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2,586 results for “Gradients”
Patterns in litterfall production from 12 forested sites along an elevation gradient in Pico del Este
We measured litterfall from 12 sites along an upper elevation gradient every two weeks from 1994 to present. Samples are being used to estimate the litterfall productivity over time and space, identify the impacts of periodic events, and help us understand the drivers of ecosystem and biogeochemical processes with climate and vegetation change. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
Terrestrial gastropods abundance data along an elevational gradient within the Sonadora River watershed
The data set includes 3 files that contain abundance data for terrestrial gastropods along an elevational gradient within the Sonadora River watershed. Two files (1 and 2) contain data from the same transect but differ in the year during which they were collected (2007 and 2008). The third file (3) contains data from a separate elevational transect (sites were located at the same elevation as in files 1 and 2) in palm dominated forest within the same watershed that was collected during the same time period in 2008 as data from file 2. Note: Plots at 250 m of elevation were not sampled in 2008 on either transect and a plot at elevation 750 m in the palm transect was never sampled. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
Elevation Gradient (EG) Soil Microbial diversity FAME and TRFLP data
Soil fungal communities respond to multiple abiotic and biotic factors that change along elevation gradients. The limited information available on fungi and microbial processes along elevation gradients is primarily from temperate areas and very few from tropical regions. This study documents changes in fungal and bacterial diversity, and abundance and composition of microbial functional groups along a subtropical elevation gradient. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
Elevational gradients of walking stick (Lamponius portoricensis) abundance
Abundance data were collected for Lamponius portoricensis from a mixed forest transect and from a palm dominated transect set along an elevational gradient in the Sonadora watershed. Each transect ranged from 300 m to 1000 m in elevation, with elevational strata located at 50 m intervals and 10 plots per stratum. No palm dominated forest could be located at 700 m in the watershed, resulting in 15 strata (150 plots) along the mixed forest transect and 14 strata (140 plots) along the palm forest transect. The data set includes 5 files that contain abundance data for walking sticks (Lamponius portoricensis) along an elevational gradient within the Sonadora River watershed. Three files contain data from the mixed forest transect but differ in the year during which they were collected (2007, 2008, 2017). The 'Walking Stick Palm" files contains data from a palm forest elevational transect from 2008 and 2017, for which all sites were located in palm dominated forest in the same watershed. Note: Plots at 250 m of elevation were only sampled during 2007, no palm dominated forest could be located at 750 m of elevation; that elevation is omitted from the palm transect. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
Rainfall and ion composition data from multiple weather stations along an elevation gradient in northeastern Puerto Rico (2009-2018)
The data archive is here: https://doi.org/10.2737/RDS-2021-0013 please use this DOI when citing this dataset. Rainfall and ionic composition data were collected at 21 sites along the elevational gradient of the Luquillo Mountains, in Puerto Rico. Stations were selected along the east coast of the island and follow the steep slope of the mountains until the highest peaks. Rainfall data were collected every two weeks and are provided in this data publication as monthly rainfall from January 2009 through May 2019. Also included are pH and conductivity which are provided monthly starting roughly in November 2011 and continue through May 2019. Monthly ionic composition data from rainwater samples collected during the last two weeks of each month are also included from January 2009 through December 2017. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
Northeastern Puerto Rico open-canopy and under-canopy temperature and moisture data on an elevational gradient
The data archive is here:https://doi.org/10.2737/RDS-2022-0051 please use this DOI when citing this dataset. This data publication contains monthly means of temperature and moisture data collected from August 2006 through September 2021 from 22 locations along an elevational gradient, from 0 to 1045 meters, in Northeastern Puerto Rico. The higher elevational data are in the Luquillo Experimental Forest (El Yunque National Forest). Five kinds of data are included: air temperature and precipitation measured in the open (not under canopy) at 20 locations, air temperature and soil temperature both measured under the canopy at all 22 locations, and soil moisture under the canopy at 4 locations. Two locations have 3 sites each, measured in different canopy types at the same location. The other 20 locations have one site each, making a total of 26 measurement sites. Data are provided as monthly averages at each site. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
Litterfall along topographic gradients at lower Bisley
