Ensembl - adding value to animal genomes through high quality annotation
Lead Research Organisation:
University of Edinburgh
Department Name: The Roslin Institute
Abstract
This project will deliver high quality up-to-date annotated genomes for key farmed and domesticated animals to enable research on these economically and socially important species.
Research on domesticated animals has important socio-economic impacts, including underpinning and accelerating improvements in the animal sector of agriculture, contributing to medical research by providing animal models, improving animal health and welfare and informing understanding of natural and wild animal populations. High quality annotated genome sequences are key resources to enable such research.
The sequence of almost all genes (a reference genome sequence) has been determined for major farmed and domesticated animal species such as cattle, goats, sheep, pigs, chickens, ducks, turkeys, dogs and horses as well as for several important fish species, including cod, rainbow trout, salmon and tilapia. However, the strings of billions of bases (symbolised as four letters A, C, G, T) that constitute these genome sequences are not particularly useful or understandable on their own. Once a genome has been sequenced, it needs to be 'annotated' (i.e. explanatory notes need to be added to identify key features within the genome sequence) in order for research scientists to make sense of it.
Annotating reference genome sequences with features such as where the coding and regulatory parts of genes are located, and the bases which differ between individuals within a species (genetic variants) greatly enhances the value and utility of the genome sequence. Visualising the genome sequences complete with annotations in a freely accessible manner further improves the value of the information.
Ensembl provides a means for researchers to look at or 'browse' the annotated genome information. The databases and tools provided by Ensembl have been shown to be a powerful and effective means of annotating the complex genomes of animal species including humans, mice and more recently farmed and domesticated animals.
Enabled by advances in genome sequencing technologies and associated computational methods scientists around the world are generating more and better genome sequences. As the genome sequence of a single individual does not completely represent the genetic make-up of a species, scientists are also sequencing multiple individuals within a species. Individual research groups and international consortia are also generating sequence information that can be used in the annotation and analysis pipelines that we will run to identify both coding and regulatory sequences. We will use these data to annotate the genomes of farmed and domesticated animals, including aquaculture species. We will run comparative analyses to compare genomes both between species and between individuals within a species.
These richly annotated genome sequences, which are in effect maps of where the coding gene content and regulatory sequences are located, will be made freely available to the scientific community and others via the Ensembl Genome Browser mounted on the World Wide Web as well as via an Application Programming Interface for power users. We will also provide between and within species comparative views.
The annotated genomes that we will deliver are valuable not only to academic researchers, but also to scientists working in industry, including those in the animal breeding, animal health and pharmaceutical sectors. Keeping this information up-to-date, by characterising new genome sequences and integrating new data as it becomes available, is essential for reference genome sequences to remain current and useful.
Research on domesticated animals has important socio-economic impacts, including underpinning and accelerating improvements in the animal sector of agriculture, contributing to medical research by providing animal models, improving animal health and welfare and informing understanding of natural and wild animal populations. High quality annotated genome sequences are key resources to enable such research.
The sequence of almost all genes (a reference genome sequence) has been determined for major farmed and domesticated animal species such as cattle, goats, sheep, pigs, chickens, ducks, turkeys, dogs and horses as well as for several important fish species, including cod, rainbow trout, salmon and tilapia. However, the strings of billions of bases (symbolised as four letters A, C, G, T) that constitute these genome sequences are not particularly useful or understandable on their own. Once a genome has been sequenced, it needs to be 'annotated' (i.e. explanatory notes need to be added to identify key features within the genome sequence) in order for research scientists to make sense of it.
Annotating reference genome sequences with features such as where the coding and regulatory parts of genes are located, and the bases which differ between individuals within a species (genetic variants) greatly enhances the value and utility of the genome sequence. Visualising the genome sequences complete with annotations in a freely accessible manner further improves the value of the information.
Ensembl provides a means for researchers to look at or 'browse' the annotated genome information. The databases and tools provided by Ensembl have been shown to be a powerful and effective means of annotating the complex genomes of animal species including humans, mice and more recently farmed and domesticated animals.
Enabled by advances in genome sequencing technologies and associated computational methods scientists around the world are generating more and better genome sequences. As the genome sequence of a single individual does not completely represent the genetic make-up of a species, scientists are also sequencing multiple individuals within a species. Individual research groups and international consortia are also generating sequence information that can be used in the annotation and analysis pipelines that we will run to identify both coding and regulatory sequences. We will use these data to annotate the genomes of farmed and domesticated animals, including aquaculture species. We will run comparative analyses to compare genomes both between species and between individuals within a species.
These richly annotated genome sequences, which are in effect maps of where the coding gene content and regulatory sequences are located, will be made freely available to the scientific community and others via the Ensembl Genome Browser mounted on the World Wide Web as well as via an Application Programming Interface for power users. We will also provide between and within species comparative views.
The annotated genomes that we will deliver are valuable not only to academic researchers, but also to scientists working in industry, including those in the animal breeding, animal health and pharmaceutical sectors. Keeping this information up-to-date, by characterising new genome sequences and integrating new data as it becomes available, is essential for reference genome sequences to remain current and useful.
Technical Summary
High quality annotated genomes are essential resources for life sciences research.
Draft reference genome sequences have been established for several farmed and domesticated animals: cattle, goat, pig, sheep; chicken, duck, turkey; dog, horse; rainbow trout, salmon, tilapia. Substantially improved genome assemblies have been established for goat, pig, cattle, sheep, water buffalo, chicken) using long read sequencing technologies. There are gaps in the annotation of these genomes in terms of transcript complexity, non-coding genes, pseudogenes and regulatory sequences. Moreover, the pseudo haploid genome sequence of one individual provides an incomplete view of a species' genome.
Scientists are generating more and better genome sequences for additional species and individuals within a species. Researchers, especially in the FAANG and FAASG consortia are generating functional data for annotation of coding, non-coding and regulatory sequences.
We will analyse and annotate farmed and domesticated animal genomes as they are released, exploiting the growing volumes of functional data (short and long read RNA-seq / transcript sequences; ChIP-seq; ATAC-Seq; CAGE; bisulfite sequence) to identify coding genes, non-coding genes and regulatory sequences. We will acquire data from re-sequencing projects to characterise genetic variation within species (SNPs, indel, structural variants) and display this variation in its genomics context. We will run comparative genomics analyses both between species and within species.
We will disseminate the resulting richly annotated genome sequences freely via the Ensembl Genome Browser and via an API for power users. These annotated genomes will provide an integrated view of functional sequences (coding, non-coding and regulatory) and sequence variation for a single or multiple individuals for key farmed and domesticated animals.
To maximise use of this resource we will provide demonstrations, on-line and face-to-face training.
Draft reference genome sequences have been established for several farmed and domesticated animals: cattle, goat, pig, sheep; chicken, duck, turkey; dog, horse; rainbow trout, salmon, tilapia. Substantially improved genome assemblies have been established for goat, pig, cattle, sheep, water buffalo, chicken) using long read sequencing technologies. There are gaps in the annotation of these genomes in terms of transcript complexity, non-coding genes, pseudogenes and regulatory sequences. Moreover, the pseudo haploid genome sequence of one individual provides an incomplete view of a species' genome.
Scientists are generating more and better genome sequences for additional species and individuals within a species. Researchers, especially in the FAANG and FAASG consortia are generating functional data for annotation of coding, non-coding and regulatory sequences.
We will analyse and annotate farmed and domesticated animal genomes as they are released, exploiting the growing volumes of functional data (short and long read RNA-seq / transcript sequences; ChIP-seq; ATAC-Seq; CAGE; bisulfite sequence) to identify coding genes, non-coding genes and regulatory sequences. We will acquire data from re-sequencing projects to characterise genetic variation within species (SNPs, indel, structural variants) and display this variation in its genomics context. We will run comparative genomics analyses both between species and within species.
We will disseminate the resulting richly annotated genome sequences freely via the Ensembl Genome Browser and via an API for power users. These annotated genomes will provide an integrated view of functional sequences (coding, non-coding and regulatory) and sequence variation for a single or multiple individuals for key farmed and domesticated animals.
To maximise use of this resource we will provide demonstrations, on-line and face-to-face training.
Planned Impact
Who will benefit?
We expect that the beneficiaries will include: academic and industry researchers, animal breeding companies, owners or farmed and domesticated animals, suppliers of 'omics tools and wider society.
How will they benefit?
The Ensembl farmed and domesticated animal resources facilitates research on domesticated animals that has important socio-economic impacts, including underpinning improvements in the livestock sector, contributions to medical research, animal health and welfare, the evolution of domestication and the understanding of natural animal populations. Thus, the benefits to wider society are expected to be the result of research enabled by the Ensembl resources.
1. academic and industry researchers
High quality annotated animal genomes enable a wide range of research, including genetics studies of the target species, understanding gene networks that drive developmental biology and the development of improved animal models using precision genome editing.
2. animal breeding companies
Genomic prediction and selection has delivered significant improvements in the accuracy of selective animal breeding. Geneticists and breeders in the world's leading animal breeding and aquaculture breeding companies, of which some of the largest are UK companies will have access to improved annotation of functional sequences and sequence variation that will allow them to develop more sophisticated models for genomic prediction.
3. owners of farmed and domesticated animals
Owners of farmed animals will benefit indirectly through the supply of superior breeding stock and greater confidence in the genetic merit and performance of the resulting production animals. Owners of domestic and companion animals will also benefit indirectly through the use of genetic tests for inherited conditions developed through research enabled by the Ensembl resources.
4. suppliers of 'omics tools
Suppliers 'omics tools such as expression arrays, exon and other sequence capture products and SNP chips will also benefit from access to annotated genomes sequences that be used to design species specific products.
5. infrastructure and capacity building
The proposed project will contribute directly to capacity building by providing training including demonstrations, online tutorials and workshops in the use of the genome portal. This programme trains PhD students, Post Docs and research scientists to develop their skills in genome annotation, genome browsing and importantly how to interpret and understand their own data. Finally, the Ensembl - farmed and domesticated animals resource contributes to infrastructure to support the life sciences and is recognised as an ELIXIR resource in this context.
