Functional Annotation of the Sheep Genome

Lead Research Organisation: University of Edinburgh
Department Name: The Roslin Institute

Abstract

Animals and humans are made up of many different kinds of organs and cells, each of which requires the actions of a subset of the genes in the genome. We currently know the function of only a subset of the genes in the genome. Much of what we know comes from studies of rodents but their biology is quite different to humans and their small size compromises their use. In the current study we will examine how individual genes are used in every tissue and cell of the sheep. From that information, we will be able to identify sets of genes that are always used together, and infer the function of genes of unknown function from the company they keep. That information will, in turn, allow us to interpret studies of the genetics and genomics of large animals, including humans (this study could not be done on a human). This will, in turn, inform the rational breeding of livestock for improved performance and welfare through selection for disease resistance. It will also give us a better understanding of the basic biology of humans that can be translated in better lifelong health.

Technical Summary

The current proposal seeks to establish a gene expression atlas for the domestic sheep, based upon a comprehensive transcriptomic analysis of hundreds of cell and tissue samples using RNAseq, genome-scale 5' RACE (CAGE) and high throughput sequencing. We will use that information to annotate the genome of sheep and other ruminants. We will also use the atlas to identify novel candidate genes underlying complex traits in large animals, including humans, to infer gene function and orthology relationships across species and to gain insights into evolution of the mammalian transcriptome, to assess the prevalence and significance of expressed genetic variation and allelic imbalance in gene expression, to examine in detail the expression of genes involved in immune function and to examine the role of promoter evolution and functional site turnover as a major driver of species divergence. We will develop web tools to provide an online resource for the livestock and health science research community.

Planned Impact

Who will benefit from our research?
The scientific community will provide expression-based annotations of the sheep genome that can be translated across to other ruminants and large animals (including humans). The biomedical research community will benefit from a resource that could provide a rational base for connection of genotype and phenotype in humans, especially in interpretation of genome-wide association studies. In the animal health sector, the information will also underpin sustainable improvements in production and resistance against infectious diseases, many of which (e.g. salmonella, influenza) are zoonotic. Thus our proposal will bridge fundamental and applied science; a One Biology:One Health agenda within two BBSRC grand challenges; Food Security and Basic Bioscience Underpinning Health. The further development of genome editing in livestock in the sheep model also falls within the province of synthetic biology and has the potential to produce novel livestock breeds with improved performance and reduce environmental footprint.
Small ruminants are a major livestock species in developing countries, and a focus of international efforts at improvement, especially for disease resistance. In the long term, the research will benefit the poorest farmers.
How will they benefit from this research?
We will contribute data that will be publicly available in appropriate international databases for the wider research community to access and exploit. We interact directly with many breeding companies to develop tools that utilise genomic evaluation in breeding strategies. Our project will thus provide added value to the international efforts to generate and maintain genomic information.
What will be done to ensure that the benefits from this research arise?
Scientific community: This project is a key component of the UK contribution to International Genome Projects and will contribute critically to the Sheep Genome Consortium and to ruminant and mammalian functional genomics. Primary data will be made available through multiple web sites and databases, notably ENSEMBL. We will also present the results and publicise the resources at key scientific meetings (ISAG, PAG, BSAS) and will particularly seek to engage a wide spectrum of researchers from the fields of genetic and genomics,agriculture, immunology and veterinary pathology and to emphasise the cross-disciplinarity of the research.
Industry: We will engage with livestock, animal health and biomedical industries through the University's commercialisation arm Edinburgh Research and Innovation. Roslin has 3 permanent business development staff who have helped to host multiple events over the past three years specifically showcasing the institute's work to industry partners.
Public: We (will) provide information about our research through our web sites (with project-specific information), talks and discussion groups and direct interaction with the media. The Roslin Institute encourages clear and open communication and has a policy of promoting Public Engagement by means of interaction with the media, presentations, publications, exhibitions and schools activities. Roslin provides support for staff and students wishing to undertake such activities. The Roslin Institute's Scientific Administrator oversees both internal and external communication of the research performed at the institute.
Track record: We have an excellent track record for translating the outcomes of our research and Roslin was considered an exemplar of good practice in KEC evaluation during the most recent ISPG review. We hold regular Industry Open Days, and have more than 40 existing industry partnerships. The individual PIs have existing collaborations with multiple companies including Genus, Pfizer, AMGEN, Affymetrix, Merck, Novartis, Aviagen and several SMEs. Our major partner, the breeding company Genus, has provided a letter of support.

Publications

10 25 50
 
Description We have produced a high resolution atlas of gene expression for the domestic sheep, which makes a major contribution to the identifying the function of many of the genes in the sheep genome. Our data also provides an insight into the basic mechanisms of crossbreeding and hybrid vigour, which forms the basis of modern animal breeding and production. Sheep are a key source of meat, milk and fibre for the global livestock sector, and an important biomedical model. Previous studies applying analysis of gene expression across multiple tissues have aided genome annotation and supported functional annotation of mammalian genes. The sheep gene expression atlas, funded by this research grant, includes gene expression data from all major organ systems from adult sheep and from several juvenile, neonatal and prenatal developmental time points. We have used the dataset to describe the overall patterns of gene expression across tissues and cell types in sheep and assigned those signatures, where possible, to specific cell populations or biological pathways. We were able to relate our findings particularly to innate immunity by focusing on clusters of genes with an immune signature, and to the advantages of cross-breeding (hybrid vigour) by examining the patterns of genes exhibiting the greatest expression differences between purebred and crossbred animals. The high-resolution gene expression atlas for sheep we have built with the research funded on this grant, is to our knowledge, the largest transcriptomic dataset from any livestock species to date. It provides a resource to improve the annotation of the current reference genome for sheep, presenting a model transcriptome for ruminants and insight into gene, cell and tissue function at multiple developmental stages.
Exploitation Route We are working on applications of the data, methods and technology to a new genome assembly for the sheep, and to the study of productivity and resilience in tropically-adapted breeds in LMIC countries. The datasets generated by the sheep gene expression atlas project, including gene expression estimates and raw data, have been made public and are a valuable resource for the functional annotation of animal genomes (FAANG) consortium. They were used for bench marking FAANG metadata and data analysis standards, which has provided useful information for researchers within the consortium. The sheep gene expression atlas datasets are being used by researchers in the UK (University of Glasgow and the Pirbright Institute) and by colleagues in the United States to add additional insights to their own research questions related to ruminant immunity. The searchable database on BioGPS will be accessed by researchers globally, providing a means to look at transcription across tissues in a ruminant mammal. This research grant has also led to future funding in a USDA Tools and Resources Grant for functional annotation of the new sheep assembly (rambouillet version1) with collaborators in the USA and Australia in which The Roslin Institute is a Co-I. The sheep gene expression atlas and these new resources will be used by researchers within the sheep genomics research community to improve the functional annotation of the sheep genome further, with the goal of improving it to the level of particularly advanced reference assemblies such as pig and goat. Via a BBSRC New Investigator AWARD we are building on the foundation provided by the sheep gene expression atlas to look further at allele- and isoform- specific expression and transcription through early and post natal development. Our aim is that insights from these studies will provide predictive information that can be added to genomic selection strategies to improve for example innate immunity, growth and productivity and improve the efficiency of sheep breeding systems, in the UK and across the globe.
Sectors Agriculture, Food and Drink

