Table_1_Tissue Resources for the Functional Annotation of Animal Genomes.xlsx

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.为构建驱动家畜基因组表达的功能元件图谱，动物基因组功能注释（Functional Annotation of Animal Genome, FAANG）计划采用的策略为：从不同物种、性别、年龄及生产阶段的少量个体中采集多种组织样本。本文展示了由法国国家农业食品与环境研究院（INRAE）与加州大学戴维斯分校开展的两个试点项目所采集的四个物种的组织样本集，涉及物种包括3种哺乳动物（牛、山羊与猪）及1种鸟类（鸡）。 该数据集描述了四类参考样本集的元数据特征：(1) 供体动物的起源、选育历史、生理状态与环境条件；(2) 样本的采集位点与组织/细胞处理流程；(3) 质量控制相关信息；(4) 存储与后续分发相关信息。本次共划定三类样本集：集1包含可标准化采集且代表性等分样本易于分发的组织，具体包括肝脏、脾脏、肺脏、心脏、脂肪垫、皮肤、肌肉与外周血单个核细胞；集2包含因细胞异质性需采用特殊处理流程的组织，例如大脑、消化道、分泌器官、性腺与配子、生殖道、免疫组织与软骨；集3包含特定细胞制剂，如免疫细胞与气管上皮细胞。 专门的采样方案已制定完成并上传至https://data.faang.org/protocol/samples。当存在相关研究需求时，会对哺乳动物与鸡之间的特异性差异进行说明。本次共采集73种不同组织或组织切片，其中21种组织为四个物种所共有。共享统一的组织样本集将有助于实现物种内部及跨物种间的知识传递，并助力减少动物实验。对同一样本集的数据进行整合分析，也将进一步推动数据融合。 部分组织已完成RNA提取与RNA质量检测流程。目前已有超过5000份样本完成存储并分配唯一标识符，其中4000余份样本已上传至生物样本（Biosamples）数据库，前提是可通过标准本体论完成样本描述。诸多组织样本已被用于开展FAANG相关检测并已发表研究成果。所有样本均无限制开放用于后续检测，其申请流程已在文中说明。FAANG成员可依据FAIR（可发现、可访问、可互操作、可复用）数据原则，采用一系列分子检测手段对采集样本的功能状态进行表征，并共享相关研究结果。