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1,179 results for “Probe”
Van Allen Probes Occurrence Rates of Electromagnetic Ion Cyclotron (EMIC) Waves with Rising Tones
<p>CSV files with the values for the occurrence rates of electromagnetic ion cyclotron (EMIC) waves with rising tones observed by the Van Allen Probes from 2012-09-07 to 2016-07-01 from the paper</p><p>Sigsbee, K., Kletzing, C. A., Faden, J., & Smith, C. W. (2023). Occurrence rates of electromagnetic ion cyclotron (EMIC) waves with rising tones in the Van Allen Probes data set. Journal of Geophysical Research: Space Physics, 128, e2022JA030548. https://doi.org/10.1029/2022JA030548 </p><p>The below files contain the values from Figures 5 and 6. The first row of each file gives the lower value of each L shell bin (0.0, 0.5, 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0, 4.5, 5.5, 6.0, 7.0, 7.5). The first column of each file gives the magnetic local time (MLT) values (0-23) for each bin. </p><p>rbspab_lshellmlt_minutes_20120907_to_20160701.csv gives the number of minutes spent by the Van Allen Probes in each bin of L shell and MLT.</p><p>rbspab_emic_lshellmlt_pcnt_20120907_to_20160701.csv gives the percentage of minutes all EMIC waves were observed in each bin of L shell and MLT.</p><p>rbspab_h_lshellmlt_pcnt_20120907_to_20160701.csv gives the percentage of minutes H+ band EMIC waves were observed in each bin of L shell and MLT.</p><p>rbspab_hr_lshellmlt_pcnt_20120907_to_20160701.csv gives the percentage of minutes H+ band EMIC waves with rising tones were observed in each bin of L shell and MLT.</p><p>rbspab_he_lshellmlt_pcnt_20120907_to_20160701.csv gives the percentage of minutes He+ band EMIC waves were observed in each bin of L shell and MLT.</p><p>rbspab_her_lshellmlt_pcnt_20120907_to_20160701.csv gives the percentage of minutes He+ band EMIC waves with rising tones were observed in each bin of L shell and MLT.</p><p>rbspab_o_lshellmlt_pcnt_20120907_to_20160701.csv gives the percentage of minutes O+ band EMIC waves with rising tones were observed in each bin of L shell and MLT.</p><p>The below files contain the values from Figures 7-13. The first row of each file gives the lower value of each bin of the radial distance RXY in the XY SM plane (0.0, 0.5, 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0, 4.5, 5.5, 6.0, 7.0, 7.5) in Earth radii (RE). The first column of each file gives the lower value of each bin of Z SM in RE (-2.0, -1.75, -1.5, -1.25, -1.0, 0.0, 1.0, 1.25, 1.50, 1.75). Separate files are provided for four MLT sectors: midnight (21 MLT to 3 MLT), dawn (3 MLT to 9 MLT), noon (9 MLT to 15 MLT), and dusk (15 MLT to 21 MLT).</p><p>Number of minutes spent by the Van Allen Probes in bins of RXY and Z SM (Figure 7):</p><p>rbspab_rxyzsm_minutes_midnight_20120907_to_20160701.csv, rbspab_rxyzsm_minutes_dawn_20120907_to_20160701.csv, rbspab_rxyzsm_minutes_noon_20120907_to_20160701.csv, rbspab_rxyzsm_minutes_dusk_20120907_to_20160701.csv </p><p>Percentage of minutes all EMIC waves were observed in bins of RXY and Z SM (Figure 8):</p><p>rbspab_emic_rxyzsm_pcnt_midnight_20120907_to_20160701.csv, rbspab_emic_rxyzsm_pcnt_dawn_20120907_to_20160701.csv, rbspab_emic_rxyzsm_pcnt_noon_20120907_to_20160701.csv, rbspab_emic_rxyzsm_pcnt_dusk_20120907_to_20160701.csv </p><p>Percentage of minutes H+ band EMIC waves were observed in bins of RXY and Z SM (Figure 9):</p><p>rbspab_h_rxyzsm_pcnt_midnight_20120907_to_20160701.csv, rbspab_h_rxyzsm_pcnt_dawn_20120907_to_20160701.csv, rbspab_h_rxyzsm_pcnt_noon_20120907_to_20160701.csv, rbspab_h_rxyzsm_pcnt_dusk_20120907_to_20160701.csv </p><p>Percentage of minutes He+ band EMIC waves were observed in bins of RXY and Z SM (Figure 10):</p><p>rbspab_he_rxyzsm_pcnt_midnight_20120907_to_20160701.csv, rbspab_he_rxyzsm_pcnt_dawn_20120907_to_20160701.csv, rbspab_he_rxyzsm_pcnt_noon_20120907_to_20160701.csv, rbspab_he_rxyzsm_pcnt_dusk_20120907_to_20160701.csv </p><p>Percentage of minutes O+ band EMIC waves were observed in bins of RXY and Z SM (Figure 