URL http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006997
 
Description Empowering sheep breeding by identifying variants associated with growth traits using allele-specific expression
Amount £426,983 (GBP)
Funding ID BB/S01540X/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2020 
End 01/2023
 
Description Ovine FAANG Project
Amount $500,000 (USD)
Organisation U.S. Department of Agriculture USDA 
Sector Public
Country United States
Start 04/2017 
End 04/2020
 
Title Sheep Gene Expression Atlas Tissue Sample Archive 
Description We have archived ~2600 tissue and cell samples from the sheep, for the sheep gene expression atlas project in the -80 freezer barn at the Roslin Institute. These tissue samples are either snap frozen or stored in RNAlater. Sample metadata is available via https://www.ebi.ac.uk/biosamples/groups/SAMEG317052 and on the FAANG data portal. The samples are available to the livestock genomics community. 
Type Of Material Biological samples 
Year Produced 2017 
Provided To Others? Yes  
Impact The tissue and cell sample archive for the sheep gene expression atlas was published in 2017 with the sheep gene expression atlas manuscript. Several groups at the Roslin Institute have utilised the samples. We have also received requests from collaborators to use the samples in grant applications for collaborative funding. 
URL https://www.ebi.ac.uk/biosamples/groups/SAMEG317052
 
Title Goat Mini Atlas Gene Expression Estimates on the UoE Datashare portal 
Description We have uploaded the averaged and unaveraged gene expression estimates for the goat mini gene expression atlas project, generated by the transcript quantification tool Kallisto, to the University of Edinburgh data portal in order to make them publicly available. These estimates were used to create the gene to gene and sample to sample network graphs described in the sheep gene expression atlas publication. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact There are no notable impacts from this dataset to date. 
URL https://datashare.is.ed.ac.uk/handle/10283/3379
 
Title Ovine FAANG Project CAGE Dataset from 56 tissues 
Description We have generated CAGE libraries (Cap Analysis Gene Expression) from 56 tissues from the reference Rambouillet sheep. This data will be used to annotate transcription start sites in the new highly contiguous Rambouillet v1 genome for sheep. The raw data and BAM analysis files are currently publicly available on the ENA and with our collaborators within the Ovine FAANG group we are using it for isoform validation with Iso-Seq data. The libraries for this project were generated by the Clinical Research Facility at Western General, University of Edinburgh. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact This data will be used to improve the annotation of the new highly contiguous Rambouillet v1 genome for sheep, significantly improving the genomic resources available for ruminants. 
URL https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB34864
 
Title PRJEB19199 - Sheep Atlas 438 RNASeq libraries from TxBF Sheep 
Description The raw data, in the form of .fastq files, for the 438 TxBF RNA-Seq libraries generated for the sheep gene expression atlas project is deposited in the European Nucleotide Archive under study accession number PRJEB19199. We have also uploaded the analysis files (BAM files) created for this project to the same accession in the ENA. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact This sheep gene expression atlas raw data has been made available publicly under the data sharing agreement of the FAANG consortium. It was the first and largest dataset of it's type to be uploaded to the ENA as a 'FAANG' dataset and was used to test metadata standards and data upload requirements. it provides a valuable information to the livestock genomics community. 
URL http://www.ebi.ac.uk/ena/data/view/PRJEB19199
 
Title PRJEB23196 - 54 RNA-Seq libraries from goat 
Description We have uploaded to the European Nucleotide Archive under accession number PRJEB23196 the raw data in the form of .fastq files from 54 RNA-Seq libraries from tissues and cell types from domestic goats. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact No impact yet. 
URL https://www.ebi.ac.uk/ena/data/view/PRJEB23196
 
Title Sheep Atlas GI Tract Expression Estimates on UoE Data Share Portal 
Description We have uploaded the averaged and unaveraged gene expression estimates for the gastrointestinal tract dataset from the sheep gene expression atlas project, generated by the transcript quantification tool Kallisto, to the University of Edinburgh Data Share portal in order to make them publicly available. These estimates were used to create the gene to gene and sample to sample network graphs described in the publication "Comprehensive Transcriptional Profiling of the Gastrointestinal Tract of Ruminants from Birth to Adulthood Reveals Strong Developmental Stage Specific Gene Expression." PMID: 30530642. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact By making this dataset available we have provided a baseline estimate of gene expression in GI tract tissues for sheep, this has allowed other groups to utilise the data, maximised the usage of the dataset and reduced the need to sacrifice additional sheep. 
URL https://datashare.is.ed.ac.uk/handle/10283/3113
 
Title Sheep Atlas Gene Expression Estimates UoE Data Portal 
Description We have uploaded the averaged and unaveraged gene expression estimates for the sheep gene expression atlas project, generated by the transcript quantification tool Kallisto, to the University of Edinburgh data portal in order to make them publicly available. These estimates were used to create the gene to gene and sample to sample network graphs described in the sheep gene expression atlas publication. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact The averaged gene expression estimates from the data portal were used by colleagues at the Scripps Institute to create the sheep atlas in BioGPS, another publicly available searchable resource for the project. 
URL http://dx.doi.org/10.7488/ds/2112
 
Title Sheep Gene Expression Atlas Dataset in BioSamples 
Description With help from our collaborators at the FAANG data coordination centre at EBI have uploaded all the sample metadata associated with the animals, tissue samples and cells used in the sheep gene expression atlas to the BioSamples database. We have provided the metadata to the specifications and standards required by the FAANG consortium. This includes details on animal age, sex, breed, tissue and cell type ontologies, dates of sample collection and sample collection protocols. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact By uploading comprehensive metadata for this large scale gene expression dataset from a livestock species we set a precedent for other research groups to do the same. The sheep gene expression atlas datasets was one the first large large metadata dataset to be added to BioSamples for the FAANG consortium and was used as a pilot for validation and improvement for upload of subsequent projects. 
URL https://www.ebi.ac.uk/biosamples/groups/SAMEG317052
 
Title Sheep Gene Expression Atlas Samples on FAANG Data Portal 
Description FAANG is the Functional Anotation of ANimal Genomes project which is working to understand the genotype to phenotype link in domesticated animals. The data portal is designed to help find and browse FAANG's data. With our collaborators at EBI we have uploaded all of the samples for the sheep gene expression atlas into this data portal. The data portal includes links to the sample and animal metadata in the BioSamples database and the experimental metadata linked to any sample in the sequence archives. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact By uploading the sample metadata from the sheep gene expression atlas to the FAANG data portal and associated links to the information in BioSamples and the sequencing archives we have made this information accessible to members of the FAANG consortium. This has led to enquires regarding sharing of the tissue samples for grant applications and funded studies broadening the scope of the research and ensuring redundancy of tissue collection, data generation and animal use in minimised. 
URL http://data.faang.org/organism?organism=Ovis%20aries
 
