Find research datasets worth reusing

opencc-by-4.0Apr 2023View details →

ALIMA range-corrected photon count profiles and spectral analysis output

The dataset includes a .nc file of range-corrected and background-corrected photon counts measured by ALIMA (Airborne Lidar for Middle Atmosphere research) from six research flights (ST08, ST09, ST10, ST11, ST12, ST14) during the SouthTRAC-GW campaign in September 2019. These corrected photons counts are proportional to the atmospheric density. The data resolution (t, z) is (10s, 100m) but not yet vertically smoothed nor temporally integrated. A vertical smoothing of 900 m and a temporal integration of 1 min is recommended to obtain a sufficient signal-to-noise-ratio. Furthermore, .nc files containing spectral power density (PSD) for selected legs of each research flight averaged over 10 km altitude ranges based on vertically smoothed and temporally integrated range- and background-corrected photon counts by ALIMA are included.

opencc-by-4.0May 2023View details →

TCGA RNA-Seq normalized rsem data, TCGA clinical data and mutational signature profiles

Normalized rsem RNA-Seq data for each of the 33 TCGA tumor types named as "tumortypernaSeq.tar", a file containing TCGA clinical data ("cliDat_tcga_18.tar") and a text file with single base substitution mutational signatures for each sample from COSMIC (https://cancer.sanger.ac.uk/cosmic, “signatureProfileSample.txt.zip”).

opencc-by-4.0May 2023View details →

Asphalt profile temperatures and weather data of CyPaTs test track

This dataset includes asphalt temperature measurements and weather data of CyPaTs test track located at Campus Groenenborger, University of Antwerp, Antwerp, Belgium. The recorded asphalt temperature measurements and weather data is between March 17th, 2021, and March 14th, 2022. There are five sheets in each excel file, containing asphalt temperatures at various depths (near-surface, 4cm, 7cm and 10 below asphalt surface), and corresponding weather data. The total number of data points is 371707, with each of these data points including information on weather parameters and 45 sensors embedded in different layers of the asphalt pavement. <ol> <li>Date (time): time of the recorded data</li> <li>TC_x-x: label of the temperature sensor embedded in asphalt pavement, in °C</li> <li>Ta: ambient air temperature, in °C</li> <li>RH: relative humidity, in %</li> <li>FF: wind speed, in m/s</li> <li>SR: solar radiation, in W/m2</li> </ol>

opencc-zeroMay 2023View details →

Functional profiling and evolutionary analysis of a marine microalgal virus pangenome

Phycodnaviridae are large double-stranded DNA viruses, which facilitate studies of host–virus interactions and co-evolution due to their prominence in algal infection and their role in the life cycle of algal blooms. However, the genomic interpretation of these viruses is hampered by a lack of functional information, stemming from the surprising number of hypothetical genes of unknown function. It is also unclear how many of these genes are widely shared within the clade. Using one of the most extensively characterized genera, Coccolithovirus, as a case study, we combined pangenome analysis, multiple functional annotation tools, AlphaFold structural modeling, and literature analysis to compare the core and accessory pangenome and assess support for novel functional predictions. We determined that the Coccolithovirus pangenome shares 30% of its genes with all 14 strains, making up the core. Notably, 34% of its genes were found in at most three strains. Core genes were enriched in early expression based on a transcriptomic dataset of Coccolithovirus EhV-201 algal infection, were more likely to be similar to host proteins than the non-core set, and were more likely to be involved in vital functions such as replication, recombination, and repair. In addition, we generated and collated annotations for the EhV representative EhV-86 from 12 different annotation sources, building up information for 142 previously hypothetical and putative membrane proteins. AlphaFold was further able to predict structures for 204 EhV-86 proteins with a modelling accuracy of good–high. These functional clues, combined with generated AlphaFold structures, provide a foundational framework for the future characterization of this model genus (and other giant viruses) and a further look into the evolution of the Coccolithovirus proteome.

opencc-by-4.0May 2023View details →

Turbulent dissipation rate and velocity spectrum at two radar wind profiler sites in North China