Litterfall (fine and coarse) due to Hurricane Hugo and subsequent fine annual litterfall inputs (1, 2 and 5 yr after Hugo) were determined for two sites (El Verde and Bisley) in the Luquillo Experimental Forest in Puerto Rico. Litter transfers into streams, riparian and upslope areas were determined within each catchment. The recovery rate of aboveground fine litterfall (leaf, fine wood <1 cm diameter, and other miscellaneous inputs) to predisturbance levels were determined 1, 2, and 5 yr after Hurricane Hugo. The amount of total litter transfers and their individual components into the riparian and upslope areas due to Hurricane Hugo varied significantly by catchments within the Luquillo Experimental Forest. At El Verde, 26-39%, 31- 35%, 14-35% and 7-12% of the total litter transfers were contributed by leaf litter, fine wood, coarse wood and fine roots, respectively. At Bisley, 28-31%, 26-29%, 33-35% and 8-10% of the litter transfers were contributed by the same categories. Differential decay rates contributed to the relative importance of fine and coarse litter inputs. The recovery of fine aboveground litterfall to pre-hurricane levels after 5 yr varied by topographic location (streams had the slowest recovery, upslope areas the highest) and catchment (El Verde: 55-77%; Bisley: 39-82% of pre-hurricane values). Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
Soil bacterial diversity inventories along small-scale stress gradients in the Arctic, Antarctic, and Chihuahuan Deserts (2022-2023)
Bacteria form the foundation of soil ecosystems in desert ecosystems, driving soil function, diversity, and ecology. Soil physicochemistry is largely dictated by larger topographical variations and can directly drive bacterial community composition and the relationships within. Bacteria may form complex networks of interactions with other bacteria and other soil taxa that have implications for emergent properties such as diversity and stability, but the way these interactions are impacted by environmental stressors remains poorly understood. Here, we sampled soil bacterial communities of three desert ecosystems at different latitudes: the McMurdo Dry Valleys, Antarctica; the northern Chihuahuan Desert, Jornada Experimental Range (JER), New Mexico, USA; and the Arctic tundra at the Canadian High Arctic Research Research Station (CHARS), Victoria Island, Nunavut, Canada. In each system, a holistic stress-gradient was sampled based on local topographical variation, vegetation cover, and water availability. Sampling along the stress-gradient was conducted at four distinct stress levels, namely lower elevation with vegetation cover, lower elevation without vegetation cover, higher elevation with vegetation cover, and higher elevation without vegetation cover. To allow robust biodiversity inference and co-occurrence network construction, 30 replicates were collected at each stress level, and this was done at two independent stress gradients for the Chihuahuan Desert and Arctic sites. The Antarctic samples consisted of two independent stress gradients, one ranging from low, middle to high elevation without vegetation cover, and one consisting of two levels with and without vegetation cover. For each site, soil pH and gravimetric water content was also measured. Each replicate was then sequenced on an Illumina MiSeq for 2x250 paired-end sequencing of the 16S rRNA marker. Sequences were archived in NCBI under BioProject PRJNA1098956, with accession numbers included herein.
Data from: Competition among eggs shifts to cooperation along a sperm supply gradient in an external fertilizer
Purple sea urchin, Strongylocentrotus purpuratus, are broadcast spawners. Empirical and theoretical exploration of this trade-off in broadcast spawners has focused heavily on the role of sperm availability. In contrast, the particular manner in which egg concentrations alter both fertilization and polyspermy remains less explored. These data are from a laboratory experiment with a factorial design (six sperm concentrations x four egg concentrations replicated across multiple male-female pairs), to measure fertilization and polyspermy of purple sea urchins. Data were used to evaluate the impact of egg concentration on fertilization, and to explicitly test for random versus nonlinear sperm-egg collision rates. A new dynamic model was developed that expands upon existing models. Observations of fertilization and polyspermy were also used to parameterize and compare the performance of existing models that included random or or nonlinear collision parameters by utilizing several different basic model forms. For more information, see paper with published results or data set methods. Results for these data are pulished in Okamoto. D. K. 2016 Competition among eggs shifts to cooperation along a sperm supply gradient in an external fertilizer. The American Naturalist. 187:5, E129-E142. DOI: 10.1086/685813
Modifications of the plant-pollinator network structure and species' roles along a gradient of urbanization
<p>This file includes data and codes used in the article titled: " Modifications of the plant-pollinator network structure and species’ roles along a gradient of urbanization".</p> <p>Data include plant-pollinator interactions sampled in each site (1-12) at each sampling event (6 events) in the three urbanization classes (low, medium, high). Each row is a single insect pollinator X plant interaction. Full species names and abbreviations used in figures in the Supplementary Information are reported.<br> The data file is .txt with tab-separated values.</p>
Argo-based ocean surface mixed layer depths using the buoyancy gradient definition of Whitt Nicholson and Carranza (2019)
<p>Argo-based mixed layer depth profiles derived from the CORA product as described in Whitt Nicholson Carranza. A binned 2-degree climatology was published previously:</p> <p>https://github.com/danielwhitt/globalimpacts_2019_whittetal/blob/master/MonthlyClimatology_ARGO_MLDbmax_TEOS10_Copernicus_PF_2000-2017_all_jun252019_nc.nc</p> <p>with:</p> <p>Whitt, D. B., Nicholson, S. A., & Carranza, M. M. (2019). Global Impacts of Subseasonal (< 60 Day) Wind Variability on Ocean Surface Stress, Buoyancy Flux, and Mixed Layer Depth. <em>Journal of Geophysical Research: Oceans</em>, <em>124</em>(12), 8798-8831</p> <p>Contact the authors with questions. </p> <p>The chosen mixed layer depth definition is the same as "HMXL", a standard output of the Community Earth System Model (CESM) ocean component.</p>
Eddy Kinetic Energy and SST gradients global datasets and trends. Additionally, this dataset includes ocean basins and ocean processes masks.