11):</p><p>rbspab_o_rxyzsm_pcnt_midnight_20120907_to_20160701.csv, rbspab_o_rxyzsm_pcnt_dawn_20120907_to_20160701.csv, rbspab_o_rxyzsm_pcnt_noon_20120907_to_20160701.csv, rbspab_o_rxyzsm_pcnt_dusk_20120907_to_20160701.csv </p><p>Percentage of minutes H+ band EMIC waves with rising tones were observed in bins of RXY and Z SM (Figure 12):</p><p>rbspab_hr_rxyzsm_pcnt_midnight_20120907_to_20160701.csv, rbspab_hr_rxyzsm_pcnt_dawn_20120907_to_20160701.csv, rbspab_hr_rxyzsm_pcnt_noon_20120907_to_20160701.csv, rbspab_hr_rxyzsm_pcnt_dusk_20120907_to_20160701.csv </p><p>Percentage of minutes He+ band EMIC waves with rising tones were observed in bins of RXY and Z SM (Figure 13):</p><p>rbspab_her_rxyzsm_pcnt_midnight_20120907_to_20160701.csv, rbspab_her_rxyzsm_pcnt_dawn_20120907_to_20160701.csv, rbspab_her_rxyzsm_pcnt_noon_20120907_to_20160701.csv, rbspab_her_rxyzsm_pcnt_dusk_20120907_to_20160701.csv </p>
Dataset for: Stereorandomization as a Method to Probe Peptide Bioactivity
<p>The upload contains additional primary data associated with the publication, including raw data in the original file format whenever possible.</p> <p>Data content: HRMS, HPLC-MS, CD, MD, TEM, Serum stability, Vesicle leakage assay, Cytotoxicity, Hemolysis.</p>
PROBE iEEG
Open the record for dataset details and reuse information.
Data From: Exploring Gelatin-A and Mouse Proline-Rich Protein 5 as Probes for Wine Polyphenols analysis by Quartz Crystal Microbalance with Dissipation Monitoring
<p>Polyphenols are essential in winemaking, affecting the wine's quality, color, astringency, bitterness, and chemical stability. Conventional methods for assessing polyphenolic content are both expensive and time-intensive, underscoring the need for new, efficient techniques.</p> <p>The Quartz Crystal Microbalance with Dissipation Monitoring (QCM-D) sensor is recognized for its speed and reliability as a label-free detection tool. This study applies QCM-D to evaluate Gelatin Type A (Gel-A) from porcine skin and Mouse Proline-Rich Protein 5 (MP5) for polyphenol analysis in red wines without pre-treatment. MP5 notably exhibited a linear dissipation signal response with both total polyphenol and hydroxybenzoic acid concentrations. These findings highlight the potential for creating a stand-alone sensor platform for real-time polyphenol monitoring in winemaking.</p>
Data for: The thermo-optical coefficient as an alternative probe for the structural arrest of polymeric glass formers
<p>The data is supplementary to the publication "The thermo-optical coefficient as an alternative probe for the structural arrest of polymeric glass formers", DOI: <a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.polymer.2024.126868" target="_blank" rel="noreferrer noopener">10.1016/j.polymer.2024.126868</a>, and contains processed raw data.</p> <p>Key words: Temperature-modulated optical refractometry, Solidification, Glass transition temperature, Thermo-optical coefficient, Structural arrest</p> <p>The data sets contain measured data on Temperature-modulated optical refractometry (TMOR) of a model epoxy polymer from the viscoelastic temperature range, through the glass transition to the glassy state. The data sets were collected via the temperature-jump method.</p> <p>Material details:</p> <ul> <li>Bisphenol A Diglycidyl ether (DGEBA, DER332, CAS 1675-54-3) + Difunctional and trifunctional carbocylic acids (Pripol1040, Croda) +1,5,7-triazabicyclo[4.4.0]dec-5-en (TBD, CAS 5807-14-7, 10 mol-% relative to carboxylic acid functions)</li> </ul> <p>Funding received from:</p> <ul> <li>German Research Foundation (DFG), project number: 521902629</li> </ul>
Confocal Microscopy Visualizes Particle-Crack Interactions in Epoxy Composites with Optical Force Probe-Crosslinked Rubber Particles
<p>Data (*.csv and *.lif) corresponding to Figures 2-7 of the manuscript and Figures S1-S2 of the Supporting Information.</p>
Data to the journal article "The capping agent is the key: Structural alterations of Ag NPs during CO2 electrolysis probed in a zero-gap gas-flow configuration"
<p>This data set corresponds to the journal article "The capping agent is the key: Structural alterations of Ag NPs during CO2 electrolysis probed in a zero-gap gas-flow configuration"</p>
