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2,308 results for “repeatability”
The dynamics of marsh-channel slump blocks: an observational study using repeated drone imagery
We analyzed the spatial and temporal dynamics of slump blocks within Dean Creek, a creek located on Sapelo Island (GA) and surrounded by salt marsh. To accomplish this, we utilized 11 images of Dean Creek captured between March 2020 and March 2021, which were acquired by using a DJI Matrice 210 UAV. For each image, we manually digitized the perimeters of slump blocks, which have the distance from intact marsh boundary exceeding 0.3 m. These digitized perimeters were subsequently converted into polygons to determine the size, number and cumulative area of slump blocks in each image. Temporal changes to the slump blocks between subsequent images were also analysed. The coordinate system of these polygon data is WGS 1984 UTM Zone 17N.
Creating multi-themed ecological regions for macroscale ecology: Testing a flexible, repeatable, and accessible clustering method
This dataset was created for the following publication: Cheruvelil, K.S., S. Yuan, K.E. Webster, P.-N. Tan, J.-F. Lapierre, S.M. Collins, C.E. Fergus, C.E. Scott, E.N. Henry, P.A. Soranno, C.T. Filstrup, T. Wagner. Under review. Creating multi-themed ecological regions for macrosystems ecology: Testing a flexible, repeatable, and accessible clustering method. Submitted to Ecology and Evolution July 2016. This dataset includes lake total phosphorus (TP) and Secchi data from summer, epilimnetic water samples, as well as 52 geographic variables at the HU-12 scale; it is a subset of the larger LAGOS-NE database (Lake multi-scaled geospatial and temporal database, described in Soranno et al. 2015). LAGOS-NE compiles multiple, individual lake water chemistry datasets into an integrated database. We accessed LAGOSLIMNO version 1.054.1 for lake water chemistry data and LAGOSGEO version 1.03 for geographic data. In the LAGOSLIMNO database, lake water chemistry data were collected from individual state agency sampling and volunteer programs designed to monitor lake water quality. Water chemistry analyses follow standard lab methods. In the LAGOSGEO database geographic data were collected from national scale geographic information systems (GIS) data layers. The dataset is a subset of the following integrated databases: LAGOSLIMNO v.1.054.1 and LAGOSGEO v.1.03. For full documentation of these databases, please see the publication below: Soranno, P.A., E.G. Bissell, K.S. Cheruvelil, S.T. Christel, S.M. Collins, C.E. Fergus, C.T. Filstrup, J.F. Lapierre, N.R. Lottig, S.K. Oliver, C.E. Scott, N.J. Smith, S. Stopyak, S. Yuan, M.T. Bremigan, J.A. Downing, C. Gries, E.N. Henry, N.K. Skaff, E.H. Stanley, C.A. Stow, P.-N. Tan, T. Wagner, K.E. Webster. 2015. Building a multi-scaled geospatial temporal ecology database from disparate data sources: Fostering open science and data reuse. GigaScience 4:28 doi:10.1186/s13742-015-0067-4 .