<p>This dataset includes the post-processed data used for the paper titled "Mesoscale kinetic energy response to changing oceans". The original data was obtained from AVISO+ SSH altimetry and NOAA optimal interpolated sea surface temperature (OISST):</p> <p>AVISO+ SSH: https://www.aviso.altimetry.fr/en/data/products/sea-surface-height-products/global/gridded-sea-level-heights-and-derived-variables.html</p> <p>NOAA-OISST: https://www.ncdc.noaa.gov/oisst</p> <p>From satellite observations of sea surface height (SSH) and sea surface temperature (SST) over the satellite record (1993 - 2019), EKE and SST gradients are derived. </p> <p>Then the fields are then temporally smoothed using a running average of 12 months. Trends and the significance of each field are finally computed with linear regression and a modified Mann–Kendall test (https://github.com/josuemtzmo/xarrayMannKendall).</p> <p>Geographical regions consist of the following ocean basins: the Southern Ocean, the Indian Ocean, the Pacific Ocean, and the Atlantic ocean. These ocean basins were expert-defined to capture ocean processes at all scales (ocean_basins_and_dynamical_masks.nc).</p> <p>Dynamical regions (Fig. 5d): the Antarctic Circumpolar Current (ACC), the boundary currents and their extensions, the tropics, the subtropical ocean gyres, and the remaining regions (ocean_basins_and_dynamical_masks.nc).</p> <p>Further information and scripts to reproduce the result of the manuscript can be found at: https://github.com/josuemtzmo/EKE_SST_trends</p>
Brachypodium distachyon images used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE et al.
<p>Brachypodium distachyon images used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE, Anthony FRATAMICO, Frédéric BOUCHÉ, Samuel HUERGA-FERNÁNDEZ, Pierre TOCQUIN, Claire PÉRILLEUX</p>
Euphorbia peplus images used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE et al.
<p>Euphorbia peplus images used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE, Anthony FRATAMICO, Frédéric BOUCHÉ, Samuel HUERGA-FERNÁNDEZ, Pierre TOCQUIN, Claire PÉRILLEUX</p>
Arabidopsis thaliana images used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE et al.
<p><em>Arabidopsis thaliana</em> images used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE, Anthony FRATAMICO, Frédéric BOUCHÉ, Samuel HUERGA-FERNÁNDEZ, Pierre TOCQUIN, Claire PÉRILLEUX</p>
Oryza sativa images used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE et al.
<p><em>Oryza sativa</em> images used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE, Anthony FRATAMICO, Frédéric BOUCHÉ, Samuel HUERGA-FERNÁNDEZ, Pierre TOCQUIN, Claire PÉRILLEUX</p>
Solanum lycopersicum images used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE et al.
<p><em>Solanum lycopersicum</em> images used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE, Anthony FRATAMICO, Frédéric BOUCHÉ, Samuel HUERGA-FERNÁNDEZ, Pierre TOCQUIN, Claire PÉRILLEUX</p>
Ocimum basilicum images used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE et al.
