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The regulatory GENomE of SWine and CHicken: functional annotation during development

Deliverables

Reproducible, scale-able workflows for FAANG data analysis

We will release on GitHub workflows that are 100% reproducible and scale-able from laptop to HPC to cloud, using a workflow language such as Snakemake or NextFlow, integrating best-in-class bioinformatics open-source software

Raw sequences of WGBS and RRBS delivered to ENA and FAANG

fastq files and metadata available at FAANG and ENA.

Raw sequences of RNA-seq delivered to ENA and FAANG

fastq files and metadata available at FAANG and ENA.

Bio-repository of 3120 samples

A list of 3120 samples corresponding to 10 aliquots * 13 tissues * 4 replicates * 3 developmental stages * 2 species

Project Management Guidelines

Report compiling the guidelines and rules in place for the coordination, reporting and quality control of the project.

Report on coordinated data production, recording and archiving within the European node of FAANG DCC

Report on the establishment of the European node of the FAANG Data Coordination Centre through agreement of scope, remit, objectives and priorities between the SFS-30 funded projects. The report will outline the interoperability development work, a basis for sharing of data and analysis methodologies and framework that will lead to cross project comparative analyses.

Outreach, dissemination, and training plan

D61 will be used to implement and evaluate the progress of the activities targeted to relevant stakeholders

GENE-SWitCH Data Management Plan

Report on the data management plan for GENE-SWitCH in accordance with the latest FAANG data standards, SOPs and FAANG Data Sharing Principles.

Searching for OpenAIRE data...

Publications

Microbial Regulation of Host Physiology by Short-chain Fatty Acids

Author(s): Bart van der Hee; Jerry M. Wells
Published in: Trends in Microbiology, Aug;29(8): 2021, 2021, Page(s) 700-712, ISSN 0966-842X
Publisher: Elsevier BV
DOI: 10.1016/j.tim.2021.02.001

From FAANG to fork: application of highly annotated genomes to improve farmed animal production

Author(s): Emily L. Clark, Alan L. Archibald, Hans D. Daetwyler, Martien A. M. Groenen, Peter W. Harrison, Ross D. Houston, Christa Kühn, Sigbjørn Lien, Daniel J. Macqueen, James M. Reecy, Diego Robledo, Mick Watson, Christopher K. Tuggle, Elisabetta Giuffra
Published in: Genome Biology, 21/1, 2020, ISSN 1474-760X
Publisher: Springer
DOI: 10.1186/s13059-020-02197-8

The European Nucleotide Archive in 2019

Author(s): Clara Amid, Blaise T F Alako, Vishnukumar Balavenkataraman Kadhirvelu, Tony Burdett, Josephine Burgin, Jun Fan, Peter W Harrison, Sam Holt, Abdulrahman Hussein, Eugene Ivanov, Suran Jayathilaka, Simon Kay, Thomas Keane, Rasko Leinonen, Xin Liu, Josue Martinez-Villacorta, Annalisa Milano, Amir Pakseresht, Nadim Rahman, Jeena Rajan, Kethi Reddy, Edward Richards, Dmitriy Smirnov, Alexey Sokolov, Sen
Published in: Nucleic Acids Research, 2019, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz1063

Accounting for overlapping annotations in genomic prediction models of complex traits

Author(s): Mollandin, F., Gilbert, H., Croiseau, P., and Rau, A.
Published in: BMC Bioinformatics, 2022, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-022-04914-5

Ensembl 2022

Author(s): Fiona Cunningham, James E Allen, Jamie Allen, Jorge Alvarez-Jarreta, M Ridwan Amode, Irina M Armean, Olanrewaju Austine-Orimoloye, Andrey G Azov, If Barnes, Ruth Bennett, Andrew Berry, Jyothish Bhai, Alexandra Bignell, Konstantinos Billis, Sanjay Boddu, Lucy Brooks, Mehrnaz Charkhchi, Carla Cummins, Luca Da Rin Fioretto, Claire Davidson, Kamalkumar Dodiya, Sarah Donaldson, Bilal El Houdaigui, Tama
Published in: Nucleic Acids Research, 2022, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab1049

The FAANG Data Portal: Global, Open-Access,“FAIR”, and Richly Validated Genotype to Phenotype Data for High-Quality Functional Annotation of Animal Genomes

Author(s): Peter W Harrison, Alexey Sokolov, Akshatha Nayak, Jun Fan, Daniel Zerbino, Guy Cochrane, Paul Flicek
Published in: Frontiers in Genetics, 12 2021/6/17, 2021, Page(s) 873, ISSN 1664-8021
Publisher: Frontiers Media
DOI: 10.3389/fgene.2021.639238

Ensembl 2021

Author(s): Kevin L Howe, Premanand Achuthan, James Allen, Jamie Allen, Jorge Alvarez-Jarreta, M Ridwan Amode, Irina M Armean, Andrey G Azov, Ruth Bennett, Jyothish Bhai, Konstantinos Billis, Sanjay Boddu, Mehrnaz Charkhchi, Carla Cummins, Luca Da Rin Fioretto, Claire Davidson, Kamalkumar Dodiya, Bilal El Houdaigui, Reham Fatima, Astrid Gall, Carlos Garcia Giron, Tiago Grego, Cristina Guijarro-Clarke, Lea
Published in: Nucleic Acids Research, 49/D1, 2020, Page(s) D884-D891, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa942

The European Nucleotide Archive in 2020

Author(s): Peter W Harrison, Alisha Ahamed, Raheela Aslam, Blaise T F Alako, Josephine Burgin, Nicola Buso, Mélanie Courtot, Jun Fan, Dipayan Gupta, Muhammad Haseeb, Sam Holt, Talal Ibrahim, Eugene Ivanov, Suran Jayathilaka, Vishnukumar Balavenkataraman Kadhirvelu, Manish Kumar, Rodrigo Lopez, Simon Kay, Rasko Leinonen, Xin Liu, Colman O’Cathail, Amir Pakseresht, Youngmi Park, Stephane Pesant, Nadim Rahm
Published in: Nucleic Acids Research, 49/D1, 2020, Page(s) D82-D85, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa1028

An evaluation of the predictive performance and mapping power of the BayesR model for genomic prediction

Author(s): Mollandin, F., Rau, A., and Croiseau, P.
Published in: G3 Genes|Genomes|Genetics, 2022, ISSN 2160-1836
Publisher: Genetics Society of America
DOI: 10.1093/g3journal/jkab225

Prediction performance of linear models and gradient boosting machine on complex phenotypes in outbred mice

Author(s): B. C. Perez, M. C. A. M. Bink, K. L. Svenson, G. A. Churchill and M. P. L. Calus
Published in: G3 Genes|Genomes|Genetics, 12; 4; 2022, 2022, Page(s) jkac039, ISSN 2160-1836
Publisher: Genetics Society of America
DOI: 10.1093/g3journal/jkac039

Identifying muscle transcriptional regulatory elements in the pig genome

Author(s): D. Crespo-Piazuelo , O. González-Rodríguez, M. Mongellaz, H. Acloque, M.-J. Mercat, M. C. A. M. Bink, A. E. Huisman, Y. Ramayo-Caldas, J. P. Sánchez, and M. Ballester
Published in: ISAG 2021 Book of abstracts, 2021, Page(s) 19; 113
Publisher: -