Find research datasets worth reusing

opencc-by-4.0Oct 2019View details →

Physiological parameters for three farm animal species (cattle, sheep, and swine) as the basis for the development of generic physiologically based kinetic models

IMPORTANT : PLEASE DISREGARD VERSION 1 OF THIS UPLOAD SINCE IT INCLUDES ERRONEOUS INFORMATION. This excel file (DOI: 10.5281/zenodo.3433224) provides physiological parameters and their inter-individual variability (mean, coefficient of variation, sample size) for three farm animal species: cattle (Bos taurus), sheep (Ovis aries), and swine (Sus scrofa domesticus). These physiological parameters were estimated based on the results of extensive literature searches and specific experimental data described in Lautz et al., (2020). This file is associated with R codes (DOI: 10.5281/zenodo.3432796) for generic PBK models, partition coefficient Quantitative Structure Activity Relationship (QSAR) models for each farm animal species and parameterisation of the model. The full data collection and implementation of the models using case studies are described in Lautz et al., 2020 (10.1016/j.toxlet.2019.10.008).

opencc-by-4.0Dec 2023View details →

Sheep videos taken from drone at low altitude

The data below are part of the European H2020 project ICAERUS regarding the livestock monitoring use case. More information here : https://icaerus.eu/ Counting sheep is particularly challenging for farmers with thousand of animals in a flock. Our objective is to develop methodology based on computer vision to counting sheep when they are passing in a corridor to coming back in a park or a pen. This first dataset will support our work.  The dataset encompasses 16 .MP4 videos from drone (DJI mavic 3 Enterprise or Thermal) of around 50 sheep crossing a gate.  The videos were taken from 5m to 10m of height and to an horizontal distance of the gate from 0m to 10m.  More videos will be published in the next months. For more information, please contact: adrien.lebreton@idele.fr  The authors are opened to any collaborations on this topic.

opencc-by-4.0Jan 2022View details →

Sheep Creek Flowlines Generalized for 1:100,000 scale Representation

This dataset comprises original and simplified versions of 28 hydrographic flowline features in North Dakota, USA. The original data were derived from National Hydrography Dataset (NHD) data for the 1:24,000 Sheep Creek Dam topographic map quadrangle. Flowline features were selected for 1:100,000 scale (100k) representation using the NHD VisibilityFilter attribute and further filtered and merged to form a contiguous network. Features were then simplified for 100k representation using a combination of automated and manual operations. The dataset was created for the 24th ICA Workshop on Map Generalisation and Multiple Representation; further details can be found in the workshop abstract. The dataset is intended to serve as a benchmark for cartographic generalization algorithms used to simplify and smooth hydrographic flowline features.   Statistics: Original vertices: 9620 Simplified vertices: 1485 Vertex reduction: 84.6%   <table> <tbody> <tr> <td>   </td> <td> Producer's Modified Hausdorff Distance (m) </td> <td> Producer's Average Distance (Vertex Influence Method) </td> <td> Sinuosity Reduction (%) </td> <td> Average Angular Deflection (degrees) </td> <td> Max Angular Deflection (degrees) </td> </tr> <tr> <td> AVG </td> <td> 24.08 </td> <td> 4.75 </td> <td> 5.23 </td> <td> 29.61 </td> <td> 46.55 </td> </tr> <tr> <td> MIN </td> <td> 0.00 </td> <td> 0.00 </td> <td> -0.49 </td> <td> 5.23 </td> <td> 5.23 </td> </tr> <tr> <td> MAX </td> <td> 38.88 </td> <td> 14.56 </td> <td> 30.40 </td> <td> 33.97 </td> <td> 53.80 </td> </tr> </tbody> </table>

opencc-by-4.0Nov 2023View details →

Videos during training and acquisition of awake Sheep MRI

These videos are provided in support of Pluchot, C., Adriaensen, H., Parias, C. et al. Sheep (Ovis aries) training protocol for voluntary awake and unrestrained structural brain MRI acquisitions. Behav Res (2024). <a href="https://doi.org/10.3758/s13428-024-02449-6" target="_blank" rel="noopener">https://doi.org/10.3758/s13428-024-02449-6</a> . One illustrates our technique to train sheep to lie down, while the other shows the acquisition of a T1-weighted image from an awake and unrestrained sheep. This Version 2 also includes the file Sheepvoice-V3.mp4, which contains footage of several training steps.

