PIGOME

In addition to being a major source of animal protein, pigs are an important model for studying development and diseases in humans. Over the past two decades, thousands of high-throughput sequencing studies in pigs have been performed using a variety of tissues from different breeds and developmental stages. However, multi-omics databases specifically designed for pig functional genomics research are still limited. Here, we present PIGOME, a user-friendly database of pig multi-omics. PIGOME currently contains seven types of pig omics datasets, including whole-genome sequencing (WGS), RNA sequencing (RNA-seq), microRNA sequencing (miRNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), assay for transposase-accessible chromatin sequencing (ATAC-seq), bisulfite sequencing (BS-seq), and methylated RNA immunoprecipitation sequencing (MeRIP-seq), from 6901 samples and 392 projects with manually curated metadata, integrated gene annotation, and quantitative trait locus information. Furthermore, various “Explore” and “Browse” functions have been established to provide user-friendly access to omics information. PIGOME implements several tools to visualize genomic variants, gene expression, and epigenetic signals of a given gene in the pig genome, enabling efficient exploration of spatiotemporal gene expression/epigenetic patterns, functions, regulatory mechanisms, and associated economic traits. Collectively, PIGOME provides valuable resources for pig breeding and is helpful for human biomedical research.

猪不仅是动物蛋白的重要来源，同时也是研究人类发育与疾病的关键模式生物。近二十年来，学界已针对不同品种、不同发育阶段的猪多种组织开展了数千项高通量测序研究。然而，专门面向猪功能基因组学研究的多组学数据库仍较为匮乏。在此，我们推出PIGOME——一款面向猪多组学研究的易用型数据库。目前，PIGOME收录了来自6901个样本、392个项目的7类猪组学数据集，涵盖全基因组测序（whole-genome sequencing, WGS）、RNA测序（RNA sequencing, RNA-seq）、微小RNA测序（microRNA sequencing, miRNA-seq）、染色质免疫沉淀测序（chromatin immunoprecipitation sequencing, ChIP-seq）、转座酶可及性染色质测序（assay for transposase-accessible chromatin sequencing, ATAC-seq）、亚硫酸氢盐测序（bisulfite sequencing, BS-seq）以及甲基化RNA免疫沉淀测序（methylated RNA immunoprecipitation sequencing, MeRIP-seq），并附带人工整理的元数据、整合的基因注释信息与数量性状位点（quantitative trait locus, QTL）数据。此外，数据库搭建了多种"Explore"与"Browse"功能模块，便于用户便捷获取组学相关信息。PIGOME集成了多款可视化工具，可针对猪基因组中特定基因的基因组变异、基因表达及表观遗传信号进行可视化展示，助力用户高效探索基因表达/表观遗传的时空模式、基因功能、调控机制以及相关经济性状。综上，PIGOME为猪育种研究提供了宝贵的资源，同时也可为人类生物医学研究提供助力。

搜集汇总

背景与挑战

背景概述

PIGOME是一个专注于猪功能基因组学研究的综合性多组学数据库，包含7种数据类型和近7000个样本，覆盖113个品种、71种组织和29个发育阶段。该数据库提供了丰富的统计信息和多种工具，支持基因变异、表达、表观遗传修饰等功能研究。