This dataset includes the monthly mean velocity spectrum width and turbulence dissipation rate from 0900 local standard time (LST)  to 1700 LST in 2021, which are retrieved from the radar wind profiler measurements at Baoding (urban) and Zhangbei (plateau) stations. Each data file is stored in xlsx format and contains two sheets, and each sheet is a two-dimensional data, including velocity spectrum width and turbulence dissipation rate. These two variables are stored in a matrix of 30 rows and 9 columns. The row refers to the height at an interval of 120 meters, and the columns refers to time which corresponds to 0900 to 1700 LST.

opencc-by-4.0Jun 2023View details →

TAN2006 TOPAS subbottom profiler dataset

Processed TOPAS subbottom profiler (SBP) dataset acquired during research voyage TAN2006 in 2020. Processing workflow <ol> <li>CRS (projected): EPSG:32760</li> <li>REPROJECT (bytes:73,77)</li> <li>STATIC CORRECTION:amp (byte:103) with SCALAR (byte:233) -> SEAFLOOR (byte:237) with SCALAR (byte:233)</li> <li>TIDE COMPENSATION</li> <li>MISTIE</li> <li>DESPIKE</li> </ol> SEG-Y file metadata EBCDIC Text Header Encoding Big Endian byte order # Traces                 : 3113 # Trace Samples     : 10000 Sample Format        : IEEE Float(32 bit) Sample Interval (uS) : 25 Time Length            : 249.975 ------------------------------------------ Header First trace Last trace SP          163374      166486 FFID        163374      166486

opencc-by-4.0Jun 2023View details →

Inferring phenotypes of single cells based on the expression profiles of phenotype-associated marker genes in bulks and single cells

The datasets analysed in the manuscript "Inferring phenotypes of single cells based on the expression profiles of phenotype-associated marker genes in bulks and single cells".

opencc-by-4.0Jun 2023View details →

Spectral data used in "Stratospheric-trace-gas-profile retrievals from balloon-borne limb imaging of mid-infrared emission spectra"

The calibrated spectral data used in the trace gas retrievals by the Limb Imaging Fourier Transform Spectrometer Experiment (LIFE).

opencc-zeroJun 2023View details →

Single-cell chromatin accessibility profiling reveals a self-renewing muscle satellite cell state

A balance between self-renewal and differentiation is critical for the regenerative capacity of tissue-resident stem cells. In skeletal muscle, successful regeneration requires the orchestrated activation, proliferation, and differentiation of muscle satellite cells (MuSCs) that are normally quiescent. A subset of MuSCs undergoes self-renewal to replenish the stem cell pool, but the features that identify and define self-renewing MuSCs remain to be elucidated. Here, through single-cell chromatin accessibility analysis, we reveal the self-renewal versus differentiation trajectories of MuSCs over the course of regeneration in vivo. We identify Betaglycan as a unique marker of self-renewing MuSCs that can be purified and efficiently contributes to regeneration after transplantation. We also show that SMAD4 and downstream genes are genetically required for self-renewal in vivo by restricting differentiation. Our study unveils the identity and mechanisms of self-renewing MuSCs while providing a key resource for comprehensive analysis of muscle regeneration.

opencc-zeroJun 2023View details →

Analysis of the proteomic profile in serum of irradiated nonhuman primates treated with Ex-Rad, a radiation medical countermeasure

There are currently four radiation medical countermeasures that have been approved by the United States Food and Drug Administration to mitigate hematopoietic acute radiation syndrome, all of which are repurposed radiomitigators. The evaluation of additional candidate drugs that may also be helpful for use during a radiological/nuclear emergency is ongoing. A chlorobenzyl sulfone derivative (organosulfur compound) known as Ex-Rad, or ON01210, is one such candidate medical countermeasure, being a novel, small-molecule kinase inhibitor that has demonstrated efficacy in the murine model. In this study, nonhuman primates exposed to ionizing radiation were subsequently administered Ex-Rad as two treatment schedules (Ex-Rad I administered 24 and 36 h post-irradiation, and Ex-Rad II administered 48 and 60 h post-irradiation) and the proteomic profiles of serum using a global molecular profiling approach were assessed. We observed that administration of Ex-Rad post-irradiation is capable of mitigating radiation-induced perturbations in protein abundance, particularly in restoring protein homeostasis and immune response and mitigating hematopoietic damage, at least in part after acute exposure. Taken together, restoration of functionally significant pathway perturbations may serve to protect damage to vital organs and provide long-term survival benefits to the afflicted population.

