AUTHOR=Tixier-Boichard Michèle , Fabre Stéphane , Dhorne-Pollet Sophie , Goubil Adeline , Acloque Hervé , Vincent-Naulleau Silvia , Ross Pablo , Wang Ying , Chanthavixay Ganrea , Cheng Hans , Ernst Catherine , Leesburg Vicki , Giuffra Elisabetta , Zhou Huaijun , Collaborative Working Group , Taragnat Catherine , Berri Cecile , Jardet Déborah , Godet Estelle , Laurent Fabrice , Gomot Gilles , Dardente Hughes , Grasseau Isabelle , Dubois Jean-Philippe , Gautron Joel , Gérard Nadine , Quéré Pascale , Lavocat Roger-Paul , Dalbies-Tran Rozenn , Métayer Sonia , Marthey Sylvain , Coustham Vincent , Druart Xavier TITLE=Tissue Resources for the Functional Annotation of Animal Genomes JOURNAL=Frontiers in Genetics VOLUME=12 YEAR=2021 URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2021.666265 DOI=10.3389/fgene.2021.666265 ISSN=1664-8021 ABSTRACT=

In order to generate an atlas of the functional elements driving genome expression in domestic animals, the Functional Annotation of Animal Genome (FAANG) strategy was to sample many tissues from a few animals of different species, sexes, ages, and production stages. This article presents the collection of tissue samples for four species produced by two pilot projects, at INRAE (National Research Institute for Agriculture, Food and Environment) and the University of California, Davis. There were three mammals (cattle, goat, and pig) and one bird (chicken). It describes the metadata characterizing these reference sets (1) for animals with origin and selection history, physiological status, and environmental conditions; (2) for samples with collection site and tissue/cell processing; (3) for quality control; and (4) for storage and further distribution. Three sets are identified: set 1 comprises tissues for which collection can be standardized and for which representative aliquots can be easily distributed (liver, spleen, lung, heart, fat depot, skin, muscle, and peripheral blood mononuclear cells); set 2 comprises tissues requiring special protocols because of their cellular heterogeneity (brain, digestive tract, secretory organs, gonads and gametes, reproductive tract, immune tissues, cartilage); set 3 comprises specific cell preparations (immune cells, tracheal epithelial cells). Dedicated sampling protocols were established and uploaded in https://data.faang.org/protocol/samples. Specificities between mammals and chicken are described when relevant. A total of 73 different tissues or tissue sections were collected, and 21 are common to the four species. Having a common set of tissues will facilitate the transfer of knowledge within and between species and will contribute to decrease animal experimentation. Combining data on the same samples will facilitate data integration. Quality control was performed on some tissues with RNA extraction and RNA quality control. More than 5,000 samples have been stored with unique identifiers, and more than 4,000 were uploaded onto the Biosamples database, provided that standard ontologies were available to describe the sample. Many tissues have already been used to implement FAANG assays, with published results. All samples are available without restriction for further assays. The requesting procedure is described. Members of FAANG are encouraged to apply a range of molecular assays to characterize the functional status of collected samples and share their results, in line with the FAIR (Findable, Accessible, Interoperable, and Reusable) data principles.