PsPM-FER02: PSR, SCR, ECG and respiration measurements from a 3 conditions x 3 experimental sessions repeated-measures design to assess the return of fear
<p>This dataset includes pupil size response (PSR), skin conductance response (SCR), electrocardiogram (ECG) and respiration measurements. Also included are CS and US information, keypress responses, keypress response times, key correctness and shock expectancy ratings at the end of the experiment for 74 healthy unmedicated participants (33 males and 41 females aged 24.2+/-3.9 years) participating in a 3 conditions x 3 experimental sessions repeated-measures design to assess the return of fear. CS were colored triangles (yellow/red/blue). US consisted of a 500 ms train of 250 square pulses with individual pulse width of 0.2 ms. SOA between the CS onset and US was 3.5 s. CS and US co-terminated. The ITI was randomly determined as discrete values between 7-11 seconds (mean 9 seconds).</p>
Repeat overhead photographs of microplots in a cross-scale interactions experiment (CSIS) at Jornada Basin LTER, 2013-ongoing
This dataset contains archived overhead photos collected from microplots in a long-term experiment (2013-present) of cross-scale interactions (CSIs) at the Jornada Basin LTER site in southern New Mexico, U.S.A. Experimental treatments were initiated in 2013 at 15 experimental blocks, each with 4 treatment plots: plant-scale herbicide of mesquite shrubs, patch-scale connectivity modifiers (ConMods), herbicide + ConMods, and control without manipulations. Repeat, overhead (downward-looking) photographs of ten "microplots" in each plot were taken for estimation of litter, soil, and vegetation cover in the experimental treatment and control plots over time. Photographs have been rotated and then cropped to provide standardized areas for this analysis. The photographs are archived by year in Zip files. This study is ongoing and new photos will be added annually. Cover estimates derived from these photos are in EDI dataset knb-lter-jrn.210413005.
Repeat lateral photographs of microplots in a cross-scale interactions experiment (CSIS) at Jornada Basin LTER, 2013-2017
This dataset contains archived lateral photos collected from microplots in a long-term experiment (2013-2017) of cross-scale interactions (CSIs) at the Jornada Basin LTER site in southern New Mexico, U.S.A. Experimental treatments were initiated in 2013 at 15 experimental blocks, each with 4 treatment plots: plant-scale herbicide of mesquite shrubs, patch-scale connectivity modifiers (ConMods), herbicide + ConMods, and control without manipulations. Repeat, lateral (side-looking) photographs of ten "microplots" in each plot were taken for estimation of the vertical accumulation of litter, soil, and vegetation in the experimental treatment and control plots over time. The photographs are archived by year in Zip files. This study is complete and new photos will not be added. Litter/soil accumulation estimates derived from these photos are in EDI dataset knb-lter-jrn.210413007.
Unexplained Repeated Pregnancy Loss is Associated with Altered Perceptual and Brain Responses to Men’s Body-Odor
Open the record for dataset details and reuse information.
Detecting repeating earthquakes on the San Andreas Fault with unsupervised machine-learning of spectrograms (supplementary material)
<p>Supplementary material for Sawi et al., 2023, <i>Detecting repeating earthquakes on the San Andreas Fault with unsupervised machine-learning of spectrograms </i>(The Seismic Record). Catalog of repeating earthquakes in sequences on a 10-km long segment of the San Andreas Fault in California from 1984-2019. </p><p> </p><p><strong>Catalog Header</strong></p><p>YR/MO/DY...........Date of event</p><p>HR/MN/SC...........Time of event</p><p>LAT/LON/DEP........Location of event</p><p>EX/EY/EZ...........Relative location uncertainty (in m)</p><p>MAG................NCSN magnitude</p><p>evID.................NCSN event ID</p><p>seqID................Repeating earthquake sequence ID</p><p>isRESp............Is quasi-periodic RES (bool)</p><p> </p><p><strong>References: </strong></p><p>Sawi T., Waldhauser F., Holtzman B. K., Groebner, N. (2023) Detecting repeating earthquakes on the San Andreas Fault with unsupervised machine-learning of spectrograms. The Seismic Record. </p><p>Waldhauser, F., and Schaff, D. P. (2021). A Comprehensive Search for Repeating Earthquakes in Northern California: Implications for Fault Creep, Slip Rates, Slip Partitioning, and Transient Stress. J Geophys Res B Solid Earth, 126(11), 1–22. <a href="https://doi.org/10.1029/2021JB022495">https://doi.org/10.1029/2021JB022495</a></p>
Repeating low frequency icequakes in the Mont-Blanc massif
<p>This dataset provides catalogs of low-frequency icequakes detected in the Mont-Blanc massif (Alps) between 2017 and 2022.</p>
Physarum polycephalum Repeated Maze Honors Thesis, Tulane University, SE Louisiana 2024-2025
We conducted an experimental maze study from January to March, 2025, on Physarum polycephalum at Tulane University in New Orleans, Louisiana. We collected data on changes in locomotive behavior as P. polycephalum repeatedly solved the same maze. From daily photographs of growth, we recorded path choice, contamination presence and location, number of times P. polycephalum grew directly over maze walls, how many of the four dead-ends P. polycephlaum grew down, and efficiency through surface area covered. Data collection is complete. We found a significant increase in efficiency, and a significant decrease in both dead-end paths and wall jumping, as maze repetitions increased. This points to evidence of information storage and retrieval, and therefore cognitive processes such as memory, within the single-cellular protist Physarum polycephalum.