Experimental layout of pump-repump-probe on ELYSE platform
<p>This scheme represents the experimental layout designated for conducting electron pulse broad supercontinuum probe and pulse-repump-probe spectroscopy on linear electron accelerator ELYSE. </p>
Probing center vortices and deconfinement in SU(2) lattice gauge theory with persistent homology — data release
<p>This release contains all data used to prepare the publication <a href="https://arxiv.org/abs/2207.13392">Probing center vortices and deconfinement in SU(2) lattice gauge theory with persistent homology</a>.</p> <p>Included are:</p> <ul> <li>The raw log output from the simulations and computed persistence images for the analysis in Section IV.B of the <a href="https://arxiv.org/abs/2207.13392">paper</a> in 'raw_data.zip'.</li> <li>The values of the action and Polyakov loop from the above logs, along with the persistence images restructured into netCDF4 format for convenience, in the files 'Nt=*_Ns=*_pis_actions_polyakovs.nc'.</li> <li>The values of the observable m_2 (as defined in the <a href="https://arxiv.org/abs/2207.13392">paper</a>) for configurations for the twisted boundary conditions analysis in netCDF4 format in 'Nt=4_Ns=12_16_20_m2.nc'.</li> <li>The example persistence diagrams used in the <a href="https://arxiv.org/abs/2207.13392">paper</a> in netCDF4 format in 'Nt=4_Ns=12_example_pds.nc'.</li> </ul>
Parker Solar Probe Filtered Ion Scale Wave Activity for Encounters 8 to 16
<p>The following datasets are the result of filtering algorithm applied to a wave analysis of Parker Solar Probe data from Encounters 8 to 16. The wave analysis was conducted by Kristoff Paulson using a Short-Time Fourier Transform (STFT) approach based on polarization techniques derived by Means, 1972 (DOI: <a href="http://doi.org/10.1029/JA077i028p05551">10.1029/JA077i028p055511135</a>). Included is a jupyter notebook containing the filtering algorithm, the results of the filtering, and a demonstration of how to best open the files. The dataset for each encounter contains 9 columns that correspond with:</p> <ol> <li>Date in CDF epoch</li> <li>Left-handed (LH) Integrated Wave Power (nT^2) where integration is over frequency space (0-32 Hz) of filtered activity</li> <li>Right-handed (RH) Integrated Wave Power (nT^2)</li> <li>LH median ellipticity where median is over frequency space</li> <li>RH median ellipticity</li> <li>LH median coherency</li> <li>RH median coherency</li> <li>LH median wave normal angle (deg)</li> <li>RH median wave normal angle (deg)</li> </ol> <p>In all cases, ellipticity is measured in the Parker Solar Probe spacecraft frame. Ellipticity measures the ellipticity of the polarization ellipse and takes on values between -1 and 1. Values of 1 correspond with RH circular polarization and -1 with LH circular polarization. Coherency takes on values between 0 and 1. It measures how interrelated fluctuations are where 0 represents noise and 1 represents coherent fluctuations. The wave normal angle is the angle between the wave vector, k, and the local mean magnetic field, B. Since there are inherent ambiguities in the direction of the wave vector for single spacecraft measurements, the wave normal angle is calculated such that it takes on angles from 0 to 90 degrees. The filtering algorithm selects activity in which coherency is above 0.8, absolute value of ellipticity is above 0.5, and wave normal angle is below 45 degrees such that coherent, circularly polarized, near parallel propagating wave activity on ion scales is selected. <strong>If wave power for a given time has value of 0.0, then no fluctuations in the magnetic field data passed the required filters at that time.</strong></p> <p>:</p>
Seeing nanoscale electrocatalytic reactions at individual MoS2 particles under an optical microscope: probing sub-mM oxygen reduction reaction
