Data from: Profile of the Spleen Transcriptome in Beef Steers with Variation in Gain and Feed Intake

We have previously identified components of the immune system contributing to feed intake and gain in both the rumen and small intestine of beef steers. In this study, we examined the spleen, a major lymphatic organ near the digestive tract, to determine whether it was also influencing individual feed efficiency status through immune responses. Animals (n = 16) that were divergent for gain and intake were selected for tissue sampling. The spleen transcriptomes were evaluated by microarray. A total of 1216 genes were identified as differentially expressed. Genes were over-represented in Kyoto encyclopedia of genes and genomes (KEGG) pathways including biological regulation, protein folding, cell communication, immune systems process, response to stress, and RNA metabolic process. Several stress response or heat shock genes including HSPH1, HSPA1A, HSPA4, DNAJB4, DNAJA4, etc., were identified as a stress response functional gene cluster in the low gain-low intake animals. These genes were up-regulated amongst the low gain-low intake animals compared to all other groups. Canonical pathways associated with the differentially expressed genes included the coagulation system, extrinsic prothrombin activation, protein ubiquitination, unfolded protein response, and aldosterone signaling in epithelial cells. An analysis of expressed copy number variable (CNV) genes in the spleen produced some of the same genes and gene families that were differentially expressed. Our data suggests the splenic contribution to some of the underlying variation among gain and intake within this group of animals may be a result of immune function and stress response. In addition, some of the differences in immune response functions may be related to gene copy number.

Resources in this dataset:
Resource Title: Supplemental Table 1. Differentially expressed genes in steer spleen. (xlsx download).
File Name: Web Page, url: https://www.frontiersin.org/articles/file/downloadfile/195479_supplementary-materials_tables_1_xlsx/octet-stream/Table 1.xlsx/2/195479
LSMEANS and fold changes by phenotypic quadrant are presented.

本团队此前已明确，肉牛阉牛的瘤胃与小肠中，存在参与调控采食量与增重的免疫系统组分。本研究聚焦于消化道附近的主要淋巴器官——脾脏，旨在探究其是否亦可通过免疫应答调控个体的饲料利用效率状态。本研究选取了16头增重与采食量表型差异显著的个体进行脾脏组织采样。通过基因芯片（microarray）对脾脏转录组进行检测分析，最终共鉴定得到1216个差异表达基因。差异表达基因在京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）通路中显著富集，富集通路涵盖生物调控、蛋白质折叠、细胞通讯、免疫系统过程、应激响应以及RNA代谢过程等。在低增重低采食量组的个体中，包括HSPH1、HSPA1A、HSPA4、DNAJB4、DNAJA4等在内的多个应激响应或热休克基因，共同构成了应激响应功能基因簇；相较于其余所有组别，该基因簇在低增重低采食量组中呈现上调表达。与差异表达基因相关的经典通路包括凝血系统、外源性凝血酶原激活通路、蛋白质泛素化、未折叠蛋白响应以及上皮细胞醛固酮信号通路。对脾脏中表达的拷贝数变异（Copy Number Variable, CNV）基因进行分析后，发现部分基因与基因家族同时为差异表达基因。本研究数据表明，在本次受试群体中，脾脏对增重与采食量表型差异的部分调控作用，可能源于免疫功能与应激响应过程。此外，免疫响应功能的部分差异可能与基因拷贝数变异相关。

本数据集包含以下资源：
资源标题：附表1. 肉牛阉牛脾脏差异表达基因（可下载xlsx格式文件）。
文件信息：网页，链接：https://www.frontiersin.org/articles/file/downloadfile/195479_supplementary-materials_tables_1_xlsx/octet-stream/Table 1.xlsx/2/195479
该文件提供了按表型象限划分的最小二乘均值（Least Squares Means, LSMEANS）与倍数变化值。