Genetics and Genomics
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To advance understanding of complex animal systems and the development of improved predictive models through the application of numerical and computational approaches in the analysis, interpretation, modelling and prediction of complex animal systems from the level of the DNA and other molecules, through cellular and gene networks, tissues and organs to whole organisms and interacting populations of organisms.
Image: Detail from Fig. 1 of Regan et al.(2018) which uses data from: Regan, Tim; Freeman, Tom; Barnett, Mark. (2018). Characterisation of the UK honey bee metagenome, 2016-2017 [dataset]. The Roslin Institute. University of Edinburgh. https://doi.org/10.7488/ds/2453.
Items in this Collection
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GenOMICC Covid-19 summary statistics European ancestry
GWAS summary statistics for European ancestry, from the GenOMICC Covid-19 critical illness study. GWAS was performed with 1676 Europeans and 5*1676 controls and validated using 100K Genomics England controls and Generation ... -
GenOMICC Covid-19 critical illness summary statistics non-European ancestries
Non-European ancestries GWAS summary statistics for Covid-19 critical illness from the GenOMICC study -
2020_Thesis_SupplementaryData_s1569052_Tissue-resident immune cells in health and disease: their heterogeneity and associated gene signatures
The dataset includes supplementary figures and tables in support of the University of Edinburgh thesis titled "Tissue-resident immune cells in health and disease: their heterogeneity and associated gene signatures". -
XP-EHH and XP-CLR scores across water buffalo and cattle breeds
This dataset consists of XP-EHH and XP-CLR scores calculated using the hapbin (https://github.com/evotools/hapbin) and xpclr (https://github.com/hardingnj/xpclr) software with default parameters across 79 water buffalo and ... -
Gene expression in the cardiovascular system of the domestic sheep (Ovis aries)
This dataset includes gene expression estimates, from RNA-Seq, for seven cardiovascular and one skeletal muscle tissue from the sheep gene expression atlas dataset (https://journals.plos.org/plosgenetics/article?id=10.13 ... -
A comparison of livestock movement network-methods and implications for disease control in developing countries
The use of network analysis to support livestock disease control in low middle-income countries (LMICs) has historically been hampered by the cost of generating empirical data in the absence of animal movement recording ... -
SUPERSEDED - Water buffalo and cattle XPEHH scores across breeds
## SUPERSEDED - This dataset has been replaced by the one which can be found at https://doi.org/10.7488/ds/2849 . ## This dataset consists of XP-EHH scores calculated using the hapbin software (https://github.com/evotools/hapbin) ... -
A putative genomic map for resistance of Bos indicus cattle in Cameroon to bovine tuberculosis
Bovine Tuberculosis (bTB) caused by Mycobacterium bovis is a livestock disease of global economic and public health importance. There are currently no effective vaccines available for livestock and so control relies on ... -
Metagenome assembled rumen-uncultured genomes (RUGs)
DNA was sequenced from rumen contents from cattle, sheep, red deer and reindeer. We constructed 391 metagenome assembled rumen-uncultured genomes (RUGs). -
An eQTL in the cystathionine beta synthase gene is linked to osteoporosis in laying hens
"An eQTL in the cystathionine beta synthase gene is linked to osteoporosis in laying hens" Dirk-Jan De Koning, Nazaret Dominguez-Gasca, Robert H. Fleming, Andrew Gill, Dominic Kurian, Andrew Law, Heather A. McCormack, ... -
Variant discovery from whole genome sequence data from a commercial broiler line and a CSFIR- mApple reporter transgenic layer line
The data comprises variants calls from whole genome sequencing (WGS) data from a set of founder broilers (n=10) and transgenic layers (n=10). The broiler samples belong to commercial Ross 308 founder population and were ... -
Unnormalised raw count estimates for the sheep gene expression atlas dataset
This dataset contains the estimated unnormalised raw counts generated using Kallisto for all RNA-Seq libraries included in the sheep gene expression atlas. ## Format ## The plain text file contains 1,954 rows of ... -
Cow genotypes before quality control in PLINK format. Dataset pertains to manuscript "Quantitative trait loci mapping for lameness associated phenotypes in Holstein Friesian dairy cattle"
Cow genotypes in PLINK format before quality control used for a GWAS study of lameness associated phenotypes in Holstein Friesian dairy cattle. Genotypes were merged from Affymetrix and Illumina SNP chips. -
A mini-atlas of gene expression for the domestic goat
The goat mini-atlas dataset includes 54 mRNA-Seq (poly-A selected) 75bp paired-end libraries from 20 tissues and 2 cell types from neonatal crossbred dairy goats. Gene level expression estimates, for the goat mini-atlas, ... -
Chicken cecal metagenome assembled genomes
We sequenced DNA from cecal contents samples taken from 24 chickens belonging to either a fast or slower growing breed consuming either a vegetable-only diet or a diet containing fish meal. We utilised 1.6T of Illumina ... -
De novo gene and transcript models created for a gene expression atlas of the domestic water buffalo (Bubalus bubalis)
The domestic water buffalo (Bubalus bubalis) makes a major contribution to the global agricultural economy in the form of milk, meat, hides and draught power. The global water buffalo population is predominantly found in ... -
The genomic and proteomic landscape of the rumen microbiome revealed by comprehensive genome-resolved metagenomics
"Metagenomic and proteomic datasets from: The genomic and proteomic landscape of the rumen microbiome revealed by comprehensive genome-resolved metagenomics Rob. D. Stewart, Marc D. Auffret, Amanda Warr, Alan Walker, ... -
Characterisation of the UK honey bee metagenome
The European honey bee (Apis mellifera) plays a major role in pollination and food production, but is under threat from emerging pathogens and agro-environmental insults. As with other organisms, honey bee health is a ... -
Open prediction of polysaccharide utilisation loci (PUL) in 5414 public Bacteroidetes genomes using PULpy
Polysaccharide utilisation loci (PUL) are regions within the genomes of Bacteroidetes that encode all the necessary machinery for the cleavage of particular carbohydrates. Prediction of PUL from genomic data alone involves ...
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