Repeat photography of tidal fresh forest trees along the salinity gradient of the Altamaha River, GA
We established a transect of 42 stations for repeat photography of tidal fresh forest trees along the salinity gradient of the Altamaha River estuary. Target trees are located approximately every km on both the north and south banks, beginning at km 20 (with 0 at the mouth of the estuary) up to km 41, for a total of 21 km. We used a small boat to travel to each station and take digital photographs of target trees facing the river in Nov 2017, Feb, May, Aug of 2018. In Oct 2018 we extended the transect an additional 5 km downstream so that it now starts at km 16, with 5 more stations on the north bank and 5 on the south bank. All 52 stations were photographed in Oct 2018 and Oct 2019. These photos will be used to distinguish healthy, stressed and dead trees in each image and how they change over time.
Diffraction images of crystals of the first and second spectrin repeats (mutant C420A/C435A) of human plectin (PDB code 2ODV): 2-wavelength SeMet MAD dataset
<p>Diffraction images of SeMet labeled crystals of a fragment of human plectin that includes the first and second spectrin repeats (SR1-SR2) of the plakin domain. The two Cys in the wild type sequence were replaced by Ala.</p> <p>This Se-Met MAD dataset was used for the <em>de novo</em> phasing of the pdb entry 2ODV (http://www.rcsb.org/pdb/explore/explore.do?structureId=2ODV).</p> <p> </p> <p>Data was collected at the BM14 beamline of the European Synchrotron Radiation Facility (ESRF, Grenoble, France) using a Mar CCD detector. Data from the same crystal were collected at two wavelengths :</p> <ul> <li>Remote wavelength (0.9185 Å): 180 images (1 degree oscillation per image).</li> <li>Peak wavelength ( 0.9785 Å): 360 images (1 degree oscillation per image).</li> </ul>
Genome, repeat, and functional annotation associated with the naked mole-rat genome assembly, mHetGlaV3 (GCA_964261345.1)
<p>The naked mole-rat (NMR; Heterocephalus glaber) is a eusocial subterranean rodent with a highly unusual set of physiological traits, such as extreme longevity, that has attracted great interest amongst the scientific community. However, the genetic basis of most of these traits has not been elucidated. To facilitate our understanding of the molecular mechanisms underlying NMR physiology and behaviour, we generated a long-read chromosomal-level genome assembly of the NMR. This genome, mHetGlaV2, was subsequently annotated and incorporated into a “91 eutherian mammals” multiple whole genome alignment in Ensembl. </p> <p>We identified intra-chromosomal misassemblies within mHetGlaV2. We fixed these misassemblies by comparing syntenic blocks between this assembly and the Canadian Porcupine (EreDor) genome assembly (https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_028451465.1/) and a FISH-Karyotype of the naked mole-rat completed by Romanenko et al., 2023 (PMID: 380307020) to address any misassemblies and place centromeres. Chromosome numbering was identified from a composite karyogram of karyotypes from over 350 cells. This scaffold-corrected assembly is labelled mHetGlaV3 (https://www.ebi.ac.uk/ena/browser/view/GCA_964261345.1).</p> <p>This repository stores the repeat, genome, and epigenome annotations for HetGlaV3.</p> <p>mHetGlaV3.primary.gtf.gz. Gene structures and gene symbols are transferred from ENSEMBL annotations of mHetGlaV2 using liftOff with default parameters. Additional gene symbols were identified using TOGA and manual curation.</p> <p>mHetGlaV3.primary.gtf.gz. Simple repetitive regions and transposable elements were annotated using EarlGrey (https://github.com/TobyBaril/EarlGrey) using "Rodentia" annotations for RepeatMasker.</p> <p>mHetGlaV3.primary.genesymbol_table.txt.txt.gz. A tab-delimited file where rows are gene IDs and columns are gene symbols generated with each method. "Consensus" shows the best matching gene symbol for each gene ID.