We expect that the beneficiaries will include: academic and industry researchers, animal breeding companies, owners or farmed and domesticated animals, suppliers of 'omics tools and wider society.
How will they benefit?
The Ensembl farmed and domesticated animal resources facilitates research on domesticated animals that has important socio-economic impacts, including underpinning improvements in the livestock sector, contributions to medical research, animal health and welfare, the evolution of domestication and the understanding of natural animal populations. Thus, the benefits to wider society are expected to be the result of research enabled by the Ensembl resources.
1. academic and industry researchers
High quality annotated animal genomes enable a wide range of research, including genetics studies of the target species, understanding gene networks that drive developmental biology and the development of improved animal models using precision genome editing.
2. animal breeding companies
Genomic prediction and selection has delivered significant improvements in the accuracy of selective animal breeding. Geneticists and breeders in the world's leading animal breeding and aquaculture breeding companies, of which some of the largest are UK companies will have access to improved annotation of functional sequences and sequence variation that will allow them to develop more sophisticated models for genomic prediction.
3. owners of farmed and domesticated animals
Owners of farmed animals will benefit indirectly through the supply of superior breeding stock and greater confidence in the genetic merit and performance of the resulting production animals. Owners of domestic and companion animals will also benefit indirectly through the use of genetic tests for inherited conditions developed through research enabled by the Ensembl resources.
4. suppliers of 'omics tools
Suppliers 'omics tools such as expression arrays, exon and other sequence capture products and SNP chips will also benefit from access to annotated genomes sequences that be used to design species specific products.
5. infrastructure and capacity building
The proposed project will contribute directly to capacity building by providing training including demonstrations, online tutorials and workshops in the use of the genome portal. This programme trains PhD students, Post Docs and research scientists to develop their skills in genome annotation, genome browsing and importantly how to interpret and understand their own data. Finally, the Ensembl - farmed and domesticated animals resource contributes to infrastructure to support the life sciences and is recognised as an ELIXIR resource in this context.
Organisations
- University of Edinburgh (Lead Research Organisation)
- ETH Zurich (Collaboration)
- Baylor College of Medicine (Collaboration)
- University of Minnesota (Collaboration)
- Aquicultura Balear SA (Collaboration)
- University of Liege (Collaboration)
- Jeju National University (Collaboration)
- Polish Academy of Sciences (Collaboration)
- GLASGOW CALEDONIAN UNIVERSITY (Collaboration)
- Centre for Genomic Regulation (CRG) (Collaboration)
- The Wellcome Trust Sanger Institute (Collaboration)
- Stolt-Nielsen (Collaboration)
- University of California, Berkeley (Collaboration)
- EMBL European Bioinformatics Institute (EMBL - EBI) (Collaboration)
- UNIVERSITY OF BIRMINGHAM (Collaboration)
- Edinethics (Collaboration)
- Science for Life Laboratory (Collaboration)
- Seoul National University (Collaboration)
- AquaGen (Collaboration)
- Huazhong Agricultural University (Collaboration)
- European Forum of Farm Animal Breeders (EFFAB) (Collaboration)
- Aarhus University (Collaboration)
- University of Copenhagen (Collaboration)
- University of Illinois at Urbana-Champaign (Collaboration)
- Norwegian University of Life Sciences (NMBU) (Collaboration)
- Panittica Italia Societa Agricola SRL (Collaboration)
- Faculdade de Medicina de Marília (Collaboration)
- Korea Research Institute of Bioscience and Biotechnology (KRIBB) (Collaboration)
- European Federation of Animal Science (Collaboration)
- National Institute of Animal Science, Korea (Collaboration)
- Commonwealth Scientific and Industrial Research Organisation (Collaboration)
- French Poultry and Aquaculture Breeders Association (Collaboration)
- Government of Catalonia (Collaboration)
- Wageningen University & Research (Collaboration)
- Washington State University (Collaboration)
- Uppsala University (Collaboration)
- Konkuk University (Collaboration)
- Parco Tecnologico Padano (Collaboration)
- AgResearch (Collaboration)
- Valle Ca' Zuliani (S.R.L.) (Collaboration)
- UNIVERSITY OF EDINBURGH (Collaboration)
- National Institute of Agrobiological Science, Japan (Collaboration)
- EARLHAM INSTITUTE (Collaboration)
- Natural Resources Institute Finland (Collaboration)
- Swedish University of Agricultural Sciences (Collaboration)
- Catalan Institution for Research and Advanced Studies (ICREA) (Collaboration)
- ABERYSTWYTH UNIVERSITY (Collaboration)
- Diagenode (Collaboration)
- Iowa State University (Collaboration)
- University of Padova (Collaboration)
- Penn State University (Collaboration)
- Utrecht University (Collaboration)
- Aarhus University Hospital (Collaboration)
- French National Institute of Agricultural Research (Collaboration)
- DURHAM UNIVERSITY (Collaboration)
- University of Limoges (Collaboration)
- Utah State University (Collaboration)
- UNIVERSITY OF ABERDEEN (Collaboration)
- U.S. Department of Agriculture USDA (Collaboration)
- University of Leipzig (Collaboration)
- University of Adelaide (Collaboration)
- University of Barcelona (Collaboration)
- University of Santiago de Compostela (Collaboration)
- University of Alberta (Collaboration)
- Eversole Associates (Collaboration)
- University College London (Collaboration)
- JSR Genetics (Collaboration)
- Martin Luther University of Halle-Wittenberg (Collaboration)
- OVAPISCIS SA (Collaboration)
- Beijing Genomics Institute (Collaboration)
- IMPERIAL COLLEGE LONDON (Collaboration)
- University of Idaho (Collaboration)
- Geneaqua SL (Collaboration)
- Genetic Information Research Institute (Collaboration)
- Hendrix Genetics (Collaboration)
- Leibniz Association (Collaboration)
- University of California, Davis (Collaboration)
- Cytocell Ltd (Collaboration)
- University of Illinois Urbana-Champaign (Collaboration)
- Hellenic Centre for Marine Research (HCMR) (Collaboration)
- Kansas State University (Collaboration)
- UNIVERSITY OF KENT (Collaboration)
- Xelect Ltd (Collaboration)
- National Health and Medical Research Council (Collaboration)
Publications
Archibald A
(2020)
An improved pig reference genome sequence to enable pig genetics and genomics research
in GigaScience
Clark EL
(2020)
From FAANG to fork: application of highly annotated genomes to improve farmed animal production.
in Genome biology
Cunningham F
(2022)
Ensembl 2022.
in Nucleic acids research
Davenport K
(2022)
An improved ovine reference genome assembly to facilitate in-depth functional annotation of the sheep genome
in GigaScience
Eory L
(2019)
Suina genomes and phylogenomics
Howe KL
(2021)
Ensembl 2021.
in Nucleic acids research
Hunt SE
(2022)
Annotating and prioritizing genomic variants using the Ensembl Variant Effect Predictor-A tutorial.
in Human mutation
Low WY
(2020)
Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle.
in Nature communications
Martin FJ
(2021)
Accessing Livestock Resources in Ensembl.