<p><span>Data in this repository include raw iSCAT optical microscopy movies for the operando monitoring of oxygen reduction reaction at bare ITO and MoS2-coated ITO electrodes in KCl solution in the presence or absence of La<sup>3+</sup> with their respective electrochemical data (voltammograms). </span></p>
Two-probe macaque monkey auditory LFP
<p>Dataset accompanying paper Klein, N., Siegle, J.H., Teichert, T., Kass, R.E. (2021) "Cross-population coupling of neural activity based on Gaussian process current source densities". </p> <p>Auditory local field potential (LFP) recordings and evoked multi-unit activity (MUA) from two 24-electrode linear probes (V-Probes from Plexon) inserted in primary auditory cortex of a macaque monkey. The probes were arranged parallel to the iso-frequency bands in primary auditory cortex (A1), and had similar tonal response fields with preferred frequencies close to 1000 Hz. The first probe (which we call the lateral probe) was located centrally in A1, while the second probe (which we call the medial probe) was located more medially and closer to the boundary of A1 with the medio-lateral belt. The medial probe had lower response threshold, shorter MUA latencies, and overall stronger current sinks and sources than the lateral probe. The spacing between electrodes on each probe was 100 microns so that the probe spanned 2,300 microns. The treatment of the animals was in accordance with the guidelines set by the U.S. Department of Health and Human Services (NIH) for the care and use of laboratory animals, and all methods were approved by the Institutional Animal Care and Use Committee at the University of Pittsburgh.</p> <p>See README.txt for precise description of data files.</p>
Atom probe tomography nomad-FAIR demonstrator dataset R76-23219-v01.epos.apth5
<p>This is the dataset of an atom probe tomography experiment which is provided open source for testing the possibility of implementing an open source encyclopedia for experimental materials science datasets, including techniques to begin with such as Scanning Transmission Electron Microscopy (STEM), Multidimensional Photo Emission Spectroscopy (MPES), and Atom Probe Tomography (APT) / Field Ion Microscopy (FIM).</p> <p><strong>This repository serves three aims:</strong></p> <p>1. The dataset is of scientific interest. Specifically, it captures the result of a cutting-edge APT experiment detailed exemplarily in DOI: 10.1038/s41467-018-03115-0 (Fig. 6a "Se+Na2Se treatment") by Torsten Schwarz and coworkers.</p> <p>2. The dataset contributes to tests of an extension to "The NOMAD Laboratory" (https://nomad-coe.eu/): nomad-FAIR. Specifically, to test various aspects of an automatized metadata parsing and processing pipeline to enable the extraction of domain-specific JSON metadata files into a NOMAD-conformant JSON file, ultimately aiming for searchable and repurposable dataset documentation. This serves two purposes: on the one hand to contextualize each dataset within NOMAD. On the other hand to serve as a starting point to parse potential interesting content from the heavy data HDF5 file to reduce unnecessary file access.<br> The implementation of nomad-FAIR is coordinated by Markus Scheidgen.<br> The APT domain-specific parser is developed by Markus Kühbach.</p> <p>3. The dataset constitutes further a test of an open format specification for storing atom probe tomography data using the Hierarchical Data Format (HDF5). This is a recent initiative of the International Field Emission Society's (IFES) atom probe tomography technical committee. In this repository it is detailed an exemplar proposal of how to store acquisition-side relevant results and context of an APT experiment into a HDF5 file and complementary metadata files such as JSON. Implementation of this HDF5-based storage solution for APT data is lead by Markus Kühbach.</p> <p><br> <strong>The organization of this repository with respect to above aims is as follows:</strong></p> <p>-The original EPOS file of the measured is contained in the compressed *.epos.tar.gz archive.</p> <p>-The *.apth5 file is a transcoded version of the EPOS file. Therein, x,y,z data columns are stripped.</p> <p>-The correspondingly named *.json file is the file which nomad-FAIR parses metadata from.</p> <p>-Other files constitute logs of the transcoding process.</p> <p><br> <strong>Funding:</strong><br> The work was partially supported by BiGmax, the Max Planck Society's Research Network on Big-Data-Driven Materials-Science.</p>