</p> <p>mHetGlaV3.primary_annotated_blacklist.bed.gz. Provides an assembly "blacklist" for mHetGlaV3. This blacklist is a bed file annotating assembly breakpoints between HetGlaV2 and HetGlaV3. This blacklist contains additional columns (e.g., closest gene, overlapping TE etc.) and should therefore be filtered to the first column before being incorporated into traditional genomic pipelines.</p> <p>mHetGlaV3.primary_hypothalamus_ABC_enhancer.bedpe.gz. Activity-By-Contact enhancers (https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction) generated in the female subordinate naked mole-rat hypothalamus using Hi-C-seq, ChIP-seq of H3K27Ac data, ATAC-seq, and RNA-seq information.</p> <p>mHetGlaV3.primary_hypothalamus_chromHMM.bed.gz. Chromatin states (using Chromhmm) annotating the female subordinate naked mole-rat hypothalamus using H3K4me3 (promoter), H4K4me2 (promoter-enhancer), H3K27Ac (active enhancer), H3K36me3 (elongated), H3K27me3 (polycomb repressed), H3K9me3 (heterochromatin), and CTCF (whole brain) ChIP-seq data, as well as ATAC-seq and RNA-seq data.</p> <p>mHetGlaV3.primary.fa.gz. Genome assembly fasta file for the naked mole-rat (V3, primary assembly). This assembly matches the primary assembly stored on ENA, however the chromosome names match these files, rather than have chromosome names processed by ENA (e.g. chr 1 instead of "OZ179169.1 Heterocephalus glaber genome assembly, chromosome: 1").</p> <p> </p> <p>UPDATES:</p> <p>* The 1.2 update fixed unscaffolded contig names from those used in-lab to those compatible with ENA.</p> <p>* The 1.3 update added small (50~100kbp) contigs onto mHetGlaV3.primary.fa.gz that were filtered before the ENA submission.</p> <p>* The 1.4 update fixed a small chromosome naming inconsistency spotted in the 1.3 update.</p>
Understory plant community data from repeated plot sampling (1978-2019) in old-growth northern hardwood forest, northern Michigan (Dukes RNA, Hiawatha National Forest)
This data-set includes long-term, permanent-plot-based data for understory plant communities in old-growth mixed northern hardwood-hemlock forest and forested peatland in the Upper Great Lakes region. Data for over 900 understory quadrats (all associated with long-term canopy data from larger permanent plots) included multiple (2-5) remeasurements over 23-40 years, with longest periods and most remeasurements for upland forest types. The Dukes Research Natural Area (RNA) (https://www.fs.usda.gov/research/nrs/rnas/locations/dukes) in the Hiawatha National Forest (Marquette Co., MI) includes ca. 100 ha of largely unlogged, original forest. Publications cited below include more detailed information about the site. About half of the RNA supports upland forests intergrading from hemlock (Tsuga candensis) dominance to mixtures of hemlock and northern hardwoods species. Sugar maple (Acer saccharum) is dominant over much of the upland area, with, locally, significant admixtures of beech (Fagus grandifolia), yellow birch (Betula alleghaniensis), and red maple (Acer rubrum). Topographic relief is very slight with total elevational change within the RNA only about 10 m. The stand is within a few km of the western limit of the continuous range of beech. In 1935, 248 continuing forest inventory (CFI) plots (circular, 0.2 acre) were established on a regular grid throughout the RNA, and these have been the subject of repeated sampling through 2018-2019 and support continuing long-term study addressing canopy tree communities (canopy data to be deposited in a separate project). Examples of resulting publications are cited elsewhere in metadata, and can provide more detailed information about the RNA. In 1978-80, U.S. Forest Service researchers, directed by Jan Schultz and Frederick Metzger, initiated studies of understory communities, including herbaceous species and woody seedlings. Data were derived from four sub-quadrats within each of the CFI plots. These quadrats were re-estab
Repeated vegetation monitoring for riparian forest restoration project, Santa Clara River, CA, 2015-2023.