Title The Sheep Atlas Gene Expression Dataset in BioGPS 
Description The set of gene expression estimates averaged across samples for the sheep gene expression atlas, as TPM generated by the transcript quantification tool Kallisto, can be downloaded as a complete dataset from the BioGPS website. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact This set of gene expression estimates are a valuable resource for researchers interested in transcription in livestock species and are accessible to the whole community via the BioGPS website which has considerable reach internationally and within the mammalian genomics field. 
URL http://biogps.org/dataset/BDS_00015/sheep-atlas/
 
Title The Sheep Atlas on BioGPS 
Description BioGPS is free extensible and customizable gene annotation portal, a complete resource for learning about gene and protein function. it was developed by our colleagues at the Scripps Institute in California, USA. We have made the expression estimates across tissues for all annotated genes for sheep, from the sheep gene expression atlas dataset available in BioGPS. This allows users to input a gene name, probably of a gene are working on, and then see the expression of that gene across tissues in sheep, providing useful baseline date for analysis. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact Several researchers have contacted me to ask which time points or tissues to focus on when they are interested in the expression pattern of a particular gene and I have been able to direct them to the BioGPS tool. BioGPS outreach have also run a "spotlight" on the dataset which generate some attention on twitter and widen the impact of the dataset. I believe it is being used by researcher across the globe, predominantly those working on sheep but also but more widely for ruminants and other livestock. 
URL http://biogps.org/sheepatlas/#goto=welcome
 
Description Collaboration with Dominique Rocha's group INRA, Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France 
Organisation French National Institute of Agricultural Research
Department GABI: Animal Genetics and Integrative Biology unit
Country France 
Sector Private 
PI Contribution We have been collaborating with Dominique Rocha's group at INRA for allele specific expression analysis in the sheep and water buffalo gene expression atlas projects. We hosted GG a PhD student in Dominque Rocha's group at INRA France, and provided him with the computing facilities and datasets from the sheep and goat gene expression atlas projects to facilitate his analysis.
Collaborator Contribution GG a PhD student in Dominque Rocha's group at INRA France visited the Roslin Institute from January to April 2017 as part of STSM (Strategic Scientific Mission) funded by the FAANG-EU Cost Action. During his stay he applied a pipeline he had developed to detect Single Nucleotide Variants (SNVs) showing Allele Specific Expression (ASE) in sheep and water buffalo using the datasets from the sheep and water buffalo gene expression atlas projects.
Impact GG presented his work on the sheep gene expression data as a comparison with results he had generated in his own lab for cattle at the ISAG meeting in Dublin 2017. At the end of his 3-month mission, he trained members of the lab group he was visiting to use the pipeline he developed and provided an instruction manual for the pipeline. This pipeline will continue to be used to analyse sheep and water buffalo RNA-Seq datasets generated at Roslin and submitted to the FAANG consortium and he has continued with some of the analysis of the sheep data on his return to INRA facilitating on a continuation of the collaboration.
Start Year 2016
 
Description Collaboration with Scripps Institute for BioGPS 
Organisation Scripps Research Institute
Country United States 
Sector Charity/Non Profit 
PI Contribution We generated the sheep and water buffalo gene expression atlas dataset and provided the gene expression estimates across tissues and cells for upload on BioGPS.
Collaborator Contribution Our partners in Andrew Su's lab at the Scripps Institute uploaded the dataset to their gene annotation platform BioGPS. This generated a searchable database of gene expression profiles for all annotated genes in the sheep genome across all tissues and cell types in the sheep atlas dataset. They plan to do the same for water buffalo.
Impact A searchable database of gene expression profiles for sheep has resulted from this collaboration which is a hugely valuable resource for the livestock and mammalian genomics research communities. This sheep database is being used by ruminant researchers internationally and the water buffalo dataset is soon to be released. The collaboration is multi-disciplinary involving computing, web design and mammalian biology.
Start Year 2017
 
Description EBI FAANG Data Coordination Centre 
Organisation EMBL European Bioinformatics Institute (EMBL - EBI)
Country United Kingdom 
Sector Academic/University 
PI Contribution We have made all the data and metadata information for the sheep gene expression atlas available to our collaborators at the FAANG data coordination centre at EBI in order for them to upload it to the FAANG data portal.
Collaborator Contribution Our collaborators at EBI at the FAANG data coordination centre have created links to the metadata and data for the sheep gene expression atlas in the FAANG data portal in order to facilitate data and sample sharing within the FAANG consortium.
Impact This collaboration has created an online database resource for the samples and dataset for the sheep gene expression atlas project, a large FAANG project. This facilitated data and sample sharing between research groups within the consortium and encouraging collaboration for grant applications and publications and reducing redundancy.
Start Year 2016
 
Description Functional Annotation of ANimal Genomes (FAANG) Metadata and Data Sharing (M&DS) Working group 
Organisation EMBL European Bioinformatics Institute (EMBL - EBI)
Country United Kingdom 
Sector Academic/University 
PI Contribution "The Animal Functional Genomics Resource" project is a collaboration between EMBL-EBI and The Roslin Institute and is supported through linked BBSRC grants to these two partners. The EMBL-EBI and Roslin Institute partners are also active members of the Functional Annotation of ANimal Genomes (FAANG) working group on Metadata and Data Sharing (M&DS). The Roslin partners bring knowledge of the target farmed animal species and exemplar datasets with which to test the draft data and metadata standards developed by the M&DS working group. The Roslin partners have also tested the systems for capturing metadata and for pre-publication data sharing.
Collaborator Contribution The EMBL-EBI partners are developing and hosting the FAANG Data Portal (http://data.faang.org/home). The EMBL-EBI partners are also developing common data submission tools and QC tools. Scientists from EMBL-EBI and the University of Delaware co-chair the Functional Annotation of ANimal Genomes (FAANG) Metadata and Data Sharing (M&DS) Working group. Scientists at Iowa State University provide links to the FAANG Bioinformatics and Data Analysis working group and to the USDA NRSP8 Bioinformatics Coordinator. Ninety-three of the 398 individuals who have joined as 'contributors' to the Functional Annotation of ANimal Genomes (FAANG) consortium have self-identified as members of the Metadata and Data Sharing (M&DS) Working group. For the sake of brevity only a few key partners are named here.
Impact The FAANG Data Sharing Statement (https://www.faang.org/data-share-principle) and guidance on data submission (https://www.ebi.ac.uk/seqdb/confluence/display/FAANG/FAANG+Archive+Submission+guidelines)
Start Year 2016
 
