Tissue Resources for the Functional Annotation of Animal Genomes
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 collec...
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Format: | Article |
Language: | English |
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Frontiers Media S.A.
2021-06-01
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Series: | Frontiers in Genetics |
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Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2021.666265/full |
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DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Michèle Tixier-Boichard Stéphane Fabre Sophie Dhorne-Pollet Adeline Goubil Hervé Acloque Silvia Vincent-Naulleau Pablo Ross Ying Wang Ganrea Chanthavixay Hans Cheng Catherine Ernst Vicki Leesburg Elisabetta Giuffra Huaijun Zhou Collaborative Working Group Catherine Taragnat Cecile Berri Déborah Jardet Estelle Godet Fabrice Laurent Gilles Gomot Hughes Dardente Isabelle Grasseau Jean-Philippe Dubois Joel Gautron Nadine Gérard Pascale Quéré Roger-Paul Lavocat Rozenn Dalbies-Tran Sonia Métayer Sylvain Marthey Vincent Coustham Xavier Druart |
spellingShingle |
Michèle Tixier-Boichard Stéphane Fabre Sophie Dhorne-Pollet Adeline Goubil Hervé Acloque Silvia Vincent-Naulleau Pablo Ross Ying Wang Ganrea Chanthavixay Hans Cheng Catherine Ernst Vicki Leesburg Elisabetta Giuffra Huaijun Zhou Collaborative Working Group Catherine Taragnat Cecile Berri Déborah Jardet Estelle Godet Fabrice Laurent Gilles Gomot Hughes Dardente Isabelle Grasseau Jean-Philippe Dubois Joel Gautron Nadine Gérard Pascale Quéré Roger-Paul Lavocat Rozenn Dalbies-Tran Sonia Métayer Sylvain Marthey Vincent Coustham Xavier Druart Tissue Resources for the Functional Annotation of Animal Genomes Frontiers in Genetics tissue sampling repository mammals bird cryopreservation genome |
author_facet |
Michèle Tixier-Boichard Stéphane Fabre Sophie Dhorne-Pollet Adeline Goubil Hervé Acloque Silvia Vincent-Naulleau Pablo Ross Ying Wang Ganrea Chanthavixay Hans Cheng Catherine Ernst Vicki Leesburg Elisabetta Giuffra Huaijun Zhou Collaborative Working Group Catherine Taragnat Cecile Berri Déborah Jardet Estelle Godet Fabrice Laurent Gilles Gomot Hughes Dardente Isabelle Grasseau Jean-Philippe Dubois Joel Gautron Nadine Gérard Pascale Quéré Roger-Paul Lavocat Rozenn Dalbies-Tran Sonia Métayer Sylvain Marthey Vincent Coustham Xavier Druart |
author_sort |
Michèle Tixier-Boichard |
title |
Tissue Resources for the Functional Annotation of Animal Genomes |
title_short |
Tissue Resources for the Functional Annotation of Animal Genomes |
title_full |
Tissue Resources for the Functional Annotation of Animal Genomes |
title_fullStr |
Tissue Resources for the Functional Annotation of Animal Genomes |
title_full_unstemmed |
Tissue Resources for the Functional Annotation of Animal Genomes |
title_sort |
tissue resources for the functional annotation of animal genomes |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Genetics |
issn |
1664-8021 |
publishDate |
2021-06-01 |
description |
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. |
topic |
tissue sampling repository mammals bird cryopreservation genome |
url |
https://www.frontiersin.org/articles/10.3389/fgene.2021.666265/full |
work_keys_str_mv |
AT micheletixierboichard tissueresourcesforthefunctionalannotationofanimalgenomes AT stephanefabre tissueresourcesforthefunctionalannotationofanimalgenomes AT sophiedhornepollet tissueresourcesforthefunctionalannotationofanimalgenomes AT adelinegoubil tissueresourcesforthefunctionalannotationofanimalgenomes AT herveacloque tissueresourcesforthefunctionalannotationofanimalgenomes AT silviavincentnaulleau tissueresourcesforthefunctionalannotationofanimalgenomes AT pabloross tissueresourcesforthefunctionalannotationofanimalgenomes AT yingwang tissueresourcesforthefunctionalannotationofanimalgenomes AT ganreachanthavixay