Dataset of ``Plasma Distribution Solver: A Model for Field-Aligned Plasma Profiles Based on Spatial Variation of Velocity Distribution Functions"

This dataset contains the plasma distribution data in the Jupiter–Io system, calculated from the Plasma Distribution Solver and used for figures in the paper “Plasma Distribution Solver: A model for field-aligned plasma profiles based on spatial variation of velocity distribution functions” by K. Saito et al. (2023).   The contents of files ‘all_Case_1.csv’ and ‘all_Case_2.csv’ are as follows: <ul> <li>Position along the magnetic field line (0 at the magnetic equator) [m] (column 1)</li> <li>Distance from the Jovian center [km] (column 2)</li> <li>Magnetic latitude [rad]([degree]) (column 3(4))</li> <li>Magnetic flux density [T] (column 5)</li> <li>The initial condition of electrostatic potential [V] (column 6)</li> <li>The result of electrostatic potential [V] (column 7)</li> <li>Number density profiles [m-3] (columns 8-17)</li> <li>Charge density profiles obtained from the integration of velocity distribution functions [C m-3] (column 18)</li> <li>Charge density profiles obtained from Poisson’s equation [C m-3] (column 19)</li> <li>Convergence value (column 20)</li> <li>Particle flux density [m-2 s-1] (columns 21-30)</li> <li>Mean flow velocity parallel to the field line [m s-1] (columns 31-40)</li> <li>Plasma pressure perpendicular to the field line [Pa] (columns 41-50)</li> <li>Plasma pressure parallel to the field line [Pa] (columns 51-60)</li> <li>Plasma dynamic pressure [Pa] (columns 61-70)</li> <li>Perpendicular temperature [J] (columns 71-80)</li> <li>Parallel temperature [J] (columns 81-90)</li> <li>Alfvén speed considering the displacement current term in Ampère’s law [m s-1] (column 91)</li> <li>Alfvén speed per the speed of light (column 92)</li> <li>Ion inertial length using averaged mass [m] (column 93)</li> <li>Electron inertial length [m] (column 94)</li> <li>Ion Larmor radius using averaged mass [m] (column 95)</li> <li>Ion acoustic gyroradius using averaged mass [m] (column 96)</li> <li>Electron Larmor radius [m] (column 97)</li> <li>Current density [A m-2] (column 98)</li> </ul> The Python codes ‘plot_all.py,’ ‘plot_plasma_beta_comparison.py,’ and ‘plot_Alfven_speed_comparison.py’ can plot Figures 5, 6, 7, and 9 of the paper using the above CSV files.   The files ‘boundary_conditions_Case_1.csv’ and ‘boundary_conditions_Case_2.csv’ contain the boundary conditions for Cases 1 and 2.   The zip files ‘probability_density_function_Case_1_H_Io.zip’ and ‘probability_density_function_Case_1_H_Jupiter_North.zip’ are zipped CSV files with the same name. The contents of these files are as follows: <ul> <li>Magnetic latitude [degree] (column 1)</li> <li>Perpendicular velocity at the particle position [m s-1] (column 2)</li> <li>Parallel velocity at the particle position [m s-1] (column 3)</li> <li>Perpendicular velocity at the boundary [m s-1] (column 4)</li> <li>Parallel velocity at the boundary [m s-1] (column 5)</li> <li>Probability density function [s3 m-3] (column 6)</li> <li>Differential flux per number density [cm-2 s-1 sr-1 keV-1] (column 7)</li> </ul> The Python code ‘plot_velocity_distribution_function.py’ can plot Figure 8 of the paper using this CSV file.