in Frontiers in genetics
| Description | Since the start of the current round of funding in summer 2019, there have been 10 releases of Ensembl annotation via the main Ensembl genome browser site from Ensembl Release 98 in September 2019 to Ensembl release 107 in July 2022. Ensembl Rapid Release is a new site within the Ensembl infrastructure designed to facilitate early release of annotation. During the course of the current BBSRC BBR grants the Ensembl Rapid Release site has been used as a staging post for new annotations of our target domesticated animal genomes. The key deliverables and milestones with respect to the farmed and companion animal species of interest are: Bovids: Annotation of the Water Buffalo reference genome sequence was released on the Ensembl Rapid Release site in July 2020. Goat: A second goat assembly (CVASU_BBG_1.0) has been annotated and released in May 2020 and is available under a goat breeds' tag in a manner analogous to that used for pigs and dogs. Pig: September 2019, Release 98 - a further 11 pig genome assemblies were annotated and released. These breed-specific annotations represent a significant resource for non-reference pig genomics. To better facilitate comparison between the reference and breed annotations, the reference gene set was also updated, utilising the latest gene finding code. The gene set was updated in April 2020, Release 100 and August 2020, Release 101. The number of non-coding genes and transcripts annotated have increased by 276% and 127%, respectively. Gene models built with RNA-Seq data generated by the EC H2020 GENE-SWitCH FAANG project have been added to the annotation on the Rapid Release Site prior to migrating to the main site in Release 107 in July 2022. Sheep: A new improved Rambouillet sheep reference genome assembly (Oar_rambouillet_v1.0) was annotated and released in May 2020. Annotation of the earlier draft Texel sheep reference genome sequence is also available on the main site. In a new development, variation data can be visualized in both these annotated genomes. Cat: An updated and patched genebuild was released for the Felis_catus_9.0 assembly in September 2019, Release 98 with further updates in April 2020, Release 100 and February 2021, Release 103. The updated gene set used the updated gene finding software and a wide range of transcriptomic data to significantly improve the existing annotation, particularly in terms of building more complete gene models. A further (American Shorthair) cat genome assembly has been annotated and is available on the Rapid Release site together with annotated genomes for F1 crossbreds between domestic and wild cat species. Dog: In September 2019, Release 98 an updated and patched genebuild was released for the CamFam3.1. This updated gene set used the updated gene finding software and a wide range of transcriptomic data to significantly improve the existing annotation, particularly in terms of building more complete gene models. In January 2020, Release 99 - a further 2 dog genome assemblies, Basenji and Great Dane, were annotated and released. In December 2021, Release 105 the Labrador Retriever assembly generated at Roslin and recognized as the new representative genome) was annotated and released together with an improved Boxer assembly. Annotated assemblies for a further two dogs (German Shepherds) and have been generated and are available on the Rapid Release site. Horse: In September 2019, Release 98 an updated and patched genebuild was released for the EquCab3.0 assembly. This updated gene set used the updated gene finding software and a wide range of transcriptomic data to significantly improve the existing annotation, particularly in terms of building more complete gene models. Further updates and patches to the gene set were released in January and April 2020. Chicken: Gene models built with RNA-Seq data generated by the EC H2020 GENE-SWitCH FAANG project were added to the annotation on the Rapid Release Site prior to migrating to the main site. Annotations are currently underway for layer and broiler breeds. On the main site the broiler assembly (bGalGal1.mat.broiler.GRCg7b (GCA_016699485.1)) is now recognised as the chicken reference genome, replacing the earlier reference of the Red Jungle Fowl that acted as a surrogate for the chicken. The annotated assembly of a White Leghorn layer's genome (bGalGal1.pat.whiteleghornlayer.GRCg7w, INSDC Assembly GCA_016700215.2) and an updated annotation the Red Jungle Fowl genome assembly (GRCg6a, INSDC Assembly GCA_000002315.5) are also available on the main site. Duck: A second duck genome (of a Mallard duck) was annotated and released in April 2020. Atlantic salmon: The first annotated reference genome of the Atlantic salmon was released in January 2020, Release 99. Annotation tracks from Salmobase and RefSeq were also loaded to help researchers reconstruct a clearer picture of the complex evolution of the salmon gene set. In July 2021 a new, higher quality reference (Ssal_v3.1 (GCA_905237065.2)) was annotated and released on Ensembl Rapid Release and is now available on the main site. Carp: In January 2020, Release 99 annotation for the genomes of three strains of common carp (german mirror, hebao red and huanghe) was released. In August 2021 a new, higher quality reference genome (Cypcar_WagV4.0 (GCA_905221575.1)) was annotated, released via Ensembl Rapid Release and is now available on the main site. Tilapia: In September 2019, Release 98 a new genebuild was released for the O_niloticus_UMD_NMBU assembly. This updated assembly and gene set used the updated gene finding software and a wide range of transcriptomic data to significantly improve the existing annotation, particularly in terms of building more complete gene models. We have provided deep comparative resources for both reference species and breeds. We have included all reference species on the main Ensembl website in our gene trees (as part of a collection of 200 vertebrate and model references), providing both the trees themselves and orthology/paralogy relationships. For each reference, we provide pairwise whole genome alignments to human or another suitable vertebrate reference (e.g. chicken for birds). For high quality genome assemblies, we have included them in our multi-whole genome alignments, such as our EPO alignments such as our 15 sauropsids EPO alignment, our 46 eutherian mammals EPO and our 37 fish EPO. For pig we have provided a custom breed-based comparative resource, which includes an EPO alignment of all 13 pig breeds (including the reference) and three outgroup species (cow, horse, sheep). In addition we have built gene trees for this same set of genomes. On our Rapid Release site we have begun to provide some basic comparative analyses, ahead of deeper integration on the main Ensembl website. The annotated reference genome sequences have been delivered through a series of ten Ensembl releases (Ensembl Release 98 in September 2019 to Ensembl release 107 in July 2022) and/or via the Ensembl Rapid Release. |
| Exploitation Route | The ongoing development of the richly annotated reference genomes of farmed and domestic animals is essential to research on these species and on applications that exploit genomic information. |
| Sectors | Agriculture, Food and Drink |
| URL | https://www.ensembl.org |
| Description | Annotated reference genome sequences are a key resource not only for biological research but also for the exploitation of genomic information by the private sector. For example, genomic selection, in which genome-wide genetic marker data are used to estimate genomic breeding values (GEBVs) of individuals by means of a genomic prediction equation, has facilitated significant acceleration in the genetic improvement of farmed animals, especially dairy cattle, pigs and poultry. This genomic prediction equation is calculated using a 'training' or 'reference' population where animals have both genotypes and phenotypes, and is then applied to selection candidates, which often have marker genotype information only. The annotated reference genome sequences are a key resource and framework for the identification of genetic variation such as Single Nucleotide Polymorphisms (SNPs) and subsequent development of SNP chips. The genotypic information required for implementation of genomic selection are acquired through the use of these SNP chips. This UKRI-BBSRC funded project has improved the annotation of the reference genomes of farmed animals and thus facilitated improvements to models used for implementing genomic selection in these species. |
| Sector | Agriculture, Food and Drink |
| Impact Types | Economic |
| Description | (BovReg) - BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Amount | € 6,033,458 (EUR) |
| Funding ID | 815668 |
| Organisation | European Commission |
| Sector | Public |
| Country | European Union (EU) |
| Start | 09/2019 |
| End | 08/2023 |
| Description | AQUA-FAANG: Advancing European Aquaculture by Genome Functional Annotation |
| Amount | £668,211 (GBP) |
| Organisation | European Commission |
| Sector | Public |
| Country | European Union (EU) |
| Start | 05/2019 |
| End | 04/2023 |
| Description | European Commission H2020-SFS30-2018-2020 Sustainable Food Security: The regulatory GENomE of SWine and CHicken: functional annotation during development |
| Amount | € 6,000,000 (EUR) |
| Funding ID | 817998 |
| Organisation | European Commission |
| Sector | Public |
| Country | European Union (EU) |
| Start | 07/2019 |
| End | 06/2023 |
| Description | USDA NIFA Sheep PanGenome Project |
| Amount | $500,000 (USD) |
| Organisation | U.S. Department of Agriculture USDA |
| Sector | Public |
| Country | United States |
| Start | 01/2021 |
| End | 01/2024 |
| Title | CAGE analysis pipeline for the BOVREG project (NextFlow - DSL2) |
| Description | This Github repository was created in December 2021 by Mazdak Salavati to describe an nf-core data analysis pipeline for CAGE sequencing data. The pipeline is available in NextFlow using the DSL2 programming language. The analysis pipeline was developed for the H202 BovReg project to analyse clusters of transcription start sites that are shared across tissues in cattle and to improve the annotation of the cattle genome. |
| Type Of Material | Data analysis technique |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | Collaborators in the BovReg have used data produced by this analysis pipeline to provide a novel annotation of the current reference genome for cattle. |
| URL | https://github.com/BovReg/nf-cage |
| Title | Common warthog (Phacochoerus africanus) reference genome sequence |
| Description | De novo assembly of a chromosome-level reference genome of the common warthog (Phacochoerus africanus). For the warthog assembly DNA was isolated from Pulmonary Alveolar Macrophages derived from a female individual. DNA long reads were isolated by Edinburgh Genomics and sequencing was done using Pacific Biosciences Sequel instruments at Pacific Biosciences and at Edinburgh Genomics. A total of 44 SMRT cells yielded 150Gbp of raw data with a read N50 of 13.9kbp, providing about 60x coverage of the genome. Contig level assembly was generated using Falcon and Falcon-unzip, reconstructing the 2.4 Gbp long genome in 1,500 contigs (with contig N50 of 3.2Mbp). Scaffolding was done using optical mapping data produced by Deep Seq on a Bionano Saphyr instrument, using Bionano Solve software. This was followed by scaffolding based on proximity ligation method. The Hi-C library was created using Dovetail Genomics' Hi-C library preparation kit. Refining the scaffolds were done with Dovetail Genomics' HiRise pipeline. Gaps in the assembly were filled with PBJelly using the PacBio long-read dataset. Error correction was done with Pilon, based on an Illumina short read library generated from the same warthog individual. The mitochondrial (MT) DNA was assembled from filtered, MT specific, PacBio long-read sequences using the Flye assembler and was error corrected with Illumina short-read data with Pilon. Data use: The assembly sequence is made publicly available by Prof. Alan L. Archibald, University of Edinburgh, Roslin Institute and Royal (Dick) School of Veterinary Studies, Midlothian, UK, under the terms of the Toronto Statement (Nature 2009, 461: 168) with the following understanding: Users are free to analyse these data if the providers of these data are properly cited, any whole genome analyses should follow guidelines outlined in the Ft. Lauderdale agreement on the use of this assembly and any redistribution of the data should carry this notice. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | None as yet |
| URL | https://www.ncbi.nlm.nih.gov/assembly/GCA_016906955.1/ |
| Title | PRJEB41485 ATAC-seq Frozen Pig Muscle |
| Description | This dataset contains 24 ATAC-Seq libraries generated from frozen pig muscle. The dataset was generated at the Roslin Institute to investigate gene expression and regulation in developing muscle from large white x landrace piglets of varying sizes and at multiple stages of development. A parallel RNA-Seq dataset (PRJEB41488) was also generated for this study. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | The dataset we have generated provides a powerful foundation to investigate how the genome is regulated in production pigs and contributes valuable functional annotation information to define and predict the effects of genetic variants in pig breeding programmes. The dataset will: 1) help us to understand the molecular drivers of muscle growth in pigs; 2) provide a foundation for functionally validating target genomic regions in in vitro systems and 3) identify high quality causative variants for muscle mass with the goal ofharnessing genetic variation and turning it into sustainable genetic gain in pig breeding programmes. |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB41485 |
