Identification of genetic variation in innate immune response genes associated with resistance to chicken viral infections

Lead Research Organisation: University of Edinburgh
Department Name: Genetics and Genomics

Abstract

The UK poultry industry faces increasing challenges in the 21st century. Many of the drugs used to control diseases in poultry are being withdrawn from use. At the same time, improving welfare standards mean that the industry is becoming more free-range. But the downside is that free-range chickens face higher rates of disease challenge, for example through contact with wild birds. One answer to this problem is to breed birds, which have a higher natural resistance to disease. To do this, we need to understand the bird's immunity to disease, so that we can identify ways to control that response. We already know that in birds and mammals, the immune response can be divided into two arms - the innate response and the adaptive response. The latter is a very specific response, which hopefully leads to immune 'memory', in other words the ability to respond rapidly to subsequent infections with the same pathogen. This is how vaccination works, however, it is specific to each pathogen the bird encounters, and thus would not give general resistance to disease. Our target is the innate immune response. This is a generalised response that recognises components of a wide range of pathogens, for example, specific types of molecules in a bacterial coat. It serves two roles - it limits infection until the adaptive immune response can kick in, and also provides signals that control the adaptive immune response. For many infections, a strong innate immune response is all that is needed to control the pathogen and prevent the onset of disease. Our initial aim in this project is to identify as many of the genes in the chicken as possible that are involved in the innate immune response. This is now possible since the chicken genome was sequenced last year and already almost 18,000 genes have been predicted. Our initial gene set will be determined by comparisons with similar gene sets in mammals, and what we can identify from the chicken genome sequence. The next step will be to identify which members of this predicted set of genes are actually involved in the innate immune response to infection with viruses. We will do this by infecting birds with different viruses and looking at the expression of genes following infection, on a global level using whole genome microarrays. These are glass slides containing short unique sequences corresponding to each known gene in the chicken genome that can be used to detect whether a gene is turned on or off. After complex mathematical analysis, one can examine global gene expression using these microarrays and identify which chicken genes respond to a particular viral infection. We have chickens lines, which we know differ in their resistance to viral infections. We suspect that at least some of that difference will be at the level of the innate immune response. Once we know which genes are involved in the innate response to viral infection, we will then look for sequence differences or polymorphisms between these chicken lines. We will be looking for changes at single nucleotides within the DNA sequence of these genes, known as SNPs (single nucleotide polymorphisms). We will then predict, and later test, if these SNPs are likely to make a functional difference to the protein encoded by the gene, either in its structure (for example by changing the amino acid sequence) or the level of its expression. Finally, we will then assess if individual SNPs track with resistance to viral infection using crosses between resistant and susceptible lines, in simplest terms by seeing if the SNP is always found in a resistant bird. These SNPs can then be used as selectable markers in normal breeding programmes to select birds that are naturally more resistant to viral infection. In addition, resistant poultry will represent a new tool in our defense against infectious disease in humans.