Probing Aqueous Ions with Non-local Auger Relaxation - data
<p>Data set pertaining to the article "Probing aqueous ions with non-local Auger relaxation" | Physical Chemistry Chemical Physics, <strong>24</strong>, 8661-8671 (2022). doi: <a href="http://dx.doi.org/10.1039/D2CP00227B">10.1039/D2CP00227B</a>.</p> <p>Files with extension .h5 are hdf5-files structured according to the NeXus standard v2022.06, see<br> https://www.nexusformat.org/<br> https://fairmat-experimental.github.io/nexus-fairmat-proposal/50433d9039b3f33299bab338998acb5335cd8951/mpes-structure.html<br> NeXus data files can be opened with any software capable of opening hdf5-files. The following viewers are adapted to the specifics of the NeXus data format:<br> * nexpy (distributed with python)<br> * https://h5web.panosc.eu/h5wasm (web-based NeXus viewer maintained by the European Photon and Neutron Open Science Cloud-consortium)</p> <p>In each NeXus file-entry, two types of spectra are shown:<br> 1. Sweep-averaged spectra integrated over the non-dispersive coordinate of our detector ('data').<br> 2. As-measured data ('raw').</p> <p><br> The following files are provided:</p> <p>Photoemission data pertaining to ICD measurements, and to 1s spectra shown in Supplementary Fig. S2 (Na, Al):<br> ICD_data.na.h5<br> ICD_data.mg.h5<br> ICD_data.al.h5<br> Photon energy corrections are applied as explained in the article and Supplementary Material, kinetic energy correction is applied to the dataset 'data'.</p> <p>Calibration data:<br> calibration_data.p04.h5 : Mostly photon energy calibration for ICD spectra.<br> calibration_data.bessy.mg.h5 : Spectra measured at BESSY for MgCl2 Mg 1s binding energy calibration.<br> calibration_data.bessy.al.h5 : Spectra measured at BESSY for AlCl3 Al 1s binding energy calibration.<br> calibration_data.p04.add.h5 : Additional spectra for cross-checking binding energy calibration, measured at DESY P04.<br> All calibration spectra are included as-measured. A binding energy axis, shown for some spectra, is derived as implied from the uncalibrated photon and kinetic energies.</p> <p> </p> <p>Contact: Uwe Hergenhahn, uhe@fhi.mpg.de .</p> <p>v2 release notes<br> A number of minor errors in the metadata and .hdf5-structure of the v1 dataset were corrected. The data themselves are unaffected.<br> * Names of NXdata-groups now agree to NXmpes naming-convention,<br> * incorrect value of photon energy correction of Al ICD data fixed (ICD_data.al.h5),<br> * proposal numbers added to metadata,<br> * measurements on pure water solution designated as calibration.</p>
Empirical laws of plasmapause and plasmasphere outer edge location from the Van Allen Probes
<p>This webpage provides access to empirical laws of the plasmapause position and the dense outer edge of the plasasphere position (i.e. location of the 100 #/cc electron density) established from spacecraft charging of the Van Allen Probes (RBSP), using data from Probe B from 26 September 2012 to 16 July 2019. These empirical laws are published of the following article:</p> <p>Ripoll, J.-F., Thaller, S. A., Hartley, D. P., Cunningham, G. S., Pierrard, V., Kurth, W. S., et al. (2022). Statistics and empirical models of the plasmasphere boundaries from the Van Allen Probes for radiation belt physics. Geophysical Research Letters, 49, e2022GL101402. https://doi.org/10.1029/2022GL101402.</p> <p>Please refer to the article and this link if you make any use of the data.