| Title | PRJEB41488 RNA-Seq Pig Muscle |
| Description | This dataset of 28 RNA-Seq libraries was generated at the Roslin Institute to investigate gene expression and regulation in developing muscle from large white x landrace piglets of varying sizes and at multiple developmental time points. A parallel ATAC-Seq dataset (PRJEB41485) was also generated for this study. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | The dataset we have generated provides a powerful foundation to investigate how the genome is regulated in production pigs and contributes valuable functional annotation information to define and predict the effects of genetic variants in pig breeding programmes. This dataset will: 1) help us to understand the molecular drivers of muscle growth in pigs; 2) provide a foundation for functionally validating target genomic regions in in vitro systems and 3) identify high quality causative variants for muscle mass with the goal of harnessing genetic variation and turning it into sustainable genetic gain in pig breeding programmes. |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB41488 |
| Title | PRJEB43235 BovReg cattle CAGE libraries |
| Description | This dataset includes Cap Analysis Gene Expression (CAGE) sequencing libraries from 109 tissue samples collected from two neonatal Holstein animals from Belgium , two juvenile Kinsella composite animals from Canada and two Charolais x German Holstein F2 adult animals from Germany to perform a global analysis of TSS. Included in this dataset are the raw data CAGE libraries that were prepared and sequenced and the corresponding BAM files mapped to the ARS-UCD1.2 reference genome. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | We have generated 109 CAGE libraries from bovine tissues and provided the output as BAM files. These BAM files are accessible to all partners in BovReg via the private data portal at present (ENA Accession Number PRJEB43235) and will be made publicly available according to the timeframe agreed by the consortium. We are currently performing clustering of CAGE tags to annotate TSS across tissues. The results of the clustering will then be used to provide a high resolution map of the transcribed regions of the cattle genome. We believe, based on preliminary analysis of TSS annotated in the ARS-UCD1.2 genome, that the map of transcribed regions that we will generate for BovReg will be a significant improvement on the current gene annotation information which is available for cattle. |
| URL | https://data.faang.org/dataset/PRJEB43235 |
| Title | PRJEB52247 WGS of 36 Texel x Scottish Blackface Sheep for ASE analysis |
| Description | The dataset comprises 36 whole genome sequencing (WGS) libraries (2x 150bp) with a Q30% = >88.3% and an average coverage of 32.6x (raw reads). Included in the dataset are trios of animals comprised of Texel sires, Scottish Blackface and Texel x Scottish Blackface F1 lambs. The dataset was deposited in the European Nucleotide Archive under accession PRJEB52247 on 10th April 2022. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | This dataset will be used to generate individualised genomes for trios of Texel x Scottish blackface sheep. We will phase the haplotypes and use this information to anchor the RNA-Seq to accurately generate allele-specific expression information. |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB52247 |
| Title | PRJEB52253 RNA-Seq of tissues from Texel x Scottish Blackface sheep for ASE analysis |
| Description | This dataset includes 48 RNA-Seq libraries (2 x 150bp) with a Q30% = >92.42% and on average we have generated 126,362,804 raw reads per sample. 48 tissue samples were sequenced, including liver, muscle and ovary from five different developmental stages. The RNA-Seq libraries were generated from archived tissue samples collected from Texel x Scottish Blackface sheep at multiple developmental stages to investigate differential and allele-specific expression. In 2021 an additional 24 RNA-Seq libraries were added to this dataset from tissues from 100 day foetuses including lung, kidney cortex, ileum and the frontal lobe of the brain. The data was deposited in the European Nucleotide Archive on the 10th April 2022. The primary accession is PRJEB52253 and the secondary accession is ERP136947. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | This dataset will be used perform analysis of differential gene expression through early development and allele-specific expression. We will be able to phase this data using corresponding whole genome sequencing dataset for these sheep, generated for this project, and generate individual transcriptomes. This approach will allow to investigate allele-specific expression and it's effect on muscling and growth traits in sheep. |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB52253 |
| Title | PRJEB59755 CAGE-seq data from 12 tissues from Texel x Scottish Blackface sheep for analysis of transcriptional start sites |
| Description | This dataset includes 12 CAGE libraries from liver, muscle and ovary tissue from Texel x Scottish Blackface sheep. The libraries were generated on the Illumina NextSeq platform using a custom barcode configuration by the Clinical Research Facility at Western General Hospital in Edinburgh. The CAGE libraries were generated from archived tissue samples collected from Texel x Scottish Blackface sheep at multiple developmental stages to investigate differential TSS and validate isoform models from Iso-Seq data (PRJEB59757) from the same samples usage across tissues and developmental stages. The data is deposited in the European Nucleotide archive under primary accession PRJEB59755, secondary accession ERP144813. The title is Sheep CAGE-seq analysis for transcriptional start sites and validation of the ISO-seq data.and the submission date was 9th Feb 2023 |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | This dataset will contribute to improving the annotation of the sheep genome. There are currently few long read transcriptome datasets for sheep and this dataset will help to validate the TSS for the different isoforms captured by long read transcriptome sequencing. The data includes multiple developmental stages for production relevant tissues such as muscle and liver. |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB59755 |
| Title | PRJEB59757 Iso-Seq data from 12 tissues from Scottish Blackface x Texel sheep for isoform discovery |
| Description | This dataset includes 12 Iso-Seq libraries from liver, muscle and ovary tissue from Scottish Blackface x Texel sheep. The libraries were generated on the PacBio Sequel IIe platform by the Centre for Genomic Research in Liverpool. The Iso-Seq libraries were generated from archived tissue samples collected from Texel x Scottish Blackface sheep at multiple developmental stages to investigate differential isoform usage across tissues and developmental stages. The data is deposited in the European Nucleotide archive under primary accession PRJEB59757, secondary accession ERP144815. The title is Sheep RNA isoform analysis for growth traits using ISO-Seq (HiFi) and the submission date was 9th Feb 2023 |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | This dataset will contribute to improving the annotation of the sheep genome. There are currently few long read transcriptome datasets for sheep and this dataset will contribute additional developmental stages to existing datasets and also long read transcriptome information for two additional breeds. |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB59757 |
| Title | Supporting data for "An improved ovine reference genome assembly to facilitate in depth functional annotation of the sheep genome" |
| Description | This supporting information includes a lifted over annotation for ARS-UI_Ramb_v2.0 from Oar_Rambouillet_v1.0 that we generated to facilitate genomic analysis in sheep using the most recent reference genome. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | This supporting information includes a lifted over assembly that we generated that has helped to facilitate genomic analysis in sheep using the most recent reference genome. |
| URL | http://dx.doi.org/10.5524/100944 |
| Description | AQUA-FAANG |
| Organisation | AquaGen |
| Country | Norway |
| Sector | Private |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | Aquicultura Balear SA |
| Country | Spain |
| Sector | Private |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | EMBL European Bioinformatics Institute (EMBL - EBI) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | European Forum of Farm Animal Breeders (EFFAB) |
| Country | Netherlands |
| Sector | Learned Society |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | French National Institute of Agricultural Research |
| Department | INRA Versailles |
| Country | France |
| Sector | Academic/University |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | French Poultry and Aquaculture Breeders Association |
| Country | France |
| Sector | Charity/Non Profit |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | Geneaqua SL |
| Country | Spain |
| Sector | Private |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | Hellenic Centre for Marine Research (HCMR) |
| Country | Greece |
| Sector | Private |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | Imperial College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | Norwegian University of Life Sciences (NMBU) |
| Country | Norway |
| Sector | Academic/University |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | OVAPISCIS SA |
| Country | Spain |
| Sector | Private |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | Panittica Italia Societa Agricola SRL |
| Country | Italy |
| Sector | Private |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | Polish Academy of Sciences |
| Country | Poland |
| Sector | Public |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | Stolt-Nielsen |
| Department | Stolt Sea Farm S.A. |
| Country | Spain |
| Sector | Private |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | University of Aberdeen |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | University of Barcelona |
| Country | Spain |
| Sector | Academic/University |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | University of Birmingham |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | University of Edinburgh |
| Department | The Roslin Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | University of Padova |
| Country | Italy |
| Sector | Academic/University |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | University of Santiago de Compostela |
| Country | Spain |
| Sector | Academic/University |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | Valle Ca' Zuliani (S.R.L.) |
| Country | Italy |
| Sector | Private |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | Wageningen University & Research |
| Country | Netherlands |
| Sector | Academic/University |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | AQUA-FAANG |
| Organisation | Xelect Ltd |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Roslin scientists contributed to the development of the H2020 grant application that is supporting this partnership to deliver improvements in understanding the genomes of the six most important European farmed fish species. Roslin scientists are contributing to experimental design, generation of experimental data, data analysis and interpretation. |
| Collaborator Contribution | The other partners in this partnership have a range of expertise, skills, capabilities and facilities in academia and commercial companies. These partners are contributing to experimental design, data generation, data analysis and interpretation. Some partner are also contributing to dissemination and implementation of the project results. |
| Impact | The partnership has secured 6 million Euros of Horizon 2020 funding to deliver a research project on Functional Annotation of ANimal Genomes (FAANG) in six farmed fish species. See also https://www.aqua-faang.eu/ |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Aarhus University |
| Country | Denmark |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Centre for Genomic Regulation (CRG) |
| Country | Spain |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Diagenode |
| Country | Belgium |
| Sector | Private |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | EMBL European Bioinformatics Institute (EMBL - EBI) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | ETH Zurich |
| Country | Switzerland |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Edinethics |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | European Federation of Animal Science |
| Country | Italy |
| Sector | Public |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Faculdade de Medicina de Marília |
| Country | Brazil |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | French National Institute of Agricultural Research |