Technical Summary

UK poultry industry faces many challenges to remain sustainable, including moves to extensive rearing systems, withdrawal of antibiotics and problems with anti-helminthics. These will impact on both poultry and human health. Increased incidence of zoonotic pathogens in chickens, such as avian influenza and SARS, could lead to an increase in these diseases in man. It is vital that poultry breeders can select for genetic improvement in resistance when birds are reared in such environments. This proposal seeks to identify genes controlling variation in innate immune responses; define the extent of genetic variability in these loci and relate this to resistance/susceptibility to viral diseases; provide new markers for selective breeding for improved innate resistance to viral disease and hence improved food safety. Inbred lines of chickens maintained at IAH differ greatly in their susceptibility to a wide spectrum of pathogens, including viruses. Differences in innate immune responses determine resistance to infection to Salmonella in different broiler lines. It is thus a reasonable hypothesis that a similar mechanism will influence resistance to viral infections. The availability of genome sequences, for both the pathogens under study (Marek's disease virus (MDV), Infectious Bursal Disease Virus (IBDV) and Infectious Bronchitis Virus (IBV)), and also now for the chicken, represents a major shift in our ability to understand host-pathogen interactions. From the chicken genome sequence and existing information on relevant mammalian and chicken genes, we will define a comprehensive set of chicken innate immune response genes (preliminary analysis has identified almost 400). Challenge experiments with the three viruses using inbred lines with varying degrees of resistance to them will be carried out. RNA samples will be used in high-throughput gene expression experiments using Affymetrix chips (containing genes from the chicken and the three pathogens) to identify the subset of innate immune response genes that are involved in the subsequent response. Most amino acids within proteins are under selective constraints with estimates of selection (dN/dS) values around 0.05-0.10. However genes involved in host-defense evolve more rapidly than other genes and have larger dN/dS ratios, probably due to positive selection on specific amino acids as a consequence of the host-pathogen 'arms-race'. Orthologous sequences will be isolated from turkey, duck and Zebrafinch cDNA libraries and compared with chicken genes to estimate dN/dS ratios. Single nucleotide polymorphisms (SNP) within these genes between the inbred lines will be determined by direct sequencing. For coding sequences we will sequence cDNAs from tissues isolated from inbred lines. Sequence alignment between the avian species listed above will be used in combination with SNP and other structural data to assess if a SNP is likely to be functional (i.e. likely to affect the function of the protein). For promoter polymorphisms we will sequence 500-bp of 5'-flanking region. SNP locations will be mapped onto conserved regions and likely transcription factor binding sites to predict possible functional significance. SNP assays will be established to determine segregation of these SNPs with resistance in relevant backcross populations. For MDV and IBDV the relevant DNA panels are already archived from previous experiments with associated phenotypic information. For IBV the relevant backcross population and challenge study will be carried out as part of this proposal. The impact of any segregating SNPs will then be determined with reporter gene and real-time quantitative RT-PCR assays. As a direct output, we expect to identify SNPs correlating with resistance to viral infections that can be used as selectable markers in conventional breeding programs. In addition, resistant poultry will represent a new tool in our defense against infectious disease in humans.

Publications

10 25 50

publication icon
David Burt (Author) (2008) Evolution of avian innate immune system in Developments in Biologicals

publication icon
Kaiser P (2009) Towards the selection of chickens resistant to Salmonella and Campylobacter infections. in Bulletin et memoires de l'Academie royale de medecine de Belgique

Related Projects

Project Reference Relationship Related To Start End Award Value
BB/D013704/1 13/09/2006 12/05/2008 £331,076
BB/D013704/2 Transfer BB/D013704/1 01/05/2008 31/08/2011 £191,240
 
Description Host responses to viral infections defined. Genetic marker for MDV resistance associated with IRG1 gene.
Exploitation Route Genetic markers for MDV in chicken
Sectors Agriculture, Food and Drink

 
Description FADH Call: Identification of the molecular basis of differential host responses to rapidly evolving Avian Influenza viruses in different avian species
Amount £1,300,000 (GBP)
Funding ID BB/L004666/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2014 
End 10/2017
 
Description International Avian RNA-Seq Consortium 
Organisation Agrocampus Ouest
Country France 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation Arizona State University
Country United States 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation Centre for Genomic Regulation (CRG)
Country Spain 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation EMBL European Bioinformatics Institute (EMBL - EBI)
Country United Kingdom 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation French National Institute of Agricultural Research
Department INRA Rennes Centre
Country France 
Sector Public 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation French National Institute of Agricultural Research
Department INRA Toulouse
Country France 
Sector Public 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation French National Institute of Agricultural Research
Country France 
Sector Public 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation Harvard University
Department Harvard Medical School
Country United States 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation Imperial College London
Country United Kingdom 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation Iowa State University
Country United States 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation Kenya Agriculture & Livestock Research Organization (KALRO)
Country Kenya 
Sector Private 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation Medical Research Council (MRC)
Department Medical Research Council (MRC) Centre Cambridge
Country United Kingdom 
Sector Public 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation National Institute of Allergy and Infectious Diseases (NIAID)
Country United States 
Sector Public 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation National Institute of Environmental Health Sciences
Country United States 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation Oregon State University
Country United States 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation Swedish University of Agricultural Sciences
Country Sweden 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation University of Arkansas
Country United States 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation University of California, Davis
Department UC Davis Genome Cente
Country United States 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation University of Delaware
Country United States 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation University of East Anglia
Country United Kingdom 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation University of Leipzig
Country Germany 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation University of Nottingham
Country United Kingdom 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation Weizmann Institute of Science
Country Israel 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Title AVIAN COLONY STIMULATING FACTOR 1 RECEPTOR BINDING PROTEINS 
Description Intellectual Property 
IP Reference CN102712689 
Protection Patent application published
Year Protection Granted 2012
Licensed No
Impact Used to culture avian macrophage in many grant application.
 