opencc-by-4.0Mar 2024View details →

From Fleece to Thread: Interdisciplinary Evidence for the Origins of Sheep Wool

Supplementary data for the article "From Fleece to Thread: Interdisciplinary Evidence for the Origins of Sheep Wool" by Laura C. Viñas-Caron, Mikkel Nørtoft, Peder Flemestad, Jonas Holm Jæger, Christina Margariti Wool confirmed finds file: Coordinates in X and Y columns in all tables are in the CRS: EPSG 3857 Some sites also have WGS 84 lat/long coordinates The majority of the wool finds are from the CINBA project: https://cinba.net/outputs/databases/textiles/ with additional finds by Mikkel Nørtoft.    Sheep mtDNA file: Spatiotemporal mtDNA metadata on sheep were collected by Laura C. Viñas-Caron. All sites have WGS 84 lat/long coordinates

opencc-by-4.0Jul 2022View details →

Data from: Transcriptomic meta-analysis reveals unannotated long non-coding RNAs related to the immune response in sheep

This dataset contains additional files from the manuscript: "Transcriptomic meta-analysis reveals unannotated long non-coding RNAs related to the immune response in sheep". The files included are: - All novel lncRNA transcript annotation GTF file ( lncrnas.gtf ) - High-confidence lncRNA gene annotation GTF file ( lncrnas_evidence.gtf ) - All novel lncRNA transcript annotation GTF file remapped to the ARS-UI_Ramb_v2.0 genome ( lncrnas_remapped_v2.gtf ) - Raw count estimates of the extended annotation ( rawcounts.csv ) - TPM values of the extended annotation ( tpmcounts.csv ) - Supplementary data to the published article (.xlsx, .pdf)

opencc-by-nc-4.0Jan 2017View details →

High density genotypes of French Sheep populations

Genotypes of 27 French sheep populations on the Illumina Ovine HD SNP chip. Dataset and results are presented in the preprint: High density genome scan for selection signatures in French sheep reveals allelic heterogeneity and introgression at adaptive loci. Christina Marie Rochus, Flavie Tortereau, Florence Plisson-Petit, Gwendal Restoux, Carole Moreno-Romieux, Gwenola Tosser-Klopp, Bertrand Servin. bioRxiv 103010; doi: https://doi.org/10.1101/103010

opencc-by-nc-4.0Feb 2017View details →

Raw Genotyping data from: Variation in recombination rate and its genetic determinism in sheep populations from combining multiple genomewide datasets

Data supporting : Variation in recombination rate and its genetic determinism in sheep populations from combining multiple genomewide datasets Morgane Petit, Jean-Michel Astruc, Julien Sarry, Laurence Drouilhet, Stephane Fabre, Carole Moreno, Bertrand Servin http://doi.org/10.1534/genetics.117.300123 Abstract Recombination is a complex biological process that results from a cascade of multiple events during meiosis. Understanding the genetic determinism of recombination can help to understand if and how these events are interacting. To tackle this question, we studied the patterns of recombination in sheep, using multiple approaches and datasets. We constructed male recombination maps in a dairy breed from the south of France (the Lacaune breed) at a fine scale by combining meiotic recombination rates from a large pedigree genotyped with a 50K SNP array and historical recombination rates from a sample of unrelated individuals genotyped with a 600K SNP array. This analysis revealed recombination patterns in sheep similar to other mammals but also genome regions that have likely been affected by directional and diversifying selection. We estimated the average recombination rate of Lacaune sheep at 1.5 cM/Mb, identified about 50,000 crossover hotspots on the genome and found a high correlation between historical and meiotic recombination rate estimates. A genome-wide association study revealed two major loci affecting inter-individual variation in recombination rate in Lacaune, including the RNF212 and HEI10 genes and possibly 2 other loci of smaller effects including  the KCNJ15  and FSHR genes. Finally, we compared our results to those obtained previously in a distantly related population of domestic sheep, the Soay. This comparison revealed that Soay and Lacaune males have a very similar distribution of recombination along the genome and that the two datasets can be combined to create more precise male meiotic recombination maps in sheep. Despite their similar recombination maps, we show that Soay and Lacaune males exhibit different heritabilities and QTL effects for inter-individual variation in genome-wide recombination rates.   Data files are provided in Plink format ( https://www.cog-genomics.org/plink2 ).

opencc-by-4.0Jun 2023View details →

Genotypes for ancient Baltic sheep

Pseudohaploid genotype calls for five ancient sheep genomes from the Baltic Sea region. WGS -- SNP calls at polymorphic sites ascertained from WGS data of wild sheep relatives, coordinates correspond to Oar4.0. SNPCHP -- SNP calls at polymorphic sites from the Illumina Ovine Infinium® HD 600K chip, coordinates correspond to Oar3.1 Description on data preparation and genotype calling can be found in our article.