We implemented a spatially-patterned methodology to restore 87 ha of riparian forest habitat, selectively applying multiple restoration approaches based on localized differences in degradation severity throughout the project area. This work was conducted as part of a large, collaborative effort to control invasive Arundo donax and reestablish contiguous natural habitat throughout the Santa Clara River floodplain in southern California.
Repeated synoptic watershed chemistry from three watersheds near Toolik Field Station, Alaska, summer 2016-2018
Data file describing repeated sampling of chemistry of distributed river water from the Kuparuk River, Oksrukuyik Creek, and Trevor Creek watersheds near Toolik Field Station, North Slope of Alaska. Data file includes sampling date, season, sampling point, subcatchment area, and resulting concentrations for a suite of solutes.
CEE01 The Climate Extremes Experiment (CEE): Assessing ecosystem resistance and resilience to repeated climate extremes at Konza Prairie
Climate extremes, such as drought, are increasing in frequency and intensity, and the ecological consequences of these extreme events can be substantial and widespread. Yet, little is known about the factors that determine recovery (or resilience) of ecosystem function post-drought. Such knowledge is particularly important because post-drought recovery periods can be protracted depending on drought legacy effects (e.g., loss key plant populations, altered community structure and/or biogeochemical processes). These drought legacies may alter ecosystem function for many years post-drought and may impact future sensitivity (both resistance and resilience) to climate extremes. With forecasts of more frequent drought, there is an imperative to understand whether and how post-drought legacies will affect ecosystem response to future drought events. To address this knowledge gap, we experimentally imposed over an eight year period two extreme growing season droughts, each two years in duration followed by a two-year recovery period, in annually burned tallgrass prairie.
Transcriptome analysis of the effect of over-expressing H2A.J mutants in proliferating WI38 fibroblasts for the paper entitled: The H2A.J histone variant contributes to Interferon-Stimulated Gene expression in senescence by its weak interaction with H1 and the derepression of repeated DNA sequences
<p>Abstract for overall study:</p> <p>The histone variant H2A.J was previously shown to accumulate in senescent human fibroblasts with persistent DNA damage to promote inflammatory gene expression, but its mechanism of action was unknown. We show that H2A.J accumulation contributes to weakening the association of histone H1 to chromatin and increasing its turnover. Decreased H1 in senescence is correlated with increased expression of some repeated DNA sequences, increased expression of STAT/IRF transcription factors, and transcriptional activation of Interferon-Stimulated Genes (ISGs). The H2A.J-specific Val-11 moderates the transcriptional activity of H2A.J, and H2A.J-specific Ser-123 can be phosphorylated in response to DNA damage with potentiation of its transcriptional activity by the phospho-mimetic S123E mutation. Our work demonstrates the functional importance of H2A.J-specific residues and potential mechanisms for its function in promoting inflammatory gene expression in senescence.