Profiling of transcripts expression in Rag2 KO and wild type mice spleen by BeadChip array analysis

Purpose: The purpose of the study was to investigate the differential expression pattern of genes in Rag2 KO mice spleen compared to its wild type counterpart. Methods: In this study, we have excised the spleen tissues from three Rag2 KO mice and three wild type mice, and then RNA samples were prepared with the spleen tissues for the analysis of transcriptomic profiles using the Illumina MouseRef-8 v2 Expression BeadChip platforms. The MouseRef-8 v2.0 BeadChip Kit content is derived from the national center for biotechnology information reference sequence (NCBI RefSeq) database (Build 36, Release 22). The content was supplemented with probes derived from the mouse exonic evidence based oligonucleotide (MEEBO) set, as well as standard protein-coding sequences described in the RIKEN FANTOM2 database. As well, the MouseRef-8 v2.0 BeadChip targets approximately 25,600 well-annotated RefSeq transcripts, over 19,100 unique genes, and enables the interrogation of 8 samples in parallel. The MouseRef-8 v2.0 BeadChip Kit uses the DirectHyb assay and is compatible with the iScan, HiScan, and Bead array reader systems. Result: The genes expression BeadChip array analysis showed that many genes have been expressed differentially between Rag2 KO and wild type mice spleen. These genes might be involved in the different biological and physiological processes including immune regulations. Conclusion: The differential genes expression profile will provide important insight about the immune deregulation in Rag2 KO mice. Spleen RNA derived from Rag2 KO and wild type mice were profiled by microarray, in triplicates for each sample, by the Illumina MouseRef-8 v2 Expression BeadChip platforms.

研究目的：本研究旨在探究Rag2基因敲除（Rag2 KO）小鼠脾脏相较于野生型对照小鼠的基因差异表达模式。
研究方法：本研究分别从3只Rag2基因敲除（Rag2 KO）小鼠与3只野生型小鼠体内分离摘取脾脏组织，随后以脾脏组织提取RNA样本，采用Illumina MouseRef-8 v2表达微珠芯片（Illumina MouseRef-8 v2 Expression BeadChip）平台开展转录组谱分析。该芯片试剂盒的探针序列源自美国国家生物技术信息中心参考序列（National Center for Biotechnology Information Reference Sequence, NCBI RefSeq）数据库（构建版本36，发布版本22），并补充了基于小鼠外显子证据的寡核苷酸（Mouse Exonic Evidence Based Oligonucleotide, MEEBO）集探针，以及RIKEN FANTOM2数据库中收录的标准蛋白编码序列。此外，MouseRef-8 v2.0微珠芯片可靶向检测约25600条经过良好注释的RefSeq转录本、覆盖超过19100个独特基因，并支持并行检测8个样本。该试剂盒采用直接杂交（DirectHyb）实验方案，可兼容iScan、HiScan及Bead阵列阅读器系统。
研究结果：基因表达微珠芯片阵列分析显示，Rag2基因敲除小鼠与野生型小鼠的脾脏组织间存在大量差异表达基因，此类基因可能参与免疫调控等多种生物及生理过程。
研究结论：本次获得的差异基因表达谱可为解析Rag2基因敲除小鼠的免疫失调机制提供重要参考。本研究通过Illumina MouseRef-8 v2表达微珠芯片平台，对Rag2基因敲除及野生型小鼠的脾脏RNA进行了转录组分析，每个样本设置3次生物学重复。