Description Functional Annotation of ANimal Genomes (FAANG) Metadata and Data Sharing (M&DS) Working group 
Organisation Iowa State University
Country United States 
Sector Academic/University 
PI Contribution "The Animal Functional Genomics Resource" project is a collaboration between EMBL-EBI and The Roslin Institute and is supported through linked BBSRC grants to these two partners. The EMBL-EBI and Roslin Institute partners are also active members of the Functional Annotation of ANimal Genomes (FAANG) working group on Metadata and Data Sharing (M&DS). The Roslin partners bring knowledge of the target farmed animal species and exemplar datasets with which to test the draft data and metadata standards developed by the M&DS working group. The Roslin partners have also tested the systems for capturing metadata and for pre-publication data sharing.
Collaborator Contribution The EMBL-EBI partners are developing and hosting the FAANG Data Portal (http://data.faang.org/home). The EMBL-EBI partners are also developing common data submission tools and QC tools. Scientists from EMBL-EBI and the University of Delaware co-chair the Functional Annotation of ANimal Genomes (FAANG) Metadata and Data Sharing (M&DS) Working group. Scientists at Iowa State University provide links to the FAANG Bioinformatics and Data Analysis working group and to the USDA NRSP8 Bioinformatics Coordinator. Ninety-three of the 398 individuals who have joined as 'contributors' to the Functional Annotation of ANimal Genomes (FAANG) consortium have self-identified as members of the Metadata and Data Sharing (M&DS) Working group. For the sake of brevity only a few key partners are named here.
Impact The FAANG Data Sharing Statement (https://www.faang.org/data-share-principle) and guidance on data submission (https://www.ebi.ac.uk/seqdb/confluence/display/FAANG/FAANG+Archive+Submission+guidelines)
Start Year 2016
 
Description Functional Annotation of ANimal Genomes (FAANG) Metadata and Data Sharing (M&DS) Working group 
Organisation University of Delaware
Department Department of Animal and Food Sciences
Country United States 
Sector Academic/University 
PI Contribution "The Animal Functional Genomics Resource" project is a collaboration between EMBL-EBI and The Roslin Institute and is supported through linked BBSRC grants to these two partners. The EMBL-EBI and Roslin Institute partners are also active members of the Functional Annotation of ANimal Genomes (FAANG) working group on Metadata and Data Sharing (M&DS). The Roslin partners bring knowledge of the target farmed animal species and exemplar datasets with which to test the draft data and metadata standards developed by the M&DS working group. The Roslin partners have also tested the systems for capturing metadata and for pre-publication data sharing.
Collaborator Contribution The EMBL-EBI partners are developing and hosting the FAANG Data Portal (http://data.faang.org/home). The EMBL-EBI partners are also developing common data submission tools and QC tools. Scientists from EMBL-EBI and the University of Delaware co-chair the Functional Annotation of ANimal Genomes (FAANG) Metadata and Data Sharing (M&DS) Working group. Scientists at Iowa State University provide links to the FAANG Bioinformatics and Data Analysis working group and to the USDA NRSP8 Bioinformatics Coordinator. Ninety-three of the 398 individuals who have joined as 'contributors' to the Functional Annotation of ANimal Genomes (FAANG) consortium have self-identified as members of the Metadata and Data Sharing (M&DS) Working group. For the sake of brevity only a few key partners are named here.
Impact The FAANG Data Sharing Statement (https://www.faang.org/data-share-principle) and guidance on data submission (https://www.ebi.ac.uk/seqdb/confluence/display/FAANG/FAANG+Archive+Submission+guidelines)
Start Year 2016
 
Description Sheep atlas - collaboration with Agribio, Latrobe University, Melbourne, Australia 
Organisation La Trobe University
Country Australia 
Sector Academic/University 
PI Contribution We provided raw count data from the sheep gene expression atlas to Agribio in order for them to perform a comparative analysis of the expression of mitochondrial genes in tissues and co-expression of nuclear mitochondrial protein genes and mitochondrial protein coding genes in cattle and sheep.
Collaborator Contribution Our collaborators at Agribio were investigating the expression of mitochondrial genes in tissues and co-expression of nuclear mitochondrial protein genes and mitochondrial protein coding genes in bovine tissue and were interested in validating their findings in other species including sheep. The sheep expression atlas and their bovine mitochondrial gene expression study had many tissues in common and they performed a comparative analysis of the raw count data from the sheep atlas that we provided.
Impact A manuscript from this collaboration was submitted by AgriBio to BMC Genomics entitled 'Expression of mitochondrial protein genes encoded by nuclear and mitochondrial genomes correlate with energy metabolism in dairy cattle'.
Start Year 2019
 
Description The Ovine FAANG Project 
Organisation AgResearch
Department Invermay Agricultural Centre
Country New Zealand 
Sector Private 
PI Contribution The Ovine FAANG Project is a collaborative effort by the International Sheep Genomics Consortium to provide a comprehensive annotation of the new highly contiguous reference genome for sheep Oar_rambouillet_v1.0. The project is funded by a USDA NIFA Tools and Resources grant. The Roslin Institute generated 56 CAGE libraries and produced an atlas of annotated transcription start sites across tissues using this dataset.
Collaborator Contribution The Ovine FAANG Project is a collaborative effort by the International Sheep Genomics Consortium and other partners produced 'omics datasets including ChIP-Seq, WGBS and RNA-Seq and Iso-Seq to provide a comprehensive annotation of the new highly contiguous reference genome for sheep Oar_rambouillet_v1.0.
Impact The datasets generated by the projects have been made available as a Bioproject in NCBI and the CAGE datasets are available also on the ENA with corresponding BAM files. The datasets have contributed directly to improving the annotation of the Rambouillet version 1 genome hosted on NCBI.
Start Year 2017
 
Description The Ovine FAANG Project 
Organisation Baylor College of Medicine
Country United States 
Sector Hospitals 
PI Contribution The Ovine FAANG Project is a collaborative effort by the International Sheep Genomics Consortium to provide a comprehensive annotation of the new highly contiguous reference genome for sheep Oar_rambouillet_v1.0. The project is funded by a USDA NIFA Tools and Resources grant. The Roslin Institute generated 56 CAGE libraries and produced an atlas of annotated transcription start sites across tissues using this dataset.
Collaborator Contribution The Ovine FAANG Project is a collaborative effort by the International Sheep Genomics Consortium and other partners produced 'omics datasets including ChIP-Seq, WGBS and RNA-Seq and Iso-Seq to provide a comprehensive annotation of the new highly contiguous reference genome for sheep Oar_rambouillet_v1.0.
Impact The datasets generated by the projects have been made available as a Bioproject in NCBI and the CAGE datasets are available also on the ENA with corresponding BAM files. The datasets have contributed directly to improving the annotation of the Rambouillet version 1 genome hosted on NCBI.
Start Year 2017
 
Description The Ovine FAANG Project 
Organisation Commonwealth Scientific and Industrial Research Organisation
Country Australia 
Sector Public 
PI Contribution The Ovine FAANG Project is a collaborative effort by the International Sheep Genomics Consortium to provide a comprehensive annotation of the new highly contiguous reference genome for sheep Oar_rambouillet_v1.0. The project is funded by a USDA NIFA Tools and Resources grant. The Roslin Institute generated 56 CAGE libraries and produced an atlas of annotated transcription start sites across tissues using this dataset.
Collaborator Contribution The Ovine FAANG Project is a collaborative effort by the International Sheep Genomics Consortium and other partners produced 'omics datasets including ChIP-Seq, WGBS and RNA-Seq and Iso-Seq to provide a comprehensive annotation of the new highly contiguous reference genome for sheep Oar_rambouillet_v1.0.
Impact The datasets generated by the projects have been made available as a Bioproject in NCBI and the CAGE datasets are available also on the ENA with corresponding BAM files. The datasets have contributed directly to improving the annotation of the Rambouillet version 1 genome hosted on NCBI.
Start Year 2017
 