Description Animal and Plant Health in the UK 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact working group at Animal and Plant Health in the UK (2014): an assessment of future national capability, emerging technologies, 14 Feb 2014, BIS Conference Centre, London, UK
Year(s) Of Engagement Activity 2014
 
Description Avian genome evolution and the origins of species diversity. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited lecture: Avian genome evolution and the origins of species diversity. In "Molecular evolution of avian species", SMBE2016, Queensland's Gold Coast, Australia, 3-7 July, 2016.
Year(s) Of Engagement Activity 2016
 
Description Avian genomics: current status and future opportunities 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Talk at 16th ADNAT Convention on Animal Genetics and Genomics. Talk: Avian genomics: current status and future opportunities. Hyderabad, Dec 17-19, 2012.
Year(s) Of Engagement Activity 2012
 
Description Development of New Tools for Genetic Selection for a Sustainable Poultry Industry 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented a talk: Development of New Tools for Genetic Selection for a Sustainable Poultry Industry (2014), Veterinary Advances in Animal Health and Welfare Research - Impact and Opportunities, Feb 20-24, 2014, NIANP Auditorium, Adugodi, Bangalore, India
Year(s) Of Engagement Activity 2014
 
Description From Sequences to Consequences 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact talk and meet industry at "21st Century Genomics for Animal Breeding and Animal Health. In "From Sequences to Consequences: What The Roslin Institute can do for you in the livestock sector", Industry Day. The Roslin Institute Building, Edinburgh, 18th March 2016."
Year(s) Of Engagement Activity 2016
 
Description ISAG Conference 2012. Talk: NGS of multiple chicken lines and development of a high-density 600K SNP genotyping array, 16-20 July, Cairns, Australia 2012. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented a talk at ISAG Conference 2012. Talk: NGS of multiple chicken lines and development of a high-density 600K SNP genotyping array, 16-20 July, Cairns, Australia 2012.
Year(s) Of Engagement Activity 2012
 
Description New tools and prospects for chicken genomics 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk at Genetics Society of Australia (GSA), July 2015, University of Adelaide, Australia
Year(s) Of Engagement Activity 2015
 
Description Past, Present and Future of Genomics in Poultry Breeding. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk: Past, Present and Future of Genomics in Poultry Breeding. 25th World's Poultry Congress, Beijing, 5-9 September, 2016.
Year(s) Of Engagement Activity 2016
 
Description Production Animal Health and Welfare Research: Impacts and Opportunities. 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk at Production Animal Health and Welfare Research: Impacts and Opportunities. 19-20 Feb, 2015, Indian Council for Agricultural Research (ICAR), New Delhi, India
Year(s) Of Engagement Activity 2015
 
Description The Chicken and other Avian Genomes: new insights and opportunities for all from high throughput sequencing and bioinformatics. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk: the Chicken and other Avian Genomes: new insights and opportunities for all from high throughput sequencing and bioinformatics. In "Avian Model Systems 9: a new integrative platform", Taipei, Taiwan, 38 March to 3 April, 2016.
Year(s) Of Engagement Activity 2016
 
Description The chicken genome 10 years on. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Keynote lecture: chicken genome - 10 years on. Avian Model Systems - the 8th International Meeting, Cold Spring Harbour, USA, 4-8th March, 2014.

CSHL Leading Strand - Keynote Lecture Series (http://theleadingstrand.cshl.edu/Course/Keynote/2014/AVIAN/150

The chicken genome 10 years on - BBSRC (http://www.bbsrc.ac.uk/news/events/1403-chicken-genome.aspx)
Year(s) Of Engagement Activity 2014