Find research datasets worth reusing

opencc-by-4.0Jul 2023View details →

Called peaks for 8 D. melanogaster functional genomics data sets

Analyses were performed on chromatin accessibility (ATAC-seq, DNase-seq, FAIRE-seq), histone modification ChIP-seq (H3K4me1, H3K4me3, and H3K27ac), and direct enhancer activity reporter via an ectopic plasmid based assay (STARR-seq) data sets generated from experiments in D. melanogaster. The ATAC-seq and FAIRE-seq data sets were generated using wandering third instar larvae eye antennal imaginal disc tissue extracted from the FRT82 stock (Davie et al., 2015), while all other data sets were generated from Drosophila melanogaster S2 cells (Arnold et al., 2013; Henriques et al., 2018; de Almeida et al., 2022). Sequencing reads were downloaded from the NIH SRA, cleaned and trimmed using Trimmomatic v0.39 (Bolger et al., 2014), and aligned to the D. melanogaster r6.45 genome (Hoskins et al., 2015) using BWA (bwa aln, default settings) v0.7.17-r1188 (Li and Durbin, 2009). The D. melanogaster genome was downloaded from Fly Base (Gramates et al., 2022). Aligned reads were filtered for mapping quality (-q 10 -F 0x0200 -F 0x0100 -F 0x004) using SAMTools v1.11 (using htslib v1.11-4) (Li et al., 2009). Peaks were called using MACS2 v 2.2.7.1 (Zhang et al., 2008) with FDR correction (-q 0.01) and the preset D. melanogaster genome size (-g dm). The data sets varied in terms of read lengths, single-end or paired-end, and the availability of control data, so parameters were adjusted appropriately. MACS peak calling parameters for ATAC-seq and FAIRE-seq data were taken from Davie et al. (2015).

dryad36/100

Data for: Russian honey bee genotype identification through enhanced marker panel set

Russian honey bees (RHB) are a breeding population developed by USDA-ARS as an effort to provide Varroa-resistant honey bees to beekeepers. The selection strategy for this breeding population was the first in honey bees to incorporate genetic stock identification (GSI). The original GSI approach has been in use for over a decade, and though effective, novel technologies and analytical approaches recently developed provide an opportunity for improvement. Here we outline a novel genotyping assay that capitalizes on the markers used in the GSI as well as novel loci recently identified in a whole genome pooled study of commercial honey bee stocks. Our approach utilizes a microfluidic platform and machine learning analyses to arrive at an accurate, high throughput assay. This novel approach provides an improved tool that can be readily incorporated into breeding decisions towards healthier more productive bees.

opencc-zeroJul 2023View details →

opencc-by-4.0Jul 2023View details →

Muon000 and Muon002 raw and pressure temperature corrected data set

Data from Two detectors Muon000 and Muon002. Raw coincidence counts and pressure temperature corrected data set.

opencc-by-4.0Jul 2023View details →

Performance Analysis of LoRa in Indoor Settings: A Data Descriptor

This work is a description of the experiment conducted to understand the reception of LoRa in closed environments, such as a building. The experiment was carried out on 04/05/2023, in the NW1 building of University of Bremen. The data’s primary goal is to provide researchers with the understanding of factors such as distance, obstacles, interference with other wireless devices that dictates LoRa’s performance.

Data Set: Promoting Open Science in Test-Driven Software Experiments

Data set for reproduction purposes (tabular data is stored using Apache's Parqet format).

Data set for "Neural mechanisms underlying uninstructed orofacial movements during reward-based learning tasks"

Data set for Li, Nakano, et al. (2023) Neural mechanisms underlying uninstructed orofacial movements during reward-based learning behaviors. Current Biology, https://doi.org/10.1016/j.cub.2023.07.013 The file "Li_Nakano_et_al_detaset.zip" (~45.4 GB) is a compressed version of the "Li_Nakano_et_al_detaset" folder. The uncompressed folder (~76.4 GB) houses the data and some analytical codes used in the study. Upon extraction, the folder reveals two subfolders, "Raw data" and "Source data," and a 'README' text file providing further instructions or information.

opencc-zeroAug 2023View details →

dryad36/100

Supporting information for: Integrating morphological, molecular, and cytogenetic data for F2 sea turtle hybrids diagnosis revealed balanced chromosomal sets

Hybridization could be considered part of the evolutionary history of many species. The hybridization among sea turtle species on the Brazilian coast is atypical and occurs where nesting areas and reproductive seasons overlap. Integrated analysis of morphology and genetics is still scarce, and there is no evidence of the parental chromosome set distribution in sea turtle interspecific hybrids. In this study, chromosome markers previously established for pure sea turtle species were combined with morphological and molecular analyses aiming to recognize genetic composition and chromosome sets in possible interspecific hybrids initially identified by mixed morphology. The data showed that one hybrid could be an F2 individual among Caretta caretta × Eretmochelys imbricata × Chelonia mydas, and another is resulting from backcross between C. caretta × Lepidochelys olivacea. Native alleles of different parental lineages were reported in the hybrids, and, despite this, it was verified that the hybrid chromosome sets were still balanced. Thus, how sea turtle hybridism can affect genetic features in the long term is a concern, as the implications of the crossing-over in hybrid chromosomal sets and the effects on genetic function are still unpredictable.

Correction of 4sU induced quantification bias of Spt6 data set

This data set contains the GRAND-SLAM output of the Spt6 data set (https://zenodo.org/record/4275956) after correcting the 4sU induced quantification bias using the correction approach described <a href="https://www.biorxiv.org/content/10.1101/2023.04.21.537786v1">here</a> and implemented in the <a href="https://www.nature.com/articles/s41467-023-39163-4">grandR package</a>. The zip file contains the full GRAND-SLAM output, the *.tsv.gz file is the GRAND-SLAM output table. The RData file contains the grandR object as analyzed in the original original Spt6 data set (see respective zenodo repository).