</p> <p>Specific description for this dataset:</p> <p>H2A.J differs from canonical H2A only by a valine at position 11 instead of alanine, and the 7 C-terminal amino acids containing a potential minimal phosphorylation site SQ for DNA-damage response kinases. To test the functional importance of these H2A.J-specific sequences, we mutated Val-11 to Ala as is found in all canonical H2A sequences, and we mutated Ser-123 to either Glu to mimic a phospho-serine residue or to Ala to prevent phosphorylation. We also substituted the C-terminus of H2A.J with the C-terminus of H2A. These mutants, WT-H2A.J and canonical H2A-type1 were ectopically expressed in proliferating fibroblasts, and their microarray transcriptomes were compared to that of proliferating and senescent fibroblasts without ectopic histone expression. Genome-wide transcriptome analysis indicated that senescent fibroblasts clustered distinctly from proliferating fibroblasts, and proliferating fibroblasts expressing the H2A.J-V11A and H2A.J-S123E mutants clustered distinctly from fibroblasts expressing the other H2A.J mutants, WT-H2A.J, and H2A. Hallmark gene set enrichment analysis of the transcriptomes of fibroblasts expressing H2A.J-V11A or H2A.J-S123E versus control proliferating fibroblasts indicated that they showed the same highly significant enrichment for the Epithelial-Mesenchyme Transition, TNF-Alpha Signaling Via NF-kB, and Inflammatory Response gene sets. Notable inflammatory genes including IL1A, IL1B, IL6, CXCL8, and CCL2 are contained in these gene sets and are often induced in senescence as part of the senescence-associated secretory phenotype. Heat maps showed that the H2A.J-V11A and H2A.J-S123E mutants were particularly apt at activating the expression of these inflammatory genes in proliferating fibroblasts</p>
Body measurements of human adults, with repeated readings
<p>This data file contains body measurements of participants of a course in morphometrics. The data are entirely anonymized and the compliance for publication of the data in the present form was obtained from each person.</p> <p>The participants were asked to measure themselves twice at intervals of one or two days, which resulted in reading a and reading b. The following measurements were taken (in mm):</p> <p>arm.l -> arm length<br> bod.h -> total body height<br> foo.l -> foot length<br> hea.c -> head circumference<br> leg.l -> leg length</p> <p>The dataset may be considered for demonstration of measurement error.</p>
Diffraction images of crystals of the first and second spectrin repeats (mutant C420A/C435A) of human plectin (PDB code 2ODV)
<p>Diffraction images of a native crystals of a fragment of human plectin that includes the first and second spectrin repeats (SR1-SR2) of the plakin domain. The two Cys in the wild type sequence were replaced by Ala.</p> <p>Images correspond to the dataset used to refine the pdb entry 2ODV (http://www.rcsb.org/pdb/explore/explore.do?structureId=2ODV).</p> <p> </p> <p>Data was collected at the BM14 beamline of the European Synchrotron Radiation Facility (ESRF, Grenoble, France) using radiation of 0.9785 Å wavelength and a Mar CCD detector. The dataset consists of 360 images (1 degree oscillation per image). Data extend to ~1.85 Å resolution.</p>
Diffraction images of a crystal of the spectrin repeats 7, 8, and 9 (SR7-SR9) of the plakin domain of human plectin (PDB code 5J1I)
<p>Diffraction images of crystals of a fragment of the plakin domain of human plectin that includes the spectrin repeats 7 to 9 (SR7-SR9).</p> <p>Images correspond to the dataset used to solve and refine the pdb entry 5J1I (http://www.rcsb.org/pdb/explore/explore.do?structureId=5J1I).</p> <p>Data were collected on a single crystal at the beamline 14.2 of the European Synchrotron Radiation Facility (ESRF, Grenoble, France) using radiation of 0.9330 Å wavelength and an ADSC Q4 CCD detector. The dataset consists of 360 images (1 degree oscillation per image).</p> <p>Diffraction data is highly anisotropic. Based on analysis with the STARANISO server (http://staraniso.globalphasing.org/) data extend approximately to 5.0, 3.8, and 2.6 Å resolution along the three principal directions of anisotropy, which are 0.555 a*+ 0.832 c*, b*, and -0.361 a* + 0.932 c*, respectively.</p>
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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.