset results
1,154 results for “Pooling”
Subsampling and DNA pooling can increase gains through genomic selection in switchgrass
<p>Genomic selection (GS) can accelerate breeding cycles in perennial crops such as the bioenergy grass switchgrass (<i>Panicum virgatum</i> L.). The sequencing costs of GS can be reduced by pooling DNA samples in the training population (TP), only sequencing TP phenotypic outliers, or pooling candidate population (CP) samples. These strategies were simulated for two traits (spring vigor and anthesis date) in three breeding populations. Sequencing only the outlier 50% of the TP phenotype distribution resulted in a penalty of <5% of the predictive ability, measured using cross-validation. Predictive ability also decreased when sequencing progressively fewer TP DNA pools, but TPs constructed from only two phenotypically contrasting DNA samples retained a mean of >80% predictive ability relative to individual TP sequencing. Novel group testing methods allowed greater than one CP individual to be screened per sequenced DNA sample but resulted in a predictive ability penalty. To determine the impact of reduced sequencing, genetic gain was calculated for seven GS scenarios with variable sequencing budgets. Reduced TP sequencing and most CP pooling methods were superior to individual sequence-based GS when sequencing resources were restricted (2,000 DNA samples per 5-yr cycle). Only one scenario was superior to individual sequencing when sequencing budgets were large (8,000 DNA samples per 5-yr cycle). This study highlights multiple routes for reduced sequencing costs in GS.</p>
Taxonomic and functional diversity covary in rock pool microalgal communities despite their different drivers - Environmental and diatom data
<p>We sampled 30 brackish‐watered, isolated rock pools once a month (17 May, 22 June, and 22 July) in 2016 on a granitic outcrop in the western island of Pihlajasaari (66°68′449″N, 38°40′48″E), ca. 2 km south of Helsinki, Finland on the coast of the northern Baltic Sea. We examined the drivers and covariance of taxonomic and functional diversity among the rock pool communities. We measured water pH, conductivity, and temperature in the field, and pool morphometrics (i.e., max depth, length, and width) to the nearest centimeter, and calculated pool area (length * width). We collected a 0.5 L water sample from each pool for the determination of total P (SFS‐EN ISO 2004). We estimated pool X and Y coordinates (based on the perpendicular pool distance from the shore and the horizontal pool distance from the map origin in the southern end parallel to the shoreline, respectively) and mean isolation as a mean Euclidean distance (i.e., the sum of distances to five closest pools divided by five; Vanschoenwinkel et al. 2007) for each pool from a drawn grid map of the study area showing the relative location of the sampled pools to each other and to the seashore.</p> <p>We sampled benthic diatoms by collecting epilithic samples (ca. 25 cm<sup>2</sup>) from each pool bottom with a toothbrush, following EN 13946 standard (2003). A total of 500 valves per sample were counted and identified to the lowest taxonomic level possible (mostly species level) with a light microscope. We created a taxonomic site‐species matrix based on species relative abundances.</p> <p>The identified diatom species were classified into 21 partly overlapping functional groups. We first divided the species into five size classes after their biovolume (determined by cell length, width, thickness, and shape) and 14 life‐form categories after interspecific morphological adaptations to physical and chemical disturbance (i.e., cell motility, posture, and type of adhesion) following Rimet & Bouchez (2012). A single taxon may have various successive life forms and may thus be classified into multiple life‐form categories. We further classified the species after their preferences for nutrient concentration and physical disturbance into four ecological guilds (high profile, low profile, motile and planktonic) after Passy (2007) and Rimet & Bouchez (2012). Finally, we separated between acid‐tolerant (acidobiontic or acidophilus species with pH optimum <7 in Van Dam et al. (1994), and nitrogen‐fixing species (with cyanobacterial endosymbionts capable of fixing atmospheric nitrogen). In the species‐trait matrix, each species belonging to a given guild (other than continuous biovolume guild on a scale 1–5) was given a value of 1; otherwise, the value was set to 0. Each species could be characterized by multiple traits and could thus belong to more than only one guild.</p>
Supplementary material 1 from: Niehues A, de Visser C, Hagenbeek FA, Karu N, Kindt ASD, Kulkarni P, Pool R, Boomsma DI, van Dongen J, van Gool AJ, `t Hoen PAC (2022) A Multi-omics Data Analysis Workflow Packaged as a FAIR Digital Object. Research Ideas and Outcomes 8: e94042. https://doi.org/10.3897/rio.8.e94042
Members of the ACTION Consortium
Supplementary material 1 from: DeWalt RE, South EJ (2015) Ephemeroptera, Plecoptera, and Trichoptera on Isle Royale National Park, USA, compared to mainland species pool and size distribution. ZooKeys 532: 137-158. https://doi.org/10.3897/zookeys.532.6478
Table S1. Raw specimen data in the form of an Excel comma delimited file:
Figure 2 from: Kwun H, Park J, Kim H, Kim J, Park H (2017) Checklist of the tidal pool fishes of Jeju Island, Korea. ZooKeys 709: 135-154. https://doi.org/10.3897/zookeys.709.14711
Figure 2 - A Hyporhamphus sajori, MFD-746, 77.3 mm standard length (SL) B Sebastes inermis, MFD-902, 47.5 mm SL.
Figure 10 from: Kwun H, Park J, Kim H, Kim J, Park H (2017) Checklist of the tidal pool fishes of Jeju Island, Korea. ZooKeys 709: 135-154. https://doi.org/10.3897/zookeys.709.14711
Figure 10 - A Lepadichthys frenatus, MFD-318, 47.5 mm SL B Luciogobius guttatus, MFD-144, 50.2 mm SL.