Description The Ovine FAANG Project 
Organisation U.S. Department of Agriculture USDA
Department U.S. Meat Animal Research Center
Country United States 
Sector Public 
PI Contribution The Ovine FAANG Project is a collaborative effort by the International Sheep Genomics Consortium to provide a comprehensive annotation of the new highly contiguous reference genome for sheep Oar_rambouillet_v1.0. The project is funded by a USDA NIFA Tools and Resources grant. The Roslin Institute generated 56 CAGE libraries and produced an atlas of annotated transcription start sites across tissues using this dataset.
Collaborator Contribution The Ovine FAANG Project is a collaborative effort by the International Sheep Genomics Consortium and other partners produced 'omics datasets including ChIP-Seq, WGBS and RNA-Seq and Iso-Seq to provide a comprehensive annotation of the new highly contiguous reference genome for sheep Oar_rambouillet_v1.0.
Impact The datasets generated by the projects have been made available as a Bioproject in NCBI and the CAGE datasets are available also on the ENA with corresponding BAM files. The datasets have contributed directly to improving the annotation of the Rambouillet version 1 genome hosted on NCBI.
Start Year 2017
 
Description The Ovine FAANG Project 
Organisation University of Idaho
Country United States 
Sector Academic/University 
PI Contribution The Ovine FAANG Project is a collaborative effort by the International Sheep Genomics Consortium to provide a comprehensive annotation of the new highly contiguous reference genome for sheep Oar_rambouillet_v1.0. The project is funded by a USDA NIFA Tools and Resources grant. The Roslin Institute generated 56 CAGE libraries and produced an atlas of annotated transcription start sites across tissues using this dataset.
Collaborator Contribution The Ovine FAANG Project is a collaborative effort by the International Sheep Genomics Consortium and other partners produced 'omics datasets including ChIP-Seq, WGBS and RNA-Seq and Iso-Seq to provide a comprehensive annotation of the new highly contiguous reference genome for sheep Oar_rambouillet_v1.0.
Impact The datasets generated by the projects have been made available as a Bioproject in NCBI and the CAGE datasets are available also on the ENA with corresponding BAM files. The datasets have contributed directly to improving the annotation of the Rambouillet version 1 genome hosted on NCBI.
Start Year 2017
 
Description The Ovine FAANG Project 
Organisation Utah State University
Country United States 
Sector Academic/University 
PI Contribution The Ovine FAANG Project is a collaborative effort by the International Sheep Genomics Consortium to provide a comprehensive annotation of the new highly contiguous reference genome for sheep Oar_rambouillet_v1.0. The project is funded by a USDA NIFA Tools and Resources grant. The Roslin Institute generated 56 CAGE libraries and produced an atlas of annotated transcription start sites across tissues using this dataset.
Collaborator Contribution The Ovine FAANG Project is a collaborative effort by the International Sheep Genomics Consortium and other partners produced 'omics datasets including ChIP-Seq, WGBS and RNA-Seq and Iso-Seq to provide a comprehensive annotation of the new highly contiguous reference genome for sheep Oar_rambouillet_v1.0.
Impact The datasets generated by the projects have been made available as a Bioproject in NCBI and the CAGE datasets are available also on the ENA with corresponding BAM files. The datasets have contributed directly to improving the annotation of the Rambouillet version 1 genome hosted on NCBI.
Start Year 2017
 
Description The Ovine FAANG Project 
Organisation Washington State University
Department Washington State University Spokane
Country United States 
Sector Academic/University 
PI Contribution The Ovine FAANG Project is a collaborative effort by the International Sheep Genomics Consortium to provide a comprehensive annotation of the new highly contiguous reference genome for sheep Oar_rambouillet_v1.0. The project is funded by a USDA NIFA Tools and Resources grant. The Roslin Institute generated 56 CAGE libraries and produced an atlas of annotated transcription start sites across tissues using this dataset.
Collaborator Contribution The Ovine FAANG Project is a collaborative effort by the International Sheep Genomics Consortium and other partners produced 'omics datasets including ChIP-Seq, WGBS and RNA-Seq and Iso-Seq to provide a comprehensive annotation of the new highly contiguous reference genome for sheep Oar_rambouillet_v1.0.
Impact The datasets generated by the projects have been made available as a Bioproject in NCBI and the CAGE datasets are available also on the ENA with corresponding BAM files. The datasets have contributed directly to improving the annotation of the Rambouillet version 1 genome hosted on NCBI.
Start Year 2017
 
Description 'What have DNA sequencing technologies ever done for the animal sciences?' BSAS Meeting 2015 Sheep Gene Expression Atlas 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact In 2015 the British Society for Animal Sciences Meeting was entitled 'What have DNA sequencing technologies ever done for the animal sciences?' and it was held at the Roslin Institute. There were over 100 delegates from academia, the animal breeding industry and the some members of the general public. Emily Clark gave a short presentation on the Sheep Gene Expression Atlas Project which sparked some interesting questions related to sample collection and the microbiome.
Year(s) Of Engagement Activity 2015
 
Description A Gene Expression Atlas for Sheep - AG100 Eskdale Show 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact In September 2019 as part of the Centenary of Animal Genetics in Edinburgh celebrations the Animal Genetics 100 Roadshow attended the Easkdale Show in Lake District. The Eskdale Show is the largest show for Herdwick sheep in the world and attended by more than 100 sheep farmers, breeders and members of the general public. We had a pop-up display entitled a 'Gene expression atlas for sheep' which was taken to this event and several other in the AG100 roadshow. Emily Clark attended and answered several questions from interested visitors to the show, many of whom were stakeholders in the sheep sector. She was also featured as an AG100 researcher on the Roslin Institute website.
Year(s) Of Engagement Activity 2019
URL https://www.ed.ac.uk/roslin/engage-with-us/ag100/ag-100-researchers
 
Description AAABG Meeting - Functional Annotation of Animal Genomes 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact David Hume was a plenary speaker at the Association for the Advancement of Animal Breeding and Genetics Meeting in Townsville, Queensland in July 2017. He introduced ideas more broadly relating to animal functional genomics and included the sheep and water buffalo gene expression project results. At the meeting there were animal breeders and industry representatives present as well as academic delegates.
Year(s) Of Engagement Activity 2017
URL http://www.aaabg2017.org/program/
 
Description BBSRC Cross Institute Workshop on Precision Breeding Functional Genomics Presentation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact In October 2018 the Roslin Institute hosted a one day workshop on "Precision breeding: genetic and genomic approaches to food security" that covered plants, animals and fish, and topics such as breeding and quantitative genetics, genomics and functional genomics, and genome editing. Delegates from John Innes, Rothamsted, Pirbirght, NIAB, Earlham, and Babraham attended. Emily Clark gave a presentation on the sheep gene expression atlas and functional genomics more widely and how information from functional assays can be applied to improve animal breeding in the context outlined in the workshop. A report from this meeting was prepared and sent to BBSRC.
Year(s) Of Engagement Activity 2018
 