| Department | INRA Versailles |
| Country | France |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Leibniz Association |
| Department | Leibniz Institute for Farm Animal Biology |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Martin Luther University of Halle-Wittenberg |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Natural Resources Institute Finland |
| Country | Finland |
| Sector | Public |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Polish Academy of Sciences |
| Department | Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences |
| Country | Poland |
| Sector | Public |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | University of Alberta |
| Country | Canada |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | University of Edinburgh |
| Department | The Roslin Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | University of Liege |
| Country | Belgium |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | University of Limoges |
| Country | France |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Utrecht University |
| Country | Netherlands |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle |
| Organisation | Wageningen University & Research |
| Country | Netherlands |
| Sector | Academic/University |
| PI Contribution | Scientists at The Roslin Institute contributed to the development of the H2020 grant application that supports the BovReg project. Roslin scientists are contributing to experimental design, data generation and analysis. |
| Collaborator Contribution | The other partners in this partnership have a range of different expertise, skills, capabilities and facilities. They are contributing to sample collection and processing, generation of experimental data, data analysis and interpretation. Some partners have specific responsibilities for training and dissemination. |
| Impact | This partnership has secured 6 million Euros from Horizon 2020 for research in cattle within the scope of the Functional Annotation of ANimal Genomes (FAANG) initiative. |
| Start Year | 2017 |
| Description | Development of tools to detect chromosomal translocations in pigs |
| Organisation | Cytocell Ltd |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | I provided my detailed knowledge of the Swine Genome Sequencing Consortium's project that produced the draft pig reference genome sequence (Sscrofa10.2) as described by Groenen et al. 2012. Pig genomes provide insight into porcine demography and evolution. Nature 491: 393-398 and the pig physical mapping project as described by Humphray et al. 2007. A high utility integrated map of the pig genome. Genome Biology 8:R139. My research team had also established the bacterial artificial chromosome (BAC) library resource described by Anderson et al. 2000. A large fragment porcine genomic library resource in a BAC vector. Mammalian Genome 11, 811-814. BAC clones from this library were used as probes for fluorescent in situ hybridisation (FISH) experiments in this collaborative project. My knowledge of the pig physical mapping and pig genome sequencing projects was critical in interpreting the anomalous and unexpected results from the initial FISH experiments. |
| Collaborator Contribution | This collaboration was initiated and led by Prof Darren Griffin and colleagues at the University of Kent. In addition to leading the collaboration the Kent team delivered the expertise in cytogenetics analysis. JSR Genetics provided animal materials and phenotypes. Cytocell Ltd provided technical expertise and the Chromoprobe Multiprobe System. The work was funded by an Innovate UK Knowledge Transfer Partnership to Prof Darren Griffin and Cytocell Ltd. |
| Impact | The project has demonstrated that FISH-based translocation screening is a powerful and reliable approach to screening for chromosomal translocation that can have adverse effects on fertility. The device described by O'Connor et al. (see below) is now a commercial product marketed by Cytocell Ltd. The project results have been useful if anchoring the new improved pig reference genome sequence to chromosomes and confirming the order and orientation for each chromosomal sequence. The results of the study have been published by O'Connor et al. Isolation of subtelomeric sequences of porcine chromosomes for translocation screening reveals errors in the pig genome assembly. Animal Genetics (in press). The research undertaken by Rebecca O'Connor is a major component of her PhD research studies. |
| Start Year | 2014 |
| Description | Development of tools to detect chromosomal translocations in pigs |
| Organisation | JSR Genetics |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | I provided my detailed knowledge of the Swine Genome Sequencing Consortium's project that produced the draft pig reference genome sequence (Sscrofa10.2) as described by Groenen et al. 2012. Pig genomes provide insight into porcine demography and evolution. Nature 491: 393-398 and the pig physical mapping project as described by Humphray et al. 2007. A high utility integrated map of the pig genome. Genome Biology 8:R139. My research team had also established the bacterial artificial chromosome (BAC) library resource described by Anderson et al. 2000. A large fragment porcine genomic library resource in a BAC vector. Mammalian Genome 11, 811-814. BAC clones from this library were used as probes for fluorescent in situ hybridisation (FISH) experiments in this collaborative project. My knowledge of the pig physical mapping and pig genome sequencing projects was critical in interpreting the anomalous and unexpected results from the initial FISH experiments. |
| Collaborator Contribution | This collaboration was initiated and led by Prof Darren Griffin and colleagues at the University of Kent. In addition to leading the collaboration the Kent team delivered the expertise in cytogenetics analysis. JSR Genetics provided animal materials and phenotypes. Cytocell Ltd provided technical expertise and the Chromoprobe Multiprobe System. The work was funded by an Innovate UK Knowledge Transfer Partnership to Prof Darren Griffin and Cytocell Ltd. |
| Impact | The project has demonstrated that FISH-based translocation screening is a powerful and reliable approach to screening for chromosomal translocation that can have adverse effects on fertility. The device described by O'Connor et al. (see below) is now a commercial product marketed by Cytocell Ltd. The project results have been useful if anchoring the new improved pig reference genome sequence to chromosomes and confirming the order and orientation for each chromosomal sequence. The results of the study have been published by O'Connor et al. Isolation of subtelomeric sequences of porcine chromosomes for translocation screening reveals errors in the pig genome assembly. Animal Genetics (in press). The research undertaken by Rebecca O'Connor is a major component of her PhD research studies. |
| Start Year | 2014 |
| Description | Development of tools to detect chromosomal translocations in pigs |
| Organisation | University of Kent |
| Department | Medway School of Pharmacy |
| Country | United Kingdom |
| Sector | Hospitals |
| PI Contribution | I provided my detailed knowledge of the Swine Genome Sequencing Consortium's project that produced the draft pig reference genome sequence (Sscrofa10.2) as described by Groenen et al. 2012. Pig genomes provide insight into porcine demography and evolution. Nature 491: 393-398 and the pig physical mapping project as described by Humphray et al. 2007. A high utility integrated map of the pig genome. Genome Biology 8:R139. My research team had also established the bacterial artificial chromosome (BAC) library resource described by Anderson et al. 2000. A large fragment porcine genomic library resource in a BAC vector. Mammalian Genome 11, 811-814. BAC clones from this library were used as probes for fluorescent in situ hybridisation (FISH) experiments in this collaborative project. My knowledge of the pig physical mapping and pig genome sequencing projects was critical in interpreting the anomalous and unexpected results from the initial FISH experiments. |
| Collaborator Contribution | This collaboration was initiated and led by Prof Darren Griffin and colleagues at the University of Kent. In addition to leading the collaboration the Kent team delivered the expertise in cytogenetics analysis. JSR Genetics provided animal materials and phenotypes. Cytocell Ltd provided technical expertise and the Chromoprobe Multiprobe System. The work was funded by an Innovate UK Knowledge Transfer Partnership to Prof Darren Griffin and Cytocell Ltd. |
| Impact | The project has demonstrated that FISH-based translocation screening is a powerful and reliable approach to screening for chromosomal translocation that can have adverse effects on fertility. The device described by O'Connor et al. (see below) is now a commercial product marketed by Cytocell Ltd. The project results have been useful if anchoring the new improved pig reference genome sequence to chromosomes and confirming the order and orientation for each chromosomal sequence. The results of the study have been published by O'Connor et al. Isolation of subtelomeric sequences of porcine chromosomes for translocation screening reveals errors in the pig genome assembly. Animal Genetics (in press). The research undertaken by Rebecca O'Connor is a major component of her PhD research studies. |
| Start Year | 2014 |
| Description | Ensembl - farmed and companion animals 2014 |
| Organisation | EMBL European Bioinformatics Institute (EMBL - EBI) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | This partnership continues a 10 year collaborative effort to annotate the reference genome sequences of the major farmed animal species. The Roslin Institute partner contributes reference genome sequences for some of these farmed animal species through its leadership and participation in international farm animal genome sequencing projects / consortia. The Roslin Institute partner also provides ancillary sequence data which are used for annotation, such as extensive RNA-seq data from multiple sheep tissues. Finally, the Roslin Institute partner also provides key links to the farm animal genetics and genomics research community and the user communities in academia and industry. |
| Collaborator Contribution | The Ensembl team at EMBL-EBI provide the expertise semi-automated genome sequence annotation, including gene builds, comparative genome analyses, functional annotation and evaluation of sequence variants. The EMBL-EBI also provide the compute infrastructure for the annotation processing and for access to the annotated genomes via the Ensembl Genome Browser. Finally, the EMBL-EBI team lead the training activities. |
| Impact | The primary output from this collaboration are annotated reference genome sequences for farmed and companion animal species, including chickens, duck, turkey, pig, sheep, cattle, dog and horse. |
| Description | Functional Annotation of Animal Genomes (FAANG) |
| Organisation | AgResearch |
| Department | Invermay Agricultural Centre |
| Country | New Zealand |
| Sector | Private |
| PI Contribution | I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young). |
| Collaborator Contribution | The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term. |
| Impact | 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site. |
| Start Year | 2012 |
| Description | Functional Annotation of Animal Genomes (FAANG) |
| Organisation | EMBL European Bioinformatics Institute (EMBL - EBI) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young). |
| Collaborator Contribution | The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term. |
| Impact | 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site. |
| Start Year | 2012 |
| Description | Functional Annotation of Animal Genomes (FAANG) |
| Organisation | French National Institute of Agricultural Research |
| Country | France |
| Sector | Academic/University |
| PI Contribution | I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young). |
| Collaborator Contribution | The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term. |
| Impact | 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site. |
| Start Year | 2012 |
| Description | Functional Annotation of Animal Genomes (FAANG) |
| Organisation | Iowa State University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young). |
| Collaborator Contribution | The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term. |
| Impact | 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site. |
| Start Year | 2012 |
| Description | Functional Annotation of Animal Genomes (FAANG) |
| Organisation | Swedish University of Agricultural Sciences |
| Country | Sweden |
| Sector | Academic/University |
| PI Contribution | I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young). |
| Collaborator Contribution | The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term. |
| Impact | 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site. |
| Start Year | 2012 |
| Description | Functional Annotation of Animal Genomes (FAANG) |
| Organisation | U.S. Department of Agriculture USDA |
| Department | Avian Disease and Oncology Laboratory (ADOL) |
| Country | United States |
| Sector | Public |
| PI Contribution | I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young). |
| Collaborator Contribution | The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term. |