The AUX1-AFB1-CNGC14 module establishes a longitudinal root surface pH profile main figures

Raw microscopy data associated with the publication "The AUX1-AFB1-CNGC14 module establishes a longitudinal root surface pH profile" in elife journal. Main figures

Doppler lidar wind profiles from Rzecin during POLIMOS 2018

This is data set includes Doppler wind lidar quantities which were calculated from measurements performed between May and September 2018 at PolWET site in Rzecin, Poland (52.75°N, 16.30°E, 59 m a.s.l.) of the Poznan University of Life Sciences The system is a Doppler lidar Stream Line (Halo Photonics), which is part of ACTRIS-Cloudnet (Illingworth et al., 2007). The system laser emits at 1.5 μm and the detector is heterodyne using fiber-optic technology. The measurements for this data set consisted of  conical scans (VAD) with constant elevation of 70° and 12 equidistant azimuth points performed every 30 min. A more detailed description of the instrument can be found in (Ortiz-Amezcua et al., 2022)

Aluminum Billett 3D profile

The dataset is divided in two folders: calibration and case study. In calibration there are three folders: camera, translation and rotation. In camera there are the .btp files acquired to calibrate the camera. In translation, there are the images of the center of the line. Each picture  corresponds to an increase of 0.1 mm. The images are named after each increment. In rotation, there are the images of the laser line. Each picture corresponds to an incremental rotation of 2 degrees. The images are named after  each increment.  In case study there are two folders: straight and not straight. The straight folder contains the acquired data for a straight billet. The not straight folder contains the acquired data for a not straight billet. Each of these folders contain three folders: profiles, rotation and translation. Profiles contain the .csv file acquired by the laser profilometer. The sub folder cleaned profiles contains just the x and z coordinates of the acquisition.  Rotation, contains .btp images acquired with a higher exposure time: all the line is visible.  Translation, contains .btp images acquired with a lower exposure time: only the center of the line is visible. In each folder of case study, the files are named according to the position measured by the encoder of the motorized drive.

3D simulations of the Archean Earth including photochemical haze profiles [dataset]

Dataset of 3D simulations of the Archean Earth including photochemical haze profiles We present results from 3D simulations of the Archean Earth including a prescribed spherical haze generated through a 1D photochemical model. Our simulations suggest that a thin haze layer, formed when CH4/CO2 = 0.1, leads to global warming of ~10.6K due to the change of water vapour and cloud feedback, compared to the simulation without any haze. However, a thicker haze layer, formed when CH4/CO2 > 0.1, leads to global cooling of up to ~65K as the scattering and absorption of shortwave radiation from the haze reduces the radiation from reaching the planetary surface. A thermal inversion is formed with a lower tropopause as the CH4/CO2 ratio increases. The haze reaches an optical threshold thickness when CH4/CO2 ~ 0.175 beyond which the atmospheric structure and the global surface temperature do not vary much.   The IRIS python package developed by the Met Office is needed to analyse the data.

opencc-by-4.0Apr 2023View details →

Datasets for "Scalable, flexible carbon fiber electrode thread arrays for three-dimensional spatial profiling of neurochemical activity in deep brain structures of rodents"

Datasets used in the manuscript titled, "Scalable, flexible carbon fiber electrode thread arrays for three-dimensional spatial profiling of neurochemical activity in deep brain structures of rodents" are uploaded here.  Brightfield and fluorescent stained images of brain tissue used for Fig. 5(a): Malt3-20190624_Region 009_DAPI.png Malt3-20190624_Region 009_qCy5.png Malt3-20190624_Region 009_qFITC.png Malt3-20190624_Region 009_qTexasRed.png Malt3_BF20190628_Region 001.png Fluorescent image of brain with embedded CFETs: MALT2_Rat_100um_MOR1_x500_TSA_AF488.jpg Rat_100um_MOR1_x500_TSA.czi In vivo dopamine recording data for Fig. 3: ratarrays822_163.mat ratarrays822_57.mat

opencc-zeroJul 2023View details →

Data from: Sorghum bicolor TX08001 nodal root tissue development gene expression profiling