Description BSAS Bacon, Beer and Biofuels Meeting 2014 Sheep Atlas Project Poster 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact The BSAS held a special meeting and Roslin Institute in 2014 entitled 'Bacon, Beer and Biofuels'. Emily Clark presented a poster at this meeting with an overview of the sheep gene expression atlas project. The meeting was attended by 100+ delegates and provided an opportunity to talk to some representatives from industry.
Year(s) Of Engagement Activity 2014
 
Description Big Data in Agriculture Meeting Speed Presentation Sheep Atlas Project 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Emily Clark gave a one minute speed presentation summarising the sheep gene expression atlas project at the Big Data in Agriculture Symposium that was held at the Roslin Institute in May 2019. Delegates included representatives from industry as well as scientific researchers from across the globe. She also presented a poster on the sheep gene expression atlas in the poster session.
Year(s) Of Engagement Activity 2018
 
Description Big Data in Agriculture Symposium Poster Presentation Allele Specific Expression Pipeline 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact In May 2018 at the Big Data in Agriculture Symposium at the Roslin Institute Mazdak Salavati presented a poster detailing a pipeline he had developed with colleagues in Germany to investigate allele specific expression across tissues in livestock, using the sheep gene expression atlas dataset as a model. During the poster session several delegates asked him questions relating to the methodology he had used.
Year(s) Of Engagement Activity 2018
 
Description BioGPS Spotlight on the Sheep Gene Expression Atlas 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Our collaborators in Andrew Su's lab at the Scripps Institute in California, run the BioGPS gene annotation portal where the sheep gene expression atlas is available. They have a website dedicated to public outreach and regularly run "spotlight" articles on datasets in BioGPS. For the article I was asked a number of questions relating to the dataset and it's scope and application. The reach of the article was international and sparked some interesting discussion and attention on Twitter.
Year(s) Of Engagement Activity 2017
URL http://sulab.org/2017/11/biogps-spotlight-on-the-sheep-gene-expression-atlas/?utm_source=feedburner&...
 
Description Easter Bush Research Seminar The Sheep Gene Expression Atlas 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact In April 2019 Emily Clark was invited to give the Easter Bush Campus Research Seminar at the Roslin Institute. She gave a seminar entitled 'The sheep gene expression atlas project and beyond'. During the seminar she described the sheep gene expression atlas project and work in CTLGH sequencing the genomes of tropically adapted sheep and goats. In the audience were researchers from the Roslin Institute, postgraduate and undergraduate students and some clinicians, as well as researchers from the Moredun Institute. There were a number of questions, relating to transcriptomics in sheep and goats and a number of opportunities for further collaboration were discussed.
Year(s) Of Engagement Activity 2019
URL https://www.ed.ac.uk/roslin/news-events/scientific-events/archive/building-model-transcriptome-rumin...
 
Description Edinburgh University Zoological Society Invited Speaker 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Undergraduate students
Results and Impact The Edinburgh University Zoological Society is run by undergraduate students in biological sciences, they invite speakers, usually one per month from within and outwith the University of Edinburgh to come and give a seminar on a wednesday evening. These seminars are usually well attended with up to 50 undergraduate and occasionally postgraduate students. Emily Clark spoke first to the group in 2015 at the start of the sheep gene expression atlas project and then again November 2017 at the end of the project. Both times the students were very engaged and asked several interesting questions.
Year(s) Of Engagement Activity 2015,2017
 
Description FAANG Metadata Workshop EBI Cambridge 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact The Functional Annotation of Animal Genomes Data Coordination Centre (FAANG-dcc) held a metadata entry and management workshop at the European Bioinformatics Institute in April 2016. This workshop provided training in entering and uploading metadata for tissue and cell samples for all FAANG projects to BioSamples according the FAANG defined metadata and data sharing standards. Emily Clark and Rachel Young attended the workshop and were able to implement this training in uploading all of the metadata for the sheep and water buffalo gene expression atlas projects to the BioSamples database.
Year(s) Of Engagement Activity 2016
 
Description Goat and Sheep Comparative Analysis Poster PAG 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Charity Muriuki a Newton Funded PhD student at Roslin presented a poster at the Plant and Animal Genomes Conference January 2018 entitled "Transcriptomics of Innate Immune Response in the Domestic Goat and Comparative Analysis with Sheep". The data see presented included data generated from the sheep gene expression atlas and the goat mini-atlas which was created using additional funding from her PhD studentship. The poster session at PAG is very popular and her poster was visited many times with interesting questions and discussion relating to where to take the analysis of the data and possible additional uses for the wider dataset.
Year(s) Of Engagement Activity 2018
URL https://pag.confex.com/pag/xxvi/meetingapp.cgi/Paper/30319
 
Description International Sheep Veterinary Society Conference 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact In July 2017 the International Sheep Veterinary Society Conference was held in Harrogate, UK. This international conference brings delegates from across the world. Some are from academia but a large proportion of practicing vets and representatives from the industry sector also attend. Emily Clark presented the sheep gene expression atlas project and Charity Muriuki presented the goat gene expression atlas work, both gave oral presentations and displayed posters in the poster session. The conference provided an excellent opportunity to present the gene expression atlas work and engage with stakeholders, both in industry and the veterinarians. There were several interesting questions focused on practical applications of the work such as what benefits the gene expression atlas will bring to farmers and how the information from the atlas can be used to inform new therapeutics for example.
Year(s) Of Engagement Activity 2017
 
Description International Society for Animal Genetics Poster 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact In 2017 the International Society of Animal Genetics meeting was held in Dublin. Emily Clark presented a poster at this meeting on the sheep gene expression atlas. The poster session was well attended and it provided an opportunity to raise the profile of the sheep gene expression atlas which has just been released on BioGPS and become a freely available resource for the ruminant genomics community. This conference also provided the opportunity to meet with the Ovine FAANG group to discuss the further funding from USDA.
Year(s) Of Engagement Activity 2017
 
Description Livestock Genomics Conference 2018 Sheep Atlas GI Tract Presentation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Emily Clark gave a presentation at the Livestock Genomics Meeting in Cambridge in September 2018. She presented the comprehensive transcriptional profiling of the ruminant gastrointestinal tract from birth to adulthood that was published at the end of 2018 in G3:Genes,Genomes,Genetic. This work used the gastrointestinal time series dataset from the sheep gene expression atlas project. There were approximately 60 people in the audience primarily research scientists but also representatives from industry. Questions and requests for further information related to the analysis software used, particularly for network cluster analysis were raised.
Year(s) Of Engagement Activity 2018
 
Description Livestock Genomics Meeting Cambridge 2018 Sheep Atlas Project ASE Presentation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Mazdak Salavati gave a presentation entitled "Analysis of allele-specific expression in immune-related tissues and cell types from the sheep gene expression atlas" at the Livestock Genomics meeting in Cambridge in 2018. This analysis used the dataset from the sheep gene expression atlas project. Questions were raised about the methodology and included some requests for further details and collaboration.
Year(s) Of Engagement Activity 2018
 
