Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken.
Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken.
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DOI：
10.1186/s12864-018-4972-7
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发表时间：
2018-08-07
期刊：
影响因子：
4.4
通讯作者：
Hume DA
中科院分区：
文献类型：
--
作者：
Bush SJ;Freem L;MacCallum AJ;O'Dell J;Wu C;Afrasiabi C;Psifidi A;Stevens MP;Smith J;Summers KM;Hume DA
家鸡（Gallus gallus）被广泛用作发育生物学的模型，也是重要的家畜品种。我们描述了一种新的数据集成方法，使用各种公开存档的 RNA-seq 数据集和来自免疫细胞和组织的新数据，为鸡生成跨越主要组织类型和发育阶段的 mRNA 表达图谱。将 RNA-seq 数据集随机下采样到共同深度，并使用 mRNA 定量工具 Kallisto 对参考转录组进行定量表达，确保不同的数据集探索可比较的转录组空间。网络分析工具 Graphia 用于从生成的表达图谱中提取共表达基因簇，其中许多是组织或细胞类型限制的，包含先前参与其调节的转录因子，或者以其他方式与生物过程（例如细胞周期）相关。该图谱为目前只有基因座 ID 的基因的功能注释提供了资源。我们将 RNA-seq 图集与公开的胚胎 Cap 基因表达分析 (CAGE) 数据集交叉引用，以推断器官系统的发育时间进程，并识别发育过程中组织巨噬细胞群扩张的特征。从公共 RNA-seq 数据集中获得的表达谱（尽管是由不同实验室使用不同方法生成的）可以相互比较。这种 RNA-seq 荟萃分析方法可以通过新组织的新数据集进行扩展，并且适用于任何物种。本文的在线版本 (10.1186/s12864-018-4972-7) 包含补充材料，可供授权用户使用。
The domestic chicken (Gallus gallus) is widely used as a model in developmental biology and is also an important livestock species. We describe a novel approach to data integration to generate an mRNA expression atlas for the chicken spanning major tissue types and developmental stages, using a diverse range of publicly-archived RNA-seq datasets and new data derived from immune cells and tissues. Randomly down-sampling RNA-seq datasets to a common depth and quantifying expression against a reference transcriptome using the mRNA quantitation tool Kallisto ensured that disparate datasets explored comparable transcriptomic space. The network analysis tool Graphia was used to extract clusters of co-expressed genes from the resulting expression atlas, many of which were tissue or cell-type restricted, contained transcription factors that have previously been implicated in their regulation, or were otherwise associated with biological processes, such as the cell cycle. The atlas provides a resource for the functional annotation of genes that currently have only a locus ID. We cross-referenced the RNA-seq atlas to a publicly available embryonic Cap Analysis of Gene Expression (CAGE) dataset to infer the developmental time course of organ systems, and to identify a signature of the expansion of tissue macrophage populations during development. Expression profiles obtained from public RNA-seq datasets – despite being generated by different laboratories using different methodologies – can be made comparable to each other. This meta-analytic approach to RNA-seq can be extended with new datasets from novel tissues, and is applicable to any species. The online version of this article (10.1186/s12864-018-4972-7) contains supplementary material, which is available to authorized users.
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