Data Set Accompanying "Free Energy Decompositions Illuminate Synergistic Effects in Interfacial Binding Thermodynamics of Mixed Surfactant Systems"

This data set accompanies "Free Energy Decompositions Illuminate Synergistic Effects in Interfacial Binding Thermodynamics of Mixed Surfactant Systems" by Colin K. Egan and Ali Hassanali.  It includes example GROMACS input files for all simulations analyzed in the paper, as well as example data sets and analysis scripts.  See https://doi.org/10.26434/chemrxiv-2023-h11k5 for the preprint manuscript.

opencc-by-nc-sa-4.0Aug 2023View details →

Ibn ʿAsākir and His History of Damascus (Data Set)

This release pertains to a series of seven blog posts that investigate the working methods of ʿAlī Ibn ʿAsākir (d. 571/1176) in his The History of Damascus (Tārīkh madīnat Dimashq, hereafter TMD). The data set is oriented to the following questions: <ol> <li> The TMD’s isnāds name individuals who, in one way or another, transferred information to Ibn ʿAsākir.  When we read the isnāds en masse, what can we learn about his reliance on the people he cites as his direct informants? From approximately how many people did Ibn ʿAsākir obtain information directly? How vast was his source base? What can we learn about his reliance on different people? </li> <li> How does Ibn ʿAsākir cite his sources within isnāds? What vocabulary does he use and what might it mean? Did he acquire the information on his own, or as part of a group; through oral communication, in writing or via a mix of the two?  </li> <li> Previous historians have written about a ‘library’ used by Ibn ʿAsākir and listed books and book titles that it might have contained. When author names appear within isnāds, what do the names signify for Ibn ʿAsākir? What can isnāds reveal about his reliance on books? How does Ibn ʿAsākir cite books themselves?  </li> <li>Outside of isnāds, how does Ibn ʿAsākir cite books and other written materials</li> </ol> To generate our data, we relied on the version of Ibn ʿAsākir’s text contained in the <a href="https://zenodo.org/record/6808108">2022.1.6</a> release of the OpenITI corpus through Zenodo. This same release provided the basis for the text reuse alignments provided here. We used the <a href="https://zenodo.org/record/7687795">2022.2.7</a> version of the corpus in just one case: the ‘IsnadFractions_ML’ data.

Data set for "Electrical detection of the flat band dispersion in van der Waals field-effect structures"

Data set for "Electrical detection of the flat band dispersion in van der Waals field-effect structures" paper published in doi:10.1038/s41565-023-01489-x

openother-openAug 2023View details →

Agriculture Futures and Climate Data Set

This is the second release. The agriculturefuturedata.mat includes the realized volatility series of corn, cotton, palm, wheat, and soybean futures. The climatedata.mat includes the average air pollution variables, weighted average air pollution variables, weighted average weather variables, attention to climate change variables, and attention to extreme weather variables.

Data set for the publication " Evaluation of the Accuracy and Frequency Response of Medium-Voltage Instrument Transformers under the Combined Influence Factors of Temperature and Vibration"

This is dataset for paper published: Agazar, M.; Istrate, D.; Pradayrol, P. Evaluation of the Accuracy and Frequency Response of Medium-Voltage Instrument Transformers under the Combined Influence Factors of Temperature and Vibration. Energies 2023, 16, 5012. https://doi.org/10.3390/en16135012

opencc-by-4.0Oct 2020View details →

Data set used in article: On the Potential of Reduced Order Models for Wind Farm Control: A Koopman Dynamic Mode Decomposition Approach

Step-wise pitch simulation of two wind turbines interacting using SOWFA. More information in the paper.

(Data Set) Shielding Factors for a Fission-Powered Mars Exploration Rover

Data Set to Accompany Technical Paper:  A. BENDOYRO et al., Shielding Factors for a Fission-Powered Mars Exploration Rover, 2023

Data set for fossil Co2 emission in Nigeria

Here is a dataset that captures fossil Co2 emission in Nigeria.

Data sets of measured cross-sectional area coordinates and material properties of an old Vindeby blade

Data sets of measured cross-sectional area coordinates and material properties of an old Vindeby blade

Data set for early carpal tunnel syndrome diagnostic

This dataset represents the minimum dataset to replicate the results obtained in the article "A coupled electro-mechanical approach for early diagnosis of carpal tunnel syndrome" by Saveliy Peshin, Julia Karakulova, Alex G. Kuchumov. The dataset includes 3D models used in FEM calculations, Python-based code for a motion capture program, MatLab-based code for determining the conductance of a deformed median nerve, and MRI images used to construct 3D geometries. All folders have a README text file that contains a detailed description of usage.

In-situ stress data set of Xianshuihe fault zone, Southwest China.

306 sets of in situ stress data were collected from 48 sites on the Xianshuihe fault zone, used in literature and reports from 1982 to 2022. The detailed data of the in-situ stress include Stress value、Direction、Depth、Longitude、Latitude, Testing method, and the data source. Of these, the in-situ stress measurement methods include hydraulic fracturing, stress relief, acoustic emission, and stress recovery.

Url of the Fire-induced Carbon Emissions Dataset in Africa 2014-2021. (1.0) [Data set].

Estimated carbon emission data from biomass burning in Africa from 2014 to 2021, based on the GABAM 30m burning area product. This product uses the WGS84 horizontal datum and the 0.00025° (approximately 30 meter) resolution for geographic (latitude/longitude) projection of the EGM96 vertical datum, consisting of 10° x 10° blocks covering the entire African region.