Description Livestock Genomics Meeting Cambridge Sheep Gene Expression Atlas Project 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact The Livestock Genomics Meeting run by the European Bioinformatics Institute is held every second year. There are around 400 delegates from predominantly Europe and the US institutions. Emily Clark presented the sheep gene expression atlas project at this meeting and was asked several interesting questions relating to the cell populations used and planned allele specific expression analysis.
Year(s) Of Engagement Activity 2016
 
Description Moredun Research Seminar Sheep Gene Expression Atlas 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact In November 2017 Emily Clark was asked to give the research seminar at the Moredun Research Institute on the Sheep Gene Expression Atlas project. The audience included scientists doing applied livestock research which can influence diagnostics, policy and decision making at a national scale. There were several requests for access to the dataset and enquiries about potential collaboration.
Year(s) Of Engagement Activity 2017
 
Description Next Generation Sequencing applications to improve livestock welfare, food security and socioeconomic stability in Brazil 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Emily Clark attended this workshop in Sao Paulo in Brazil funded by the Newton Fund. The aim of the workshop was to provide the opportunity for early career researchers from the UK and Brazil to meet and exchange ideas and forge new research collaborations that they could then take forward independently. She gave an overview of the sheep gene expression atlas project at the workshop and participated in networking and discussion on a diverse range of topics related to utilising NGS techology in Brazil.
Year(s) Of Engagement Activity 2015
 
Description Oral Presentation Cattle/Sheep/Goat Session Plant and Animal Genomes Conference 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact The Plant and Animal Genomes conference take place in San Diego USA every year in January. There are several sessions on livestock species. Emily Clark was invited to present the sheep gene expression atlas work in the Cattle/Sheep/Goat session. This was an excellent opportunity to engage with experts in the field of livestock genomics and transcriptomics and to demonstrate the utility of the sheep transcriptional atlas as a resource for the ruminant genomics community to use. There were some interesting questions and discussion that highlighted the potential for further work and acquisition of additional funding.
Year(s) Of Engagement Activity 2018
URL https://pag.confex.com/pag/xxvi/meetingapp.cgi/Paper/30388
 
Description Oral Presentation FAANG Session Plant and Animal Genomes Conference 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact The functional annotation of animal genomes consortium (FAANG) is an international consortium dedicated to improving the livestock genomes and linking genotype to phenotype. This was the first year that there was a half day dedicated session organised by the FAAAG consortium at the international plant and animal genomes conference in San Diego, January 2018. Emily Clark was invited to present an overview of the water buffalo and sheep transcriptome work to members of the consortium in this session. There were interesting questions raised and the opportunity to present the work to an audience of 50+ livestock genomics researchers both raised the profile of the atlas projects as a resource for the community to use and highlighted the potential for further related activity.
Year(s) Of Engagement Activity 2018
URL https://pag.confex.com/pag/xxvi/meetingapp.cgi/Paper/31781
 
Description Plant and Animal Genome XXIV Conference 2017 Update on the Sheep Gene Expression Atlas Project 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Emily Clark was invited to present on update on the Sheep Gene Expression Atlas Project at the International Sheep Genomics Consortium Workshop at PAG conference in San Diego. This workshop is very well attended with delegates from industry and academia. It provides an interesting forum for discussion, networking and collaboration. She also displayed a poster in sheep poster session on the sheep gene expression atlas. The poster sessions at PAG are also very well attended and she was asked several questions about the work.
Year(s) Of Engagement Activity 2017
 
Description Plant and Animal Genome XXV Conference 2016 Sheep Atlas Project Overview 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Emily Clark presented an overview of the planned work for the Sheep Gene Expression Atlas Project at the International Sheep Genomics Consortium Workshop at PAG conference in San Diego in 2016. This workshop is very well attended with international delegates from industry and academia. It provides an interesting forum discussion, networking and collaboration. She also displayed a poster in sheep poster session with an overview of the sheep gene expression atlas. The poster sessions at PAG are also very well attended and she was asked several questions about her work.
Year(s) Of Engagement Activity 2016
 
Description Plant and Animal Genome XXVII Conference 2019 Sheep Genomics Consortium Workshop Sheep Atlas GI Tract Presentation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Emily Clark gave a presentation in the International Sheep Genomics Consortium Workshop at the Plant and Animal Genomes Conference 2019. She presented the comprehensive transcriptional profiling of the ruminant gastrointestinal tract from birth to adulthood that was published at the end of 2018 in G3:Genes,Genomes,Genetic. This work used the gastrointestinal time series dataset from the sheep gene expression atlas project. There were approximately 60 people in the audience primarily research scientists but also representatives from industry. Questions and requests for further information related to the analysis software used, particularly for network cluster analysis and to the quality of the annotation of the current goat genome for comparative analysis.
Year(s) Of Engagement Activity 2019
URL https://pag.confex.com/pag/xxvii/meetingapp.cgi/Paper/35719
 
Description Research Seminar Royal Veterinary College Ruminant Transcriptomics 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact In February 2019 Emily Clark was asked to give the research seminar at the Royal Veterinary College. She gave a seminar entitled 'The sheep gene expression atlas project - building a model transcriptome for ruminants'. In the audience were researchers from the Royal Veterinary College and some clinicians. There were a number of questions and a number of opportunities for further collaboration particularly relating to innate immunity and disease phenotypes in sheep and goats were identified.
Year(s) Of Engagement Activity 2019
 
Description Ruminant Functional Genomics Research Group Website 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact In 2019 we launched webpages for the ruminant functional genomics research group at the Roslin Institute led by Emily Clark. These pages were put together by Mazdak Salavati and Emily Clark to represent the research programme and some key projects including the sheep gene expression atlas and population sequencing of tropically adapted sheep and goats. The reach of web pages should be international and they have led to several enquiries from visiting scientists and other requests for further information.
Year(s) Of Engagement Activity 2019
URL https://www.ed.ac.uk/roslin/ruminant-functional-genomics
 
Description Scotsman Newspaper Article the Sheep Gene Expression Atlas 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact The Scotman newspaper farming section ran an article on the sheep gene expression atlas entitled 'Sheep sector is following in the footsteps of Dolly'. Emily Clark and Alan Archibald were both interviewed for this article. The focus of the article was on how the sheep gene expression atlas could provide fresh insights into the genetic code of sheep and how this information could be used for accelerating breeding programmes aimed at improving their health and productivity. The article will have been read by industry stakeholders, farmers and members of the general public as the Scotsman is a national newspaper with wide and varied readership.
Year(s) Of Engagement Activity 2017
URL https://www.scotsman.com/business/companies/farming/sheep-sector-is-following-in-the-footsteps-of-do...
 