</p> <p>We first deliver 3 files which contain the plasmapause position versus a given geomagnetic index, either Kp, AE, or Dst. These data files are MLT-averaged. The filename is Lpp_v_XX_stats_1.txt with XX the index name. </p> <p>We then deliver 3 files which contains the plasmapause position versus a geomagnetic starred index (i.e. a max taken during the last 24 hours for Kp and AE and a min for Dst), either Kp*, AE*, or Dst* for 4 MLT sectors written successively in each file and then for all sectors averaged together. These data files are MLT-dependent for the 4 first blocks and then MLT-averaged in the fifth block. The filename is Lpp_v_XX_star_MLT_stats_2-1.txt with XX the starred index name. </p> <p>The MLT range is given in the last two columns. When the plasmapause location is undetermined (i.e. Lpp = 0 or no value), there is no MLT, so that in the file we just have the total number of points (all real) and not the three values of total, number of real, number of Nans.</p> <p>Similarly, we deliver 3 files which contains the plasmapause position versus a geomagnetic non starred index, either Kp, AE, or Dst for 4 MLT sectors written successively in each file. Filenames have the form "Lpp_v_XX_MLT_stats_1.txt" with XX the name of the index. Figures associated to this data were not given in the article and have been added here with a filename of the form Lpp_by_mlt_XX.pdf with XX the name of the index.</p> <p>Finally, the zip file "RBSP-A Figures and Laws" contains Figures (same format as each figure of Figure 4 in the article) and empirical laws (same format as above) for RBSP-A data (10/2012-04/2016). Being more limited in time, we rather recommend to use RBSP B data. They are provided to confirm both RBSP A and B data agree when statistics are converged.</p>
Performance Data of an Ice-Melting Probe from Field Tests in two Different Ice Environments
<p>This dataset was acquired at field tests of the steerable ice-melting probe "EnEx-IceMole" (Dachwald et al., 2014). A field test in summer 2014 was used to test the melting probe's system, before the probe was shipped to Antarctica, where, in international cooperation with the MIDGE project, the objective of a sampling mission in the southern hemisphere summer 2014/2015 was to return a clean englacial sample from the subglacial brine reservoir supplying the Blood Falls at Taylor Glacier (Badgeley et al., 2017, German et al., 2021).</p> <p>The standardized log-files generated by the IceMole during melting operation include more than 100 operational parameters, housekeeping information, and error states, which are reported to the base station in intervals of 4 s. Occasional packet loss in data transmission resulted in a sparse number of increased sampling intervals, which where compensated for by linear interpolation during post processing. The presented dataset is based on a subset of this data: The penetration distance is calculated based on the ice screw drive encoder signal, providing the rate of rotation, and the screw's thread pitch. The melting speed is calculated from the same data, assuming the rate of rotation to be constant over one sampling interval. The contact force is calculated from the longitudinal screw force, which es measured by strain gauges. The used heating power is calculated from binary states of all heating elements, which can only be either switched on or off. Temperatures are measured at each heating element and averaged for three zones (melting head, side-wall heaters and back-plate heaters).</p>
Supplementary Materials for "Exploration of User Privacy in 802.11 Probe Requests with MAC Address Randomization Using Temporal Pattern Analysis"
<p>Supplementary Materials for "Exploration of User Privacy in 802.11 Probe Requests with MAC Address Randomization Using Temporal Pattern Analysis"</p> <p>This package contains an anonymized packets of 802.11 probe requests captured in in December 2021 at Universitat Jaume I . The packet capture file is in the standardized *.pcap binary format and can be opened with any packet analysis tool such as Wireshark or scapy (Python packet analysis and manipulation package).</p>
ASM01 Soil water content measured by neutron probe at Konza Prairie
Data set contains measurements of soil moisture (%volume) at various depths (25-200 cm) in deep (lowland) soils collected on LTER grazed and ungrazed watersheds burned at 1-, 4-, and 20-year intervals. Soil moisture measured by the neutron probe method.