| Impact | 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site. |
| Start Year | 2012 |
| Description | Functional Annotation of Animal Genomes (FAANG) |
| Organisation | U.S. Department of Agriculture USDA |
| Department | National Animal Disease Center |
| Country | United States |
| Sector | Public |
| PI Contribution | I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young). |
| Collaborator Contribution | The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term. |
| Impact | 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site. |
| Start Year | 2012 |
| Description | Functional Annotation of Animal Genomes (FAANG) |
| Organisation | University of Adelaide |
| Department | School of Animal and Veterinary Sciences |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young). |
| Collaborator Contribution | The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term. |
| Impact | 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site. |
| Start Year | 2012 |
| Description | Functional Annotation of Animal Genomes (FAANG) |
| Organisation | University of California, Davis |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young). |
| Collaborator Contribution | The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term. |
| Impact | 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site. |
| Start Year | 2012 |
| Description | Functional Annotation of Animal Genomes (FAANG) |
| Organisation | Uppsala University |
| Department | Department of Medical Biochemistry and Microbiology |
| Country | Sweden |
| Sector | Academic/University |
| PI Contribution | I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young). |
| Collaborator Contribution | The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term. |
| Impact | 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site. |
| Start Year | 2012 |
| Description | Functional Annotation of Animal Genomes (FAANG) |
| Organisation | Wageningen University & Research |
| Country | Netherlands |
| Sector | Academic/University |
| PI Contribution | I was a major initiator of the Functional Annotation of Animal Genomes (FAANG) initiative. Initially this initiative was known as AgENCODE. Scientists at The Roslin Institute contribute to this collaboration through membership of the FAANG Steering Committee (A Archibald, D Burt, M Watson); the Animals, Samples and Assays committee (D Burt, E Clark, M McCulloch, J Smith, M Watson, R Young); the Bioinformatics and Data Analysis committee (M Watson (co-chair), D Burt, L Eory, R Kuo, M McCulloch); Communication (A Archibald, M Watson); and Metadata and Data Sharing committee (A Archibald, S Bush, E Clark, M Watson, R Young). |
| Collaborator Contribution | The FAANG initiative is an open international collaborative project. The project partners are developing agreed standards for i) experiments to generate the data required for functional annotation of animal genomes, ii) meta data, iii) data analysis and iv) data sharing. A few partners have secured funding for pilot data generation efforts and are producing initial data sets. The partners at EMBL-European Bioinformatics Insitute are establishing the Data Coordination Centre (DCC) function for FAANG. The EMBL-EBI partners, together with A Archibald and D Burt at The Roslin Institute are seeking funding to support the DCC in the medium term. |
| Impact | 280 scientists from around the world have identified themselves as contributors to FAANG. To date (March 2016) the listed collaborators are limited to those institutions from which the authors of the paper below are drawn. The FAANG Consortium published their vision for this collaborative venture (The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elsik, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khattib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulu, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Boichard, M., Tosser-Klop, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S. and Zhou, H., 2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16: 57). A workshop (GO-FAANG) to launch FAANG and to engage with potential funders was held at the US National Academy of Sciences, Washington DC over 7-8 October 2015. Funding has been secured to establish a COST Action Functional Annotation of Animal Genomes - European network (FAANG-Europe)) CA1152. A data sharing agreement has been completed and individuals who sign up as FAANG contributors are expected to comply with the data sharing agreement, including placing experimental data in the public domain in advance of publication. Further outcomes can be monitored through the FAANG web-site. |
| Start Year | 2012 |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Aarhus University Hospital |
| Country | Denmark |
| Sector | Hospitals |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Aberystwyth University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Beijing Genomics Institute |
| Country | China |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Catalan Institution for Research and Advanced Studies (ICREA) |
| Department | ICREA Centre for Research in Agricultural Genomics (CRAG) |
| Country | Spain |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Durham University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | EMBL European Bioinformatics Institute (EMBL - EBI) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Earlham Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Eversole Associates |
| Country | United States |
| Sector | Private |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | French National Institute of Agricultural Research |
| Department | GABI: Animal Genetics and Integrative Biology unit |
| Country | France |
| Sector | Private |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | French National Institute of Agricultural Research |
| Department | Physiology of Reproduction and Behavior |
| Country | France |
| Sector | Private |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | French National Institute of Agricultural Research |
| Country | France |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Genetic Information Research Institute |
| Country | United States |
| Sector | Charity/Non Profit |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Glasgow Caledonian University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Huazhong Agricultural University |
| Country | China |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Iowa State University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Jeju National University |
| Country | Korea, Republic of |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Kansas State University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Konkuk University |
| Country | Korea, Republic of |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Konkuk University |
| Country | Korea, Republic of |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Korea Research Institute of Bioscience and Biotechnology (KRIBB) |
| Country | Korea, Republic of |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | National Health and Medical Research Council |
| Country | Australia |
| Sector | Public |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | National Institute of Agrobiological Science, Japan |
| Country | Japan |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | National Institute of Animal Science, Korea |
| Country | Korea, Republic of |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | National Institute of Animal Science, Korea |
| Country | Korea, Republic of |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Parco Tecnologico Padano |
| Country | Italy |
| Sector | Private |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Penn State University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Science for Life Laboratory |
| Country | Sweden |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Seoul National University |
| Country | Korea, Republic of |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | The Wellcome Trust Sanger Institute |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | U.S. Department of Agriculture USDA |
| Department | Beltsville Agricultural Research Center |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | U.S. Department of Agriculture USDA |
| Department | U.S. Meat Animal Research Center |
| Country | United States |
| Sector | Public |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | U.S. Department of Agriculture USDA |
| Country | United States |
| Sector | Public |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | University College London |
| Department | Division of Infection and Immunity |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | University of California, Berkeley |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | University of California, Davis |
| Department | UC Davis Genome Cente |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | University of Copenhagen |
| Department | Department of Basic Animal and Veterinary Sciences (IBHV) |
| Country | Denmark |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | University of Illinois |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | University of Illinois at Urbana-Champaign |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | University of Illinois at Urbana-Champaign |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | University of Illinois at Urbana-Champaign |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | University of Illinois at Urbana-Champaign |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | University of Illinois at Urbana-Champaign |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | University of Kent |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | University of Leipzig |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | University of Minnesota |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Uppsala University |
| Country | Sweden |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Uppsala University |
| Country | Sweden |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | International Swine Genome Sequencing Consortium |
| Organisation | Wageningen University & Research |
| Country | Netherlands |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner in the Swine Genome Sequencing Consortium contributed to the leadership of the pig genome sequencing project, coordination of analysis and annotation and writing the genome paper. On-going commitments to the SGSC include efforts to improve the reference genome sequence and assembly, including generating additional genome sequence data and ancillary sequence data for annotation. |
| Collaborator Contribution | The other partners in the SGSC have contributed in multiple roles, including genome sequencing and analysis. The roles of each partner are recorded in the pig genome sequence paper as published in Nature in 2012 (Groenen et al. 2012. Nature 491: 393-398) |
| Impact | The primary output from this collaborative partnership was the publication of the draft reference genome sequence of the pig (Sus scrofa) in Nature in November 2012. Groenen et al. 2012. Nature 491: 393-398 and associated companion papers. The genome sequence data are accessible in the public DNA sequence repositories and the annotated sequence can be accessed in the three main genome browsers (Ensembl, NCBI, UCSC). The SGSC has a continuing interest in improving the reference genome sequence. However, this task is mainly being pursued by the founding core partners. |
| Description | Pig T2T Genome Assembly |
| Organisation | U.S. Department of Agriculture USDA |
| Department | U.S. Meat Animal Research Center |
| Country | United States |
| Sector | Public |
| PI Contribution | To provide samples to generate a new telomere to telomere genome assembly for pig, we collected tissues from a Hampshire x (Large white x Landrace) F1 fetus at 72 days of gestation and shipped these to USMARC. We also collected samples to generate DNA from the two parent animals and sent these to NeoGen to generate Illumina short read data for haplotype phasing, which we also subsequently transferred to USMARC. We plan to generate RNA from the tissue samples and send this for long read isoform sequencing. We routinely participate in swine genomics consortium calls with US collaborators to progress generating the T2T assembly and annotation. |
| Collaborator Contribution | Our collaborators at USMARC and USDA-ARS in Beltsville received the tissue samples and have generated PacBio HiFi, and Oxford Nanopore data to build a telomere to telomere assembly for pig. They will use a trio-binning approach to generate the assembly, and also plan to generate methylation data for several of the tissues. |
| Impact | No outputs yet, data is still being generated. |
| Start Year | 2022 |
| 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | The Ovine PanGenome Project |
| Organisation | AgResearch |
| Department | Invermay Agricultural Centre |
| Country | New Zealand |
| Sector | Private |
| PI Contribution | The Ovine Pangenome project is funded by USDA NIFA. We are co-investigators in the project and will provide expertise in analysing allele-specific expression in a set of tissues collected from F1 crosses of divergent sheep breeds. The project will generate at least 10 new long read genome assemblies for sheep and the RNA-Seq and allele-specific expression analysis will be used to generate breed specific transcriptomes and identify unique expressed variants to each of the breeds. One of the crosses we will generate new assemblies for is the Texel x Scottish Blackface which will complement ongoing UKRI grants. |