Description Sheep Atlas Project - Invited Speaker FANTOD Project 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Emily Clark was invited to present the sheep gene expression atlas project at a meeting for the FANTOD project (Functional Annotation of Dog Genomes) in Helsinki, Finland in November 2018. This was a small meeting of ~30 people working on the FANTOD project and two invited speakers. The sheep gene expression atlas was of particular interest to the group and they were keen to hear about the similarities between the two projects and any potential insights into how they could ensure the success of the FANTOD project in terms of lessons learned from the sheep atlas project related to tissue collection, project analysis and outputs.
Year(s) Of Engagement Activity 2017
 
Description Sheep Gene Expression Atlas Article in Farmers Weekly Magazine 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact The national farming magazine 'Farmers Weekly' ran an article on the 'Sheep Gene Expression Atlas Project' entitled 'Sheep gene 'atlas' could match cattle genomics'. Emily Clark and Alan Archibald were both interviewed for the article and provided some insight into the benefits to farmers that might be gained from the project and the dataset. Farmers Weekly is read by industry, stakeholders, veterinarians and farmers as well as members of the general public therefore the article would have reached a large and important audience to disseminate the research.
Year(s) Of Engagement Activity 2017
URL http://www.fwi.co.uk/livestock/sheep-gene-atlas-match-cattle-genomics.htm
 
Description Sheep Gene Expression Atlas Pop Up Sheep Roslin Open Day 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact The Roslin Institute Open Day is part of the Midlothian Science Festival, an annual science public engagement event for the region. The open day itself attracts 100's of visitors to the institute, including members of the general public, school children, media and also some attendees from business and stake holders. We designed a pop up anatomy sheep game to demonstrate gene expression across tissues to children between 7-16 years of age. The exhibit was designed around attaching the organs to the pop up sheep in the appropriate place and then choosing a ping pong ball with a gene name on it out of bucket and matching that to where the gene was expressed in the sheep and what function that gene that might have. The gene was then linked to a set of cards with different functions including immunity, pollness and mastitis. 100+ children played the game over the course of the day and many were very interested particularly in how a sheep differs in it's anatomy and gene expression from a human.
Year(s) Of Engagement Activity 2016
 
Description Sheep Gene Expression Atlas Pop Up Sheep Royal Highland Show 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact The Royal Highland Show at Ingliston Edinburgh occurs annually and is Scotland's largest agricultural show. The show itself attracts 1000's of visitors, including members of the general public, school children, media, farmers, vets and also other industry stake holders. We designed a pop up anatomy sheep game to demonstrate gene expression across tissues to children between 7-16 years of age, for the Roslin Institutes display. The exhibit was designed around attaching the organs to the pop up sheep in the appropriate place and then choosing a ping pong ball with a gene name on it out of bucket and matching that to where the gene was expressed in the sheep and what function that gene that might have. The gene was then linked to a set of cards with different functions including immunity, pollness and mastitis. 50+ children per day played the game over the course of the four days of the show and many were very interested particularly in how a sheep differs in it's anatomy and gene expression from a human. Several adults, including a handful of farmers also asked some questions and were interested in the uses of the atlas data set and how it might be used to answer questions related to productivity and disease resistance.
Year(s) Of Engagement Activity 2016
 
Description Sheep Gene Expression Atlas Poster PAG 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact The Plant and Animal Genome conference has a popular poster session for all delegates. Emily Clark presented a poster on the "Sheep Gene Expression Atlas Project" which included links to the data and associated resources. She spoke to 20+ delegates during the poster session about the work displayed on the poster and several asked for more information as they saw the potential to utilise the atlas dataset as a valuable resource to apply to their own research questions.
Year(s) Of Engagement Activity 2018
URL https://pag.confex.com/pag/xxvi/meetingapp.cgi/Paper/29349
 
Description Sheep Gene Expresson Atlas Article Scottish Farmer 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact The Scottish Farmer, Scotland's leading agricultural magazine ran a print only article on the sheep gene expression atlas project and the potential implications and benefits to farmers and other industry stakeholders of the work. The scope and popularity of this magazine and it's wide and varied readership meant the article will have reached a significant proportion of the national farming community.
Year(s) Of Engagement Activity 2017
 
Description Small ruminant functional genomics - 'Nuffield Council Working Group' on 'Genome Editing and Farm Animals' 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact In September 2019 Emily Clark gave a short presentation entitled 'Functional Genomics and Gene Editing in Small Ruminants Nuffield Council Working Group' on 'Genome Editing and Farm Animals'. She described how gene expression atlases can highlight potential targets for gene editing and how we can apply this technology in small ruminants. The working group asked several questions and reported that they found this presentation and the other presentations on the day very interesting and useful in compiling their review on genome editing and farmed animals for the Nuffield Council.
Year(s) Of Engagement Activity 2019
URL https://www.nuffieldbioethics.org/publications/genome-editing-and-farmed-animals
 
Description Sustainable African Goat Productivity Gains Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact In December 2014 Emily Clark travelled to the International Livestock Research Institute in Nairobi for a workshop on Sustainable African Goat Productivity Gains. She presented the plan for the sheep gene expression atlas and participated in facilitated discussions on stakeholder engagement, sustainable production and community based breeding programmes for goats. Numerous small ruminant scientists from across Africa attended and this meeting facilitated a collaboration with the University of DSchang in Cameroon which is still ongoing.
Year(s) Of Engagement Activity 2014
 
Description Texel Society R&D Visit November 2017 Sheep Atlas 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Joanne Connington from SRUC organises a regular meeting with the Texel Sheep Society, as part of her ongoing collaborations with them. During the working group meeting in November 2017 Emily Clark attended to discuss the sheep gene expression atlas project. She presented the work in a short informal discussion and suggested ways that the work might link with the priorities of the society and any potential overlap with current research and development goals. We would like to take a collaboration forward with the society to expand on the sheep atlas project, perhaps involving eQTL analysis with a large phenotyped population of sheep and both the Texel Society and Jo Connington at SRUC were keen to discuss and progress this further. The meeting was an excellent opportunity to engage with the sheep breeding industry and representatives from that sector and overall the society were very interested and the outcome overall was positive.
Year(s) Of Engagement Activity 2017
 
Description Transcriptomics of Innate Immune Response in the Domestic Goat and Comparative Analysis with Sheep PAG 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Charity Muriuki a PhD student working on Newton Funded PhD Studentship was invited to present her comparative analysis of some goat RNA-Seq data she had generated with the sheep gene expression dataset at the International Goat Genomics Consortium Workshop at the Plant and Animal Genomes Conference 2018 in San Diego USA. There were 50+ conference delegates in the audience, including many livestock geneticists and genomicists. There were several requests for more information following her presentation and also requests for access to the dataset, particularly as the dataset is being used to annotate the new goat reference assembly which was also mentioned during this workshop.
Year(s) Of Engagement Activity 2018
URL https://pag.confex.com/pag/xxvi/meetingapp.cgi/Paper/28600
 
Description University of Edinburgh Press Release Sheep Gene Expression Atlas Project 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact When the sheep gene expression atlas was published in PLoS Genetics the University of Edinburgh generated a press release describing the project entitled 'Sheep gene insights could help farmers breed healthier animals'. There was a particular focus on the implications of the work for improving sheep breeding and productivity and sub title of the article was 'Fresh insights into the genetic code of sheep could aid breeding programmes to improve their health and productivity.'. Emily Clark was interviewed for the article and helped the UoE press officer Jen Middleton to put it together. The press release triggered interest from the wider media and led to articles in Farmers Weekly, the Scottish Farmer, the Courier and farming section of the Scotsman newspaper.
Year(s) Of Engagement Activity 2017
URL https://www.ed.ac.uk/roslin/news-events/latest-news/sheep-gene-helps-breed-healthier-animals