Crossreactive probes on Illumina DNA methylation arrays: a large study on ALS shows that a cautionary approach is warranted in interpreting epigenome-wide association studies
<p>Data corresponding to the paper "Crossreactive probes on Illumina DNA methylation arrays: a large study on ALS shows that a cautionary approach is warranted in interpreting epigenome-wide association studies."<br> <br> Corresponding scripts can be found at: <a href="https://github.com/pjhop/dnamarray_crossreactivity">https://github.com/pjhop/dnamarray_crossreactivity</a><br> All downstream analyses in <a href="https://github.com/pjhop/dnamarray_crossreactivity/blob/master/analysis/c9_analysis.Rmd">c9_analysis.Rmd</a> and in<a href="https://github.com/pjhop/dnamarray_crossreactivity/blob/master/analysis/supplementary_note.Rmd"> supplementary_note.Rmd</a> can be reproduced using the deposited data as follows:</p> <ul> <li>Clone the dnamarray_crossreactivity repository: < git clone https://github.com/pjhop/dnamarray_crossreactivity.git ></li> <li>Download the data ('data.zip') and place it in the 'dnamarray_crossreactivity' folder.</li> <li>Unzip the data.zip folder</li> </ul> <p>Scripts used to generate the data in each subdirectory can be found at:</p> <ul> <li>data/processed/c9_matches/: <a href="https://github.com/pjhop/dnamarray_crossreactivity/tree/master/analysis/c9_matches">https://github.com/pjhop/dnamarray_crossreactivity/tree/master/analysis/c9_matches</a></li> <li>data/output/ewas/: <a href="https://github.com/pjhop/dnamarray_crossreactivity/tree/master/analysis/ewas">https://github.com/pjhop/dnamarray_crossreactivity/tree/master/analysis/ewas</a></li> <li>data/output/figs/: empty folder, running 'c9_analysis.Rmd' will save figures here.</li> <li>data/misc/: <a href="https://github.com/pjhop/dnamarray_crossreactivity/tree/master/analysis/other">https://github.com/pjhop/dnamarray_crossreactivity/tree/master/analysis/other</a></li> <li>data/extdata: <ul> <li>Zhou <em>et al.</em> annotations (EPIC.hg19.manifest.tsv.gz, HM450.hg19.manifest.pop.tsv.gz, HM450.hg19.manifest.tsv.gz) were downloaded from: <a href="https://zwdzwd.github.io/InfiniumAnnotation">https://zwdzwd.github.io/InfiniumAnnotation</a> (downloaded at 17/09/2020)</li> <li>Naeem <em>et al.</em><em> </em>data (12864_2013_7006_MOESM2_ESM.csv) was downloaded from: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3943510/">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3943510/</a></li> <li>Chen <em>et al.</em> data (48639-non-specific-probes-Illumina450k.xlsx) was downloaded from <a href="https://github.com/Jfortin1/funnorm_repro/blob/master/bad_probes/48639-non-specific-probes-Illumina450k.xlsx">https://github.com/Jfortin1/funnorm_repro/blob/master/bad_probes/48639-non-specific-probes-Illumina450k.xlsx</a></li> <li>The anno_450k.txt.gz and anno_EPIC.txt.gz are subsets of the annotation files included in the following package respectively: <a href="https://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylation450kanno.ilmn12.hg19.html">https://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylation450kanno.ilmn12.hg19.html</a> and <a href="https://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylationEPICanno.ilm10b2.hg19.html">https://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylationEPICanno.ilm10b2.hg19.html</a></li> </ul> </li> <li> data/genome_bs: Scripts used to generate these data can be found at <a href="https://github.com/pjhop/DNAmCrosshyb/blob/master/data-raw/bisulfite_convert_hg19.R">https://github.com/pjhop/DNAmCrosshyb/blob/master/data-raw/bisulfite_convert_hg19.R</a> and <a href="https://github.com/pjhop/DNAmCrosshyb/blob/master/data-raw/bisulfite_convert_hg38.R">https://github.com/pjhop/DNAmCrosshyb/blob/master/data-raw/bisulfite_convert_hg38.R</a> .</li> <li> data/raw: Individual-level data is available upon access at: <a href="https://ega-archive.org/studies/EGAS00001004587">https://ega-archive.org/studies/EGAS00001004587</a></li> </ul>
Oligonucleotide probes used for comparative mapping in lupin species
<p>The supplementary list of oligonucleotide probes generated in Chorus software. Filtered probes were used in oligo-FISH comparative mapping of lupin species. Detailed description provided in the article: 'The puzzling fate of a lupin chromosome revealed by reciprocal oligo-FISH and BAC-FISH mapping'.</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.