Figure 4 from: Kwun H, Park J, Kim H, Kim J, Park H (2017) Checklist of the tidal pool fishes of Jeju Island, Korea. ZooKeys 709: 135-154. https://doi.org/10.3897/zookeys.709.14711
Figure 4 - A Pseublennius percoides, MFD-671, 47.8 mm SL B Pseudoblennius marmoratus, MFD-927, 19.3 mm SL.
Figure 6 from: Kwun H, Park J, Kim H, Kim J, Park H (2017) Checklist of the tidal pool fishes of Jeju Island, Korea. ZooKeys 709: 135-154. https://doi.org/10.3897/zookeys.709.14711
Figure 6 - A Plesiops coeruleolineatus, MFD-860, 82.8 mm SL B Lutjanus fulviflamma, MFD-866, 101.1 mm SL.
Figure 9 from: Kwun H, Park J, Kim H, Kim J, Park H (2017) Checklist of the tidal pool fishes of Jeju Island, Korea. ZooKeys 709: 135-154. https://doi.org/10.3897/zookeys.709.14711
Figure 9 - A Stethojulis interrupta terina, MFD-850, 92.9 mm SL B Stethojulis trilineata, MFD-482, 25.7 mm SL.
Fig. 11 in Pools and rapids as spawning and nursery areas for fish in a river stretch without floodplains
Fig. 11. Conceptual model of the distribution patterns of eggs and larvae in the early stages of two environments in the Peixe River (upper Uruguay River), from October 2011 to March 2012.
Fig. 6 in Pools and rapids as spawning and nursery areas for fish in a river stretch without floodplains
Fig. 6. Average density ± standard deviation of the macrozooplankton organisms captured in both environments (rapids and pool) of the Peixe River, between October 2011 and March 2012.
Fig. 4 in Pools and rapids as spawning and nursery areas for fish in a river stretch without floodplains
Fig. 4. Average repletion degree (%) of the captured larvae digestive tract from both environments of the Peixe River, from October 2011 to March 2012. Number of larvae examined is shown in brackets. Repletion degree: E - empty; PE - partially empty; PF - partially full; F - full.
Fig. 8 in Pools and rapids as spawning and nursery areas for fish in a river stretch without floodplains
Fig. 8. Average density ± standard error of the larvae captured in the Peixe River with light traps in different environments and months from October 2011 to March 2012.
Fig. 5 in Pools and rapids as spawning and nursery areas for fish in a river stretch without floodplains
Fig. 5. Average flow and precipitation ratings registered in the Peixe River, from October 2011 to March 2012. Source: Consórcio de Itá.
Fig. 5 in New record of four ciliates (Protozoa, Ciliophora) collected from rocky intertidal pools of South Korea
Fig. 5. Photomicrographs of Dysteria semilunaris from living specimens (A-D) and protargol impregnated specimens (E, F). A. Left lateral view of typical individual. B. longitudinal groove on left plate (arrowheads). C. Ventral view. D. Right lateral view showing the two contractile vacuoles (arrows) and the longitudinal groove on the right plate (arrowheads). E, F. Left views of stained specimens showing infraciliature, arrow denotes the short row below the end of the frontoventral kineties. Co, circumoral kineties; CVP, contractile vacuole pore; Cy, cytopharynx; EF, equatorial fragment; FVK, frontoventral kineties; LF, left frontal kineties; LK, left kineties; Ma, macronucleus; P, podite; Pr, preoral kinety; RK, right kineties; TF, terminal fragment. Scale bars: 20 μm.
Fig. 2 in New record of four ciliates (Protozoa, Ciliophora) collected from rocky intertidal pools of South Korea
Fig. 2. Photomicrographs of Aspidisca polypoda from living specimens (A-D), protargol impregnated specimens (E, F), and illustrations (G-J). A. Ventral view showing posterior part of the adoral membranelles (arrowhead). B. Eight distinctive ridges (arrowheads) and contractile vacuole (arrow). C. Anterior part of the adoral membranelles (arrowhead). D. Separated into two parts of leftmost transverse cirri (arrowhead). E, F. Ventral and dorsal view of stained specimens. G-J. Illustrations showing main characteristics. AZM 1 and 2, adoral zone of membranelles 1 and 2; CV, contractile vacuole; DK, dorsal kineties; FVC, frontoventral cirri; MA, macronucleus; TC, transverse cirri. Scale bars: 20 μm.
Cold pool collisions
<p>This dataset contains data used in a publication regarding cold pool collisions.</p>
Figure 9 from: Ando K (2019) The study of amphipods in rimstone pools of Akiyoshi-do Cave, Japan. Subterranean Biology 32: 81-94. https://doi.org/10.3897/subtbiol.32.35031
Figure 9 Result of CCA analysis on the amphipod abundances and water characteristics. TN: total nitrogen, TP: total phosphorus, TB: total number of bacteria, TVB: total number of viable bacteria. Other symbols mean pools surveyed in each season by "month-pool number": for example, 5-CH1 corresponds to CH1 pool surveyed in May.
Figure 5 from: Ando K (2019) The study of amphipods in rimstone pools of Akiyoshi-do Cave, Japan. Subterranean Biology 32: 81-94. https://doi.org/10.3897/subtbiol.32.35031
Figure 5 Pools with arrows pointing the flowing directions. Water from the walls and drips was supplied to CH4 and water flowed to CH2 and CH1 via CH5. Pumped cave river water was supplied to CH8 and CH9 and water flowed to CH6 and CH7.
Figure 8 from: Ando K (2019) The study of amphipods in rimstone pools of Akiyoshi-do Cave, Japan. Subterranean Biology 32: 81-94. https://doi.org/10.3897/subtbiol.32.35031
Figure 8 Fluctuation of the population density of Gammarus nipponensis in the type C pools (1971–1975, 2015–2016).
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.