<div class="page"> <div class="section"> <div class="layoutArea"> <div class="column"> Bioenergy sorghum's large nodal root system enables deposition of soil organic carbon deep in soil profiles aiding production of low carbon intensity biofuels from this crop. During bioenergy sorghum's long growing season, plants produce ~175 nodal roots In review bearing lateral roots that take up water and nutrients from >2 m deep in soil profiles, and aerial roots that support a complex phyllosphere. In the current study, nodal root bud development, a slow process spanning ~40 days, was characterized using microscopy and transcriptome analysis. A first ring of 10-15 nodal root buds was initiated in the stem pulvinus of phytomer 7 near sub-epidermal vascular bundles. A second ring of buds formed above the first ring much later in phytomer development. Nascent nodal root buds from phytomer 7 exhibited relatively high expression of pericycle marker genes (PFA) and genes involved in auxin transport (ABCB19, PIN4, LAX2), cytokinin signaling (TSO, MYB3R1), and cell proliferation (CYCB2;4, CDKB2;1, REM1). Following initiation, expression of genes involved in cell proliferation and cytokinin-signaling decreased while expression of genes involved in proliferative arrest, ABA-signaling, dormancy and stress tolerance increased. Further bud development was correlated with increased expression of WOX11 and PLT5 followed by PLT2, PLT4 and genes encoding RGF peptides that regulate PLT-expression and bud development. Expression of the ARF7-regulated LBD29, a gene required for nodal root formation, increased in parallel with increasing bud size to a maximum late in NRB development. Appearance of the nodal root bud cap late in development coincided with expression of SMB and FEZ, whereas genes such as WOX5 and two MYB36 family members were expressed at higher levels in outgrowing aerial roots. Genes involved in gibberellin, brassinosteroid, strigolactone, ethylene, jasmonate, salicyclic acid, and eATP signaling showed complex patterns of expression during nodal root bud formation. Overall, this study provides a detailed description of bioenergy sorghum nodal root bud development and transcriptome information useful for molecular analysis of networks that regulate nodal root development. </div> </div> </div> </div>

Matrix Profile of Seismological Data Repository

The Computed Matrix Profile (MP) repository for seismic data. Please see below the archived manuscript of Shakibay Senobari et al., (Submitted to JGR, under review) for more information regarding the Matrix Profile and data set: essopenarchive.org/604953/p1vlDMs-5b0zsrs7C033Ug https://doi.org/10.1002/essoar.10512525.1

opencc-by-4.0Aug 2023View details →

Molecular profiling of sponge deflation reveals an ancient relaxant-inflammatory response

A hallmark of animals is the coordination of whole-body movement. Neurons and muscles are central to this, yet coordinated movements also exist in sponges that lack these cell types. Sponges are sessile animals with a complex canal system for filter-feeding. They undergo whole-body movements resembling “contractions'' that lead to canal closure and water expulsion. Here, we combine 3D optical coherence microscopy, pharmacology, and functional proteomics to elucidate anatomy, molecular physiology, and control of these movements. We show that they are driven by the relaxation of actomyosin stress fibers in epithelial canal cells, which leads to whole-body deflation via collapse of the incurrent and expansion of the excurrent system, controlled by an Akt/NO/PKG/A pathway. A concomitant increase in reactive oxygen species and secretion of proteinases and cytokines indicate an inflammation-like state reminiscent of vascular endothelial cells experiencing oscillatory shear stress. This suggests an ancient relaxant-inflammatory response of perturbed fluid-carrying systems in animals. File descriptions: <ul> <li>pharma_*.avi: Exemplary videos for pharmacological treatments of Spongilla lacustris, related to Fig. 2</li> <li>OCM_tomographic_scan: 2D scan through an unsegmented sponge body. First a x-z scan, afterwards a x-y scan. </li> <li>ink_treatment_suppl_figS3.mov: Video of ink treated Spongilla lacustris specimen, related to Fig. S3</li> <li>S_lacustris_annotations_emapper: EggNOG mapper (v2.1.9) results used for GO term enrichment analysis</li> <li>S_lacustris_proteome: Proteome file used as database for proteomic searches</li> <li>S_lacustris_scRNAseq.h5ad: file containing scRNAseq and cell type information of Spongilla lacustris. </li> <li>Suppl_file_*.xlsx: Tables of proteomics (TPP, phophoproteomics, secretomics) results</li> </ul>