tissueresourcesforthefunctionalannotationofanimalgenomes AT hanscheng tissueresourcesforthefunctionalannotationofanimalgenomes AT catherineernst tissueresourcesforthefunctionalannotationofanimalgenomes AT vickileesburg tissueresourcesforthefunctionalannotationofanimalgenomes AT elisabettagiuffra tissueresourcesforthefunctionalannotationofanimalgenomes AT huaijunzhou tissueresourcesforthefunctionalannotationofanimalgenomes AT collaborativeworkinggroup tissueresourcesforthefunctionalannotationofanimalgenomes AT catherinetaragnat tissueresourcesforthefunctionalannotationofanimalgenomes AT cecileberri tissueresourcesforthefunctionalannotationofanimalgenomes AT deborahjardet tissueresourcesforthefunctionalannotationofanimalgenomes AT estellegodet tissueresourcesforthefunctionalannotationofanimalgenomes AT fabricelaurent tissueresourcesforthefunctionalannotationofanimalgenomes AT gillesgomot tissueresourcesforthefunctionalannotationofanimalgenomes AT hughesdardente tissueresourcesforthefunctionalannotationofanimalgenomes AT isabellegrasseau tissueresourcesforthefunctionalannotationofanimalgenomes AT jeanphilippedubois tissueresourcesforthefunctionalannotationofanimalgenomes AT joelgautron tissueresourcesforthefunctionalannotationofanimalgenomes AT nadinegerard tissueresourcesforthefunctionalannotationofanimalgenomes AT pascalequere tissueresourcesforthefunctionalannotationofanimalgenomes AT rogerpaullavocat tissueresourcesforthefunctionalannotationofanimalgenomes AT rozenndalbiestran tissueresourcesforthefunctionalannotationofanimalgenomes AT soniametayer tissueresourcesforthefunctionalannotationofanimalgenomes AT sylvainmarthey tissueresourcesforthefunctionalannotationofanimalgenomes AT vincentcoustham tissueresourcesforthefunctionalannotationofanimalgenomes AT xavierdruart tissueresourcesforthefunctionalannotationofanimalgenomes |
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doaj-7c495e08d881437aad0a5971029104be2021-06-21T10:03:39ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-06-011210.3389/fgene.2021.666265666265Tissue Resources for the Functional Annotation of Animal GenomesMichèle Tixier-Boichard0Stéphane Fabre1Sophie Dhorne-Pollet2Adeline Goubil3Hervé Acloque4Silvia Vincent-Naulleau5Pablo Ross6Ying Wang7Ganrea Chanthavixay8Hans Cheng9Catherine Ernst10Vicki Leesburg11Elisabetta Giuffra12Huaijun Zhou13Collaborative Working GroupCatherine TaragnatCecile BerriDéborah JardetEstelle GodetFabrice LaurentGilles GomotHughes DardenteIsabelle GrasseauJean-Philippe DuboisJoel GautronNadine GérardPascale QuéréRoger-Paul LavocatRozenn Dalbies-TranSonia MétayerSylvain MartheyVincent CousthamXavier DruartUniversity Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, FranceGenPhySe, INRAE, ENVT, ENSAT, Castanet-Tolosan, FranceUniversity Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, FranceUniversity Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, FranceUniversity Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, FranceUniversity Paris-Saclay, CEA, IRCM, Fontenay-aux-Roses, FranceUC Davis Department of Animal Science, University of California, Davis, Davis, CA, United StatesUC Davis Department of Animal Science, University of California, Davis, Davis, CA, United StatesUC Davis Department of Animal Science, University of California, Davis, Davis, CA, United StatesUSDA-ARS Avian Disease and Oncology Laboratory, East Lansing, MI, United StatesDepartment of Animal Science, Michigan State University, East Lansing, MI, United StatesUSDA-ARS, Fort Keogh Livestock and Range Research Laboratory, Miles City, MT, United StatesUniversity Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, FranceUC Davis Department of Animal Science, University of California, Davis, Davis, CA, United StatesIn 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.https://www.frontiersin.org/articles/10.3389/fgene.2021.666265/fulltissue samplingrepositorymammalsbirdcryopreservationgenome |