<p><em>Ocimum basilicum</em> images used in the paper entitled "Led Color Gradient As A New Screening Tool For Rapid Phenotyping Of Plant Responses To Light Quality" by Pierre LEJEUNE, Anthony FRATAMICO, Frédéric BOUCHÉ, Samuel HUERGA-FERNÁNDEZ, Pierre TOCQUIN, Claire PÉRILLEUX</p>
Range expansion is slower and more variable with rapid evolution across a spatial gradient in temperature
<p><span>Rapid evolution in colonizing populations can alter our ability to predict future range expansions. Recent theory suggests that the dynamics of replicate range expansions are less variable, and hence more predictable, with increased selection at the expanding range front. Here, we test whether selection from environmental gradients across space produces more consistent range expansion speeds, using the experimental evolution of replicate duckweed populations colonizing landscapes with and without a temperature gradient. We found that range expansion across a temperature gradient was slower on average, with range-front populations displaying higher population densities, and genetic signatures and trait changes consistent with directional selection. Despite this, we found that with a spatial gradient range expansion speed became more variable and less consistent among replicates over time. Our results therefore challenge current theory, highlighting that chance can still shape the genetic response to selection to influence our ability to predict range expansion speeds.</span></p>
The North Pacific Eukaryotic Gene Catalog: Raw assemblies from Gradients 1, 2 and 3
<p>The North Pacific Eukaryotic Gene Catalog consolidates eukaryotic metatranscriptome data from three latitudinal transects of the North Pacific transition zone and one cruise in the subtropical gyre. Metatranscriptomes were gathered from latitudinally-resolved surface samples, and diel-resolved temporal studies, with samples taken in triplicate or duplicate and collected on 0.2-100 μm, 0.2-3 μm, and 3 μm-100 or 200 μm size fractions. These metatranscriptome data were <em>de novo</em> assembled into 175 independent assemblies, totalling 182 million clustered nucleotide contigs. Assemblies were annotated by taxonomy and function. This catalog provides assembled environmental contigs, their translated peptide sequences, and their taxonomic and functional annotations with the aim of facilitating continued discoveries about the molecular ecology of microbial eukaryotes in the North Pacific.<br><br>A full description of this data is published in Scientific Data, available here: <a href="https://www.nature.com/articles/s41597-024-04005-5" target="_blank" rel="noopener">The North Pacific Eukaryotic Gene Catalog of metatranscriptome assemblies and annotations</a>. Please cite this publication if your research uses this data:<br><br>Groussman, R. D., Coesel, S. N., Durham, B. P., Schatz, M. J., & Armbrust, E. V. (2024). The North Pacific Eukaryotic Gene Catalog of metatranscriptome assemblies and annotations. <em>Scientific Data</em>, <em>11</em>(1), 1161.</p> <div> <p>This dataset repository is associated with a codebase and documentation repository:<br><a href="https://github.com/armbrustlab/NPac_euk_gene_catalog" target="_blank" rel="noopener">https://github.com/armbrustlab/NPac_euk_gene_catalog</a><br>Please see this code repository for additional data and project updates<br><br>Translated and processed protein sequences and their annotations are available in this repository: <br><a href="../doi/10.5281/zenodo.10472589">https://zenodo.org/doi/10.5281/zenodo.10472589</a><br><br>99% identity clustered nucleotide sequences and kallisto enumerations are available here:<br><a href="../doi/10.5281/zenodo.10570448">https://zenodo.org/doi/10.5281/zenodo.10570448</a></p> </div> <div> <p>File contents: this repository contains five .tar.gz compressed tarballs with raw de novo Trinity assemblies of poly-A selected metatranscriptomes from the Gradients 1 through 3 cruises, and a plain-text file with the custom spike-in mRNA standards (CustomStandardSequences.txt)</p> </div> <div> <p><strong><br>Gradients1.KOK1606.PA.assemblies.tar.gz</strong><br>- Link to <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/tree/main/projects/G1PA" target="_blank" rel="noopener">G1PA project github page</a><br>- Simons CMAP cruise page and datasets: <a href="https://simonscmap.com/catalog/cruises/KOK1606" target="_blank" rel="noopener">https://simonscmap.com/catalog/cruises/KOK1606</a><br>- Short read processing code: <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/blob/main/scripts/G1PA.process_short_reads.sh" target="_blank" rel="noopener">G1PA.process_short_reads.sh</a><br>- Trinity assembly code: <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/blob/main/scripts/G1PA.trinity_assemblies.sh" target="_blank" rel="noopener">G1PA.trinity_assemblies.sh</a></p> </div> <div> <p><strong><br>Gradients2.MGL1704.PA.assemblies.tar.gz</strong><br>- Link to <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/tree/main/projects/G2PA" target="_blank" rel="noopener">G2PA project github page</a><br>- Simons CMAP cruise page and datasets: <a href="https://simonscmap.com/catalog/cruises/MGL1704" target="_blank" rel="noopener">https://simonscmap.com/catalog/cruises/MGL1704</a><br>- Short read processing code: <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/blob/main/scripts/G2PA.process_short_reads.sh" target="_blank" rel="noopener">G2PA.process_short_reads.sh</a><br>- Trinity assembly code: <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/blob/main/scripts/G2PA.trinity_assemblies.sh" target="_blank" rel="noopener">G2PA.trinity_assemblies.sh</a></p> </div> <div> <p><strong><br>Gradients3.KM1906.PA.assemblies.tar.gz</strong><br>- Link go <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/tree/main/projects/G3PA" target="_blank" rel="noopener">G3PA project github page</a><br>- Simons CMAP cruise page and datasets: <a href="https://simonscmap.com/catalog/cruises/KM1906" target="_blank" rel="noopener">https://simonscmap.com/catalog/cruises/KM1906</a><br>- Short read processing code: <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/blob/main/scripts/G3PA_UW.process_short_reads.sh" target="_blank" rel="noopener">G3PA_UW.process_short_reads.sh</a><br>- Trinity assembly code: <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/blob/main/scripts/G3PA_UW.trinity_assemblies.sh" target="_blank" rel="noopener">G3PA_UW.trinity_assemblies.sh</a></p> </div> <div> <p><strong><br>G3_diel.KM1906.PA.assemblies.tar.gz</strong><br>- Link go <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/tree/main/projects/G3PA" target="_blank" rel="noopener">G3PA project github page</a><br>- Simons CMAP cruise page and datasets: <a href="https://simonscmap.com/catalog/cruises/KM1906" target="_blank" rel="noopener">https://simonscmap.com/catalog/cruises/KM1906</a><br>- Short read processing code: <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/blob/main/scripts/G3PA_diel.process_short_reads.sh" target="_blank" rel="noopener">G3PA_diel.process_short_reads.sh</a><br>- Trinity assembly code: <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/blob/main/scripts/G3PA_diel.trinity_assemblies.sh" target="_blank" rel="noopener">G3PA_diel.trinity_assemblies.sh</a></p> </div> <div> <p><strong><br>CustomStandardSequences.txt<br></strong>- Plain-text FASTA file with the spike-in standards used during mRNA extraction and sequencing prep<br>- Link to publication of spike-in standards methods: <a href="https://www.nature.com/articles/s41564-019-0507-5" target="_blank" rel="noopener">https://www.nature.com/articles/s41564-019-0507-5</a></p> </div> <div> <p>The 2015 SCOPE Diel metatranscriptome raw assemblies have been released in a previous Zenodo repository, and are not included again in this deposition. We provide the links to the Diel1 resources here:<br>- Diel1 raw metatranscriptome assembly Zenodo repository: <a href="../records/5009803" target="_blank" rel="noopener">https://zenodo.org/records/5009803</a><br>- Dataset DOI: <a href="https://doi.org/10.5281/zenodo.5009803" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.5009803</a><br>- Associated publication: <a href="https://www.frontiersin.org/articles/10.3389/fmicb.2021.682651/full" target="_blank" rel="noopener">https://www.frontiersin.org/articles/10.3389/fmicb.2021.682651/full</a><br>- Codebase: <a href="https://github.com/armbrustlab/diel_eukaryotes" target="_blank" rel="noopener">https://github.com/armbrustlab/diel_eukaryotes</a><br>- Simons CMAP cruise page and datasets: <a href="https://simonscmap.com/catalog/cruises/KM1513" target="_blank" rel="noopener">https://simonscmap.com/catalog/cruises/KM1513</a><br>- Short read processing code: <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/blob/main/scripts/D1PA.process_short_reads.sh" target="_blank" rel="noopener">D1PA.process_short_reads.sh</a><br>- Trinity assembly code: <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/blob/main/scripts/D1PA.trinity_assemblies.sh" target="_blank" rel="noopener">D1PA.trinity_assemblies.sh</a></p> </div> <p><br><br></p>
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.