| Collaborator Contribution | This project is led by the University of Idaho. Partners in this project are generating crosses of the divergent sheep breeds to generate tissue to use to generate the long read assemblies and the transcriptomes. They are also performing library preparation and sequencing and performing genome assembly. They will make the new assemblies publicly available by uploading them to NCBI. |
| Impact | No impact yet the project is still ongoing. |
| Start Year | 2021 |
| Description | The Ovine PanGenome Project |
| Organisation | U.S. Department of Agriculture USDA |
| Department | Beltsville Agricultural Research Center |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The Ovine Pangenome project is funded by USDA NIFA. We are co-investigators in the project and will provide expertise in analysing allele-specific expression in a set of tissues collected from F1 crosses of divergent sheep breeds. The project will generate at least 10 new long read genome assemblies for sheep and the RNA-Seq and allele-specific expression analysis will be used to generate breed specific transcriptomes and identify unique expressed variants to each of the breeds. One of the crosses we will generate new assemblies for is the Texel x Scottish Blackface which will complement ongoing UKRI grants. |
| Collaborator Contribution | This project is led by the University of Idaho. Partners in this project are generating crosses of the divergent sheep breeds to generate tissue to use to generate the long read assemblies and the transcriptomes. They are also performing library preparation and sequencing and performing genome assembly. They will make the new assemblies publicly available by uploading them to NCBI. |
| Impact | No impact yet the project is still ongoing. |
| Start Year | 2021 |
| Description | The Ovine PanGenome Project |
| Organisation | U.S. Department of Agriculture USDA |
| Department | U.S. Meat Animal Research Center |
| Country | United States |
| Sector | Public |
| PI Contribution | The Ovine Pangenome project is funded by USDA NIFA. We are co-investigators in the project and will provide expertise in analysing allele-specific expression in a set of tissues collected from F1 crosses of divergent sheep breeds. The project will generate at least 10 new long read genome assemblies for sheep and the RNA-Seq and allele-specific expression analysis will be used to generate breed specific transcriptomes and identify unique expressed variants to each of the breeds. One of the crosses we will generate new assemblies for is the Texel x Scottish Blackface which will complement ongoing UKRI grants. |
| Collaborator Contribution | This project is led by the University of Idaho. Partners in this project are generating crosses of the divergent sheep breeds to generate tissue to use to generate the long read assemblies and the transcriptomes. They are also performing library preparation and sequencing and performing genome assembly. They will make the new assemblies publicly available by uploading them to NCBI. |
| Impact | No impact yet the project is still ongoing. |
| Start Year | 2021 |
| Description | The Ovine PanGenome Project |
| Organisation | University of Idaho |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The Ovine Pangenome project is funded by USDA NIFA. We are co-investigators in the project and will provide expertise in analysing allele-specific expression in a set of tissues collected from F1 crosses of divergent sheep breeds. The project will generate at least 10 new long read genome assemblies for sheep and the RNA-Seq and allele-specific expression analysis will be used to generate breed specific transcriptomes and identify unique expressed variants to each of the breeds. One of the crosses we will generate new assemblies for is the Texel x Scottish Blackface which will complement ongoing UKRI grants. |
| Collaborator Contribution | This project is led by the University of Idaho. Partners in this project are generating crosses of the divergent sheep breeds to generate tissue to use to generate the long read assemblies and the transcriptomes. They are also performing library preparation and sequencing and performing genome assembly. They will make the new assemblies publicly available by uploading them to NCBI. |
| Impact | No impact yet the project is still ongoing. |
| Start Year | 2021 |
| Description | The Ovine PanGenome Project |
| Organisation | Utah State University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The Ovine Pangenome project is funded by USDA NIFA. We are co-investigators in the project and will provide expertise in analysing allele-specific expression in a set of tissues collected from F1 crosses of divergent sheep breeds. The project will generate at least 10 new long read genome assemblies for sheep and the RNA-Seq and allele-specific expression analysis will be used to generate breed specific transcriptomes and identify unique expressed variants to each of the breeds. One of the crosses we will generate new assemblies for is the Texel x Scottish Blackface which will complement ongoing UKRI grants. |
| Collaborator Contribution | This project is led by the University of Idaho. Partners in this project are generating crosses of the divergent sheep breeds to generate tissue to use to generate the long read assemblies and the transcriptomes. They are also performing library preparation and sequencing and performing genome assembly. They will make the new assemblies publicly available by uploading them to NCBI. |
| Impact | No impact yet the project is still ongoing. |
| Start Year | 2021 |
| Description | The Ovine PanGenome Project |
| Organisation | Washington State University |
| Department | Washington State University Spokane |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The Ovine Pangenome project is funded by USDA NIFA. We are co-investigators in the project and will provide expertise in analysing allele-specific expression in a set of tissues collected from F1 crosses of divergent sheep breeds. The project will generate at least 10 new long read genome assemblies for sheep and the RNA-Seq and allele-specific expression analysis will be used to generate breed specific transcriptomes and identify unique expressed variants to each of the breeds. One of the crosses we will generate new assemblies for is the Texel x Scottish Blackface which will complement ongoing UKRI grants. |
| Collaborator Contribution | This project is led by the University of Idaho. Partners in this project are generating crosses of the divergent sheep breeds to generate tissue to use to generate the long read assemblies and the transcriptomes. They are also performing library preparation and sequencing and performing genome assembly. They will make the new assemblies publicly available by uploading them to NCBI. |
| Impact | No impact yet the project is still ongoing. |
| Start Year | 2021 |
| Description | The regulatory GENomE of SWine and CHicken: functional annotation during development (GENE-SWitCH) |
| Organisation | Diagenode |
| Country | Belgium |
| Sector | Private |
| PI Contribution | The Roslin Institute partner contributed to the development of the research proposal and will contribute to experimental design, data generation and data analysis |
| Collaborator Contribution | The other partners in the European Commission funded H2020 project bring a range of skills, expertise and facilities, including genomics, functional genomics, bioinformatic analyses, data management and knowledge transfer and public engagement. |
| Impact | Successful application for European Commission H2020 funding. Multidisciplinary |
| Start Year | 2017 |
| Description | The regulatory GENomE of SWine and CHicken: functional annotation during development (GENE-SWitCH) |
| Organisation | EMBL European Bioinformatics Institute (EMBL - EBI) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner contributed to the development of the research proposal and will contribute to experimental design, data generation and data analysis |
| Collaborator Contribution | The other partners in the European Commission funded H2020 project bring a range of skills, expertise and facilities, including genomics, functional genomics, bioinformatic analyses, data management and knowledge transfer and public engagement. |
| Impact | Successful application for European Commission H2020 funding. Multidisciplinary |
| Start Year | 2017 |
| Description | The regulatory GENomE of SWine and CHicken: functional annotation during development (GENE-SWitCH) |
| Organisation | European Federation of Animal Science |
| Country | Italy |
| Sector | Public |
| PI Contribution | The Roslin Institute partner contributed to the development of the research proposal and will contribute to experimental design, data generation and data analysis |
| Collaborator Contribution | The other partners in the European Commission funded H2020 project bring a range of skills, expertise and facilities, including genomics, functional genomics, bioinformatic analyses, data management and knowledge transfer and public engagement. |
| Impact | Successful application for European Commission H2020 funding. Multidisciplinary |
| Start Year | 2017 |
| Description | The regulatory GENomE of SWine and CHicken: functional annotation during development (GENE-SWitCH) |
| Organisation | European Forum of Farm Animal Breeders (EFFAB) |
| Country | Netherlands |
| Sector | Learned Society |
| PI Contribution | The Roslin Institute partner contributed to the development of the research proposal and will contribute to experimental design, data generation and data analysis |
| Collaborator Contribution | The other partners in the European Commission funded H2020 project bring a range of skills, expertise and facilities, including genomics, functional genomics, bioinformatic analyses, data management and knowledge transfer and public engagement. |
| Impact | Successful application for European Commission H2020 funding. Multidisciplinary |
| Start Year | 2017 |
| Description | The regulatory GENomE of SWine and CHicken: functional annotation during development (GENE-SWitCH) |
| Organisation | French National Institute of Agricultural Research |
| Department | INRA Toulouse |
| Country | France |
| Sector | Public |
| PI Contribution | The Roslin Institute partner contributed to the development of the research proposal and will contribute to experimental design, data generation and data analysis |
| Collaborator Contribution | The other partners in the European Commission funded H2020 project bring a range of skills, expertise and facilities, including genomics, functional genomics, bioinformatic analyses, data management and knowledge transfer and public engagement. |
| Impact | Successful application for European Commission H2020 funding. Multidisciplinary |
| Start Year | 2017 |
| Description | The regulatory GENomE of SWine and CHicken: functional annotation during development (GENE-SWitCH) |
| Organisation | French National Institute of Agricultural Research |
| Country | France |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner contributed to the development of the research proposal and will contribute to experimental design, data generation and data analysis |
| Collaborator Contribution | The other partners in the European Commission funded H2020 project bring a range of skills, expertise and facilities, including genomics, functional genomics, bioinformatic analyses, data management and knowledge transfer and public engagement. |
| Impact | Successful application for European Commission H2020 funding. Multidisciplinary |
| Start Year | 2017 |
| Description | The regulatory GENomE of SWine and CHicken: functional annotation during development (GENE-SWitCH) |
| Organisation | Government of Catalonia |
| Department | Institute for Research and Technology in Food and Agriculture |
| Country | Spain |
| Sector | Public |
| PI Contribution | The Roslin Institute partner contributed to the development of the research proposal and will contribute to experimental design, data generation and data analysis |
| Collaborator Contribution | The other partners in the European Commission funded H2020 project bring a range of skills, expertise and facilities, including genomics, functional genomics, bioinformatic analyses, data management and knowledge transfer and public engagement. |
| Impact | Successful application for European Commission H2020 funding. Multidisciplinary |
| Start Year | 2017 |
| Description | The regulatory GENomE of SWine and CHicken: functional annotation during development (GENE-SWitCH) |
| Organisation | Hendrix Genetics |
| Country | Netherlands |
| Sector | Private |
| PI Contribution | The Roslin Institute partner contributed to the development of the research proposal and will contribute to experimental design, data generation and data analysis |
| Collaborator Contribution | The other partners in the European Commission funded H2020 project bring a range of skills, expertise and facilities, including genomics, functional genomics, bioinformatic analyses, data management and knowledge transfer and public engagement. |