opencc-by-4.0Dec 2021View details →

Genome-wide analysis identified candidate variants and genes associated with heat stress adaptation in Egyptian sheep breeds

The current study was conducted from 2009 to 2019 in three hot and dry agroecological zones in Egypt: Western Desert coastal zone, New Valley desert oasis, and hot-dry Upper Egypt. Within these zones, three local sheep breeds were studied: Barki (83 ewes), Wahati (55 ewes) and Saidi (68 ewes). During the study period, the animals exercised under natural heat stress (simulating summer grazing on poor pasture). Meteorological and physiological parameters were measured and recorded. The heat tolerance index of the animals was calculated to identify animals with high and low heat tolerance based on the animals' response to the five main physiological parameters (scale from 0 to 5). DNA samples were extracted for genomic analysis. The genetic diversity measurements showed a significant influence of breed and location on the populations. The influence of breed is more significant than that of location. The inbreeding analysis shows that the desert breeds (Wahati and Barki) have lower values than the urban breed (Saidi). The high rate of sub-clustering indicates the process of sub-population through inbreeding pressure. Wahati and Barki are very distinct breeds with strong identification, while Saidi breed has crosses with other breeds. The most significant SNPs associated with heat tolerance were found in MYO5A, PRKG1, GSTCD, and RTN1 genes (P < 0.0001). MYO5A had an effect of 0.74 on the trait heat tolerance in the studied population. It produces a protein that is widely distributed in the melanin-producing neural crest of the skin. Genetic association between genetic and phenotypic variations showed that OAR1 18300122.1, located in ST3GAL3, had the greatest positive effect on heat tolerance. GWAS analysis identified SNPs associated with heat tolerance in the PLCB1, STEAP3, KSR2, UNC13C , PEBP4, and GPAT2 genes.

FIG. 10 in The biometry of prehistoric Alpine sheep: exploring four millennia of human-sheep interaction by means of osteometry

FIG. 10. — LSI of sheep bone width measurements in statistically meaningful Early/Middle Bronze Age find complexes. For Barche di Solferino, see Figure 7.

FIG. 5 in The biometry of prehistoric Alpine sheep: exploring four millennia of human-sheep interaction by means of osteometry

FIG. 5. — LSI of sheep bone width measurements in broad chronological subdivision. For the results of the significance test, see Table 3.

FIG. 4 in The biometry of prehistoric Alpine sheep: exploring four millennia of human-sheep interaction by means of osteometry

FIG. 4. — The LSI median values of width measurements compared with the shoulder height of sheep in individual find complexes. Furthermore, sample size in shoulder height values is considered. Abbreviations: BA, Bronze Age; EBA, Early Bronze Age; EIA, Early Iron Age; IA, Iron Age; LBA, Late Bronze Age; LIA, Late Iron Age; MBA, Middle Bronze Age; NCA, Neolithic/Copper Age. Site numbering, see Tables 1, 2.

FIG. 9 in The biometry of prehistoric Alpine sheep: exploring four millennia of human-sheep interaction by means of osteometry

FIG. 9. — LSI of sheep bone width measurements in Neolithic/Copper Age archaeofaunas. For the results of the significance test, see Table 3.

FIG. 6 in The biometry of prehistoric Alpine sheep: exploring four millennia of human-sheep interaction by means of osteometry

FIG. 6. — LSI of sheep bone width measurements in several micro-regions (for the results of the significance test see Table 3). The sites are arranged in chronological orders and numbering refers to Table 1. Abbreviations: a, Northern Pre-Alps and Limestone Alps; b, Inn Valley; BA, Bronze Age; c,Val Venosta; d, Isarco Valley; e, Adige Valley and surroundings; EBA, Early Bronze Age; EIA, Early Iron Age; ELT, Early La Tène Period; f, Southern drop of the Alps with Lessinian Mountains and Northern Padanian Plain;IA, Iron Age; LBA, Late Bronze Age; LIA, Late Iron Age; LLT, Late La Tène Period; MBA, Middle Bronze Age; MLT, Middle La Tène Period; NCA, Neolithic/Copper Age.

FIG. 1 in The biometry of prehistoric Alpine sheep: exploring four millennia of human-sheep interaction by means of osteometry

FIG. 1. — The percentage of the main livestock species animals in Prehistoric Alpine find complexes., Neolithic/Copper Age;, Bronze Age;, Iron Age. Site numbering, see Table 1.

FIG. 11 in The biometry of prehistoric Alpine sheep: exploring four millennia of human-sheep interaction by means of osteometry

FIG. 11. — The Bronze Age sheep populations of the Northern Alpine Foreland and the Inn Valley in LSI comparison. For the results of the significance test, see Table 3.