| Impact | Successful application for European Commission H2020 funding. Multidisciplinary |
| Start Year | 2017 |
| Description | The regulatory GENomE of SWine and CHicken: functional annotation during development (GENE-SWitCH) |
| Organisation | Uppsala University |
| Country | Sweden |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner contributed to the development of the research proposal and will contribute to experimental design, data generation and data analysis |
| Collaborator Contribution | The other partners in the European Commission funded H2020 project bring a range of skills, expertise and facilities, including genomics, functional genomics, bioinformatic analyses, data management and knowledge transfer and public engagement. |
| Impact | Successful application for European Commission H2020 funding. Multidisciplinary |
| Start Year | 2017 |
| Description | The regulatory GENomE of SWine and CHicken: functional annotation during development (GENE-SWitCH) |
| Organisation | Wageningen University & Research |
| Country | Netherlands |
| Sector | Academic/University |
| PI Contribution | The Roslin Institute partner contributed to the development of the research proposal and will contribute to experimental design, data generation and data analysis |
| Collaborator Contribution | The other partners in the European Commission funded H2020 project bring a range of skills, expertise and facilities, including genomics, functional genomics, bioinformatic analyses, data management and knowledge transfer and public engagement. |
| Impact | Successful application for European Commission H2020 funding. Multidisciplinary |
| Start Year | 2017 |
| Description | USDA Iso-Seq analysis of White Dorper x Romanov sheep |
| Organisation | U.S. Department of Agriculture USDA |
| Department | Beltsville Agricultural Research Center |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | We have employed a pipeline for the analysis of Iso-Seq data using TAMA suite of analysis tools for Iso-Seq data. TAMA tools was developed at The Roslin Institute. Using this pipeline we have analysed isoform usage across tissues from a White Dorper x Romanov 100 day sheep foetus. We performed this analysis in order to establish the analysis pipeline prior to our own Iso-Seq data becoming available. In parallel we have analyses allele-specific expression in these tissues to look at parent of origin effects and links allele and isoform specific expression information. |
| Collaborator Contribution | Our collaborators at the USDA generated the Iso-Seq data from 36 tissues from a White Dorper x Romanov 100 day sheep foetus on the PacBio Sequel II platform and then transferred this to us. In parallel they generated Ilumunia RNA-Seq on the same tissues and transferred this data to us to analyse in paralell. These datasets were generated to annotate new long read assemblies they were generated for these two breeds of sheep using a trio-binning approach. |
| Impact | No outcomes to report to date. |
| Start Year | 2021 |
| Description | USDA ONT sequencing of sheep and goat genomes |
| Organisation | U.S. Department of Agriculture USDA |
| Department | Beltsville Agricultural Research Center |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | We are working to generate long read genome assemblies for breeds of sheep and goats from across the globe to generate a pan genome. We plan to use Oxford Nanopore technologies and are extracting DNA, preparing sequencing libraries and sequencing ONT libraries at Roslin for this purpose. We plan to use a trio-binning approach and start with the Texel x Scottish Blackface cross. To this end we have brought up ovine embryonic fibroblasts from this cross and frozen cell pellets ready for DNA extraction. |
| Collaborator Contribution | The USDA are coordinating sheep and goat long read genome assembly sequencing efforts and plan to send us flow cells to generate some of these assemblies at Roslin. They are also providing their expertise in the generation of trio-binned assemblies and are facilitating acquiring some of the samples from other partners for sequencing. |
| Impact | No outputs or outcomes to report to date. |
| Start Year | 2021 |
| Description | AGGB Webinar - CTLGH Small Ruminants |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | On the 23rd November 2022 Emily Clark was invited to give a webinar by the Animal Genetics, Genomics and Breeding Forum (AGGB) entitled 'Highly annotated genomes as a resource to improve farmed animal production in the UK and the tropics'. The webinar was attended by researchers from across West and Central Africa including, Uganda, Nigeria and Ghana. There were many questions around applying functional annotation projects in tropical farmed animal systems and requests for further information. |
| Year(s) Of Engagement Activity | 2022 |
| Description | BovReg Poster FAANG Virtual Workshop Feb 2022 |
| 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 presented a virtual poster at the virtual FAANG consortium workshop on the 16th of February 2022. The poster was entitled 'Transcriptome analysis of crossbred and purebred cattle using CAGE and mRNA-Seq for the BovReg Project' and was presented via Gathertown which allow participants to ask questions. Participants at the workshop were predominantly members of the FAANG consortium, and researchers in the field of animal genetics and genomics. Several participants asked for more information about the project. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.faang.org/bbs?s=2022workshop..txt |
| Description | BovReg TSS Oral Presentation ISAG2021 Virtual Conference |
| 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 an oral presentation entitled 'Annotation of transcription start sites in the bovine genome reveals novel breed specific complexity' for the H2020 BovReg project at the International Society of Animal Genetics (ISAG) virtual conference July 26-30th, 2021. The audience included predominantly academics but also representatives from industry. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.isag.us/2021/ |
| Description | EFFAB Breeders Talk Green Webinar FAANG to Fork |
| 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 webinar on the 6th of December 2021 entitled 'From FAANG to Fork: How more will knowledge of the genetic code of farmed animals benefit animal breeding?'. The session of the 'Breeders Talk Green' webinar series was entitled 'What's Next in Animal Breeding'. EFFAB & FABRE-TP run the Webinar Series #BreederstalkGreen and the audience includes policy makers, industry representatives and scientists working in the fields of animal breeding, genetics and genomics. The webinar was watched by a large audience and recorded. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.youtube.com/watch?v=MgW4EP_fFCM |
| Description | FAANG Workshop 2022 - Next phase of FAANG roundtable |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | On February the 16th 2022 Emily Clark was the chair of a roundtable discussion on 'Implementing the next phase of FAANG.' at the FAANG consortium virtual workshop. The discussion included the bioinformatics that are necessary, continuing and facilitating further global collaboration and the results of a recent survey run by the consortium. There were just under 100 attendees and attendees were encourage to raise questions for the panel to discuss. The attendees were predominantly members of FAANG and also researchers in animal genetics and genomics. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.faang.org/bbs?s=2022workshop..txt |
| Description | FAANG to Fork summary in Gene-SWitCH Newsletter |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Emily Clark wrote an editorial summary of the FAANG to Fork manuscript for the second newsletter published in February 2021 for the H2020 Gene-SWitCH project. The newsletter was written for a general audience, widely advertised on Twitter and the social media and will be read by academic researchers and policy makers in the European Commission. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.gene-switch.eu/uploads/1/2/6/6/126678735/gene_switch_newsletter2_final.pdf |
| Description | Future of FAANG Roundtable ISAG2021 Virtual Conference |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Emily Clark took part in a roundtable discussion that focused on 'the future of FAANG' at the International Society of Animal Genetics Virtual Conference from 26th-30th 2021. The discussion focused on current and future bioformatics resources and training of the next generation of data scientists for the functional annotation of animal genomes (FAANG). Continuing and strengthening global FAANG efforts were also discussed. There were six panel members including the coordinators of FAANG. There was audience participation which was facilitated by the session chair. The audience included members of the FAANG consortium but also those working in animal genetics and genomics more broadly and representatives from industry. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.isag.us/2021/ |
| Description | Improved pig reference genome in GENE-SWitCH newsletter |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Alan Archibald wrote a article on the development and publication of an improved pig reference genome sequence for the second H2020 GENE-SWitCH newsletter published in February 2021. The newsletter was written for a general audience, widely advertised on Twitter and the social media and will be read by academic researchers and policy makers in the European Commission. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.gene-switch.eu/uploads/1/2/6/6/126678735/gene_switch_newsletter2_final.pdf |
| Description | Invited Talk UKCBCB Conference FAANG to Fork |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Emily Clark gave an invited talk at the UK Conference of Bioinformatics and Computational Biology on the 30th September 2021 entitled 'Highly Annotated Genomes as a Resource to Improve Farmed Animal Production'. The conference was held virtually by the Earlham Institute and attendees were from a range of research backgrounds with a bioinformatics or computational biology focus. The session was entitled 'Bridging the genotype to phenotype gap'. In the talk Emily presented the FAANG to Fork concept as well as work from her own research group including using allele-specific expression to predict growth traits in sheep. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.earlham.ac.uk/uk-conference-bioinformatics-and-computational-biology-21 |
| Description | Roslin Institute News - Article DNA offers insights into pig muscle development |
| 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 | Other audiences |
| Results and Impact | This article was posted as a Roslin Institute News report describing how the researchers involved in the study hope to explore their data further to identify variations in the genetic code of pigs that are linked to growth, and better understand how these differences regulate the activity of key genes involved in muscle development, to inform pig breeding programmes. The method described in the news article and associated publication using frozen tissue could be applied to investigate how the genetic code of livestock controls their characteristics. As the method can be used on samples from frozen tissue banks this can help limit the numbers of animals used for research. The research was published in G3: Genes, Genomes, Genetics https://doi.org/10.1093/g3journal/jkab424. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.ed.ac.uk/roslin/news-events/latest-news-2022/dna-offers-insights-into-pig-muscle-develop... |
| Description | University of Florida FAANG to Fork Research Seminar |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | On the 2nd of February Emily Clark was invited by Raluca Mateescu to give a research seminar describing how highly annotated genomes can provide a resource to improve farmed animal production. Emily described the research priorities outlined in the FAANG to Fork framework recently published in Genome Biology and presented some of the ongoing projects in her own research group. Including the sheep gene expression atlas and empowering sheep breeding using allele-specific expression. The seminar was attended by undergraduate and postgraduate students, teaching faculty and researchers in the livestock genomics space at the University of Florida. |
| Year(s) Of Engagement Activity | 2021 |
| Description | WCGALP BovReg CAGE Short Presentation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | The 12th World Congress in Genetics Applied to Livestock Production took place in Rotterdam in July 2022. The focus of the congress which occurs every 4 years is to promote technical and species orientated innovations in animal breeding, and the contribution of genetics to solving societal challenges. Mazdak Salavati gave a short presentation in the 'Epigenetics, structural variants and exploiting transcriptome' session entitled 'Comparative analysis of CAGE-Seq across tissues reveals transcription start sites unique to cattle'. In the presentation he described CAGE sequencing to define TSS across tissues from three different populations of cattle to provide new annotation for the cattle genome, and a resource to inform cattle breeding. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.wageningenacademic.com/pb-assets/wagen/WCGALP2022/33_005.pdf |